Cornelia Schulz and Andreas Zell

Real-Time Graph-Based SLAM with Occupancy Normal Distributions Transforms

2020 IEEE International Conference on Robotics and Automation (ICRA), Paris, France, Methods in Molecular Biology vol. , IEEE, November, 2020, pp. 8203-8208 ((accepted for publication))


Abstract

This work presents a model based traversability analysis method which employs a detailed vehicle model to perform real-time path planning in complex environments. The vehicle model represents the vehicle’s wheels and chassis, allowing it to accurately predict the vehicles 3D pose, detailed contact information for each wheel and the occurrence of a chassis collision given a 2D pose on an elevation map. These predictions are weighted, depending on the safety requirements of the vehicle, to provide a scoring function for an A*-like search strategy. The proposed method is designed to run at frame rates of 30Hz on data from a RGB-D sensor to provide reactive planning of safe paths. For evaluation, two wheeled mobile robots in different simulated and real world environment setups were tested to show the reliability and performance of the proposed method.


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BibTeX

@inproceedings{SchulzICRA2020,
  title = {{Real-Time Graph-Based SLAM with Occupancy Normal Distributions Transforms}},
  author = {Cornelia Schulz and Andreas Zell},
  booktitle = {2020 IEEE International Conference on Robotics and Automation (ICRA)},
  address = {Paris, France},
  year = {2020},
  note = {(accepted for publication)},
}

@inproceedings{SchulzIROS2019,
  title = {{Collaborative Mapping with Pose Uncertainties using different Radio Frequencies and Communication Modules}},
  author = {Cornelia Schulz and Richard Hanten and Matthias Reisenauer and Andreas Zell},
  booktitle = {2019 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)},
  pages = {8203-8208},
  address = {Macau, China},
  year = {2019},
  month = {November},
  days = {4--8},
}

@inproceedings{HantenIROS2019,
  title = {{MuSe: Multi-Sensor Integration Strategies Applied to Sequential Monte Carlo Methods}},
  author = {Richard Hanten and Cornelia Schulz and Adrian Zwiener and Andreas Zell},
  booktitle = {2019 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)},
  pages = {7792-7798},
  address = {Macau, China},
  year = {2019},
  month = {November},
  days = {4--8},
}

@inproceedings{ZwienerIROS2019,
  title = {{ARMCL: ARM Contact point Localization via Monte Carlo Localization}},
  author = {Adrian Zwiener and Richard Hanten and Cornelia Schulz and Andreas Zell},
  booktitle = {2019 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)},
  pages = {7105-7111},
  address = {Macau, China},
  year = {2019},
  month = {November},
  days = {4--8},
}

@inproceedings{SchulzECMR2019,
  title = {{Sub-Pixel Resolution Techniques for Ray Casting in Low-Resolution Occupancy Grid Maps}},
  author = {Cornelia Schulz and Andreas Zell},
  booktitle = {European Conference on Mobile Robots (ECMR)},
  pages = {},
  address = {Prague, Czech Republic},
  year = {2019},
  month = {September},
  days = {4--6},
  doi = {10.1109/ECMR.2019.8870966},
}

@inproceedings{LaubeIJCNN2019,
  title = {{ShuffleNASNets: Efficient CNN models through modified Efficient Neural Architecture Search}},
  author = {Kevin Alexander Laube and Andreas Zell},
  url = {https://arxiv.org/abs/1812.02975},
  booktitle = {IEEE International Joint Conference on Neural Networks (IJCNN)},
  year = {2019},
  address = {Budapest, Hungary},
  month = {July},
  note = {(Accepted for publication)},
}

@inproceedings{JordanICRA2019,
  title = {{Real-Time Model Based Path Planning for Wheeled Vehicles}},
  author = {Julian Jordan and Andreas Zell},
  booktitle = {IEEE International Conference on Robotics and Automation (ICRA)},
  abstract = {This work presents a model based traversability analysis method which employs a detailed vehicle model to perform real-time path planning in complex environments. The vehicle model represents the vehicle’s wheels and chassis, allowing it to accurately predict the vehicles 3D pose, detailed contact information for each wheel and the occurrence of a chassis collision given a 2D pose on an elevation map. These predictions are weighted, depending on the safety requirements of the vehicle, to provide a scoring function for an A*-like search strategy. The proposed method is designed to run at frame rates of 30Hz on data from a RGB-D sensor to provide reactive planning of safe paths. For evaluation, two wheeled mobile robots in different simulated and real world environment setups were tested to show the reliability and performance of the proposed method.},
  pages = {5787-5792},
  address = {Montreal, Canada},
  year = {2019},
  month = {May},
  days = {20--24},
}

@inproceedings{GaoIRC2019,
  title = {{Markerless Racket Pose Detection and Stroke Classification based on Stereo Vision for Table Tennis Robots}},
  author = {Yapeng Gao and Jonas Tebbe and Julian Krismer and Andreas Zell},
  booktitle = {2019 Third IEEE International Conference on Robotic Computing (IRC)},
  year = {2019},
  address = {Naples, Italy},
  month = {February},
  pages = {189-196},
}

@inproceedings{SchulzIRC2019,
  title = {{Simultaneous Collaborative Mapping Based on Low-Bandwidth Communication}},
  author = {Schulz, Cornelia and Hanten, Richard and Reisenauer, Matthias and Zell, Andreas},
  booktitle = {2019 Third IEEE International Conference on Robotic Computing (IRC)},
  abstract = {Multi-robot systems have become interesting for many robotic applications like cleaning, mowing and search and rescue (SAR) scenarios. Most applications require a consistent common map, e.g. for exploration area coverage or for the surveying task itself. Especially in absence of WiFi and in case of an autonomously operating swarm, this becomes a difficult problem. Therefore, we propose a multi-robot mapping system based on 868 MHz radio frequency modules. While other approaches only manage to map key features or communicate coarse approximations of submaps, we achieve consistent and accurate maps by exchanging small incremental updates. This way, our multiple robots obtain shared knowledge about the commonly processed area.},
  year = {2019},
  address = {Naples, Italy},
  month = {February},
  pages = {413-414},
  doi = {10.1109/IRC.2019.00076},
}

@article{huskic2019high,
  title = {High-speed path following control of skid-steered vehicles},
  author = {Huski{\'c}, Goran and Buck, Sebastian and Herrb, Matthieu and Lacroix, Simon and Zell, Andreas},
  journal = {The International Journal of Robotics Research},
  pages = {0278364919859634},
  year = {2019},
  publisher = {SAGE Publications Sage UK: London, England}
}

@inproceedings{TebbeGCPR2018,
  title = {{A Table Tennis Robot System using an industrial KUKA Robot Arm}},
  author = {Jonas Tebbe and Yapeng Gao and Marc Sastre-Rienitz and Andreas Zell},
  booktitle = {German Conference on Pattern Recognition (GCPR)},
  pages = {},
  address = {Stuttgart, Germany},
  year = {2018},
  month = {October},
  days = {10--12},
  doi = {10.1007/978-3-030-12939-2_3}
}

@inproceedings{SchulzIROS2018,
  title = {{Efficient Map Representations for Multi-Dimensional Normal Distributions Transforms}},
  author = {Cornelia Schulz and Richard Hanten and Andreas Zell},
  booktitle = {2018 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)},
  pages = {2679--2686},
  address = {Madrid, Spain},
  year = {2018},
  month = {October},
  days = {1--5},
  abstract = {Efficient 2D and 3D map representations of both static and dynamic, indoor and outdoor environments are crucial for navigation of driving and flying robots. In this paper, we propose a fast and accurate approach for 2D and 3D Normal Distributions Transform (NDT) mapping based on indexed kd-trees. Similar to other approaches, we also model free space, which allows us to obtain occupancy probabilities. Additionally, we provide optional visibility based updates to enhance map consistency in case of noisy data, e.g. from stereo cameras. Unlike other available implementations, our approach is natively applicable to large-scale environments and in real-time, because our maps are able to grow dynamically. This also offers applicability to exploration tasks. To evaluate our approach, we present experimental results on publicly available datasets and discuss the mapping efficiency in terms of accuracy, runtime and memory management. As an exemplary use case, we apply our maps to Monte Carlo Localization on a well-known large-scale dataset.},
  doi = {10.1109/IROS.2018.8593602},
}

@inproceedings{ZwienerICRA2018,
  author = {Adrian Zwiener and Christian Geckeler and Andreas Zell},
  booktitle = {2018 IEEE International Conference on Robotics and Automation (ICRA)},
  title = {Contact Point Localization for Articulated Manipulators with Proprioceptive Sensors and Machine Learning},
  year = {2018},
  volume = {},
  month = may,
  number = {},
  pages = {323-329},
  keywords = {Force;Torque;Three-dimensional displays;Robot sensing systems;Manipulator dynamics},
  doi = {10.1109/ICRA.2018.8462869},
  issn = {2577-087X},
  month = {May},
}

@inproceedings{2018_hanten_3dperson,
  title = {Robust Real-time 3D Person Detection for Indoor and Outdoor Applications},
  author = {Richard Hanten and Philipp Kuhlmann and Sebastian Otte and Andreas Zell},
  booktitle = {{IEEE} International Conference on Robotics and Automation (ICRA)},
  address = {Brisbane, Australia},
  year = {2018},
  month = may,
  pages = {2000-2006},
}

@article{huskic2018gerona,
  title = {GeRoNa: Generic Robot Navigation},
  author = {Huski{\'c}, Goran and Buck, Sebastian and Zell, Andreas},
  journal = {Journal of Intelligent \& Robotic Systems},
  pages = {1--24},
  year = {2018},
  publisher = {Springer}
}

@article{BuckJINT2018,
  author = {Buck, Sebastian
and Zell, Andreas},
  title = {CS::APEX: A Framework for Algorithm Prototyping and Experimentation with Robotic Systems},
  journal = {Journal of Intelligent {\&} Robotic Systems},
  year = {2018},
  month = {Apr},
  day = {24},
  abstract = {Robotic systems differ drastically in their sensory capabilities, their computational power and their designated tasks. For efficient algorithm development, however, we need to have a common modeling framework that enables us to generalize and re-use existing solutions. A modular approach, which is coherent across different platforms, also allows faster prototyping of new systems, given that existing functionality can be reused from already implemented modules. In this paper we develop a modeling framework based on data flow graphs that achieves the following goal: We first merge synchronous data flow and reactive programming into hybrid flow graphs, where we explicitly model synchronous and asynchronous data flow. Then we transfer concepts from finite-state machines to achieve a coherent framework which we call Activity Flow Graphs. The flow of activity enables us to model high level states directly in the data flow graph. The result is a single computation graph that can express both perception and high level control aspects of any robotic system. This theoretical foundation is the core of our open-source software framework CS::APEX, which allows the creation, manipulation and evaluation of Activity Flow Graphs and enables rapid prototyping and experimentation and can be used with any robot supporting the Robot Operating System (ROS). We then demonstrate the framework with two high level models for a fetch-and-delivery robot and a person following robot.},
  issn = {1573-0409},
  doi = {10.1007/s10846-018-0831-7},
  url = {https://doi.org/10.1007/s10846-018-0831-7},
}

@inproceedings{ZwienerIAS2018,
  title = {Configuration Depending Crosstalk Torque
Calibration for Robotic Manipulators with Deep
Neural Regression Models},
  author = {Adrian Zwiener and Sebastian Otte and Richard Hanten and Andreas Zell},
  booktitle = {Intelligent Autonomous Systems (IAS), The 15th International Conference on},
  address = {Baden-Baden, Germany},
  year = {2018},
  month = june,
  note = {(Accepted for publication)},
  abstract = {In this paper, an approach for articulated robotic manipulator which minimizes configuration depending crosstalk torques is presented. In particular, these crosstalk torques are an issue for the Kinova
Jaco 2 manipulator. We can experimentally show that the presented
approach leads to crosstalk minimization for the Kinova Jaco 2 manipulator. Crosstalk leads to a significant difference between sensor output
and inverse dynamic models using CAD rigid body parameters. As a consequence, these disturbances lead to a hindered torque control and perception. Different machine learning techniques, namely Random Forests
and various neural network architectures, are evaluated on this task. We
show that particularly deep neural regression networks are able to learn
the influence of the cross torques which improves perception.},
}

@inproceedings{JordanIROS2017,
  title = {Real-time Pose Estimation on Elevation Maps for Wheeled Vehicles},
  author = {Jordan, Julian and Zell, Andreas},
  booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)},
  address = {Vancouver, Canada},
  pages = {},
  year = {2017},
  month = sep,
  abstract = {Fast and accurate obstacle detection is a crucial
component for autonomous robot navigation. It becomes even
more important for a shared control vehicle like an electric
wheeled walker, since the safety of the vehicle and the user
depend on the correct classification of obstacles. This work
describes a method for pose estimation of four-wheeled vehicles,
which utilizes the fixed resolution of digital elevation maps to
generate a detailed vehicle model. The vehicle’s wheels are also
approximated using digital elevation maps, allowing efficient
calculation of wheel to ground contact points and therefore
fast and accurate estimation of valid vehicle poses. To evaluate
the proposed method, pose estimates are compared to three
datasets including ground truth poses: one created using an
external tracking system and two created by simulations of
wheeled robots. It is also shown that the method is fast enough
for real time operation.},
  days = {24-28},
  note = {},
}

@inproceedings{HuskicIROS2017,
  title = {Person Following at Higher Speeds using a Skid-Steered Mobile Robot},
  author = {Huski\'{c}, Goran and Buck, Sebastian and Ibarg\"uen Gonz\'alez, Luis Azareel and Zell, Andreas},
  booktitle = {Intelligent Robots and Systems (IROS), 2017 IEEE/RSJ International Conference on},
  address = {Vancouver, Canada},
  pages = {},
  year = {2017},
  month = sep,
  days = {24-28},
  note = {},
}

@inproceedings{OtteICANN2017,
  title = {Inherently Constraint-Aware Control of Many-Joint Robot Arms with Inverse Recurrent Models},
  author = {Otte, Sebastian and Zwiener, Adrian and Butz, Martin V},
  booktitle = {International Conference on Artificial Neural Networks},
  pages = {262--270},
  year = {2017},
  organization = {Springer},
}

@inproceedings{JordanECMR2017,
  title = {Kinematic Model based Visual Odometry for Differential Drive Vehicles},
  author = {Jordan, Julian and Zell, Andreas},
  booktitle = {IEEE 8th European Conference on Mobile Robots (ECMR)},
  year = {2017},
  address = {ENSTA ParisTech, Université Paris-Saclay, France},
  month = sept,
  abstract = {This work presents KMVO, a ground plane based
visual odometry that utilizes the vehicle’s kinematic model
to improve accuracy and robustness. Instead of solving a
generic image alignment problem, the motion parameters of a
differential drive vehicle can be directly estimated from RGB-
D image data. In addition, a method for outlier rejection is
presented that can deal with large percentages of outliers. The
system is designed to run in real time on a single thread of a
mobile CPU.
The results of the proposed method are compared to other
publicly available visual odometry and SLAM methods on a
set of nine real world image sequences of different indoor
environments.},
  days = {6-8},
  note = {},
}

@inproceedings{JellalECMR2017,
  title = {Outdoor Obstacle Avoidance based on Hybrid Stereo Visual SLAM for an Autonomous Quadrotor MAV},
  author = {Ait Jellal, Radouane and Zell, Andreas},
  booktitle = {IEEE 8th European Conference on Mobile Robots (ECMR)},
  year = {2017},
  address = {ENSTA ParisTech, Université Paris-Saclay, France},
  month = sept,
  abstract = {We address the problem of on-line volumentric
map creation of unknown environments and planning of safe
trajectories. The sensor used for this purpose is a stereo camera.
Our system is designed to work in GPS denied areas. We design
a keyframe based hybrid SLAM algorithm which combines
feature-based stereo SLAM and direct stereo SLAM. We use
it to grow the map while keeping track of the camera pose in
the map. The SLAM system builds a sparse map. For the path
planning we build a dense volumetric map by computing dense
stereo matching at keyframes and inserting the point clouds
in an Octomap. The computed disparity maps are reused on
the direct tracking refinement step of our hybrid SLAM. Safe
trajectories are then estimated using the RRTstar algorithm in
the SE(3) state space. In our experiments, we show that we can
map large environments with hundreds of keyframes. We also
conducted autonomous outdoor flights using a quadcopter to
validate our approach for obstacle avoidance.},
  days = {6-8},
  note = {},
  pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2017/JellalECMR17.pdf}
}

@article{Yang2017116,
  title = {Multi-camera visual \{SLAM\} for autonomous navigation of micro aerial vehicles },
  journal = {Robotics and Autonomous Systems },
  volume = {93},
  number = {},
  pages = {116 - 134},
  year = {2017},
  note = {},
  issn = {0921-8890},
  doi = {https://doi.org/10.1016/j.robot.2017.03.018},
  url = {http://www.sciencedirect.com/science/article/pii/S0921889015302177},
  author = {Shaowu Yang and Sebastian A. Scherer and Xiaodong Yi and Andreas Zell},
  keywords = {Visual SLAM},
  keywords = {Multiple cameras},
  keywords = {MAVs},
  keywords = {Autonomous navigation },
  abstract = {Abstract In this paper, we present a visual simultaneous localization and mapping (SLAM) system which integrates measurements from multiple cameras to achieve robust pose tracking for autonomous navigation of micro aerial vehicles (MAVs) in unknown complex environments. We analyze the iterative optimizations for pose tracking and map refinement of visual \{SLAM\} in multi-camera cases. The analysis ensures the soundness and accuracy of each optimization update. A well-known monocular visual \{SLAM\} system is extended to utilize two cameras with non-overlapping fields of view (FOVs) in the final implementation. The resulting visual \{SLAM\} system enables autonomous navigation of an \{MAV\} in complex scenarios. The theory behind this system can easily be extended to multi-camera configurations, when the onboard computational capability allows this. For operations in large-scale environments, we modify the resulting visual \{SLAM\} system to be a constant-time robust visual odometry. To form a full visual \{SLAM\} system, we further implement an efficient back-end for loop closing. The back-end maintains a keyframe-based global map, which is also used for loop-closure detection. An adaptive-window pose-graph optimization method is proposed to refine keyframe poses of the global map and thus correct pose drift that is inherent in the visual odometry. We demonstrate the efficiency of the proposed visual \{SLAM\} system for applications onboard of \{MAVs\} in experiments with both autonomous and manual flights. The pose tracking results are compared with ground truth data provided by an external tracking system. }
}

@inproceedings{JellalICRA2017,
  title = {LS-ELAS: Line Segment based Efficient Large Scale Stereo Matching},
  author = {Ait Jellal, Radouane and Lange, Manuel and Wassermann, Benjamin  and Schilling, Andreas and Zell, Andreas},
  booktitle = {IEEE International Conference on Robotics and Automation (ICRA)},
  year = {2017},
  address = {Singapore},
  month = may-jun,
  abstract = {We present LS-ELAS, a line segment extension to the ELAS algorithm, which increases the performance and robustness. LS-ELAS is a binocular dense stereo matching algorithm, which computes the disparities in constant time for most of the pixels in the image and in linear time for a small subset of the pixels (support points). Our approach is based on line segments to determine the support points instead of uniformly selecting them over the image range. This way we find very informative support points which preserve the depth discontinuity. The prior of our Bayesian stereo matching method is based on a set of line segments and a set of support points. Both sets are plugged into a constrained Delaunay triangulation to generate a triangulation mesh which is aware of possible depth discontinuities. We further increased the accuracy by using an adaptive method to sample candidate points along edge segments.},
  days = {29-3},
  pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2017/JellalICRA17.pdf}
}

@inproceedings{BuckICRA2017,
  title = {Multi-sensor Payload Detection and Acquisition for Truck-Trailer AGVs},
  author = {Buck, Sebastian and Hanten, Richard and Bohlmann, Karsten and Zell, Andreas},
  booktitle = {Robotics and Automation (ICRA), 2017 IEEE International Conference on},
  address = {Singapore},
  year = {2017},
  month = may-jun,
  days = {29-3},
}

@inproceedings{HuskicICRA2017,
  title = {Path Following Control of Skid-Steered Wheeled Mobile Robots at Higher Speeds on Different Terrain Types},
  author = {Huski\'{c}, Goran and Buck, Sebastian and Zell, Andreas},
  booktitle = {IEEE International Conference on Robotics and Automation (ICRA)},
  year = {2017},
  address = {Singapore},
  month = may-jun,
  abstract = {A new nonlinear control law for path following with skid-steered mobile robots is proposed. A terrain dependent kinematic model is utilized in path coordinates, and the kinematic parameters are experimentally evaluated. A kinematic path following control is developed using the Lyapunov approach. A separate linear velocity control is then proposed, taking reachable curvatures and actuator saturation into account. The proposed approach is experimentally evaluated in different terrain scenarios, and compared with two other state-of-the-art algorithms. The skid-steered vehicle used for the experiments is the Robotnik Summit XL, a well known commercial mobile robot.},
  days = {29-3},
}

@inproceedings{BuckIROS2016,
  title = {Generic 3D Obstacle Detection for AGVs using Time-of-Flight Cameras},
  author = {Buck, Sebastian and Hanten, Richard and Bohlmann, Karsten and Zell, Andreas},
  booktitle = {Intelligent Robots and Systems (IROS), 2015 IEEE/RSJ International Conference on},
  address = {Daejeon, Korea},
  doi = {10.1109/IROS.2016.7759606},
  pages = {4119 - 4124},
  year = {2016},
  month = oct,
  days = {9-14},
}

@inproceedings{2016_icann_rnnstrings,
  title = {{Investigating} {Recurrent} {Neural} {Networks} for {Feature-less} {Computational} {Drug} {Design}},
  author = {D\"orr, Alexander and Otte, Sebastian and Zell, Andreas},
  booktitle = {International Conference on Artificial Neural Networks (ICANN)},
  address = {Barcelona, Spain},
  year = {2016},
  month = sep,
  note = {(accepted for publication)},
}

@inproceedings{2016_icann_rnnrobotarm,
  title = {{Inverse} {Recurrent} {Models} -- {An} {Application} {Scenario} for {Many-Joint} {Robot} {Arm} {Control}},
  author = {Otte, Sebastian and Zwiener Adrian and Hanten, Richard and Zell, Andreas},
  booktitle = {International Conference on Artificial Neural Networks (ICANN)},
  address = {Barcelona, Spain},
  year = {2016},
  month = sep,
  pages = {149--157},
  organization = {Springer},
}

@inproceedings{2016_icann_rgbd,
  title = {{Revisiting} {Deep} {Neural} {Networks} for {RGB-D} based {Object} {Recognition}},
  booktitle = {International Conference on Artificial Neural Networks (ICANN)},
  author = {Madai-Tahy, Lorand and Otte, Sebastian and Zell, Andreas},
  address = {Barcelona, Spain},
  year = {2016},
  month = sep,
  note = {(accepted for publication)},
}

@article{Romer2016,
  abstract = {The late detection of non-genotoxic carcinogens in the drug development process can delay drug candidates for unmet medical needs from reaching the market despite considerable investments in their development. To enable faster, safer, and less expensive development of medications for patients, the MARCAR project generated a large set of transcriptomic data to investigate the underlying mechanisms of non-genotoxic hepatocarcinogenesis and to identify potential biomarkers for early detection of tumor formation in the rodent liver. The effective mining of these high-dimensional datasets is a non-trivial task that usually requires bioinformatics support to extract relevant mechanistic patterns and confirm toxicological hypotheses. Here, we present MARCARviz, a web-platform that enables biologists to (a) quickly address the most common questions associated with the MARCAR microarray data, to (b) identify relevant patterns in the data, and to (c) generate or confirm mechanistic hypotheses about non-genotoxic effects leading to cancer formation. The major advantage of MARCARviz is that there is no software or advanced technical knowledge required to perform powerful analyses and generate visualizations of the MARCAR data. MARCARviz greatly facilitates the confirmation of published MARCAR results and generation of new insights from the collected data by the greater public without the requirement for tedious pre-processing steps. MARCARviz is publicly available from https://tea.cs.uni-tuebingen.de/.},
  author = {R{\"{o}}mer, Michael and Ellinger-Ziegelbauer, Heidrun and Grasl-Kraupp, Bettina and Schwarz, Michael and Zell, Andreas},
  doi = {10.7287/peerj.preprints.2393v1},
  journal = {PeerJ Preprints},
  pages = {e2393v1},
  title = {{MARCARviz: Interactive web-platform for exploratory analysis of toxicogenomics data for nongenotoxic hepatocarcinogenesis}},
  volume = {4},
  month = aug,
  year = {2016},
}

@inproceedings{HuskicIAS2016,
  title = {A Simple and Efficient Path Following Algorithm for Wheeled Mobile Robots},
  author = {Huski\'{c}, Goran and Buck, Sebastian and Zell, Andreas},
  booktitle = {Intelligent Autonomous Systems (IAS), The 14th International Conference on},
  year = {2016},
  address = {Shanghai, CN},
  month = jul,
  abstract = {A heuristic path following algorithm for wheeled mobile robots
    is presented. This approach is based on the orthogonal projection to the
    path  and  exponential  functions  for  lateral  and  longitudinal  control.  It
    allows smooth and stable navigation in dynamic and cluttered environments,
    and does not depend on the robot's kinematics. The results are
    experimentally demonstrated using three di erent kinematic con gurations:
    omnidirectional, Ackermann- and two-steering},
  days = {3-7},
  doi = {10.1007/978-3-319-48036-7_27},
}

@inproceedings{HantenIAS2016,
  title = {Vector-AMCL: Vector based Adaptive Monte Carlo Localization for Indoor Maps},
  author = {Hanten, Richard and Buck, Sebastian and Otte, Sebastian and Zell, Andreas},
  booktitle = {Intelligent Autonomous Systems (IAS), The 14th International Conference on},
  year = {2016},
  address = {Shanghai, CN},
  month = jul,
  abstract = {For navigation of mobile robots in real-world scenarios, accurate
    and robust localization is a fundamental requirement. In this
    work we present an efficient localization approach based on adaptive
    Monte Carlo Localization (AMCL) for large-scale indoor navigation, using
     vector-based CAD floor plans. The approach is able to use the line
    segment data of these plans directly. In order to minimize the computational
    effort, a visibility lookup table is generated, reducing the amount
    of line segments to process for pose estimation. In addition, we show that
    the proposed approach performs well in cluttered as well as uncluttered
    environments. It is compared with grid map-based AMCL and is able to
    improve its results in terms of memory usage and accuracy.},
  days = {3-7},
}

@inproceedings{BuckIAS2016,
  title = {Synchronous Dataflow and Visual Programming for Prototyping Robotic Algorithms},
  author = {Buck, Sebastian and Hanten, Richard and Pech, C. Robert and Zell, Andreas},
  booktitle = {Intelligent Autonomous Systems (IAS), The 14th International Conference on},
  pages = {911--923},
  year = {2016},
  address = {Shanghai, CN},
  month = jul,
  abstract = {Robots perceive their environment by processing continuous
    streams  of  data,  which  can  be  very  naturally  modelled  as  a  dataflow
    graph. The development of new perception algorithms is often an iterative
    process, involving the investigation of a set of parameters and their
    in uence on the system. The amount of immediate feedback available to
    the developer can make these in uences more obvious and can therefore
    speed up development. We present a framework based on synchronous
    dataflow and event-based message passing that forms the basis of a visual
    programming language for rapid prototyping of robotic perception systems.
    We explicitly model algorithmic parameters in the dataflow graph,
    which results in a more expressive feature set. We provide an open-source
    implementation,  consisting  of  a  user  interface  for  immediate  feedback
    and interactive manipulation of dataflow algorithms and an independent
    execution framework that can be directly used on any robot.},
  days = {3-7},
  pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2016/BuckIAS2016.pdf},
  doi = {10.1007/978-3-319-48036-7_66},
}

@article{Jordan2016108,
  title = {Ground plane based visual odometry for RGBD-Cameras using orthogonal projection},
  journal = {IFAC-PapersOnLine},
  volume = {49},
  number = {15},
  pages = {108 - 113},
  year = {2016},
  month = jun,
  note = {9th \{IFAC\} Symposium on Intelligent Autonomous Vehicles \{IAV\} 2016, Leipzig, Germany, 29 June-1 July 2016},
  issn = {2405-8963},
  doi = {http://dx.doi.org/10.1016/j.ifacol.2016.07.717},
  url = {http://www.sciencedirect.com/science/article/pii/S2405896316309934},
  author = {Julian Jordan and Andreas Zell},
  keywords = {Mobile robots},
  keywords = {Visual},
  keywords = {Motion estimation},
  keywords = {Image registration},
  abstract = {Abstract This work presents a method for visual odometry that allows robust 3 degrees of freedom trajectory estimation for wheeled robots using a downward facing RGBD-camera. Assuming that the robot moves on a ground plane while the environment itself can have arbitrary geometry allows to estimate the frame to frame motion from orthographic projections of the RGBD-data. Instead of directly aligning these projections, the reference frame is split into blocks, which are individually registered using Efficient Second Order Minimization, and thus create several estimates of the current motion. These estimates are combined using an outlier rejection scheme to create a robust estimate of the actual motion even under challenging conditions. The results of this method are compared to the results of other state-of-the-art methods to show its accuracy and robustness.},
}

@article{2016_neurocomp_rnndynamics,
  series = {Advances in artificial neural networks, machine learning and computational intelligence -- Selected papers from the 23rd {European} {Symposium} on {Artificial} {Neural} {Networks} ({ESANN} 2015)},
  title = {Optimizing recurrent reservoirs with neuro-evolution},
  volume = {192},
  issn = {0925-2312},
  url = {http://www.sciencedirect.com/science/article/pii/S0925231216002629},
  doi = {10.1016/j.neucom.2016.01.088},
  journal = {Neurocomputing},
  author = {Otte, Sebastian and Butz, Martin V. and Koryakin, Danil and Becker, Fabian and Liwicki, Marcus and Zell, Andreas},
  month = jun,
  year = {2016},
  keywords = {Echo state networks, Learning dynamics, Neuro-Evolution, recurrent neural networks, Reservoir computing},
  pages = {128--138},
}

@article{Du2016,
  author = {Du, Bin and Zielinski, Daniel and Dr\"ager, Andreas and Tan, Justin and
    Zhang, Zhen and Ruggiero, Kayla and Arzumanyan, Garry and Palsson, Bernhard O.},
  title = {Evaluation of Rate Law Approximations in Bottom-up Kinetic Models of
    Metabolism},
  journal = {BMC Systems Biology},
  month = jun,
  year = {2016},
  abstract = {Background: The mechanistic description of enzyme kinetics in a
    dynamic model of metabolism requires specifying the numerical values of a
    large number of kinetic parameters. The parameterization challenge is often
    addressed through the use of simplifying approximations to form reaction
    rate laws with reduced numbers of parameters. Whether such simplified models
    can reproduce dynamic characteristics of the full system is an important
    question.

    Results: In this work, we compared the local transient response properties
    of dynamic models constructed using rate laws with varying levels of
    approximation. These approximate rate laws were: 1) a Michaelis-Menten rate
    law with measured enzyme parameters, 2) a Michaelis-Menten rate law with
    approximated parameters, using the convenience kinetics convention, 3) a
    thermodynamic rate law resulting from a metabolite saturation assumption,
    and 4) a pure chemical reaction mass action rate law that removes the role
    of the enzyme from the reaction kinetics. We utilized in vivo data for the
    human red blood cell to compare the effect of rate law choices against the
    backdrop of physiological flux and concentration differences. We found that
    the Michaelis-Menten rate law with measured enzyme parameters yields an
    excellent approximation of the full system dynamics, while other assumptions
    cause greater discrepancies in system dynamic behavior. However, iteratively
    replacing mechanistic rate laws with approximations resulted in a model that
    retains a high correlation with the true model behavior. Investigating this
    consistency, we determined that the order of magnitude differences among
    fluxes and concentrations in the network were greatly influential on the
    network dynamics. We further identified reaction features such as thermodynamic
    reversibility, high substrate concentration, and lack of allosteric regulation,
    which make certain reactions more suitable for rate law approximations.

    Conclusions: Overall, our work generally supports the use of approximate
    rate laws when building large scale kinetic models, due to the key role that
    physiologically meaningful flux and concentration ranges play in determining
    network dynamics. However, we also showed that detailed mechanistic models
    show a clear benefit in prediction accuracy when data is available. The work
    here should help to provide guidance to future kinetic modeling efforts on the
    choice of rate law and parameterization approaches.},
  keywords = {metabolic modeling, kinetic modeling, approximate rate laws,
    Michaelis-Menten kinetics, mass action kinetics},
  volume = {10},
  number = {1},
  pages = {1--15},
  issn = {1752-0509},
  doi = {10.1186/s12918-016-0283-2},
  url = {http://dx.doi.org/10.1186/s12918-016-0283-2},
  pdf = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895898/pdf/12918_2016_Article_283.pdf},
}

@inproceedings{2016_icra_rnnground,
  title = {{Recurrent} {Neural} {Networks} for {Fast} and {Robust} {Vibration-based} {Ground} {Classification} on {Mobile} {Robots}},
  booktitle = {IEEE International Conference on Robotics and Automation (ICRA)},
  author = {Otte, Sebastian and Weiss, Christian and Scherer, Tobias and Zell, Andreas},
  address = {Stockholm, Sweden},
  year = {2016},
  month = may,
}

@inproceedings{koch2016icra,
  author = {Artur Koch and Andreas Zell},
  title = {{RFID}-Enabled Location Fingerprinting based on Similarity Models
from Probabilistic Similarity Measures},
  booktitle = {IEEE International Conference on Robotics and Automation (ICRA)},
  year = {2016},
  address = {Stockholm, Sweden},
  month = {May},
  publisher = {IEEE},
  abstract = {In this work we present a novel fingerprint similarity sensor model for the purpose of localizing a mobile robot with passive ultra-high frequency (UHF) radio-frequency identification (RFID) through location fingerprinting. We firstly evaluate the performance of different probabilistic similarity measures applied to received signal strength (RSS) and compare them to previous results obtained with well known vector similarity measures. We furthermore extend the observation model used in a particle filter to dynamically adapt to the uncertainty of single candidate fingerprints by using their similarity to the current observation. For this purpose, we derive a new likelihood function and introduce an alternative way of selecting candidate fingerprints using a combination of their signal space similarity as well as the distance between the currently estimated pose and reference fingerprints. Results obtained from experiments in two different environments highlight the improved accuracy as well as robustness of the proposed methods.},
}

@article{Scranton2016,
  author = {Scranton, Melissa A. and Ostrand, Joseph T. and Georgianna, D. Ryan
    and Lofgren, Shane M. and Li, Daphne and Ellis, Rosalie C. and Carruthers,
    David N. and Dr\"ager, Andreas and Masica, David L. and Mayfield, Stephen P.},
  title = {{Synthetic promoters capable of driving robust nuclear gene expression
    in the green alga \emph{Chlamydomonas reinhardtii}}},
  journal = {Algal Research},
  volume = {15},
  pages = {135--142},
  year = {2016},
  month = feb,
  issn = {2211-9264},
  abstract = {Algae have enormous potential as bio-factories for the
    efficient production of a wide array of high-value products, and eventually
    as a source of renewable biofuels. However, tools for engineering the
    nuclear genomes of algae remain scarce and limited in functionality. In this
    study, synthetic algal promoters (saps) were generated as a tool for
    increasing nuclear gene expression and as a model for understanding promoter
    elements and structure in green algae. Promoters were generated to mimic
    native \emph{cis}-motif elements, structure, and overall nucleotide
    composition of top expressing genes from \emph{Chlamydomonas reinhardtii}.
    Twenty five saps were used to drive expression of a fluorescent reporter in
    transgenic algae. A majority of the promoters were functional \emph{in vivo}
    and seven were identified to drive expression of the fluorescent reporter
    better than the current best endogenous promoter in \emph{C.~reinhardtii},
    the chimeric hsp70/rbs2 promoter. Further analysis of the best synthetic
    promoter, sap11, revealed a new DNA motif essential for promoter function
    that is widespread and highly conserved in \emph{C.~reinhardtii}. These data
    demonstrate the utility of synthetic promoters to drive gene expression in
    green algae, and lays the groundwork for the development of a suite of saps
    capable of driving the robust and complex gene expression that will be
    required for algae to reach their potential as an industrial platform for
    photosynthetic bio-manufacturing.},
  keywords = {Algal engineering, C. reinhardtii, Synthetic biology, Nuclear promoters, Cis-motifs, Flow cytometry},
  doi = {10.1016/j.algal.2016.02.011},
  url = {http://www.sciencedirect.com/science/article/pii/S2211926416300443},
  pdf = {http://www.sciencedirect.com/science/article/pii/S2211926416300443/pdfft?md5=a0e0ddab3712c8312e0504b9b98e094f&pid=1-s2.0-S2211926416300443-main.pdf},
}

@article{Braeuning2016,
  title = {Tumor promotion and inhibition by phenobarbital in livers of
    conditional Apc-deficient mice},
  author = {Braeuning, Albert and Gavrilov, Alina and Geissler, Miriam and Wenz,
    Christine and Colnot, Sabine and Templin, Markus F and Metzger, Ute and
    R\"omer, Michael and Zell, Andreas and Schwarz, Michael},
  journal = {Archives of Toxicology},
  pages = {1--14},
  year = {2016},
  month = feb,
  publisher = {Springer},
}

@article{Roemer2016a,
  author = {R\"omer, Michael and Eichner, Johannes and Dr\"ager, Andreas and
    Wrzodek, Clemens and Wrzodek, Finja and Zell, Andreas},
  title = {{ZBIT Bioinformatics Toolbox: a Web-Platform for Systems Biology
    and Expression Data Analysis}},
  year = {2016},
  month = feb,
  number = {2},
  volume = {11},
  pages = {e0149263},
  journal = {PLoS ONE},
  publisher = {Public Library of Science},
  abstract = {Bioinformatics analysis has become an integral part of research
    in biology. However, installation and use of scientific software can be
    difficult and often requires technical expert knowledge. Reasons are
    dependencies on certain operating systems or required third-party libraries,
    missing graphical user interfaces and documentation, or nonstandard input
    and output formats. In order to make bioinformatics software easily
    accessible to researchers, we here present a web-based platform. The Center
    for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based
    access to a collection of bioinformatics tools developed for systems biology,
    protein sequence annotation, and expression data analysis. Currently, the
    collection encompasses software for conversion and processing of community
    standards SBML and BioPAX, transcription factor analysis, and analysis of
    microarray data from transcriptomics and proteomics studies. All tools are
    hosted on a customized Galaxy instance and run on a dedicated computation
    cluster. Users only need a web browser and an active internet connection in
    order to benefit from this service. The web platform is designed to
    facilitate the usage of the bioinformatics tools for researchers without
    advanced technical background. Users can combine tools for complex analyses
    or use predefined, customizable workflows. All results are stored persistently
    and reproducible. For each tool, we provide documentation, tutorials, and
    example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely
    available at \url{https://webservices.cs.uni-tuebingen.de}.},
  doi = {10.1371/journal.pone.0149263},
  keywords = {Transcription factors, Bioinformatics, DNA-binding proteins, Genome analysis, Systems biology, Software tools, Carcinogens, User interfaces},
  url = {http://dx.doi.org/10.1371%2Fjournal.pone.0149263},
}

@article{Keller2016a,
  author = {Keller, Roland and Klein, Marcus and Thomas, Maria and Dr\"ager,
    Andreas and Metzger, Ute and Templin, Markus F. and Joos, Thomas O. and
    Thasler, Wolfgang E. and Zell, Andreas and Zanger, Ulrich M.},
  title = {{Coordinating role of RXR$\alpha$ in downregulating hepatic
    detoxification during inflammation revealed by fuzzy-logic modeling}},
  journal = {PLoS Computational Biology},
  publisher = {Public Library of Science},
  year = {2016},
  month = jan,
  volume = {12},
  url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1004431},
  pages = {e1004431},
  number = {1},
  doi = {10.1371/journal.pcbi.1004431},
  abstract = {During various inflammatory processes circulating cytokines
    including IL-6, IL-1$\beta$, and TNF$\alpha$ elicit a broad and
    clinically relevant impairment of hepatic detoxification that is based on
    the downregulation of many drug metabolizing enzymes and transporters but it
    remained unclear, whether a common mechanism is involved. To address this
    question we treated human primary hepatocytes with IL-6, the major mediator
    of the acute phase response in liver, and characterized acute phase and
    detoxification responses in quantitative gene expression and
    (phospho-)proteomics data sets. Selective inhibitors were used to
    disentangle the roles of JAK/STAT, MAPK, and PI3K signaling pathways. The
    extensive data sets were used to calibrate a prior knowledge-based
    fuzzy-logic model comprising signal transduction and gene regulation. Our
    model suggests a major role of MAPK and PI3K signaling, with the orphan
    nuclear receptor RXR$\alpha$ playing a central role. Validation experiments
    revealed a striking similarity of RXR$\alpha$ gene silencing and IL-6
    stimulation with respect to negative gene regulation. These results concur
    with RXR$\alpha$ functioning as obligatory heterodimerization partner for
    several nuclear receptors that regulate drug and lipid metabolism.},
}

@phdthesis{Keller2016b,
  author = {Keller, Roland},
  title = {Simulation and optimization of logical and kinetic biochemical models},
  school = {University of Tuebingen},
  year = {2016},
  address = {T\"ubingen, Germany},
  note = {in press},
}

@inproceedings{jiang_ROBIO2015,
  author = {Jiang, Lixing and Lu, Huimin and  Duc, My Vo and Koch, Artur and Zell, Andreas},
  title = {Superpixel Segmentation Based Gradient Maps on {RGB-D} Dataset},
  booktitle = {IEEE International Conference on Robotics and Biomimetics (ROBIO)},
  year = {2015},
  address = {Zhuhai, China},
  month = {December},
  url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/Jiang_ROBIO15.pdf}
}

@article{King2015b,
  author = {King, Zachary A. and Lu, Justin S. and Dr\"ager, Andreas and Miller,
    Philip C. and Federowicz, Stephen and Lerman, Joshua A and Ebrahim, Ali and
    Palsson, Bernhard O. and Lewis, Nathan E.},
  title = {{BiGG Models: A platform for integrating, standardizing, and sharing
    genome-scale models}},
  journal = {Nucleic Acids Research},
  abstract = {Genome-scale metabolic models are mathematically-structured
    knowledge bases that can be used to predict metabolic pathway usage and
    growth phenotypes. Furthermore, they can generate and test hypotheses when
    integrated with experimental data. To maximize the value of these models,
    centralized repositories of high-quality models must be established, models
    must adhere to established standards, and model components must be linked to
    relevant databases. Tools for model visualization further enhance their
    utility. To meet these needs, we present BiGG Models
    (\url{http://bigg.ucsd.edu}), a completely redesigned Biochemical, Genetic,
    and Genomic knowledge base. BiGG Models contains more than 75 high-quality,
    manually-curated genome-scale metabolic models. On the website, users can
    browse, search, and visualize models. BiGG Models connects genome-scale
    models to genome annotations and external databases. Reaction and metabolite
    identifiers have been standardized across models to conform to community
    standards and enable rapid comparison across models. Furthermore, BiGG
    Models provides a comprehensive application programming interface (API) for
    accessing BiGG Models with modeling and analysis tools. As a resource for
    highly curated, standardized, and accessible models of metabolism, BiGG
    Models will facilitate diverse systems biology studies and support
    knowledge-based analysis of diverse experimental data.},
  keywords = {genome-scale model, knowledge base, omics data},
  month = oct,
  year = {2015},
  doi = {10.1093/nar/gkv1049},
  url = {http://nar.oxfordjournals.org/content/44/D1/D515},
  pdf = {http://nar.oxfordjournals.org/content/early/2015/10/15/nar.gkv1049.full.pdf},
}

@article{Ebrahim2015,
  author = {Ebrahim, Ali and Almaas, Eivind and Bauer, Eugen and Bordbar, Aarash
    and Burgard, Anthony P. and Chang, Roger L. and Dr\"ager,  Andreas and
    Famili, Iman and Feist, Adam M. and Fleming, Ronan M.~T. and Fong, Stephen S.
    and Hatzimanikatis, Vassily and Herrg\r{a}rd, Markus J. and Holder, Allen
    and Hucka, Michael and Hyduke, Daniel and Jamshidi, Neema and Lee, Sang Yup
    and {Le Nov\`{e}re}, Nicolas and Lerman, Joshua A. and Lewis, Nathan E. and
    Ma, Ding and Mahadevan, Radhakrishnan and Maranas, Costas and Nagarajan, Harish
    and Navid, Ali and Nielsen, Jens and Nielsen, Lars K. and Nogales, Juan and
    Noronha, Alberto and Pal, Csaba and Palsson, Bernhard O. and Papin, Jason A.
    and Patil, Kiran R. and Price, Nathan D. and Reed, Jennifer L. and Saunders,
    Michael and Senger, Ryan S. and Sonnenschein, Nikolaus and Sun,  Yuekai and
    Thiele, Ines},
  title = {{Do Genome-scale Models Need Exact Solvers or Clearer Standards?}},
  journal = {Molecular Systems Biology},
  year = {2015},
  month = oct,
  volume = {11},
  number = {10},
  pages = {831},
  issn = {1744-4292},
  url = {http://dx.doi.org/10.15252/msb.20156157},
  doi = {10.15252/msb.20156157},
  pdf = {http://msb.embopress.org/content/11/10/831.full.pdf},
}

@article{Ibrahim2015,
  title = {pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening},
  author = {Ibrahim, Tamer M. and Bauer, Matthias R. and D\"orr, Alexander and Veyisoglu, Erdem and Boeckler, Frank M.},
  journal = {Journal of Chemical Information and Modeling},
  year = {2015},
  month = {October},
  publisher = {ACS Publications},
  doi = {10.1021/acs.jcim.5b00475},
  url = {http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00475}
}

@article{Draeger2015,
  author = {Dr\"ager, Andreas and Zielinski, Daniel C. and Keller, Roland and
    Rall, Matthias and Eichner, Johannes and Palsson, Bernhard O. and Zell, Andreas},
  title = {{SBMLsqueezer~2: Context-sensitive creation of kinetic equations in biochemical networks}},
  journal = {BMC Systems Biology},
  volume = {9},
  number = {1},
  pages = {1--17},
  issn = {1752-0509},
  month = sep,
  year = {2015},
  doi = {10.1186/s12918-015-0212-9},
  url = {http://dx.doi.org/10.1186/s12918-015-0212-9},
  abstract = {Background: The size and complexity of published biochemical
    network reconstructions are steadily increasing, expanding the potential
    scale of derived computational models. However, the construction of large
    biochemical network models is a laborious and error-prone task. Automated
    methods have simplified the network reconstruction process, but building
    kinetic models for these systems is still a manually intensive task.
    Appropriate kinetic equations, based upon reaction rate laws, must be
    constructed and parameterized for each reaction. The complex
    test-and-evaluation cycles that can be involved during kinetic model
    construction would thus benefit from automated methods for rate law
    assignment.

    Results: We present a high-throughput algorithm to automatically suggest and
    create suitable rate laws based upon reaction type according to several
    criteria. The criteria for choices made by the algorithm can be influenced
    in order to assign the desired type of rate law to each reaction. This
    algorithm is implemented in the software package SBMLsqueezer~2. In
    addition, this program contains an integrated connection to the kinetics
    database SABIO-RK to obtain experimentally-derived rate laws when desired.

    Conclusions: The described approach fills a heretofore absent niche in
    workflows for large-scale biochemical kinetic model construction. In several
    applications the algorithm has already been demonstrated to be useful and
    scalable. SBMLsqueezer is platform independent and can be used as a
    stand-alone package, as an integrated plugin, or through a web interface,
    enabling flexible solutions and use-case scenarios.},
  pdf = {http://www.biomedcentral.com/content/pdf/s12918-015-0212-9.pdf},
}

@article{Hucka2015,
  author = {Hucka, Michael and Bergmann, Frank T. and Dr\"ager, Andreas and
    Hoops, Stefan and Keating, Sarah M. and {Le Nov\`{e}re}, Nicolas and Myers,
    Chris J. and Olivier, Brett G. and Sahle, Sven and Schaff, James C. and
    Smith, Lucian P. and Waltemath, Dagmar and Wilkinson, Darren J.},
  title = {{Systems Biology Markup Language (SBML) Level 2 Version 5: Structures
    and Facilities for Model Definitions}},
  journal = {Journal of Integrative Bioinformatics},
  volume = {12},
  number = {2},
  pages = {271},
  month = sep,
  year = {2015},
  doi = {10.2390/biecoll-jib-2015-271},
  abstract = {Computational models can help researchers to interpret data,
    understand biological function, and make quantitative predictions. The
    Systems Biology Markup Language (SBML) is a file format for representing
    computational models in a declarative form that can be exchanged between
    different software systems. SBML is oriented towards describing biological
    processes of the sort common in research on a number of topics, including
    metabolic pathways, cell signaling pathways, and many others. By supporting
    SBML as an input/output format, different tools can all operate on an
    identical representation of a model, removing opportunities for translation
    errors and assuring a common starting point for analyses and simulations.
    This document provides the specification for Version 5 of SBML Level 2. The
    specification defines the data structures prescribed by SBML as well as
    their encoding in XML, the eXtensible Markup Language. This specification
    also defines validation rules that determine the validity of an SBML
    document, and provides many examples of models in SBML form. Other materials
    and software are available from the SBML project web site,
    \url{http://sbml.org}},
  url = {http://journal.imbio.de/article.php?aid=271},
  pdf = {http://journal.imbio.de/articles/pdf/jib-271.pdf},
}

@article{Mittag2015,
  abstract = {Various attempts have been made to predict the individual disease risk based on genotype data from genome-wide association studies (GWAS). However, most studies only investigated one or two classification algorithms and feature encoding schemes. In this study, we applied seven different classification algorithms on GWAS case-control data sets for seven different diseases to create models for disease risk prediction. Further, we used three different encoding schemes for the genotypes of single nucleotide polymorphisms (SNPs) and investigated their influence on the predictive performance of these models. Our study suggests that an additive encoding of the SNP data should be the preferred encoding scheme, as it proved to yield the best predictive performances for all algorithms and data sets. Furthermore, our results showed that the differences between most state-of-the-art classification algorithms are not statistically significant. Consequently, we recommend to prefer algorithms with simple models like the linear support vector machine (SVM) as they allow for better subsequent interpretation without significant loss of accuracy.},
  author = {Mittag, Florian and R\"omer, Michael and Zell, Andreas},
  doi = {10.1371/journal.pone.0135832},
  editor = {Raghava, Gajendra P. S.},
  issn = {1932-6203},
  journal = {PLoS ONE},
  publisher = {Public Library of Science},
  month = aug,
  number = {8},
  pages = {e0135832},
  pmid = {26285210},
  publisher = {Public Library of Science},
  title = {{Influence of Feature Encoding and Choice of Classifier on Disease Risk Prediction in Genome-Wide Association Studies}},
  url = {http://dx.doi.org/10.1371/journal.pone.0135832 http://dx.plos.org/10.1371/journal.pone.0135832},
  volume = {10},
  year = {2015},
}

@article{Yang2015,
  author = {Yang, Laurence and Tan, Justin and O'Brien, Edward J. and
    Monk, Jonathan and Kim, Donghyuk and Lia, Howard J. and Charusantia, Pep
    and Ebrahim, Ali and Lloyd, Colton J. and Yurkovich,  James T. and Du, Bin
    and Dr\"ager, Andreas and Thomas, Alex and Sun, Yuekai and Saunders, Michael A.
    and Palsson, Bernhard O.},
  title = {Systems biology definition of the core proteome of metabolism and
    expression is consistent with high-throughput data},
  journal = {Proceedings of the National Academy of Sciences},
  abstract = {Finding the minimal set of gene functions needed to sustain life
    is of both fundamental and practical importance. Minimal gene lists have
    been proposed using comparative genomics-based core proteome definitions.
    A definition of a core proteome that is supported by empirical data, is
    understood at the systems-level, and provides a basis for computing
    essential cell functions is lacking. Here, we use a systems biology-based
    genome-scale model of metabolism and expression to define a functional core
    proteome consisting of 356 gene products, accounting for 44\% of the
    \emph{Escherichia coli} proteome by mass based on proteomics data. This
    systems biology core proteome includes 212 genes not found in previous
    comparative genomics-based core proteome definitions, accounts for 65\% of
    known essential genes in \emph{E.~coli}, and has 78\% gene function overlap with
    minimal genomes (\emph{Buchnera aphidicola} and \emph{Mycoplasma genitalium}).
    Based on transcriptomics data across environmental and genetic backgrounds,
    the systems biology core proteome is significantly enriched in non-differentially
    expressed genes, and depleted in differentially expressed genes. Compared to
    the non-core, core gene expression levels are also similar across genetic
    backgrounds (two times higher Spearman rank correlation), and exhibit
    significantly more complex transcriptional and post-transcriptional regulatory
    features (40\% more transcription start sites per gene, 22\% longer 5'UTR).
    Thus, genome-scale systems biology approaches rigorously identify a
    functional core proteome needed to support growth. This framework, validated
    using high-throughput datasets, facilitates a mechanistic understanding of
    systems-level core proteome function through in silico models; it
    \emph{de facto} defines a paleome.},
  year = {2015},
  month = aug,
  url = {http://www.pnas.org/content/early/2015/08/05/1501384112},
  pdf = {http://www.pnas.org/content/early/2015/08/05/1501384112.full.pdf},
  doi = {10.1073/pnas.1501384112},
}

@article{King2015a,
  author = {King, Zachary A. and Dr\"ager, Andreas and Ebrahim, Ali and
    Sonnenschein, Nikolaus and Lewis, Nathan E. and Palsson, Bernhard O.},
  title = {Escher: A web application for building, sharing, and embedding
    data-rich visualizations of biological pathways},
  abstract = {Escher is a web application for visualizing data on biological
    pathways. Three key features make Escher a uniquely effective tool for
    pathway visualization. First, users can rapidly design new pathway maps.
    Escher provides pathway suggestions based on user data and genome-scale
    models, so users can draw pathways in a semi-automated way. Second, users
    can visualize data related to genes or proteins on the associated reactions
    and pathways, using rules that define which enzmyes catalyze each reaction.
    Thus, users can identify trends in common genomic data types (e.g., RNA-Seq,
    proteomics, ChIP) in conjunction with metabolite- and reaction-oriented data
    types (e.g., metabolomics, fluxomics). Third, Escher harnesses the strengths
    of web technologies (SVG, D3, developer tools) so that visualizations can be
    rapidly adapted, extended, shared, and embedded. This paper provides
    examples of each of these features and explains how the development approach
    used for Escher can be used to guide the development of future visualization
    tools.},
  doi = {10.1371/journal.pcbi.1004321},
  publisher = {Public Library of Science},
  journal = {PLoS Computational Biology},
  month = aug,
  pages = {e1004321},
  volume = {11},
  number = {8},
  url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1004321},
  year = {2015},
  keywords = {Data visualization; Metabolites; Web-based application; Genomic databases; Genome analysis; Enzymes; Protein metabolism; Genomic libraries},
}

@inproceedings{BuckICAR2015,
  title = {Conclusions from an Object-Delivery Robotic Competition: SICK Robot Day 2014},
  author = {Buck, Sebastian and Hanten, Richard and Huski\'{c}, Goran and Rauscher, Gerald and
            Kloss, Alina and Leininger, Jan and Ruff, Eugen and Widmaier, Felix and Zell, Andreas},
  booktitle = {Advanced Robotics (ICAR), The 17th International Conference on},
  year = {2015},
  address = {Istanbul, TR},
  month = {July},
  pages = {137-143},
  abstract = {Contrary to controlled experiments in a laboratory,
    robotics competitions pose a real challenge to an intelligent
    autonomous system. To allow a good performance, robotic systems
    have to be very robust to unforeseen circumstances in a
    highly constrained time frame. In this paper we present the
    design, implementation and performance of the robotic system
    we developed for participation in the SICK robot day 2014, with
    which we achieved very good results, placing second, with the
    same maximum score as the first. The task of this competition was
    to alternately fetch and deliver objects in a simplified warehouse
    scenario. Participating robots had to be able to carry out different
    tasks, such as detecting filling and delivery stations, receiving and
    analysing bar-code labelled objects as well as navigating in an
    arena among three other robots.},
  days = {27-31},
  pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/BuckICAR2015.pdf},
  url = {http://dx.doi.org/10.1109/ICAR.2015.7251446},
  doi = {10.1109/ICAR.2015.7251446}
}

@inproceedings{Ait_JellalICAR2015,
  title = {A fast dense stereo matching algorithm with an application to 3D occupancy mapping using quadrocopters},
  author = {Radouane Ait Jellal and Andreas Zell},
  booktitle = {The 17th International Conference on Advanced Robotics (ICAR)},
  year = {2015},
  address = {Istanbul, TR},
  month = jul,
  pages = {587 - 592},
  abstract = {We propose a fast algorithm for computing stereo correspondences and correcting the mismatches. The correspondences are computed using stereo block matching and refined with a depth-aware method. We compute 16 disparities at the same time using SSE instructions. We evaluated our method on the Middlebury benchmark and obtained promosing results for practical realtime applications. The use of SSE instructions allows us to reduce the time needed to process the Tsukuba stereo pair to 8 milliseconds (125 fps) on a Core i5 CPU with 2X3.3 GHz. Our disparity refinement method has corrected 40\% of the wrong matches with an additional computational time of 5.2\% (0.41ms). The algorithm has been used to build 3D occupancy grid maps from stereo images. We used the datasets provided by the EuRoC Robotic Challenge. The reconstruction was accurate enough to perform realtime safe navigation.},
  days = {27-31},
  pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/Ait_JellalICAR2015.pdf},
  url = {http://ieeexplore.ieee.org/Xplore/defdeny.jsp?url=http\%3A\%2F\%2Fieeexplore.ieee.org\%2Fstamp\%2Fstamp.jsp\%3Ftp\%3D\%26arnumber\%3D7251515\%26userType\%3Dinst&denyReason=-134&arnumber=7251515&productsMatched=null&userType=inst}
}

@inproceedings{otte_ijcnn_2015,
  title = {{An} {Analysis} {of} {Dynamic} {Cortex} {Memory} {Networks}},
  booktitle = {International Joint Conference on Neural Networks (IJCNN)},
  author = {Otte, Sebastian and Liwicki, Marcus and Zell, Andreas},
  address = {Killarney, Ireland},
  pages = {3338--3345},
  isbn = {978-1-4799-1959-8},
  year = {2015},
  month = jul,
}

@article{Rodriguez2015,
  author = {Rodriguez, Nicolas and Thomas, Alex and Watanabe, Leandro and
    Vazirabad, Ibrahim Y. and Kofia, Victor and G\'{o}mez, Harold F. and Mittag,
    Florian and Matthes, Jakob and Rudolph, Jan D. and Wrzodek, Finja and Netz,
    Eugen and Diamantikos, Alexander and Eichner, Johannes and Keller, Roland
    and Wrzodek, Clemens and Fr\"ohlich, Sebastian and Lewis, Nathan E. and
    Myers, Chris J. and {Le Nov\`{e}re}, Nicolas and Palsson, Bernhard {\O}. and
    Hucka, Michael and Dr\"ager, Andreas},
  title = {{JSBML 1.0: providing a smorgasbord of options to encode systems biology models}},
  journal = {Bioinformatics},
  year = {2015},
  month = jun,
  doi = {10.1093/bioinformatics/btv341},
  abstract = {Summary: JSBML, the official pure Java programming library for the
    SBML format, has evolved with the advent of different modeling formalisms in
    systems biology and their ability to be exchanged and represented via
    extensions of SBML. JSBML has matured into a major, active open-source
    who not only maintain compatibility with SBML, but also drive steady
    improvements to the Java interface and promote ease-of-use with end users.

    Availability: Source code, binaries and documentation for JSBML can be
    freely obtained under the terms of the LGPL 2.1 from the website
    \url{http://sbml.org/Software/JSBML}.

    Supplementary Information: More information about JSBML can be found in the
    user guide at \url{http://sbml.org/Software/JSBML/docs/}.

    Contact: \url{mailto:jsbml-development@googlegroups.com}},
  url = {http://bioinformatics.oxfordjournals.org/content/31/20/3383},
  eprint = {http://bioinformatics.oxfordjournals.org/content/early/2015/06/30/bioinformatics.btv341.full.pdf+html},
  pdf = {http://bioinformatics.oxfordjournals.org/content/early/2015/06/30/bioinformatics.btv341.full.pdf},
}

@inproceedings{scherer2015,
  title = {DCTAM: Drift-corrected tracking and mapping for autonomous micro aerial vehicles},
  author = {Sebastian A. Scherer and Shaowu Yang and Andreas Zell},
  booktitle = {Unmanned Aircraft Systems (ICUAS), 2015 International Conference on},
  year = {2015},
  address = {Denver, CO, USA},
  month = {June},
  pages = {1094-1101},
  abstract = {Visual odometry, especially using a forward-looking camera only,
	can be challenging: It is doomed to fail from time to time and will
	inevitably drift in the long run. We accept this fact and present
	methods to cope with and correct the effects for an autonomous MAV
	using an RGBD camera as its main sensor. We propose correcting drift
	and failure in visual odometry by combining its pose estimates with
	information about efficiently detected ground planes in the short term
	and running a full SLAM back-end incorporating loop closures and
	ground plane measurements in pose graph optimization. We show that the
	system presented here achieves accurate results on several instances
	of the TUM RGB-D benchmark dataset while being computationally
	efficient enough to enable autonomous flight of an MAV.},
  days = {9-12},
  pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/scherer2015.pdf},
  url = {http://dx.doi.org/10.1109/ICUAS.2015.7152401}
}

@inproceedings{Jiang2015icra,
  author = {Lixing Jiang and Artur Koch and Andreas Zell},
  title = {Salient Regions Detection for Indoor Robots using {RGB-D} Data},
  booktitle = {IEEE International Conference on Robotics and Automation (ICRA)},
  year = {2015},
  address = {Seattle, USA},
  month = {May},
  url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/Jiang_ICRA15.pdf}
}

@article{GraslKraupp2015,
  author = {Grasl-Kraupp, Bettina and Riegler, Teresa and Nejabat, Marzieh and Paur, Jakob and Eichner, Johannes and R\"omer, Michael and Zell, Andreas and Schulte-Hermann, Rolf and Huber, Wolfgang},
  title = {Abstract 810: Non-genotoxic hepatocarcinogens induce growth and anti-apoptotic pathways in hepatocytes via mesenchymal cytokines},
  volume = {75},
  month = {April},
  number = {15 Supplement},
  pages = {810},
  year = {2015},
  doi = {10.1158/1538-7445.AM2015-810},
  abstract = {Purpose of study. Chemical carcinogens are categorized as either genotoxic or non-genotoxic. While most genotoxic carcinogens are known to interfere with DNA, the mode of action of non-genotoxic carcinogens (NGC) is far from being understood. Many steroid hormones act as NGC and account for cancer of the breast, prostate, or other organs. As ligands of nuclear receptors hormones induce growth in target tissues and support the outgrowth of mutated cells to malignancy. An almost identical principle is underlying the action of NGC producing liver tumors in long-term rodent bioassays. This group of compounds comprises drugs prescribed to hundred-thousands of humans, like hypolipidemic and antidiabetic drugs, or synthetic steroid hormones. A thorough knowledge of the mode of action of NGC is of utmost importance in order to estimate the risk of exposed humans.Conventional notion regards the action of NGC an autonomous process largely confined to parenchymal cells. Here, we aim to elucidate the role of the hepatic mesenchyme for the action of two prototypical NGC, phenobarbital (PB), an anti-epileptic drug, and cyproterone acetate (CPA), a gestagen used in contraceptive pills.Experimental procedures. Mesenchymal liver cells (MC) and hepatocytes (HC) were isolated from control and PB/CPA-treated rat livers by collagenase perfusion and subsequent low-speed centrifugation. Transcriptomics was performed by oligo-array analyses (Affymetrix). Cytokine levels were determined by ELISA. Nuclear translocation of NFkB was shown by immunoblotts of nuclear extracts and by reporter gene assay.Results: Analyses by oligo-arrays revealed that PB and CPA altered the transcriptome profiles of HC and MC. In PB-treated MC, there were deregulations of pro-inflammatory cytokines and chemokines of the TNF-, CCL- and CXCL-family. PB treatment in vivo or in vitro elevated the production and release of tumor necrosis factor alpha (TNFalpha)from MC. The secretome of PB-treated MC induced in HC a pro-inflammatory reaction and nuclear translocation of nuclear factor-kB (NFkB), an effect also observed with recombinant TNFalpha. Both, TNFalpha and the secretome of PB-treated MC, protected HC from pro-apoptotic stimuli.Transcriptome analyses of CPA-treated MC revealed enhanced expression not only of pro-inflammatory cytokines but also of several potent growth factors. Accordingly, the supernatant of CPA-treated MC enhanced considerably the DNA replication of preneoplastic hepatocytes.Conclusion: PB and CPA appear to alter considerably the function of the hepatic mesenchyme. The resulting release of cytokines induces growth and/or activates anti-apoptotic pathways in HC which may contribute to the tumor promoting activity of these compounds. Thus, epithelial-mesenchymal interactions appear crucial in NGC-driven hepatocarcinogenesis.Project MARCAR, funded by IMI JU under grant agreement Nr 115001.Citation Format: Bettina Grasl-Kraupp, Teresa Riegler, Marzieh Nejabat, Jakob Paur, Johannes Eichner, Michael Roemer, Andreas Zell, Rolf Schulte-Hermann, Wolfgang Huber. Non-genotoxic hepatocarcinogens induce growth and anti-apoptotic pathways in hepatocytes via mesenchymal cytokines. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 810. doi:10.1158/1538-7445.AM2015-810},
  url = {http://cancerres.aacrjournals.org/content/75/15_Supplement/810.abstract},
  journal = {Cancer Research},
}

@inproceedings{otte_esann_2015a,
  title = {{Learning} {Recurrent} {Dynamics} {using} {Differential} {Evolution}},
  booktitle = {European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN)},
  author = {Otte, Sebastian and Becker, Fabian and Butz, Martin V. and Liwicki, Marcus and Zell, Andreas},
  address = {Bruges, Belgium},
  year = {2015},
  month = apr,
  pages = {65--70},
}

@inproceedings{otte_esann_2015b,
  title = {{Robust} {Visual} {Terrain} {Classification} {with} {Recurrent} {Neural} {Networks}},
  booktitle = {European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN)},
  author = {Otte, Sebastian and Laible, Stefan and Hanten, Richard and Liwicki, Marcus and Zell, Andreas},
  address = {Bruges, Belgium},
  year = {2015},
  month = apr,
  pages = {451--456},
}

@article{Ohrnberger2014,
  author = {Ohrnberger, Stefan and Thavamani, Abhishek and Braeuning, Albert
	and Lipka, Daniel B and Kirilov, Milen and Geffers, Robert and Authenrieth,
	Stella E and R\"omer, Michael and Zell, Andreas and Bonin, Michael
	and Schwarz, Michael and Sch\"{u}tz, G\"{u}nther and Schirmacher,
	Peter and Plass, Christoph and Longerich, Thomas and Nordheim, Alfred},
  title = {{Dysregulated serum response factor triggers formation of hepatocellular carcinoma}},
  journal = {Hepatology},
  year = {2015},
  month = mar,
  doi = {10.1002/hep.27539},
  issn = {1527-3350},
  pmid = {25266280},
  abstract = {The ubiquitously expressed transcriptional regulator serum
    response factor (SRF) is controlled by both Ras/MAPK (mitogen-activated
    protein kinase) and Rho/actin signaling pathways, which are frequently
    activated in hepatocellular carcinoma (HCC). We generated \emph{SRF-VP16\textsuperscript{iHep}} mice,
    which conditionally express constitutively active SRF-VP16 in hepatocytes,
    thereby controlling subsets of both Ras/MAPK- and Rho/actin-stimulated
    target genes. All \emph{SRF-VP16\textsuperscript{iHep}} mice develop hyperproliferative liver nodules
    that progresses to lethal HCC. Some murine (m)HCCs acquire \emph{Ctnnb1} mutations
    equivalent to those in human (h)HCC. The resulting transcript signatures
    mirror those of a distinct subgroup of hHCCs, with shared activation of
    oncofetal genes including \emph{Igf2}, correlating with CpG hypomethylation at the
    imprinted \emph{Igf2/H19} locus.

    \emph{Conclusion:}
    \emph{SRF-VP16\textsuperscript{iHep}} mHCC reveal convergent Ras/MAPK and Rho/actin signaling as a
    highly oncogenic driver mechanism for hepatocarcinogenesis. This suggests
    simultaneous inhibition of Ras/MAPK and Rho/actin signaling as a treatment
    strategy in hHCC therapy.},
  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365683/},
  pdf = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365683/pdf/hep0061-0979.pdf},
}

@inproceedings{2015_nc2_eegrnn,
  title = {{On} the {Applicability} of {Recurrent} {Neural} {Networks} for {Pattern} {Recognition} in {Electroencephalography} {Signals}},
  author = {Binz, Marcel and Otte, Sebastian and Zell, Andreas},
  booktitle = {Machine Learning Reports 03/2015, Workshop New Challenges in Neural Computation},
  year = {2015},
  pages = {85--92},
}

@article{Doerr2014b,
  author = {D\"{o}rr, Alexander and Rosenbaum, Lars and Zell, Andreas},
  title = {A Ranking Method for the Concurrent Learning of Compounds with Various
	Activity Profiles},
  journal = {J. Cheminf.},
  year = {2015},
  volume = {7},
  number = {1},
  month = jan,
}

@inproceedings{Lu2015iros,
  author = {Huimin Lu and Lixing Jiang and Andreas Zell},
  title = {Long Range Traversable Region Detection Based on Superpixels Clustering for Mobile Robots},
  booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems
	({IROS})},
  year = {2015},
  address = {Hamburg, Germany},
  month = {Sept.},
  url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2015/Lu_IROS15.pdf}
}

@article{Ran_IJDSN_2015,
  author = {Ran Liu and Goran Huski\'{c} and Andreas Zell},
  title = {{On Tracking Dynamic Objects with Long Range Passive UHF RFID Using a Mobile Robot}},
  journal = {International Journal of Distributed Sensor Networks (IJDSN)},
  year = {2015},
  volume = {Article ID 781380},
  issn = {781380},
  publisher = {Hindawi},
  url = {http://dx.doi.org/10.1155/2015/781380}
}

@article{yuyiliu14,
  author = {Liu, Yuyi and {van Schijndel}, Jos and Longo, Stefano and Kerrigan, Eric C.},
  title = {{UAV} Energy Extraction with Incomplete Atmospheric Data Using {MPC}},
  journal = {{IEEE} Transactions on Aerospace and Electronic Systems},
  year = {2015},
  volume = {51},
  number = {2},
  pages = {1203-1215},
}

@inproceedings{yuyiliu15,
  author = {Liu, Yuyi and Montenbruck, Jan Maximilian and Stegagno, Paolo and Allg\"ower, Frank and Zell, Andreas},
  title = {A Robust Nonlinear Controller for Nontrivial Quadrotor Maneuvers: Approach and Verification},
  booktitle = {Proc. 2015 {IEEE/RSJ} International Conference on Intelligent Robots and Systems},
  year = {2015},
  pages = {5410-5416},
}

@article{Doerr2014a,
  author = {D\"orr, Alexander and Keller, Roland and Zell, Andreas and Dr\"ager,
	Andreas},
  title = {{SBMLsimulator: a Java tool for model simulation and parameter estimation
	in systems biology}},
  journal = {Computation},
  year = {2014},
  volume = {2},
  pages = {246--257},
  number = {4},
  month = dec,
  abstract = {The identification of suitable model parameters for biochemical reactions
	has been recognized as a quite difficult endeavor. Parameter values
	from literature or experiments can often not directly be combined
	in complex reaction systems. Nature-inspired optimization techniques
	can find appropriate sets of parameters that calibrate a model to
	experimentally obtained time series data. We present SBMLsimulator,
	a tool that combines the Systems Biology Simulation Core Library
	for dynamic simulation of biochemical models with the heuristic optimization
	framework EvA2. SBMLsimulator provides an intuitive graphical user
	interface with various options as well as a fully-featured command-line
	interface for large-scale and script-based model simulation and calibration.
	In a parameter estimation study based on a published model and artificial
	data we demonstrate the capability of SBMLsimulator to identify parameters.
	SBMLsimulator is useful for both, the interactive simulation and
	exploration of the parameter space and for the large-scale model
	calibration and estimation of uncertain parameter values.},
  doi = {10.3390/computation2040246},
  issn = {2079-3197},
  keywords = {SBML; ODE modeling; Simulation; Parameter estimation},
  pdf = {http://www.mdpi.com/2079-3197/2/4/246/pdf},
  url = {http://www.mdpi.com/2079-3197/2/4/246}
}

@article{Draeger2014,
  author = {Dr\"ager, Andreas and Palsson, Bernhard {\O}.},
  title = {Improving collaboration by standardization efforts in systems biology},
  journal = {Frontiers in Bioengineering},
  year = {2014},
  volume = {2},
  number = {61},
  month = dec,
  abstract = {Collaborative genome-scale reconstruction endeavors of metabolic networks
	would not be possible without a common, standardized formal representation
	of these systems. The ability to precisely define biological building
	blocks together with their dynamic behavior has even been considered
	a prerequisite for upcoming synthetic biology approaches.

	Driven by the requirements of such ambitious research goals, standardization
	itself has become an active field of research on nearly all levels
	of granularity in biology. In addition to the originally envisaged
	exchange of computational models and tool interoperability, new standards
	have been suggested for an unambiguous graphical display of biological
	phenomena, to annotate, archive, as well as to rank models, and to
	describe execution and the outcomes of simulation experiments. The
	spectrum now even covers the interaction of entire neurons in the
	brain, three-dimensional motions, and the description of pharmacometric
	studies.

	Thereby, the mathematical description of systems and approaches for
	their (repeated) simulation are clearly separated from each other
	and also from their graphical representation. Minimum information
	definitions constitute guidelines and common operation protocols
	in order to ensure reproducibility of findings and a unified knowledge
	representation. Central database infrastructures have been established
	that provide the scientific community with persistent links from
	model annotations to on-line resources. A rich variety of open-source
	software tools thrives for all data formats, often supporting a multitude
	of programming languages. Regular meetings and workshops of developers
	and users lead to continuous improvement and ongoing development
	of these standardization efforts.

	This article gives a brief overview about the current state of the
	growing number of operation protocols, markup languages, graphical
	descriptions, and fundamental software support with relevance to
	systems biology.},
  doi = {10.3389/fbioe.2014.00061},
  issn = {2296-4185},
  keywords = {model formats, modeling guidelines, ontologies, model databases, network
	visualization, software support},
  pdf = {http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00061/pdf},
  url = {http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00061/}
}

@inproceedings{voduc2014_2,
  author = {My Vo Duc and Lixing Jiang and Andreas Zell},
  title = {Real time Multiple Person Detection and Tracking Using {RGB-D} Images
	for Mobile Robots},
  booktitle = {IEEE International Conference on Robotics and Biomimetics 2014},
  year = {2014},
  address = {Bali, Indonesia},
  month = {December},
  url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/voduc2014_robio.pdf}
}

@article{Roemer2014b,
  author = {R\"omer, Michael and Backert, Linus and Eichner, Johannes and Zell,
	Andreas},
  title = {ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases
	for Drug Candidates},
  journal = {International Journal of Molecular Sciences},
  year = {2014},
  volume = {15},
  pages = {19037--19055},
  number = {10},
  month = {October},
  doi = {10.3390/ijms151019037},
  issn = {1422-0067},
  url = {http://www.mdpi.com/1422-0067/15/10/19037}
}

@inproceedings{laible2014iros,
  author = {Stefan Laible and Andreas Zell},
  title = {Building Local Terrain Maps Using Spatio-Temporal Classification
	for Semantic Robot Localization},
  booktitle = {Intelligent Robots and Systems (IROS 2014), 2014 IEEE/RSJ International
	Conference on},
  year = {2014},
  pages = {4591--4597},
  address = {Chicago, IL},
  month = {September},
  organization = {IEEE},
  publisher = {IEEE},
  abstract = {The correct classification of the surrounding terrain is an important
	ability of a mobile robot that drives in outdoor environments. Our
	robot uses a 3D LIDAR and a camera to classify terrain as either
	asphalt, cobblestones, grass, or gravel. We build on previous work
	where we modeled the terrain as a Conditional random field to account
	for spatial dependencies, which improved results substantially. We
	now show how to speed up the spatial classification by defining a
	new energy term for neighborhood relations. Moreover, we now also
	consider temporal dependencies as the robot moves. This not only
	further improves the results, but makes it possible to build local
	terrain maps of the environment. We describe how to efficiently integrate
	the classification results of each time step into the map in a probabilistic
	manner. By also detecting obstacles with the LIDAR, the robot can
	build combined terrain and elevation maps. We show that these maps
	can be used for semantic robot localization.},
  doi = {10.1109/IROS.2014.6943213},
  pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/laible2014iros.pdf},
}

@incollection{otte_dcm_2014,
  series = {Lecture {Notes} in {Computer} {Science}},
  title = {Dynamic {Cortex} {Memory}: {Enhancing} {Recurrent} {Neural} {Networks} for {Gradient}-{Based} {Sequence} {Learning}},
  isbn = {978-3-319-11178-0, 978-3-319-11179-7},
  shorttitle = {Dynamic {Cortex} {Memory}},
  abstract = {In this paper a novel recurrent neural network (RNN) model for gradient-based sequence learning is introduced. The presented dynamic cortex memory (DCM) is an extension of the well-known long short term memory (LSTM) model. The main innovation of the DCM is the enhancement of the inner interplay of the gates and the error carousel due to several new and trainable connections. These connections enable a direct signal transfer from the gates to one another. With this novel enhancement the networks are able to converge faster during training with back-propagation through time (BPTT) than LSTM under the same training conditions. Furthermore, DCMs yield better generalization results than LSTMs. This behaviour is shown for different supervised problem scenarios, including storing precise values, adding and learning a context-sensitive grammar.},
  language = {en},
  number = {8681},
  booktitle = {Artificial {Neural} {Networks} and {Machine} {Learning} -- {ICANN} 2014},
  publisher = {Springer International Publishing},
  author = {Otte, Sebastian and Liwicki, Marcus and Zell, Andreas},
  editor = {Stefan Wermter et al},
  month = sep,
  year = {2014},
  pages = {1--8},
}

@inproceedings{Masselli2014ICPR,
  author = {Andreas Masselli and Andreas Zell},
  title = {A New Method for Solving the Perspective-Three-Point Problem},
  booktitle = {International Conference on Pattern Recognition (ICPR 2014)},
  year = {2014},
  address = {Stockholm, Sweden},
  month = {August},
  note = {Accepted for publication},
}

@inproceedings{otte_antsac_2014,
  title = {{ANTSAC}: {A} {Generic} {RANSAC} {Variant} {Using} {Principles} of {Ant} {Colony} {Algorithms}},
  shorttitle = {{ANTSAC}},
  doi = {10.1109/ICPR.2014.612},
  abstract = {In this paper, we present a new variant of the well-known Random Sample Consensus (RANSAC) algorithm for robust estimation of model parameters. The idea of our method is based on a kind of volatile memory which is similar to the pheromone evaporation in the ant colony optimization algorithm. Therefore, we call our improved RANSAC like algorithm ANTSAC. We describe our new approach and the influence of its relevant parameters to the achieved performance in detail. ANTSAC is computationally efficient and convincingly easy to implement. It turns out that ANTSAC significantly outperforms RANSAC regarding the number of inliers after a given number of iterations. Further, we show that the advantage of ANTSAC increases with the complexity of the problem, i.e., with the number of model parameters, as well as with the relative number of outliers. ANTSAC is entirely generic, such that no further domain knowledge is required, as it is for many other RANSAC extensions. Nevertheless, we show that it is competitive to state-of-the-art methods even in domain specific scenarios.},
  booktitle = {2014 22nd {International} {Conference} on {Pattern} {Recognition} ({ICPR})},
  author = {Otte, Sebastian and Schwanecke, Ulrich and Zell, Andreas},
  month = aug,
  year = {2014},
  pages = {3558--3563},
}

@inproceedings{voduc2014,
  author = {My Vo Duc and Andreas Zell},
  title = {Real time Face Recognition using Local Ternary Patterns with Collaborative
	Representation based Classification for Mobile Robots},
  booktitle = {International Conference on Intelligent Autonomous Systems (IAS-13)},
  year = {2014},
  address = {Padova, Italy},
  month = {July},
  url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/voduc2014.pdf}
}

@inproceedings{jiang_IAS13,
  author = {Jiang, Lixing and Koch, Artur and Zell, Andreas},
  title = {Object Recognition and Tracking for Indoor Robots using an {RGB-D}
	Sensor},
  booktitle = {International Conference on Intelligent Autonomous Systems (IAS-13)},
  year = {2014},
  address = {Padova, Italy},
  month = {July},
  abstract = {In this paper we extend and generalize our previously published approach
	on RGB-D based fruit recognition to be able to recognize different
	kinds of objects in front of our mobile system. We therefore firstly
	extend our segmentation to use depth filtering and clustering with
	a watershed algorithm on the depth data to detect the target to be
	recognized. We forward the processed data to extract RGB-D descriptors
	that are used to recoup complementary object information for the
	classification and recognition task. After having detected the object
	once, we apply a simple tracking method to reduce the object search
	space and the computational load through frequent detection queries.
	The proposed method is evaluated using the random forest (RF) classifier.
	Experimental results highlight the effectiveness as well as real
	time suitability of the proposed extensions for our mobile system
	based on real RGB-D data.},
  url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/IAS14_jiang.pdf}
}

@inproceedings{Masselli2014IAS,
  author = {Andreas Masselli and Richard Hanten and Andreas Zell},
  title = {Localization of Unmanned Aerial Vehicles Using Terrain Classification
	from Aerial Images},
  booktitle = {2014 International Conference on Intelligent Autonomous Systems (IAS-13)},
  year = {2014},
  address = {Padova, Italy},
  month = {July},
  abstract = {In this paper we investigate the benefit of terrain classification
	for self-localization of a flying robot. The key idea is to use aerial
	images, which are already available from online databases such as
	GoogleMaps TM , as reference map and to match images taken with a
	downward looking camera with this map. Using different terrain classes
	as features, we can make sure that our method is invariant to lighting/weather
	changes as well as seasonal variations or minor changes in the environment.
	A particle filter is used to register the query image with parts
	of the map. The proposed method has shown to work on image data from
	both simulated and real flights.},
}

@inproceedings{Rauscher2014IAS,
  author = {Gerald Rauscher and Daniel Dube and Andreas Zell},
  title = {A Comparison of 3D Sensors for Wheeled Mobile Robots},
  booktitle = {2014 International Conference on Intelligent Autonomous Systems (IAS-13)},
  year = {2014},
  address = {Padova, Italy},
  month = {July},
  abstract = {

3D Sensors are used for many different applications, e.g. scene reconstruction, object detection and mobile robots, etc. Several studies on usability and accuracy have been done for different sensors. However, all these studies have used different settings for the different sensors. For this reason we compare five 3D sensors, including the structured light sensors Microsoft Kinect and ASUS Xtion Pro Live and the time of flight sensors Fotonic E70P, IFM O3D200 and Nippon Signal FX6, using the same settings. The sensor noise, absolute error and point detection rates are compared for different depth values, environmental illumination and different surfaces. Also simple models of the noise depending on the measured depth are proposed. It is found that the structured light sensors are very accurate for close ranges. The time of flight sensors have more noise, but the noise does not increase as strongly with the measured distance. Further, it is found that these sensors can be used for outdoor applications.

}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/rauscher2014ias.pdf}, } @inproceedings{Yang14c, author = {Shaowu Yang and Sebastian A. Scherer and Andreas Zell}, title = {Robust Onboard Visual {SLAM} for Autonomous {MAVs}}, booktitle = {2014 International Conference on Intelligent Autonomous Systems (IAS-13)}, year = {2014}, address = {Padova, Italy}, month = {July}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/ias14_yang.pdf}, } @article{Eichner2014c, author = {Eichner, Johannes and Heubach, Yvonne and Ruff, Manuel and Kohlhof, Hella and Strobl, Stefan and Mayer, Barbara and Pawlak, Michael and Templin, Markus F. and Zell, Andreas}, title = {{RPPApipe: A pipeline for the analysis of reverse-phase protein array data}}, journal = {BioSystems}, year = {2014}, month = jun, keywords = {Reverse-phase protein arrays; Web application; Statistical analysis; Clustering; Pathway analysis; Visualization}, abstract = {Background and scope: Today, web-based data analysis pipelines exist for a wide variety of microarray platforms, such as ordinary gene-centered arrays, exon arrays and SNP arrays. However, most of the available software tools provide only limited support for reverse-phase protein arrays (RPPA), as relevant inherent properties of the corresponding datasets are not taken into account. Thus, we developed the web-based data analysis pipeline RPPApipe, which was specifically tailored to suit the characteristics of the RPPA platform and encompasses various tools for data preprocessing, statistical analysis, clustering and pathway analysis. Implementation and performance: All tools which are part of the RPPApipe software were implemented using R/Bioconductor. The software was embedded into our web-based ZBIT Bioinformatics Toolbox which is a customized instance of the Galaxy platform. Availability: RPPApipe is freely available under GNU Public License from \url{http://webservices.cs.uni-tuebingen.de}. A full documentation of the tool can be found on the corresponding website \url{http://www.cogsys.cs.uni-tuebingen.de/software/RPPApipe}. \textcopyright{} 2014 Elsevier Ireland Ltd.}, doi = {10.1016/j.biosystems.2014.06.009}, url = {http://www.sciencedirect.com/science/article/pii/S0303264714000902}, pdf = {http://www.sciencedirect.com/science/article/pii/S0303264714000902/pdfft?md5=8824813e798bbc740be6b96c29e944e2&pid=1-s2.0-S0303264714000902-main.pdf}, publisher = {Elsevier}, } @inproceedings{Yang14b, author = {Shaowu Yang and Sebastian A. Scherer and Andreas Zell}, title = {Visual {SLAM} for Autonomous {MAVs} with Dual Cameras}, booktitle = {2014 International Conference on Robotics and Automation (ICRA'14)}, year = {2014}, address = {Hongkong, China}, month = {June}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/ICRA14_yang_final.pdf}, } @article{Eichner2014a, author = {Johannes Eichner and Lars Rosenbaum and Clemens Wrzodek and Hans-Ulrich H\"aring and Andreas Zell and Rainer Lehmann}, title = {{Integrated enrichment analysis and pathway-centered visualization of metabolomics, proteomics, transcriptomics, and genomics data by using the InCroMAP software}}, journal = {Journal of Chromatography B}, year = {2014}, month = may, doi = {http://dx.doi.org/10.1016/j.jchromb.2014.04.030}, issn = {1570-0232}, keywords = {Metabolomics}, publisher = {Elsevier}, url = {http://www.sciencedirect.com/science/article/pii/S1570023214002682} } @article{Eichner2014b, author = {Johannes Eichner and Clemens Wrzodek and Michael R\"omer and Heidrun Ellinger-Ziegelbauer and Andreas Zell}, title = {{Evaluation of toxicogenomics approaches for assessing the risk of nongenotoxic carcinogenicity in rat liver}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2014}, volume = {9}, pages = {e97678}, number = {5}, month = may, doi = {10.1371/journal.pone.0097678}, publisher = {Public Library of Science}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0097678} } @inproceedings{koch2014icra, author = {Artur Koch and Andreas Zell}, title = {Mapping of Passive {UHF} {RFID} Tags with a Mobile Robot using Outlier Detection and Negative Information}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA)}, year = {2014}, address = {Hong Kong, China}, month = {May}, publisher = {IEEE}, abstract = {In this paper we propose a novel approach to classify detection events from a stream of radio-frequency identification (RFID) measurements for the purpose of mapping RFID transponders. Since raw readings from RFID readers only provide information on positive read attempts, i.e. the detections of a tag, we propose an outlier filter method solely based on the spatial extent of the sensor model that is used for the mapping process. Furthermore, we use this filter to actually classify detections as well as non-detections of tags into valid and invalid positive as well as negative detection events. We incorporate the different classes into our mapping pipeline and introduce several extensions to improve the mapping accuracy. Experimental results including the classification and mapping accuracy are presented to prove the effectiveness of our approach.}, } @article{Roemer2014a, author = {Michael R\"omer and Johannes Eichner and Ute Metzger and Markus F. Templin and Simon Plummer and Heidrun Ellinger-Ziegelbauer and Andreas Zell}, title = {Cross-Platform Toxicogenomics for the Prediction of Non-Genotoxic Hepatocarcinogenesis in Rat}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2014}, volume = {9}, pages = {e97640}, number = {5}, month = may, abstract = {

In the area of omics profiling in toxicology, i.e. toxicogenomics, characteristic molecular profiles have previously been incorporated into prediction models for early assessment of a carcinogenic potential and mechanism-based classification of compounds. Traditionally, the biomarker signatures used for model construction were derived from individual high-throughput techniques, such as microarrays designed for monitoring global mRNA expression. In this study, we built predictive models by integrating omics data across complementary microarray platforms and introduced new concepts for modeling of pathway alterations and molecular interactions between multiple biological layers. We trained and evaluated diverse machine learning-based models, differing in the incorporated features and learning algorithms on a cross-omics dataset encompassing mRNA, miRNA, and protein expression profiles obtained from rat liver samples treated with a heterogeneous set of substances. Most of these compounds could be unambiguously classified as genotoxic carcinogens, non-genotoxic carcinogens, or non-hepatocarcinogens based on evidence from published studies. Since mixed characteristics were reported for the compounds Cyproterone acetate, Thioacetamide, and Wy-14643, we reclassified these compounds as either genotoxic or non-genotoxic carcinogens based on their molecular profiles. Evaluating our toxicogenomics models in a repeated external cross-validation procedure, we demonstrated that the prediction accuracy of our models could be increased by joining the biomarker signatures across multiple biological layers and by adding complex features derived from cross-platform integration of the omics data. Furthermore, we found that adding these features resulted in a better separation of the compound classes and a more confident reclassification of the three undefined compounds as non-genotoxic carcinogens.

}, doi = {10.1371/journal.pone.0097640}, publisher = {Public Library of Science}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0097640} } @inproceedings{Schauwecker2014b, author = {Konstantin Schauwecker and Andreas Zell}, title = {{Robust and Efficient Volumetric Occupancy Mapping with an Application to Stereo Vision}}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA)}, year = {2014}, pages = {6102--6107}, address = {Hong Kong, China}, month = {May}, pdf = {http://www.ra.cs.uni-tuebingen.de/publikationen/2014/schauwecker_icra2014.pdf}, } @article{Unterberger2014, author = {Unterberger, Elif B. and Eichner, Johannes and Wrzodek, Clemens and Lempi\"ainen, Harri and Luisier, Rapha\"elle and Terranova, R\'{e}mi and Metzger, Ute and Plummer, Simon and Knorpp, Thomas and Braeuning, Albert and Moggs, Jonathan and Templin, Markus and Honndorf, Valerie and Piotto, Martial and Zell, Andreas and Schwarz, Michael}, title = {{Metabolic Programs Orchestrated by the Activated Ha-ras and $\beta$-Catenin Oncoproteins in Mouse Liver Tumors}}, journal = {International Journal of Cancer}, year = {2014}, month = mar, doi = {10.1002/ijc.28798}, issn = {1097-0215}, publisher = {Wiley}, url = {http://dx.doi.org/10.1002/ijc.28798} } @article{Kenar2014, author = {Kenar, Erhan and Franken, Holger and Forcisi, Sara and W\F6rmann, Kilian and H\E4ring, Hans-Ulrich and Lehmann, Rainer and Schmitt-Kopplin, Philippe and Zell, Andreas and Kohlbacher, Oliver}, title = {Automated Label-free Quantification of Metabolites from Liquid Chromatography-Mass Spectrometry Data}, journal = {Molecular \& Cellular Proteomics}, year = {2014}, volume = {13}, pages = {348-359}, number = {1}, abstract = {Liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technology in metabolomics. In particular, label-free quantification based on LC-MS is easily amenable to large-scale studies and thus well suited to clinical metabolomics. Large-scale studies, however, require automated processing of the large and complex LC-MS datasets.We present a novel algorithm for the detection of mass traces and their aggregation into features (i.e. all signals caused by the same analyte species) that is computationally efficient and sensitive and that leads to reproducible quantification results. The algorithm is based on a sensitive detection of mass traces, which are then assembled into features based on mass-to-charge spacing, co-elution information, and a support vector machine-based classifier able to identify potential metabolite isotope patterns. The algorithm is not limited to metabolites but is applicable to a wide range of small molecules (e.g. lipidomics, peptidomics), as well as to other separation technologies.We assessed the algorithm's robustness with regard to varying noise levels on synthetic data and then validated the approach on experimental data investigating human plasma samples. We obtained excellent results in a fully automated data-processing pipeline with respect to both accuracy and reproducibility. Relative to state-of-the art algorithms, ours demonstrated increased precision and recall of the method. The algorithm is available as part of the open-source software package OpenMS and runs on all major operating systems.}, doi = {10.1074/mcp.M113.031278}, eprint = {http://www.mcponline.org/content/13/1/348.full.pdf+html}, url = {http://www.mcponline.org/content/13/1/348.abstract} } @inproceedings{Ran_IROS_2014, author = {Ran Liu and Goran Huski\'{c} and Andreas Zell}, title = {{Dynamic Objects Tracking with a Mobile Robot using Passive UHF RFID Tags}}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2014)}, year = {2014}, address = {Chicago, Illinois, USA}, days = {September 14--18}, } @inproceedings{Ran_IAS_2014, author = {Ran Liu and Andreas Zell}, title = {{Towards Localizing Both Static and Non-static RFID Tags with a Mobile Robot}}, booktitle = {International Conference on Intelligent Autonomous Systems (IAS-13)}, year = {2014}, address = {Padova, Italy}, days = {July 15-July 19}, } @article{Masselli2014JINT, author = {Andreas Masselli and Shaowu Yang and Karl Engelbert Wenzel and Andreas Zell}, title = {A Cross-Platform Comparison of Visual Marker Based Approaches for Autonomous Flight of Quadrocopters}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2014}, volume = {73}, pages = {349--359}, number = {1-4}, abstract = {In this paper, we compare three different marker based approaches for six degrees of freedom (6DOF) pose estimation, which can be used for position and attitude control of micro aerial vehicles (MAV). All methods are able to achieve real time pose estimation onboard without assistance of any external metric sensor. Since these methods can be used in various working environments, we compare their performance by carrying out experiments across two different platforms: an AscTec Hummingbird and a Pixhawk quadrocopter. We evaluate each method's accuracy by using an external tracking system and compare the methods with respect to their operating ranges and processing time. We also compare each method's performance during autonomous takeoff, hovering and landing of a quadrocopter. Finally we show how the methods perform in an outdoor environment. The paper is an extended version of the one with the same title published at the ICUAS Conference 2013.}, doi = {10.1007/s10846-013-9925-4}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/masselli2013JINT.pdf} } @article{Schauwecker2014, author = {Konstantin Schauwecker and Andreas Zell}, title = {{On-Board Dual-Stereo-Vision for the Navigation of an Autonomous MAV}}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2014}, volume = {74}, pages = {1--16}, number = {1-2}, month = {January}, note = {[The final publication is available at link.springer.com].}, abstract = { We present a quadrotor Micro Aerial Vehicle (MAV) equipped with four cameras, which are arranged in two stereo configurations. The MAV is able to perform stereo matching for each camera pair on-board and in real-time, using an efficient sparse stereo method. In case of the camera pair that is facing forward, the stereo matching results are used for a reduced stereo SLAM system. The other camera pair, which is facing downwards, is used for ground plane detection and tracking. Hence, we are able to obtain a full 6DoF pose estimate from each camera pair, which we fuse with inertial measurements in an extended Kalman filter. Special care is taken to compensate various drift errors. In an evaluation we show that using two instead of one camera pair significantly increases the pose estimation accuracy and robustness. }, pdf = {http://www.ra.cs.uni-tuebingen.de/publikationen/2013/schauwecker_jint2013.pdf}, publisher = {Springer}, url = {http://link.springer.com/article/10.1007/s10846-013-9907-6} } @article{YangsJINT13, author = {Shaowu Yang and Sebastian A. Scherer and Konstantin Schauwecker and Andreas Zell}, title = {{Autonomous Landing of MAVs on Arbitrarily Textured Landing Sites using Onboard Monocular Vision}}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2014}, volume = {74}, pages = {27-43}, number = {1-2}, abstract = {This paper presents a novel solution for micro aerial vehicles (MAVs) to autonomously search for and land on an arbitrary landing site using real-time monocular vision. The autonomous MAV is provided with only one single reference image of the landing site with an unknown size before initiating this task. We extend a well-known monocular visual SLAM algorithm that enables autonomous navigation of the MAV in unknown environments, in order to search for such landing sites. Furthermore, a multi-scale ORB feature based method is implemented and integrated into the SLAM framework for landing site detection. We use a RANSAC-based method to locate the landing site within the map of the SLAM system, taking advantage of those map points associated with the detected landing site. We demonstrate the efficiency of the presented vision system in autonomous flights, both indoor and in challenging outdoor environment.}, doi = {10.1007/s10846-013-9906-7}, issn = {0921-0296}, language = {English}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/JINT13_yangs.pdf}, publisher = {Springer}, url = {http://link.springer.com/article/10.1007/s10846-013-9906-7} } @article{Chaouiya2013, author = {Chaouiya, Claudine and B\'{e}renguier, Duncan and Keating, Sarah M. and Naldi, Aur\'{e}lien and van Iersel, Martijn P. and Rodriguez, Nicolas and Dr\"ager, Andreas and B\"uchel, Finja and Cokelaer, Thomas and Kowal, Bryan and Wicks, Benjamin and Gon\c{c}alves, Emanuel and Dorier, Julien and Page, Michel and Monteiro, Pedro T. and von Kamp, Axel and Xenarios, Ioannis and de Jong, Hidde and Hucka, Michael and Klamt, Steffen and Thierffry, Dennis and {Le Nov\`{e}re}, Nicolas and Saez-Rodriguez, Julio and Helikar, Tom\'{a}\v{s}}, title = {{SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools}}, journal = {BMC Systems Biology}, year = {2013}, volume = {7}, pages = {135}, number = {1}, month = dec, abstract = {Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. Results: We present the System Biology Markup Language (SBML) Qualitative Models Package (``qual''), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the cooperative development of the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyze qualitative models. Conclusion: SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.}, doi = {10.1186/1752-0509-7-135}, eprint = {1309.1910}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-135.pdf}, publisher = {Springer (Biomed Central Ltd.)}, url = {http://www.biomedcentral.com/1752-0509/7/135} } @article{Eichner2013c, author = {Eichner, Johannes and Topf, Florian and Dr\"ager, Andreas and Wrzodek, Clemens and Wanke, Dierk and Zell, Andreas}, title = {{TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2013}, volume = {8}, pages = {e82238}, number = {12}, month = dec, abstract = {One of the key mechanisms of transcriptional control are the specific connections between transcription factors (TF) and \emph{cis}-regulatory elements in gene promoters. The elucidation of these specific protein-DNA interactions is crucial to gain insights into the complex regulatory mechanisms and networks underlying the adaptation of organisms to dynamically changing environmental conditions. As experimental techniques for determining TF binding sites are expensive and mostly performed for selected TFs only, accurate computational approaches are needed to analyze transcriptional regulation in eukaryotes on a genome-wide level. We implemented a four-step classification workflow which for a given protein sequence (1) discriminates TFs from other proteins, (2) determines the structural superclass of TFs, (3) identifies the DNA-binding domains of TFs and (4) predicts their \emph{cis}-acting DNA motif. While existing tools were extended and adapted for performing the latter two prediction steps, the first two steps are based on a novel numeric sequence representation which allows for combining existing knowledge from a BLAST scan with robust machine learning-based classification. By evaluation on a set of experimentally confirmed TFs and non-TFs, we demonstrate that our new protein sequence representation facilitates more reliable identification and structural classification of TFs than previously proposed sequence-derived features. The algorithms underlying our proposed methodology are implemented in the two complementary tools TFpredict and SABINE. The online and stand-alone versions of TFpredict and SABINE are freely available to academics at \url{http://www.cogsys.cs.uni-tuebingen.de/software/TFpredict/} and \url{http://www.cogsys.cs.uni-tuebingen.de/software/SABINE/}.}, doi = {10.1371/journal.pone.0082238}, pdf = {http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0082238&representation=PDF}, publisher = {Public Library of Science}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0082238} } @inproceedings{jiang_ROBIO2013, author = {Jiang, Lixing and Koch, Artur and Scherer, Sebastian A. and Zell, Andreas}, title = {Multi-class Fruit Classification using {RGB-D} Data for Indoor Robots}, booktitle = {IEEE International Conference on Robotics and Biomimetics (ROBIO)}, year = {2013}, address = {Shenzhen, China}, month = {December}, abstract = {In this paper we present an effective and robust system to classify fruits under varying pose and lighting conditions tailored for an object recognition system on a mobile platform. Therefore, we present results on the effectiveness of our underlying segmentation method using RGB as well as depth cues for the specific technical setup of our robot. A combination of RGB low-level visual feature descriptors and 3D geometric properties is used to retrieve complementary object information for the classification task. The unified approach is validated using two multi-class RGB-D fruit categorization datasets. Experimental results compare different feature sets and classification methods and highlight the effectiveness of the proposed features using a Random Forest classifier.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/jiang_robio2013.pdf} } @article{Buechel2013b, author = {B\"uchel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek, Clemens and Czauderna, Tobias and Keller, Roland and Mittag, Florian and Schubert, Michael and Glont, Mihai and Golebiewski, Martin and {van Iersel}, Martijn and Keating, Sarah M. and Rall, Matthias and Wybrow, Michael and Hermjakob, Henning and Hucka, Michael and {B Kell}, Douglas and M\"uller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya, Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe, Camille and Dr\"ager, Andreas and {Le Nov\`{e}re}, Nicolas}, title = {{Path2Models: large-scale generation of computational models from biochemical pathway maps}}, journal = {BMC Systems Biology}, year = {2013}, volume = {7}, pages = {116}, number = {1}, month = nov, abstract = {Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data. Results: To increase the efficiency of model creation, the Path2Models representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2~600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at \url{http://www.ebi.ac.uk/biomodels-main/path2models}. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps. Conclusions: To date, the project has resulted in more than 140~000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.}, doi = {10.1186/1752-0509-7-116}, keywords = {Modular rate law, Constraint based models, Logical models, SBGN, SBML}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-116.pdf}, url = {http://www.biomedcentral.com/1752-0509/7/116} } @article{Buechel2013c, author = {B\"uchel, Finja and Saliger, Sandra and Dr\"ager, Andreas and Hoffmann, Stephanie and Wrzodek, Clemens and Zell, Andreas and Kahle, Philipp J.}, title = {{Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of $\alpha$-synuclein}}, journal = {BMC Neuroscience}, year = {2013}, volume = {14}, number = {136}, month = nov, abstract = {Background: Parkinson's disease is an age-related disease, whose pathogenesis is not completely known. Animal models exist for investigating the disease but not all results can be easily transferred to humans. Therefore, mathematical or probabilistic models for the human disease are to be constructed \emph{in-silico} in order to predict specific processes within a cell, such as the dopamine metabolism and transport processes in a neuron. Results: We present an SBML model of a whole dopaminergic nerve cell consisting of 139 reactions and 111 metabolites which includes, among others, the dopamine metabolism and transport, oxidative stress, aggregation of $\alpha$-synuclein ($\alpha$SYN), lysosomal and proteasomal degradation, and mitophagy. The predictive power of the model was investigated using flux balance analysis for the identification of steady model states. To this end, we performed six experiments: (i) investigation of the normal cell behavior, (ii) increase of O\textsubscript{2}, (iii) increase of ATP, (iv) influence of neurotoxins, (v) increase of $\alpha$SYN the cell and (vi) increase of dopamine synthesis. The SBML model is available in BioModels database with identifier MODEL1302200000. Conclusion: It is possible to simulate the normal behavior of an \emph{in-vivo} nerve cell with the developed model. We show that the model is sensitive for neurotoxins and oxidative stress. Further, an increased level of $\alhpa$SYN induces apoptosis and we observed an increased flux of $\alpha$SYN to the extracellular space.}, doi = {10.1186/1471-2202-14-136}, issn = {1471-2202}, keywords = {Parkinson's disease, Dopaminergic nerve cell model, SBML model, Flux balance analysis}, pdf = {http://www.biomedcentral.com/content/pdf/1471-2202-14-136.pdf}, url = {http://www.biomedcentral.com/1471-2202/14/136} } @inproceedings{RanArtur_IROS_2013, author = {Ran Liu and Artur Koch and Andreas Zell}, title = {{Mapping UHF RFID Tags with a Mobile Robot using 3D Sensor Model}}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2013)}, year = {2013}, address = {Big Sight, Tokyo, Japan}, month = {November}, abstract = {Recently, researchers showed growing interest in utilizing UHF Radio-Frequency Identification (RFID) technology for localizing tagged items with mobile robots in industrial scenarios. In this paper we present a novel three-dimensional (3D) probability sensor model of RFID antennas in the context of mapping passive RFID tags with mobile robots. The proposed 3D sensor model characterizes both detection rates and received signal strength (RSS). Compared to 2D-sensor model based approaches, the 3D model gains a higher mapping accuracy for 2D position estimation. Specially, with this sensor model, we are able to localize the tags in 3D by integrating the measurements from a pair of RFID antennas mounted at different heights of the robot. Furthermore, by integrating negative information (i.e., non-detections), the 3D mapping accuracy can be improved. Additionally, we utilize KLD-sampling to reduce the number of particles for our specific application, so that our algorithm can be performed online. Indoor experiments with a Scitos G5 robot demonstrate the effectiveness of our approach. }, days = {3-8}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/ran_iros_2013.pdf} } @inproceedings{scherer2013iros, author = {Scherer, Sebastian A. and Andreas Zell}, title = {{Efficient Onboard RGBD-SLAM for Fully Autonomous MAVs}}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2013)}, year = {2013}, address = {Tokyo Big Sight, Japan}, month = {November}, abstract = {We present a computationally inexpensive RGBD-SLAM solution taylored to the application on autonomous MAVs, which enables our MAV to fly in an unknown environment and create a map of its surroundings completely autonomously, with all computations running on its onboard computer. We achieve this by implementing efficient methods for both tracking its current location with respect to a heavily processed previously seen RGBD image (keyframe) and efficient relative registration of a set of keyframes using bundle adjustment with depth constraints as a front-end for pose graph optimization. We prove the accuracy and efficiency of our system based on a public benchmark dataset and demonstrate that the proposed method enables our quadrotor to fly autonomously.}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/scherer2013iros.pdf}, } @inbook{Eichner2013b, pages = {143-164}, title = {{Inference of Alternative Splicing from Tiling Array Data}}, publisher = {Humana Press}, year = {2013}, editor = {Lee, Tin-Lap and Luk, Shui and Chun, Alfred}, author = {Johannes Eichner}, volume = {1067}, series = {Methods in Molecular Biology}, month = oct, booktitle = {Tiling Arrays}, url = {http://dx.doi.org/10.1007/978-1-62703-607-8_10} } @article{Buechel2013a, author = {B\"uchel, Finja and Mittag, Florian and Wrzodek, Clemens and Zell, Andreas and Gasser, Thomas and Sharma, Manu}, title = {{Integrative pathway-based approach for genome-wide association studies: identification of new pathways for rheumatoid arthritis and type 1 diabetes}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2013}, volume = {8}, pages = e78577, number = {10}, month = sep, doi = {10.1371/journal.pone.0078577}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0078577} } @article{Eichner2013a, author = {Johannes Eichner and Nadine Kossler and Clemens Wrzodek and Arno Kalkuhl and Dorthe Bach Toft and Nina Ostenfeldt and Virgile Richard and Andreas Zell}, title = {{A Toxicogenomic Approach for the Prediction of Murine Hepatocarcinogenesis Using Ensemble Feature Selection}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2013}, volume = {8}, pages = {e73938}, number = {9}, month = sep, doi = {10.1371/journal.pone.0073938}, publisher = {Public Library of Science}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073938} } @inproceedings{jimenez2013ecmr, author = {Jimenez Lugo, Jacobo and Andreas Masselli and Andreas Zell}, title = {Following a quadrotor with another quadrotor using computer vision}, booktitle = {European Conference on Mobile Robots (ECMR 2013)}, year = {2013}, address = {Barcelona, Catalonia, Spain}, month = {September}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/JimeMassECMR13.pdf} } @inproceedings{laible2013ecmr, author = {Stefan Laible and Yasir Niaz Khan and Andreas Zell}, title = {Terrain Classification With Conditional Random Fields on Fused 3D LIDAR and Camera Data}, booktitle = {European Conference on Mobile Robots (ECMR 2013)}, year = {2013}, pages = {172--177}, address = {Barcelona, Catalonia, Spain}, month = {September}, publisher = {IEEE}, abstract = {For a mobile robot to navigate safely and efficiently in an outdoor environment, it has to recognize its surrounding terrain. Our robot is equipped with a low-resolution 3D LIDAR and a color camera. The data from both sensors are fused to classify the terrain in front of the robot. Therefore, the ground plane is divided into a grid and each cell is classified as either asphalt, cobblestones, grass or gravel. We use height and intensity features for the LIDAR data and Local ternary patterns for the image data. By additionally taking into account the context-sensitive nature of the terrain, the results can be improved significantly. We present a method based on Conditional Random Fields and compare it with a Markov Random Field based approach. We show that the Conditional Random Field model is better suited for our task. We achieve an average true positive rate of 94.2% for classifying the grid cells into the four terrain classes.}, doi = {10.1109/ECMR.2013.6698838}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/laible2013ecmr.pdf}, } @inproceedings{Masselli2013ecmr, author = {Andreas Masselli and Richard Hanten and Andreas Zell}, title = {{Robust Real-Time Detection of Multiple Balls on a Mobile Robot}}, booktitle = {European Conference on Mobile Robots (ECMR 2013)}, year = {2013}, address = {Barcelona, Catalonia, Spain}, month = {September}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/masselli2013ecmr.pdf} } @inproceedings{scherer2013ecmr, author = {Scherer, Sebastian A. and Alina Kloss and Andreas Zell}, title = {{Loop Closure Detection using Depth Images}}, booktitle = {European Conference on Mobile Robots (ECMR 2013)}, year = {2013}, address = {Barcelona, Catalonia, Spain}, month = {September}, abstract = {We investigate the question whether loop closure detection using depth images is feasible using currently available depth features. For this reason, we collected a benchmark dataset consisting of a total number of 15 logfiles with several loops in various environments, implemented a modular and easily extensible loop closure detector and used this to evaluate the adequacy of state-of-the art depth features on our benchmark dataset. To allow for a fair comparison, we determined the best values for the sometimes large number of user-chosen parameters using a large-scale grid search. Since our benchmark dataset contains both depth and RGB images, we can compare the performance relying on depth features with the performance achieved when using intensity image features.}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/scherer2013ecmr.pdf}, } @inbook{Draeger2013a, chapter = {Metabolic Networks}, pages = {1249--1251}, title = {{Encyclopedia of Systems Biology}}, publisher = {Springer-Verlag}, year = {2013}, editor = {Dubitzky, Werner and Wolkenhauer, Olaf and Yokota, Hiroki and Cho, Kwang-Hyun}, author = {Dr\"ager, Andreas and Planatscher, Hannes}, address = {Springer New York Heidelberg Dorodrecht London}, month = aug, abstract = {Metabolic networks are interconnected pathways of biochemical reactions within living cells through which building blocks or compounds necessary for cellular functioning are assembled (anabolism) or energy and matter are produced by breaking down biomolecules (catabolism). These pathways are often organized as cycles or chains of coupled reactions, in which the product of one reaction serves as the substrate of the succeeding reaction. Although all reactions are reversible in principle, thermodynamic gradients within metabolic reactions often promote one direction, yielding a flux through the metabolic pathways. In many cases distinct pathways or reactions exist for contrary flows of matter. All processes within a metabolic network are temporally and spatially organized. Often cells contain several compartments which separate parts of its reaction network into subnetworks. The reacting compounds are called metabolites or species. Additionally, modifiers can activate, inhibit or catalyze a reaction. Enzymes play a central role in metabolic networks, because they act as catalysts in the vast majority of the reactions. The interplay of its components determines the dynamic behavior of the overall network.}, doi = {10.1007/978-1-4419-9863-7_1277}, isbn = {978-1441998644}, keywords = {Biochemical network; Metabolic pathways; Pathway map; Pathways; Reaction network; Reaction pathways}, language = {eng}, url = {http://link.springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_100849} } @inbook{Draeger2013b, chapter = {{Parameter Estimation, Metabolic Network Modeling}}, pages = {1627--1631}, title = {{Encyclopedia of Systems Biology}}, publisher = {Springer-Verlag}, year = {2013}, editor = {Dubitzky, Werner and Wolkenhauer, Olaf and Yokota, Hiroki and Cho, Kwang-Hyun}, author = {Dr\"ager, Andreas and Planatscher, Hannes}, address = {Springer New York Heidelberg Dorodrecht London}, month = aug, abstract = {Metabolic networks can mathematically be modeled as a differential equation system. These models consist of a stoichiometric matrix, a modulation matrix, and a vector of reaction rates. The mathematical structure of the differential equation system is usually assumed to be known, its parameters, however, in general are not. Here the term ``parameter'' denotes all quantities within the model whose values are uncertain or difficult to obtain experimentally. In the most common case, these comprise kinetic constants, concentrations of external metabolites, enzyme concentrations or activities, and compartment sizes. The parameter estimation problem aims at estimating meaningful values for these targets by trying to coincide given experimental data with the predictions of the model. Bayesian methods, maximum likelihood estimates, and (biologically inspired) optimization procedures are frequently used estimation approaches. Experimental data usually contain a time-course or steady state of concentration values of the reacting species (compounds) within the network. Before estimating their values, a parameter identifiability analysis should be conducted. Estimated values should be analyzed regarding their thermodynamic plausibility.}, doi = {10.1007/978-1-4419-9863-7_1174}, isbn = {978-1441998644}, keywords = {Model calibration, Model fitting, Parameter fitting, Parameter identification, Regression}, language = {eng}, url = {http://link.springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_1174} } @article{Gispert12072013, author = {Gispert, Suzana and Parganlija, Dajana and Klinkenberg, Michael and Dr\"ose, Stefan and Wittig, Ilka and Mittelbronn, Michel and Grzmil, Pawel and Koob, Sebastian and Hamann, Andrea and Walter, Michael and B\"uchel, Finja and Adler, Thure and de Angelis, Martin Hrab\'{e} and Busch, Dirk H. and Zell, Andreas and Reichert, Andreas S. and Brandt, Ulrich and Osiewacz, Heinz D. and Jendrach, Marina and Auburger, Georg}, title = {Loss of mitochondrial peptidase Clpp leads to infertility, hearing loss plus growth retardation via accumulation of {CLPX, mtDNA,} and inflammatory factors}, journal = {Human Molecular Genetics}, year = {2013}, month = {July}, abstract = {The peptidase {CLPP} is conserved from bacteria to humans. In the mitochondrial matrix, it multimerizes and forms a macromolecular proteasome-like cylinder together with the chaperone CLPX. In spite of a known relevance for the mitochondrial unfolded protein response, its substrates and tissue-specific roles are unclear in mammals. Recessive CLPP mutations were recently observed in the human Perrault variant of ovarian failure and sensorineural hearing loss. Here, a first characterization of Clpp null mice demonstrated complete female and male infertility and auditory deficits. Disrupted spermatogenesis already at the spermatid stage and ovarian follicular differentiation failure were evident. Reduced pre-/post-natal survival and marked ubiquitous growth retardation contrasted with only light impairment of movement and respiratory activities. Interestingly, the mice showed resistance to ulcerative dermatitis. Systematic expression studies detected up-regulation of other mitochondrial chaperones, accumulation of CLPX and mtDNA as well as inflammatory factors throughout tissues. T-lymphocytes in the spleen were activated. Thus, murine Clpp deletion represents a faithful Perrault model. The disease mechanism probably involves deficient clearance of mitochondrial components and inflammatory tissue destruction.}, doi = {10.1093/hmg/ddt338}, eprint = {http://hmg.oxfordjournals.org/content/early/2013/07/12/hmg.ddt338.full.pdf+html}, url = {http://hmg.oxfordjournals.org/content/early/2013/07/12/hmg.ddt338.abstract} } @article{Keller2013, author = {Keller, Roland and D\"orr, Alexander and Tabira, Akito and Funahashi, Akira and Ziller, Michael J. and Adams, Richard and Rodriguez, Nicolas and {Le Nov\`{e}re}, Nicolas and Hiroi, Noriko and Planatscher, Hannes and Zell, Andreas and Dr\"ager, Andreas}, title = {The systems biology simulation core algorithm}, journal = {BMC Systems Biology}, year = {2013}, volume = {7}, pages = {55}, month = jul, abstract = {Background: With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases. Results: This article describes an efficient algorithm to solve SBML models that are interpreted in terms of ordinary differential equations. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven sophisticated interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and all models of BioModels Database. Conclusions: The formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. The reference implementation can be used as a simulation backend for Java-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from \url{http://simulation-core.sourceforge.net}. Feature requests, bug reports, contributions, or any further discussion can be directed to the mailing list \url{mailto:simulation-core-development@lists.sourceforge.net}.}, doi = {10.1186/1752-0509-7-55}, keywords = {Systems biology; Biological networks; Mathematical modeling; Simulation; Algorithms; Ordinary differential equation systems; Numerical integration; Software engineering}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-55.pdf}, url = {http://www.biomedcentral.com/1752-0509/7/55} } @article{Vlaic26062013, author = {Vlaic, Sebastian and Hoffmann, Bianca and Kupfer, Peter and Weber, Michael and Dr\"ager, Andreas}, title = {{GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML}}, journal = {Bioinformatics}, year = {2013}, volume = {29}, pages = {2216--2217}, month = jun, abstract = {Summary: GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and \emph{minimum information required in the annotation of models} registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage. Availability: GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from \url{http://www.hki-jena.de/index.php/0/2/490}. Supplementary information: General information on GRN2SBML, examples and tutorials are available at the tool's web page. Contact: \url{mailto:Sebastian.Vlaic@hki-jena.de} or \url{mailto:andraeger@eng.ucsd.edu}}, doi = {10.1093/bioinformatics/btt370}, pdf = {http://bioinformatics.oxfordjournals.org/content/29/17/2216.full.pdf}, url = {http://bioinformatics.oxfordjournals.org/content/29/17/2216.abstract} } @phdthesis{Wrzodek2013PhD, author = {Wrzodek, Clemens}, title = {Inference and integration of biochemical networks with multilayered omics data}, school = {University of Tuebingen}, year = {2013}, address = {T\"ubingen, Germany}, month = jun, abstract = { The technological advances of the last decade have led to numerous studies focusing on genome-wide transcriptomic changes. This is also reflected in a great number of publications that compare the gene expression levels of healthy and other samples. However, the detailed molecular mechanisms that cause these changes remain largely unknown. The different types of cancer are popular examples, for which altered transcriptomic expression profiles are known for a long time, and researchers nowadays focus on identifying causes and treatments against these alterations. Epigenetic effects, such as DNA methylation, have been identified as associated to most types of cancer. The integration of both omics layers---transcriptomic and epigenomic---allowed for explaining varied gene expression levels for some genes. Despite these promising results, automated methods for an integration of multiple omics datasets are still in an early stage of development. More omics layers need to be analyzed integratively and more approaches need to be developed that help researchers finding causes for varied expression levels. For this purpose, systems biology methods are required that interpret biological coherences as an overall system and help to identify complex interactions. However, the biochemical networks that underly those systems must be reconstructed before most systems biology methods can be applied or interactions can be identified. Thus, approaches for the reconstruction of biochemical networks and novel methods, which help identifying complex coherences between different omics layers are firstly described in this thesis. It thereby focuses on the inference of biochemical networks and their subsequent integration with multilayered omics data. A widely-used source for biochemical networks are biological pathways. Unfortunately, they are mostly stored as inaccurate and incomplete qualitative descriptions in proprietary formats and thus, cannot be used directly with systems biology methods. This thesis presents a method that automatically fixes those issues and translates pathways to well-defined computational models. As a result of this work, 142,050 revised models of metabolic and non-metabolic pathways have been generated and put into the popular BioModels repository for the systems biology modeling language (SBML). The ModuleMaster method is a second approach for the generation of biochemical networks. More specifically, transcriptional regulatory networks are inferred from combinations of experimental gene expression data and a priori knowledge. To this end, gene expression data is clustered and regulatory transcription factors are determined. The inferred interactions between both span the final network. The established biochemical networks are used for a joint visualization of multilayered omics data. For this purpose, it is discussed how different omics layers can be integrated into a single dataset. On this basis, a methodology has been developed that integratively depicts messenger RNA, microRNA, DNA methylation and protein data in a single network. Besides this integration technique, several further integrated omics data analysis methods are presented in this thesis. The concept of gene-set enrichment analysis is extended to multilayered omics data and methods that ease a joint inspection of these high-dimensional datasets are presented. Finally, a machine learning approach is described that links epigenetic profiles to genetic features. This is used to discover the mechanisms and features that induce changes in the epigenome.}, isbn = {978-3-8439-1116-0}, keywords = {Integrator, InCroMAP, integration of omics data, machine learning, omics data, JSBML, MARCAR, metabolic modeling, gene-regulatory network, ModuleMaster, path2models, SBML, BioPAX, KEGG, KEGGtranslator, CpG island}, InCroMAP, HepatoSys, MARCAR, NGFN-II, Spher4Sys}, publisher = {Verlag Dr.~Hut, Sternstra{\ss}e 18, M\"unchen}, url = {http://www.dr.hut-verlag.de/978-3-8439-1116-0.html} } @inproceedings{Masselli2013, author = {Andreas Masselli and Shaowu Yang and Karl Engelbert Wenzel and Andreas Zell}, title = {A Cross-Platform Comparison of Visual Marker Based Approaches for Autonomous Flight of Quadrocopters}, booktitle = {Proceedings of International Conference on Unmanned Aircraft Systems}, year = {2013}, pages = {1-9}, address = {Atlanta, Georgia, USA}, month = may, abstract = {In this paper, we compare three different marker based approaches for six degrees of freedom (6DOF) pose estimation, which can be used for position and attitude control of micro aerial vehicles (MAV). All methods are able to achieve real time pose estimation onboard without assistance of any external metric sensor. Since these methods can be used in various working environments, we compare their performance by carrying out experiments across two different platforms: An AscTec Hummingbird and a Pixhawk quadrocopter. We evaluate each method's accuracy by using an external tracking system and compare the methods with respect to their operating ranges and processing time. We finally compare each method's performance during autonomous takeoff, hovering and landing of a quadrocopter.}, days = {28-31}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/masselli2013icuas.pdf} } @inproceedings{Schauwecker2013a, author = {Schauwecker, Konstantin and Zell, Andreas}, title = {{On-Board Dual-Stereo-Vision for Autonomous Quadrotor Navigation}}, booktitle = {International Conference on Unmanned Aircraft Systems (ICUAS)}, year = {2013}, pages = {332--341}, address = {Atlanta, GA, USA}, month = {May}, publisher = {IEEE}, abstract = { We present a quadrotor Micro Aerial Vehicle (MAV) capable of autonomous indoor navigation. The MAV is equipped with four cameras arranged in two stereo configurations. One camera pair is facing forward and serves as input for a reduced stereo SLAM system. The other camera pair is facing downwards and is used for ground plane detection and tracking. All processing, including sparse stereo matching, is run on-board in real-time and at high processing rates. We demonstrate the capabilities of this MAV design in several flight experiments. Our MAV is able to recover from pose estimation errors and can cope with processing failures for one camera pair. We show that by using two camera pairs instead of one, we are able to significantly increase navigation accuracy and robustness. }, pdf = {http://www.ra.cs.uni-tuebingen.de/publikationen/2013/schauwecker_icuas2013.pdf}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6564706} } @inproceedings{YangsICUAS13, author = {Shaowu Yang and Sebastian A. Scherer and Konstantin Schauwecker and Andreas Zell}, title = {{Onboard Monocular Vision for Landing of an MAV on a Landing Site Specified by a Single Reference Image}}, booktitle = {2013 International Conference on Unmanned Aircraft Systems (ICUAS'13)}, year = {2013}, pages = {317--324}, address = {Atlanta, GA, USA}, month = {May}, abstract = {This paper presents a real-time monocular vision solution for MAVs to autonomously search for and land on an arbitrary landing site. The autonomous MAV is provided with only one single reference image of the landing site with an unknown size before initiating this task. To search for such landing sites, we extend a well-known visual SLAM algorithm that enables autonomous navigation of the MAV in unknown environments. A multi-scale ORB feature based method is implemented and integrated into the SLAM framework for landing site detection. We use a RANSAC-based method to locate the landing site within the map of the SLAM system, taking advantage of those map points associated with the detected landing site. We demonstrate the efficiency of the presented vision system in autonomous flight, and compare its accuracy with ground truth data provided by an external tracking system.}, days = {28-31}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/ICUAS13_yangs_final.pdf}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6564704} } @article{Yin2013, author = {Yin, Peiyuan and Peter, Andreas and Franken, Holger and Zhao, Xinjie and Neukamm, Sabine Sarah and Rosenbaum, Lars and Lucio, Marianna and Zell, Andreas and H\"aring, Hans-Ulrich and Xu, Guowang and Lehmann, Rainer}, title = {Pre-analytical aspects and sample quality assessment in metabolomics studies of human blood}, journal = {Clinical Chemistry}, year = {2013}, volume = {59}, pages = {833-845}, number = {5}, month = may, } @inproceedings{jimenez2013ICUAS, author = {Jimenez Lugo, Jacobo and Andreas Zell}, title = {Framework for Autonomous Onboard Navigation with the AR.Drone}, booktitle = {International Conference on Unmanned Aircraft Systems (ICUAS'13)}, year = {2013}, address = {Atlanta, Georgia, USA}, month = {April}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/jimenez_icuas_final.pdf} } @article{Beck13_1, author = {Markus Beck and Peter Bayer and Michael de Paly and Jozsef Hecht-Mendez and Andreas Zell}, title = {Geometric Arrangement and Operation Mode Adjustment in Low Enthalpy Geothermal Borehole Fields for Heating}, journal = {Energy}, year = {2013}, volume = {49}, pages = {434-443}, abstract = {The efficient operation of ground source heat pump (GSHP) systems with multiple borehole heat exchangers (BHEs) over a lifetime of decades implies an optimized performance of the BHEs and a mitigation of the environmental impact of the system. This paper introduces a new combined optimization approach, which optimizes the BHE positions as well as the individually regulated energy extraction for each single BHE within a given BHE field in conduction dominated media for a given seasonal changing load profile. The optimization of only the BHE positions without optimizing the individual BHE loads nearly produces the same improvement of the underground temperature change of approximately 12% as an optimization of the BHE loads without optimized positioning. The combination of both optimization approaches result in only slightly better results compared to a result achieved by only one of the optimization approaches. Thus for homogeneous fields without groundwater flow, an optimal load assignment can be replaced by an optimal BHE placement, which leads to a considerably reduced complexity of the BHE field.}, keywords = {shallow geothermal energy; multiple BHEs; BHE positioning; optimization; evolutionary algorithms; linear programming}, } @inproceedings{voduc2013, author = {My Vo Duc and Andreas Zell}, title = {Real Time Face Tracking and Pose Estimation Using an Adaptive Correlation Filter for Human-Robot Interaction}, booktitle = {European Conference on Mobile Robots (ECMR 2013) (Oral)}, year = {2013}, address = {Barcelona, Catalonia, Spain}, month = september, abstract = {In this paper, we present a real time algorithm for mobile robots to track human faces and estimate face poses accurately, even when humans move freely and far away from the camera or go through different illumination conditions in uncontrolled environments. We combine the algorithm of an adaptive correlation filter with a Viola-Jones object detection to track the face as well as the facial features including the two external eye corners and the nose. These facial features provide geometric cues to estimate the face pose robustly. In our method, the depth information from a Microsoft Kinect camera is used to estimate the face size and improve the performance of tracking facial features. Our method is shown to be robust and fast in uncontrolled environments.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/voduc2013.pdf} } @article{hecht_mendez13, author = {Jozsef Hecht-Mendez and Michael de Paly and Markus Beck and Peter Bayer}, title = {Optimization of energy extraction for vertical closed-loop geothermal systems considering groundwater flow}, journal = {Energy Conversion and Management}, year = {2013}, volume = {66}, pages = {1-10}, abstract = {A combined simulation-optimization procedure is presented to regulate the operation of borehole heat exchangers (BHEs) in a multiple BHE field when groundwater flow exists. Such fields are of increasing interest for large-scale geothermal heating energy supply of buildings, but so far strategic adjustment of energy extraction rates (loads) of the individual BHEs has not been considered in practice. Groundwater flow means an additional advective energy supply, which is advantageous but also complicates proper BHE adjustment. In the presented procedure, the field is simulated by temporally and spatially superimposed moving line source equations. The optimization goal is formulated in an objective function to minimize the thermal impact in the ground, to avoid extreme temperature anomalies, and by this, ultimately improve heat pump performance. For a given seasonal energy demand and total operation time, linear programming efficiently delivers optimized BHE operation patterns. For an examined square lattice of 25 BHEs, the optimized radial load patterns characteristic for conduction dominated conditions change to patterns that are oriented at the groundwater flow when advection dominates. Through this, optimization always levels the temperature distribution in the ground. Also, in comparison to routine practice, mean BHE outlet temperatures can be increased. For the small study case, numerical simulation reveals that already more than 1 K can be achieved, given a seasonal energy demand oriented at common conditions in central Europe. However, for a fixed energy demand, advective heat supply towards the BHEs increases with groundwater flow velocity and thus mitigates the benefits from optimization. }, } @article{Lehmann2013, author = {Lehmann, R. and Franken, H. and Dammeier, S. and Rosenbaum, L. and Kantartzis, K. and Peter, A. and Zell, A. and Adam, P. and Li, J. and Xu, G. and K\"onigsrainer, A. and Machann, J. and Schick, F. and Hrabe de Angelis, M. and Schwab, M. and Staiger, H. and Schleicher, E. and Gastaldelli, A. and Fritsche, A. and H\"aring, H.-U. and Stefan, N.}, title = {Circulating lyso-phosphatidylcholines are markers of ametabolically benign nonalcoholic fatty liver}, journal = {Diabetes Care}, year = {2013}, volume = {36}, pages = {2331--2338}, number = {8}, } @inproceedings{yuyiliu13, author = {Liu, Yuyi and Longo, Stefano and Kerrigan, Eric C.}, title = {Nonlinear Predictive Control of Autonomous Soaring {UAVs} Using {3DOF} Models}, booktitle = {Proc. of European Control Conference ({ECC 13})}, year = {2013}, pages = {1365-1370}, } @article{JimenezJINT13, author = {Jacobo Jimenez Lugo and Andreas Zell}, title = {Framework for Autonomous Onboard Navigation with the AR.Drone }, journal = {Journal of Intelligent \& Robotic Systems}, year = {2013}, note = {Online First}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/masselli2013JINT.pdf} } @inproceedings{Otte2013Oct, author = {Otte, S. and Otte, C. and Schlaefer, A. and Wittig, L. and Huttmann, G. and Dromann, D. and Zell, A.}, title = {{OCT A-Scan based Lung Tumor Tissue Classification with Bidirectional Long Short Term Memory Networks}}, booktitle = {Machine Learning for Signal Processing (MLSP), 2013 IEEE International Workshop on}, year = {2013}, pages = {1--6}, doi = {10.1109/MLSP.2013.6661944}, issn = {1551-2541}, keywords = {Accuracy;Biomedical optical imaging;Lungs;Needles;Optical imaging;Training;Tumors;LSTM;Long Short Term Memory;OCT;Sequence classification;bidirectional LSTM;lung tumor recognition;optical coherence tomography;recurrent neural networks;soft tissue classification}, } @article{Rosenbaum2013b, author = {Rosenbaum, Lars and D\"{o}rr, Alexander and Bauer, Matthias R. and Boeckler, Frank M. and Zell, Andreas}, title = {Inferring multi-target {QSAR} models with taxonomy-based multi-task learning}, journal = {J. Cheminf.}, year = {2013}, volume = {5}, pages = {33}, } @article{Rosenbaum2013a, author = {Lars Rosenbaum and Andreas Jahn and Alexander D\"{o}rr and Andreas Zell}, title = {Optimization and Visualization of the Edge Weights in Optimal Assignment Methods for Virtual Screening}, journal = {BioData Mining}, year = {2013}, volume = {6}, pages = {7}, } @article{Wrzodek2013a, author = {Wrzodek, Clemens and B\"uchel, Finja and Ruff, Manuel and Dr\"ager, Andreas and Zell, Andreas}, title = {Precise generation of systems biology models from {KEGG} pathways.}, journal = {BMC Systems Biology}, year = {2013}, volume = {7}, pages = {15}, number = {1}, month = jan, abstract = {Background: The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, the pathways can be extended with an enormous amount of information and provide a foundation for initial structural modeling approaches. As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and often omit important details for the sake of a clear arrangement of its entries. Thus, a direct conversion into systems biology models would produce incomplete and erroneous models. Results: Here, we present a precise method for processing and converting KEGG pathways into initial metabolic and signaling models encoded in the standardized community pathway formats SBML (Levels 2 and 3) and BioPAX (Levels 2 and 3). This method involves correcting invalid or incomplete KGML content, creating complete and valid stoichiometric reactions, translating relations to signaling models and augmenting the pathway content with various information, such as cross-references to Entrez Gene, OMIM, UniProt ChEBI, and many more. Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG to BioPAX does not involve a loss of information, whilst lossless translations to SBML can only be performed using SBML Level 3, including its recently proposed qualitative models and groups extension packages. Conclusions: Building correct BioPAX and SBML signaling models from the KEGG database is a unique characteristic of the proposed method. Further, there is no other approach that is able to appropriately construct metabolic models from KEGG pathways, including correct reactions with stoichiometry. The resulting initial models, which contain valid and comprehensive SBML or BioPAX code and a multitude of cross-references, lay the foundation to facilitate further modeling steps.}, doi = {10.1186/1752-0509-7-15}, issn = {1752-0509}, keywords = {KEGG, KGML, SBML, BioPAX, modeling, systems biology, qualitative modeling, quantitative modeling, converter, comparison}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-15.pdf}, url = {http://www.biomedcentral.com/1752-0509/7/15} } @article{YangsJINT12, author = {Shaowu Yang and Sebastian A. Scherer and Andreas Zell}, title = {An Onboard Monocular Vision System for Autonomous Takeoff, Hovering and Landing of a Micro Aerial Vehicle}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2013}, volume = {69}, pages = {499--515}, number = {1--4}, month = jan, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/yang_JINT.pdf}, publisher = {Springer}, url = {http://link.springer.com/article/10.1007/s10846-012-9749-7} } @article{Holmans2012, author = {Holmans, Peter and Moskvina, Valentina and Jones, Lesley and Sharma, Manu and {International Parkinson's Disease Genomics Consortium (IPDGC)}, The and Vedernikov, Alexey and B\"uchel, Finja and Sadd, Mohamad and Bras, Jose M. and Bettella, Francesco and Nicolaou, Nayia and Sim\'{o}n-S\'{a}nchez, Javier and Mittag, Florian and Gibbs, J. Raphael and Schulte, Claudia and Durr, Alexandra and Guerreiro, Rita and Hernandez, Dena and Brice, Alexis and Stef\'{a}nsson, Hreinn and Majamaa, Kari and Gasser, Thomas and Heutink, Peter and Wood, Nicholas W. and Martinez, Maria and Singleton, Andrew B. and Nalls, Michael A. and Hardy, John and Morris, Huw R. and Williams, Nigel M.}, title = {{A pathway-based analysis provides additional support for an immune-related genetic susceptibility to Parkinson's disease}}, journal = {Human Molecular Genetics}, year = {2012}, month = dec, abstract = {Parkinson's disease (PD) is the second most common neurodegenerative disease affecting 1-2\% in people >60 and 3-4\% in people >80. Genome-wide association (GWA) studies have now implicated significant evidence for association in at least 18 genomic regions. We have studied a large PD-meta analysis and identified a significant excess of SNPs (P < 1 $\times$ $10^16$) that are associated with PD but fall short of the genome-wide significance threshold. This result was independent of variants at the 18 previously implicated regions and implies the presence of additional polygenic risk alleles. To understand how these loci increase risk of PD, we applied a pathway-based analysis, testing for biological functions that were significantly enriched for genes containing variants associated with PD. Analysing two independent GWA studies, we identified that both had a significant excess in the number of functional categories enriched for PD-associated genes (minimum P = 0.014 and P = 0.006, respectively). Moreover, 58 categories were significantly enriched for associated genes in both GWA studies (P < 0.001), implicating genes involved in the 'regulation of leucocyte/lymphocyte activity' and also 'cytokine-mediated signalling' as conferring an increased susceptibility to PD. These results were unaltered by the exclusion of all 178 genes that were present at the 18 genomic regions previously reported to be strongly associated with PD (including the HLA locus). Our findings, therefore, provide independent support to the strong association signal at the HLA locus and imply that the immune-related genetic susceptibility to PD is likely to be more widespread in the genome than previously appreciated. }, doi = {10.1093/hmg/dds492}, pdf = {http://hmg.oxfordjournals.org/content/early/2012/12/13/hmg.dds492.full.pdf}, url = {http://hmg.oxfordjournals.org/content/early/2012/12/13/hmg.dds492.abstract} } @article{Wrzodek2012_3, author = {Wrzodek, Clemens and Eichner, Johannes and B\"uchel, Finja and Zell, Andreas}, title = {{InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway data}.}, journal = {Bioinformatics}, year = {2012}, volume = {29}, pages = {506--508}, number = {4}, month = dec, abstract = {Microarrays are commonly used to detect changes in gene expression between different biological samples. For this purpose, many analysis tools have been developed that offer visualization, statistical analysis, and more sophisticated analysis methods. Most of these tools are designed specifically for messenger RNA microarrays. However today, more and more different microarray platforms are available. Changes in DNA methylation, microRNA expression or even protein phosphorylation states can be detected with specialized arrays. For these microarray technologies, the number of available tools is very small, compared to mRNA analysis tools. Especially, a joint analysis of different microarray platforms that have been employed on the same set of biological samples is hardly supported by most microarray analysis tools. We here present InCroMAP, a tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein modification datasets. Several methods are offered that allow for an integrated analysis of data from those platforms. The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signaling pathways. InCroMAP is freely available as Java application at \url{http://www.cogsys.cs.uni-tuebingen.de/software/InCroMAP/}, including a comprehensive user's guide and example files.}, doi = {10.1093/bioinformatics/bts709}, eprint = {http://bioinformatics.oxfordjournals.org/content/29/4/506.full.pdf+html}, keywords = {Integration of omics data, Integration, omics, data, Visualization, Microarray data, Pathway, Pathways, Data integration, Microarray data analysis, MicroRNA, InCroMAP, application, software}, pdf = {http://bioinformatics.oxfordjournals.org/content/29/4/506.full.pdf}, url = {http://bioinformatics.oxfordjournals.org/content/29/4/506} } @inproceedings{bohlmann2012rose, author = {Karsten Bohlmann and Henrik Marks and Andreas Zell}, title = {Automated Odometry Self-Calibration for Car-Like Robots with Four-Wheel-Steering}, booktitle = {IEEE International Symposium on Robotic and Sensors Environments (ROSE)}, year = {2012}, address = {Magdeburg, Germany}, month = nov, note = {Accepted for publication}, } @inproceedings{voduc2012, author = {My Vo Duc and Andreas Masselli and Andreas Zell}, title = {Real Time Face Detection using Geometric Constraints, Navigation and Depth-based Skin Segmentation on Mobile Robots}, booktitle = {2012 IEEE International Symposium on Robotic and Sensors Environments}, year = {2012}, address = {Magdeburg, Germany}, month = nov, abstract = {Face detection is an important component for mobile robots to interact with humans in a natural way. Various face detection algorithms for mobile robots have been proposed; however, almost all of them have not yet met the requirements of the accuracy and the speed to run in real time on a robot platform. In this paper, we present a method of combining color and depth images provided by a Kinect camera and navigation information for face detection on mobile robots. This method is shown to be very fast and accurate and runs in real time in indoor environments.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/voduc2012.pdf} } @inproceedings{wenzel2012, author = {Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell}, title = {Visual Tracking and Following of a Quadrocopter by another Quadrocopter}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2012)}, year = {2012}, pages = {1-6}, address = {Vilamoura, Algarve, Portugal}, month = {October 7-12}, publisher = {IEEE}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/follow.pdf} } @article{Harri2012, author = {Harri Lempi\"ainen and Philippe Couttet and Federico Bolognani and Arne M\"uller and Val\'{e}rie Dubost and Rapha\"elle Luisier and Espinola Alberto {Del Rio} and Veronique Vitry and Elif B Unterberger and John P Thomson and Fridolin Treindl and Ute Metzger and Clemens Wrzodek and Florian Hahne and Tulipan Zollinger and Sarah Brasa and Magdalena Kalteis and Magali Marcellin and Fanny Giudicelli and Albert Braeuning and Laurent Morawiec and Natasa Zamurovic and Ulrich L\"angle and Nico Scheer and Dirk Sch\"ubeler and Jay Goodman and Salah-Dine Chibout and Jennifer Marlowe and Diethilde Theil and David J Heard and Olivier Grenet and Andreas Zell and Markus F Templin and Richard R Meehan and {C. Roland} Wolf and Clifford R Elcombe and Michael Schwarz and Pierre Moulin and R\'{e}mi Terranova and Jonathan G Moggs}, title = {{Identification of \emph{Dlk1}-\emph{Dio3} imprinted gene cluster non-coding RNAs as novel candidate biomarkers for liver tumor promotion}.}, journal = {Toxicological Sciences}, year = {2012}, volume = {131}, pages = {375--386}, number = {2}, month = oct, abstract = {The molecular events during non-genotoxic carcinogenesis and their temporal order are poorly understood but thought to include long-lasting perturbations of gene expression. Here, we have investigated the temporal sequence of molecular and pathological perturbations at early stages of phenobarbital-mediated liver tumor promotion in vivo. Molecular profiling (mRNA, miRNA, DNA methylation & proteins) of mouse liver during 13 weeks of phenobarbital treatment revealed progressive increases in hepatic expression of long non-coding RNAs and microRNAs originating from the Dlk1-Dio3 imprinted gene cluster, a locus that has recently been associated with stem cell pluripotency in mice and various neoplasms in humans. Phenobarbital-induction of the Dlk1-Dio3 cluster non-coding RNA Meg3 was localised to glutamine synthetase positive hypertrophic perivenous hepatocytes suggesting a role for $\beta$-catenin signaling in the dysregulation of Dlk1-Dio3 non-coding RNAs. The carcinogenic relevance of Dlk1-Dio3 locus non-coding RNA induction was further supported by in vivo genetic dependence on Constitutive Androstane Receptor (CAR) and $\beta$-catenin pathways. Our data identify Dlk1-Dio3 non-coding RNAs as novel candidate early biomarkers for mouse liver tumor promotion and provide new opportunities for assessing the carcinogenic potential of novel compounds.}, doi = {10.1093/toxsci/kfs303}, eprint = {http://toxsci.oxfordjournals.org/content/131/2/375.full.pdf+html}, institution = {Discovery and Investigative Safety, Preclinical Safety, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland.}, keywords = {Non-genotoxic carcinogenesis, Phenobarbital, biomarker, non-coding RNAs, Dlk1-Dio3 Imprinted cluster, epigenetics}, language = {eng}, pdf = {http://toxsci.oxfordjournals.org/content/131/2/375.full.pdf}, pii = {kfs303}, pmid = {23091169}, url = {http://toxsci.oxfordjournals.org/content/131/2/375.abstract} } @inproceedings{RanArtur_IROS_2012, author = {Ran Liu and Artur Koch and Andreas Zell}, title = {Path Following with Passive {UHF RFID} Received Signal Strength in Unknown Environments}, booktitle = {2012 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2012)}, year = {2012}, address = {Vilamoura, Algarve, Portugal}, month = {October}, abstract = {We present a novel approach incorporating a combination of Radio-Frequency Identification (RFID) and odometry information into the motion control of a mobile robot for the purpose of path following in unknown environments. Our method utilizes RFID measurements as landmarks and makes the mobile robot autonomously follow a path that was previously recorded in a manual training phase. The approach needs no prior information about RFID sensor models, the distribution and positioning of the tags nor does it require a map of the environment. Particularly, it is adaptive to different reader power levels and various tag densities, which have a major impact on RFID performance. Extensive experiments with a SCITOS G5 robot in different environments like a library, a supermarket and hallways confirm the effectiveness of our algorithm.}, days = {7-12}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/ran_iros_2012.pdf} } @inproceedings{Schauwecker2012b, author = {Schauwecker, Konstantin and Klette, Reinhard and Zell, Andreas}, title = {{A New Feature Detector and Stereo Matching Method for Accurate High-Performance Sparse Stereo Matching}}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)}, year = {2012}, pages = {5171--5176}, address = {Vilamoura, Algarve, Portugal}, month = {October}, publisher = {IEEE}, abstract = { Hardware platforms with limited processing power are often incapable of running dense stereo analysis algorithms at acceptable speeds. Sparse algorithms provide an alternative but generally lack in accuracy. To overcome this predicament, we present an efficient sparse stereo analysis algorithm that applies a dense consistency check, leading to accurate matching results. We further improve matching accuracy by introducing a new feature detector based on FAST, which exhibits a less clustered feature distribution. The new feature detector leads to a superior performance of our stereo analysis algorithm. In a performance evaluation the proposed stereo matching system achieves processing rates above 200 frames per second on a commodity dual core CPU, and also achieves faster than video frame-rate processing on a low-performance embedded platform. The stereo matching results prove to be superior to those achieved with ordinary sparse matching algorithms. }, pdf = {http://www.ra.cs.uni-tuebingen.de/publikationen/2012/schauwecker_iros2012.pdf}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6385492} } @inproceedings{bohlmann2012pemra, author = {Karsten Bohlmann and Andreas Beck-Greinwald and Sebastian Buck and Henrik Marks and Andreas Zell }, title = { Autonomous Person Following with 3D LIDAR in Outdoor Environments}, booktitle = {1st International Workshop on Perception for Mobile Robots Autonomy (PEMRA 2012)}, year = {2012}, address = {Poznan, Poland}, month = sep, abstract = {The capability of a robot to follow autonomously a person highly enhances its usability when humans and robots collaborate. In this paper we present a system for autonomous following of a walking person in outdoor environments while avoiding static and dynamic obstacles. The principal sensor is a 3D LIDAR with a resolution of 59x29 points. We present a combination of 3D features, motion detection and tracking with a sampling Bayesian filter which results in reliable person detection for a low-resolution 3D-LIDAR. The method is implemented on an outdoor robot with car-like steering, which incorporates the target's path into its own path planning around local obstacles. Experiments in outdoor areas validate the approach.}, affiliation = {Chair of Cognitive Systems, University of Tuebingen, Department of Computer Science, Sand 1, 72076 Tuebingen, Germany}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/bohlmann2012pemra.pdf} } @inproceedings{Schauwecker2012a, author = {Schauwecker, Konstantin and Ke, Nan Rosemary and Scherer, Sebastian A. and Zell, Andreas}, title = {{Markerless Visual Control of a Quad-Rotor Micro Aerial Vehicle by Means of On-Board Stereo Processing}}, booktitle = {22nd Conference on Autonomous Mobile Systems (AMS)}, year = {2012}, pages = {11--20}, address = {Stuttgart, Germany}, month = {September}, publisher = {Springer}, abstract = { We present a quad-rotor micro aerial vehicle (MAV) that is capable to fly and navigate autonomously in an unknown environment. The only sensory input used by the MAV are the imagery from two cameras in a stereo configuration, and data from an inertial measurement unit. We apply a fast sparse stereo matching algorithm in combination with a visual odometry method based on PTAM to estimate the current MAV pose, which we require for autonomous control. All processing is performed on a single board computer on-board the MAV. To our knowledge, this is the first MAV that uses stereo vision for navigation, and does not rely on visual markers or off-board processing. In a flight experiment, the MAV was capable to hover autonomously, and it was able to estimate its current position at a rate of 29 Hz and with an average error of only 2.8cm. }, pdf = {http://www.ra.cs.uni-tuebingen.de/publikationen/2012/schauwecker_ams2012.pdf}, url = {http://www.springerlink.com/content/x7p122p320v3q027/} } @article{Wrzodek2012_2, author = {Wrzodek, Clemens and Eichner, Johannes and Zell, Andreas}, title = {Pathway-based visualization of cross-platform microarray datasets.}, journal = {Bioinformatics}, year = {2012}, volume = {28}, pages = {3021--3026}, number = {23}, month = sep, abstract = {Motivation: Traditionally, microarrays were almost exclusively employed for the genome-wide analysis of differential gene expression. But nowadays, their scope of application has been extended to various genomic features, such as microRNAs, proteins, and DNA methylation. Most available methods for the visualization of these datasets are focused on individual platforms and are not capable of integratively visualizing multiple microarray datasets from cross-platform studies. Above all, there is a demand for methods that can visualize genomic features that are not directly linked to protein-coding genes, such as regulatory RNAs (e.g., microRNAs) and epigenetic alterations (e.g., DNA methylation), in a pathway-centered manner. Results: We present a novel pathway-based visualization method that is especially suitable for the visualization of high-throughput datasets from multiple different microarray platforms which were employed for the analysis of diverse genomic features in the same set of biological samples. The proposed methodology includes concepts for linking DNA methylation and microRNA expression datasets to canonical signaling and metabolic pathways. We further point out strategies for displaying data from multiple proteins and protein modifications corresponding to the same gene. Ultimately, we show how data from four distinct platform types (mRNA, miRNA, protein, and DNA methylation arrays) can be integratively visualized in the context of canonical pathways. Availability: The described method is implemented as part of the InCroMAP application that is freely available at \url{http://www.cogsys.cs.uni-tuebingen.de/software/InCroMAP/}. Contact: \url{mailto:clemens.wrzodek@uni-tuebingen.de}}, doi = {10.1093/bioinformatics/bts583}, eprint = {http://bioinformatics.oxfordjournals.org/content/28/23/3021.full.pdf+html}, keywords = {Integration of omics data, Integration, omics, data, Visualization, Microarray data, Pathway, Pathways, Data integration, Microarray data analysis, MicroRNA}, pdf = {http://bioinformatics.oxfordjournals.org/content/28/23/3021.full.pdf}, url = {http://bioinformatics.oxfordjournals.org/content/28/23/3021} } @article{Buechel2012a, author = {B\"uchel, Finja and Wrzodek, Clemens and Mittag, Florian and Dr\"ager, Andreas and Eichner, Johannes and Rodriguez, Nicolas and {Le Nov\`{e}re}, Nicolas and Zell, Andreas}, title = {{Qualitative translation of relations from BioPAX to SBML qual}}, journal = {Bioinformatics}, year = {2012}, volume = {28}, pages = {2648--2653}, number = {20}, month = aug, abstract = {Motivation: The Biological Pathway Exchange Language (BioPAX) and the Systems Biology Markup Language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus of SBML is quantitative modeling and dynamic simulation of models, whereas the BioPAX specification concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. In contrast, SBML core exclusively describes quantitative processes such as reactions. With the SBML Qualitative Models extension (qual), it has recently also become possible to describe relations in SBML. Before the development of SBML qual, relations could not be properly translated into SBML. Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations. Results: The entire Nature Pathway Interaction Database (PID) has been converted from BioPAX (Level 2 and Level 3) into SBML (Level 3 Version 1) including both reactions and relations by using the new qual extension package. Additionally, we present the new webtool BioPAX2SBML for further BioPAX to SBML conversions. Compared to previous conversion tools, BioPAX2SBML is more comprehensive, more robust and more exact. Availability: BioPAX2SBML is freely available at \url{http://webservices.cs.uni-tuebingen.de/} and the complete collection of the PID models at \url{http://www.cogsys.cs.uni-tuebingen.de/downloads/Qualitative-Models/}. Contact: \url{mailto:finja.buechel@uni-tuebingen.de} Supplementary Information: Supplementary data is available at Bioinformatics online.}, doi = {10.1093/bioinformatics/bts508}, keywords = {SBML, BioPAX, qual extension, qualitative model, quantitative model, conversion}, pdf = {http://bioinformatics.oxfordjournals.org/content/28/20/2648.full.pdf}, url = {http://bioinformatics.oxfordjournals.org/content/28/20/2648.abstract} } @article{jiang2012, author = {Lixing Jiang and Jin Hou}, title = {Image Annotation Using the Ensemble Learning}, journal = {Acta Automatica Sinica}, year = {2012}, volume = {38}, pages = {1257-1262}, number = {8}, month = {August}, eid = {1257}, keywords = {Automatic image annotation;machine learning;ensemble learning;fast random forest ({FRF})}, numpages = {5}, publisher = {Acta Automatica Sinica}, url = {http://www.aas.net.cn/EN/abstract/abstract17735.shtml#} } @inproceedings{Beck12, author = {Markus Beck and Michael de Paly and Jozsef Hecht-Mendez and Peter Bayer and Andreas Zell}, title = {{Evaluation of the Performance of Evolutionary Algorithms for Optimization of Low-Enthalpy Geothermal Heating Plants}}, booktitle = {Genetic and Evolutionary Computation Conference, GECCO-2012}, year = {2012}, pages = {1047-1054}, address = {Philadelphia, USA}, month = jul, abstract = {In this paper, we present the application of Evolutionary Algorithms (EAs) and linear programming for minimizing thermal impacts in the ground by operating a low-enthalpy geothermal plant with a field of multiple borehole heat exchangers (BHEs). The new methodology is demonstrated on two synthetic case studies with 36 BHEs that are grounded in reality and operated to produce given seasonal heating energy demand. We compare the performance of six different Evolutionary Algorithms (EAs) (two Differential Evolution variants, Particle Swarm Optimization, two Evolution Strategy based Algorithms, real valued Genetic Algorithm) and Monte-Carlo random search to find the optimal BHE positions. Additionally, linear programming is applied to adjust the energy extraction (loads) for the individual BHEs in the field. Both optimization steps are applied separately and in combination, and the achieved system improvements are compared to the conditions for the non-optimized case. The EAs were able to find constellations that cause less pronounced temperature changes in the subsurface (18% - 25%) than those associated with non-optimized BHE fields. Further, we could show that exclusive optimization of BHE energy extraction rates delivers slightly better results than the optimization of BHE positions. Combining both optimization approaches is the best choice and, ideally, adjusts the geothermal plant.}, } @article{Koenig05072012, author = {K\"onig, Matthias and Dr\"ager, Andreas and Holzh\"utter, Hermann-Georg}, title = {{CySBML: a Cytoscape plugin for SBML}}, journal = {Bioinformatics}, year = {2012}, volume = {28}, pages = {2402--2403}, number = {18}, month = jul, abstract = {Summary: CySBML is a plugin designed to work with SBML in Cytoscape having the following features: SBML import, support of the SBML Layout and Qualitative Model packages, navigation in network layouts based on SBML structure, access to MIRIAM and SBO-based annotations, and SBML validation. CySBML includes an importer for BioModels to load SBML from standard repositories. Availability and implementation: Freely available for noncommercial purposes via the Cytoscape plugin manager or for download at \url{http://sourceforge.net/projects/cysbml/}. Contact: \url{mailto:cysbml-team@lists.sourceforge.net} Supplementary information: Tutorial, usage guide, installation instructions and additional figures are available for download at \url{http://www.charite.de/sysbio/people/koenig/software/cysbml/}.}, doi = {10.1093/bioinformatics/bts432}, url = {http://bioinformatics.oxfordjournals.org/content/28/18/2402.abstract} } @article{Mittag2012_1, author = {Florian Mittag and Finja B\"uchel and Mohamad Saad and Andreas Jahn and Claudia Schulte and Zoltan Bochdanovits and Javier Sim\'{o}n-S\'{a}nchez and Mike A Nalls and Margaux Keller and Dena Hernandez and Raphael Gibbs and Suzanne Lesage and Alexis Brice and Peter Heutink and Maria Martinez and Nicholas W Wood and John Hardy and Andrew B. Singleton and Andreas Zell and Thomas Gasser and Manu Sharma}, title = {{Use of Support Vector Machines for Disease Risk Prediction in Genome-Wide Association Studies: Concerns and Opportunities}}, journal = {Human Mutation}, year = {2012}, volume = {33}, pages = {1708--1718}, number = {12}, month = jun, abstract = {The success of genome-wide association studies (GWAS) in deciphering the genetic architecture of complex diseases has fueled the expectations whether the individual risk can also be quantified based on the genetic architecture. So far, disease risk prediction based on top-validated single-nucleotide polymorphisms (SNPs) showed little predictive value. Here, we applied a support vector machine (SVM) to Parkinson disease (PD) and type 1 diabetes (T1D), to show that apart from magnitude of effect size of risk variants, heritability of the disease also plays an important role in disease risk prediction. Furthermore, we performed a simulation study to show the role of uncommon (frequency 1-5\%) as well as rare variants (frequency <1%) in disease etiology of complex diseases. Using a cross-validation model, we were able to achieve predictions with an area under the receiver operating characteristic curve (AUC) of ~0.88 for T1D, highlighting the strong heritable component (~90\%). This is in contrast to PD, where we were unable to achieve a satisfactory prediction (AUC ~0.56; heritability ~38\%). Our simulations showed that simultaneous inclusion of uncommon and rare variants in GWAS would eventually lead to feasible disease risk prediction for complex diseases such as PD. The used software is available at http://www.ra.cs.uni-tuebingen.de/software/MACLEAPS/. }, doi = {10.1002/humu.22161}, issn = {1098-1004}, keywords = {genome-wide association studies, disease risk prediction, machine learning, support vector machines, Parkinson disease}, publisher = {Wiley Subscription Services, Inc., A Wiley Company}, url = {http://dx.doi.org/10.1002/humu.22161} } @inproceedings{YangsICUAS12, author = {Shaowu Yang and Sebastian A. Scherer and Andreas Zell}, title = {{An Onboard Monocular Vision System for Autonomous Takeoff, Hovering and Landing of a Micro Aerial Vehicle}}, booktitle = {2012 International Conference on Unmanned Aircraft Systems (ICUAS'12)}, year = {2012}, address = {Philadelphia, PA, USA}, month = jun, days = {12-15}, } @inproceedings{scherer2012, author = {Scherer, Sebastian A. and Daniel Dube and Andreas Zell}, title = {{Using Depth in Visual Simultaneous Localisation and Mapping}}, booktitle = {IEEE International Conference on Robotics and Automation}, year = {2012}, address = {St. Paul, Minnesota, USA}, month = {May}, abstract = {We present a method of utilizing depth information as provided by RGBD sensors for robust real-time visual simultaneous localisation and mapping (SLAM) by augmenting monocular visual SLAM to take into account depth data. This is implemented based on the feely available software ``Parallel Tracking and Mapping'' by Georg Klein. Our modifications allow PTAM to be used as a 6D visual SLAM system even without any additional information about odometry or from an inertial measurement unit.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/scherer2012.pdf} } @incollection{Franken2012, author = {Franken, Holger and Seitz, Alexander and Lehmann, Rainer and H\"aring, Hans-Ulrich and Stefan, Norbert and Zell, Andreas}, title = {Inferring Disease-Related Metabolite Dependencies with a Bayesian Optimization Algorithm}, booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics}, publisher = {Springer Berlin / Heidelberg}, year = {2012}, editor = {Giacobini, Mario and Vanneschi, Leonardo and Bush, William}, volume = {7246}, series = {Lecture Notes in Computer Science}, pages = {62-73}, note = {10.1007/978-3-642-29066-4_6}, abstract = {Understanding disease-related metabolite interactions is a key issue in computational biology. We apply a modified Bayesian Optimization Algorithm to targeted metabolomics data from plasma samples of insulin-sensitive and -resistant subjects both suffering from non-alcoholic fatty liver disease. In addition to improving the classification accuracy by selecting relevant features, we extract the information that led to their selection and reconstruct networks from detected feature dependencies. We compare the influence of a variety of classifiers and different scoring metrics and examine whether the reconstructed networks represent physiological metabolite interconnections. We find that the presented method is capable of significantly improving the classification accuracy of otherwise hardly classifiable metabolomics data and that the detected metabolite dependencies can be mapped to physiological pathways, which in turn were affirmed by literature from the domain.}, affiliation = {Center for Bioinformatics (ZBIT), University of T\"ubingen, D-72076 T\"ubingen, Germany}, isbn = {978-3-642-29065-7}, keyword = {Computer Science}, url = {http://dx.doi.org/10.1007/978-3-642-29066-4_6} } @inproceedings{beck_egu_vienna12, author = {Jozsef Hecht-Mendez and Michael de Paly and Markus Beck and Phillip Blum and Peter Bayer}, title = {{Strategic optimization of large-scale vertical closed-loop shallow geothermal systems}}, booktitle = {{Geophysical Research Abstracts, EGU12079}}, year = {2012}, volume = {14}, address = {Vienna}, month = {apr}, organization = {EGU General Assembly 2012}, } @article{Margaux2012, author = {Keller, Margaux F. and Saad, Mohamad and Bras, Jose M. and Bettella, Francesco and Nicolaou, Nayia and Sim\'{o}n-S\'{a}nchez, Javier and Mittag, Florian and B\"uchel, Finja and Sharma, Manu and Gibbs, J. Raphael and Schulte, Claudia and Moskvina, Valentina and Durr, Alexandra and Holmans, Peter and Kilarski, Laura L. and Guerreiro, Rita and Hernandez, Dena and Brice, Alexis and Ylikotila, Pauli and Stef\'{a}nsson, Hreinn and Majamaa, Kari and Morris, Huw R. and Williams, Nigel and Gasser, Thomas and Heutink, Peter and Wood, Nick and Hardy, John and Martinez, Maria and Singleton, Andrew B. and Nalls, Michael A.}, title = {Using Genome-wide Complex Trait Analysis 1 to quantify 'missing heritability' in Parkinson's disease}, journal = {Human Molecular Genetics}, year = {2012}, volume = {21}, pages = {4996--5009}, number = {22}, month = august, abstract = {Genome-wide association studies (GWAS) have been successful at identifying single nucleotide polymorphisms (SNPs) highly associated with common traits, however a great deal of the heritable variation associated with common traits remains unaccounted for within the genome. Genome-wide Complex Trait Analysis (GCTA) is a statistical method that applies a linear mixed model to estimate phenotypic variance of complex traits explained by genome-wide SNPs, including those not associated with the trait in a GWAS. We applied GCTA to 8 cohorts containing 7,096 case and 19,455 control individuals of European ancestry in order to examine the missing heritability present in Parkinson's disease (PD). We meta-analyzed our initial results to produce robust heritability estimates for PD types across cohorts. Our results identify 27% (95% CI [17%, 38%], p = 8.08E-08) phenotypic variance associated with all types of PD, 15% (95% CI [-0.2%, 33%], p = 0.09) phenotypic variance associated with early onset PD, and 31% (95% CI [17%, 44%], p = 1.34E-05) phenotypic variance associated with late onset PD. This is a substantial increase from the genetic variance identified by top GWAS hits alone (between 3- 5%) and indicates there are substantially more risk loci to be identified. Our results suggest that while GWAS is a useful tool in identifying the most common variants associated with complex disease, a great deal of common variants of small effect remain to be discovered.}, doi = {10.1093/hmg/dds335}, keywords = {Parkinson's disease, missing heritability, Genome-wide Complex Trait Analysis, rare variants}, pdf = {http://hmg.oxfordjournals.org/content/21/22/4996.full.pdf}, url = {http://hmg.oxfordjournals.org/content/21/22/4996.abstract} } @article{Kenar2012, author = {Kenar, E. and Franken, H. and Rosenbaum, L. and Lehmann, R. and Forcisi, S. and W\"ormann, K. and Lucio, M. and K\"onig, A. and Rahnenf\"uher, J. and Schmidt-Kopplin, P. and H\"aring, H.-U. and Zell, A. and Kohlbacher, O.}, title = {Mit Bioinformatik zu Biomarkern}, journal = {Medizinische Welt}, year = {2012}, volume = {63}, pages = {245--250}, number = {5}, } @inproceedings{khan12, author = {Yasir Niaz Khan and Andreas Masselli and Andreas Zell}, title = {Visual Terrain Classification by Flying Robots}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA)}, year = {2012}, pages = {498 -503}, address = {St. Paul, Minnesota, USA}, month = {may}, abstract = {In this paper we investigate the effectiveness of SURF features for visual terrain classification for outdoor flying robots. A quadrocopter fitted with a single camera is flown over different terrains to take images of the ground below. Each image is divided into a grid and SURF features are calculated at grid intersections. A classifier is then used to learn to differentiate between different terrain types. Classification results of the SURF descriptor are compared with results from other texture descriptors like Local Binary Patterns and Local Ternary Patterns. Six different terrain types are considered in this approcah. Random forests are used for classification on each descriptor. It is shown that SURF features perform better than other descriptors at higher resolutions.}, doi = {10.1109/ICRA.2012.6224988}, issn = {1050-4729}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/khan2012icra.pdf} } @incollection{laible2012ams, author = {Stefan Laible and Yasir Niaz Khan and Karsten Bohlmann and Andreas Zell}, title = {3D LIDAR- and Camera-Based Terrain Classification Under Different Lighting Conditions}, booktitle = {Autonomous Mobile Systems 2012}, publisher = {Springer Berlin Heidelberg}, year = {2012}, series = {Informatik aktuell}, pages = {21--29}, abstract = {Terrain classification is a fundamental task in outdoor robot navigation to detect and avoid impassable terrain. Camera-based approaches are well-studied and provide good results. A drawback of these approaches, however, is that the quality of the classification varies with the prevailing lighting conditions. 3D laser scanners, on the other hand, are largely illumination-invariant. In this work we present easy to compute features for 3D point clouds using range and intensity values. We compare the classification results obtained using only the laser-based features with the results of camera-based classification and study the influence of different lighting conditions.}, affiliation = {Chair of Cognitive Systems, University of T\"ubingen, Department of Computer Science, Sand 1, 72076 T\"ubingen, Germany}, doi = {10.1007/978-3-642-32217-4_3}, isbn = {978-3-642-32217-4}, keyword = {Engineering}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/laible2012ams.pdf}, url = {http://dx.doi.org/10.1007/978-3-642-32217-4_3} } @misc{MasselliWenzel2012, author = {Andreas Masselli and Karl Engelbert Wenzel and Andreas Zell}, title = {{Verfahren zur Bestimmung der relativen Lage eines Objektes im Raum sowie optisches Eingabesystem}}, year = {2012}, note = {Patent, PCT/EP2012/057446, Submitted 2012.04.24}, } @inproceedings{Masselli2012, author = {Andreas Masselli and Andreas Zell}, title = {{A Novel Marker Based Tracking Method for Position and Attitude Control of MAVs}}, booktitle = {Proceedings of International Micro Air Vehicle Conference and Flight Competition}, year = {2012}, pages = {1-6}, address = {Braunschweig, Germany}, publisher = {DGON}, abstract = {In this paper we present a novel method for pose estimation for micro aerial vehicles (MAVs), which provides all six degrees of freedom (6DOF) and runs completely onboard and in real time at 60 Hz. The approach uses a distinct pattern of orange table tennis balls as passive visual markers and a monocular color camera mounted onto the MAV as the only sensor. We show that our method can be used as input of position and attitude controllers for autonomous take-off, hovering and landing of MAVs. As a testing platform we choose an AscTec Hummingbird quadrocopter, which we equipped with a Gumstix processor, running at 600 MHz. The quadrocopter is fully controlled by our method, which acts as input to four independent, classical proportional-integral-derivative (PID) controllers. }, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2012/Masselli2012IMAV.pdf} } @article{DePaly12, author = {Michael de Paly and Jozsef Hecht-Mendez and Markus Beck and Philipp Blum and Andreas Zell and Peter Bayer }, title = {Optimization of energy extraction for closed shallow geothermal systems using linear programming}, journal = {Geothermics}, year = {2012}, volume = {43}, pages = {57-65}, abstract = {The objective of the study is to optimize the performance and thereby to mitigate the environmental impact of ground source heat pump (GSHP) systems using multiple borehole heat exchangers (BHEs) by including variable energy loads. Hence, an optimization procedure is developed that is able to predict temperature distributions in the subsurface. Optimized BHE fields are able to keep the maximum temperature change in the subsurface about 18% lower than BHE fields which feature equal flow rates for all BHEs. Thus, the long-term temperature anomaly can be mitigated and the possibility of extracting a higher amount of energy, while keeping temperature thresholds or environmental constraints, arises. }, doi = {10.1016/j.geothermics.2012.03.001}, } @incollection{Rosenbaum2012a, author = {Lars Rosenbaum and Andreas Jahn and Andreas Zell}, title = {Optimizing the Edge Weights in Optimal Assignment Methods for Virtual Screening with Particle Swarm Optimization}, booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics}, publisher = {Springer Berlin / Heidelberg}, year = {2012}, editor = {Giacobini, Mario and Vanneschi, Leonardo and Bush, William}, volume = {7246}, series = {Lecture Notes in Computer Science}, pages = {26-37}, affiliation = {Center for Bioinformatics (ZBIT), University of Tuebingen, Sand 1, 72076 T\"ubingen, Germany}, isbn = {978-3-642-29065-7}, keyword = {Computer Science}, url = {http://dx.doi.org/10.1007/978-3-642-29066-4_3} } @article{springerlink:10.1007/s11428-011-0778-9, author = {W\"{o}rmann, K. and Lucio, M. and Forcisi, S. and Heinzmann, S.S. and Kenar, E. and Franken, H. and Rosenbaum, L. and Schmitt-Kopplin, P. and Kohlbacher, O. and Zell, A. and H\"{a}ring, H.-U. and Lehmann, R.}, title = {Metabolomics in der {D}iabetesforschung}, journal = {Der Diabetologe}, year = {2012}, pages = {1-5}, note = {10.1007/s11428-011-0778-9}, affiliation = {Abteilung Analytische BioGeoChemie, Helmholtz Zentrum M\"{u}nchen, M\"{u}nchen, Deutschland}, issn = {1860-9716}, keyword = {Medizin}, publisher = {Springer Berlin / Heidelberg}, url = {http://dx.doi.org/10.1007/s11428-011-0778-9} } @article{Wrzodek2012_1, author = {Wrzodek, Clemens and B\"uchel, Finja and Hinselmann, Georg and Eichner, Johannes and Mittag, Florian and Zell, Andreas}, title = {{Linking the epigenome to the genome: Correlation of different features to DNA methylation of CpG islands}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2012}, volume = {7}, pages = {e35327}, number = {4}, month = {04}, abstract = {DNA methylation of CpG islands plays a crucial role in the regulation of gene expression. More than half of all human promoters contain CpG islands with a tissue-specific methylation pattern in differentiated cells. Still today, the whole process of how DNA methyltransferases determine which region should be methylated is not completely revealed. There are many hypotheses of which genomic features are correlated to the epigenome that have not yet been evaluated. Furthermore, many explorative approaches of measuring DNA methylation are limited to a subset of the genome and thus, cannot be employed, e.g., for genome-wide biomarker prediction methods. In this study, we evaluated the correlation of genetic, epigenetic and hypothesis-driven features to DNA methylation of CpG islands. To this end, various binary classifiers were trained and evaluated by cross-validation on a dataset comprising DNA methylation data for 190 CpG islands in HEPG2, HEK293, fibroblasts and leukocytes. We achieved an accuracy of up to 91\% with an MCC of 0.8 using ten-fold cross-validation and ten repetitions. With these models, we extended the existing dataset to the whole genome and thus, predicted the methylation landscape for the given cell types. The method used for these predictions is also validated on another external whole-genome dataset. Our results reveal features correlated to DNA methylation and confirm or disprove various hypotheses of DNA methylation related features. This study confirms correlations between DNA methylation and histone modifications, DNA structure, DNA sequence, genomic attributes and CpG island properties. Furthermore, the method has been validated on a genome-wide dataset from the ENCODE consortium. The developed software, as well as the predicted datasets and a web-service to compare methylation states of CpG islands are available at http://www.cogsys.cs.uni-tuebingen.de/software/dna-methylation/.}, doi = {10.1371/journal.pone.0035327}, pdf = {http://www.ra.cs.uni-tuebingen.de/mitarb/wrzodek/publications/Linking%20the%20Epigenome%20to%20the%20Genome%20-%20Correlation%20of%20CpG%20islands.pdf}, publisher = {Public Library of Science}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0035327} } @inproceedings{dube2011, author = {Dube, Daniel and Zell, Andreas}, title = {Real-Time Plane Extraction from Depth Images with the Randomized Hough Transform}, booktitle = {IEEE ICCV Workshop on Challenges and Opportunities in Robot Perception}, year = {2011}, pages = {1084 -1091}, address = {Barcelona, Spain}, month = nov, doi = {10.1109/ICCVW.2011.6130371}, } @phdthesis{Schroeder2011d, author = {Schr\"oder, Adrian}, title = {Inference of gene-regulatory networks in primary human hepatocytes}, school = {University of Tuebingen}, year = {2011}, address = {T\"ubingen, Germany}, month = nov, abstract = {The liver is among the largest and most complex organs in the human body. It is responsible for the detoxification, metabolization, and elimination of thousands of chemically diverse substances. This essential functionality is mainly accomplished by hepatocytes, the most abundant cell type in human liver tissue. An arsenal of liver proteins that are sensitive to chemical compounds, orchestrates the activation of genes and thus the production of specific enzymes, transporters, and other proteins. These proteins transform endogenous and exogenous chemical substances into less toxic and more water soluble metabolites and promote the efflux of these compounds. The complex architecture of these regulatory programs in human liver cells is widely unknown. Defects in the regulatory mechanisms are known to be involved in the development of a variety of liver diseases. Understanding the structure and functionality of gene-regulatory networks in human liver cells is, therefore, of high medical relevance. The work at hand presents several new approaches to the reconstruction of gene-regulatory networks in primary human hepatocytes. The main building blocks of this kind of networks are transcription factors, which are able to activate genes by recognizing and binding to specific DNA sequence elements in the regulatory region of these genes. In this work, first, a new approach for the prediction of transcription factor binding specificities is proposed. Next, a new method for the reconstruction of transcriptional regulatory networks is presented that mines for patterns of transcription factor binding sites in sets of co-expressed genes. The application of this method to drug-response gene expression data revealed several new regulatory relationships that were successfully validated in wet lab experiments. Finally, genome-wide association analyses are performed to identify new associations between genetic markers and quantitative gene expression levels based on a cohort of 150 human liver samples.}, isbn = {978-3-8439-0256-4}, publisher = {Verlag Dr.~Hut, Sternstra{\ss}e 18, M\"unchen}, url = {http://www.dr.hut-verlag.de/978-3-8439-0256-4.html} } @inproceedings{vorst2011rfidta, author = {Philipp Vorst and Artur Koch and Andreas Zell}, title = {Efficient Self-Adjusting, Similarity-based Location Fingerprinting with Passive {UHF} {RFID} }, booktitle = {IEEE International Conference on RFID-Technology and Applications (RFID-TA2011)}, year = {2011}, pages = {160--167}, address = {Sitges, Barcelona, Spain}, month = {September 15-16}, publisher = {IEEE}, abstract = {In this paper we present extensive experimental results of location fingerprinting with passive UHF radio-frequency identification (RFID). As recent passive RFID hardware provides information about received signal strength (RSS), we evaluate its usefulness in the context of fingerprinting based on classical vector similarity measures. We analyze the impact of decisive parameters of the applied approach and also select them automatically via cross-validation, including the most appropriate similarity measure. A further novelty is an RSS thresholding mechanism which reduces the computational demands of comparing fingerprints. This technique is especially useful in surroundings which are densely equipped with RFID tags, such as future supermarkets or logistic centers. We conducted realworld experiments with a mobile robot and two different RFID readers. Results are reported both for global localization in each time frame and for time-filtered position tracking. We provide the experimental data of this work for download. Details on the experimental setup as well as downloadable datasets can be obtained at \url{http://www.cogsys.cs.uni-tuebingen.de/datasets/rfid-ta2011/}.}, doi = {10.1109/RFID-TA.2011.6068632}, ee = {http://dx.doi.org/10.1109/RFID-TA.2011.6068632}, isbn = {978-1-4577-0028-6}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/vorstkoch2011rfidta.pdf} } @article{Courtot2011a, author = {Courtot, M\'{e}lanie and Juty, Nick and Kn\"upfer, Christian and Waltemath, Dagmar and Zhukova, Anna and Dr\"ager, Andreas and Dumontier, Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna and Hoops, Stefan and Keating, Sarah M. and Kell, Douglas B. and Kerrien, Samuel and Lawson, James and Lister, Allyson and Lu, James and Machne, Rainer and Mendes, Pedro and Pocock, Matthew and Rodriguez, Nicolas and Vill\'{e}ger, Alice and Wilkinson, Darren J. and Wimalaratne, Sarala and Laibe, Camille and Hucka, Michael and {Le Nov\`{e}re}, Nicolas}, title = {Controlled vocabularies and semantics in systems biology}, journal = {Molecular Systems Biology}, year = {2011}, volume = {7}, pages = {543}, number = {1}, month = sep, abstract = {The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the Systems Biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of Systems Biology models, their characterization, and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments.}, doi = {10.1038/msb.2011.77}, keywords = {dynamics; kinetics; model; ontology; simulation}, pdf = {http://msb.embopress.org/content/7/1/543.full.pdf}, url = {http://dx.doi.org/10.1038/msb.2011.77} } @inproceedings{liu1109:Path, author = {Ran Liu and Philipp Vorst and Artur Koch and Andreas Zell}, title = {Path Following for Indoor Robots with {RFID} Received Signal Strength}, booktitle = {The 19th International Conference on Software, Telecommunications and Computer Networks (SoftCOM 2011)}, year = {2011}, address = {Split, Hvar, and Dubrovnik, Croatia}, month = {September}, note = {(Best paper award at the Symposium on RFID Technologies and Internet of Things)}, abstract = {We present a novel method for robot path following in an RFID-equipped corridor using received signal strength (RSS). RSS measurements are recorded as reference fingerprints during the exploration phase. These data are used to guide the robot through the corridor in the navigation phase. Distance and orientation that the robot derivates from the expected trajectory are approximated through the RSS differences and the index differences of two antennas. The RSS differences are calculated by comparing the current fingerprint to reference fingerprints, and the index differences are estimated by a particle filter. Finally, a P-controller is used for the navigation of the robot. This enables the robot to follow a certain path, which may be defined in the first phase of our approach. The actual experiments with a SCITOS G5 service robot confirm the validity and robustness of our approach.}, days = {15}, keywords = {RFID-based Navigation, Particle Filter, Fingerprints, Received Signal Strength (RSS)}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/ranliu2011-path-following-rss.pdf} } @inproceedings{schairer2011iros, author = {Timo Schairer and Benjamin Huhle and Philipp Vorst and Andreas Schilling and Wolfgang Strasser}, title = {Visual Mapping with Uncertainty for Correspondence-free Localization using {Gaussian} Process Regression}, booktitle = {Proceedings of the 2011 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2011)}, year = {2011}, address = {San Francisco, California, USA}, month = {September}, note = {Accepted for publication}, } @inproceedings{scherer2011ecmr, author = {Scherer, Sebastian A. and Daniel Dube and Philippe Komma and Andreas Masselli and Andreas Zell}, title = {{Robust Real-Time Number Sign Detection on a Mobile Outdoor Robot}}, booktitle = {Proceedings of the 6th European Conference on Mobile Robots (ECMR 2011)}, year = {2011}, address = {\"Orebro, Sweden}, month = sep, abstract = {We present the evolution of a highly-efficient system for visually detecting number signs in real-time on a mobile robot with limited computational power. The system was designed for use on a robot participating in the 2010 ``SICK robot day'' robotics challenge, in which the robot needed to autonomously find 10 number signs and drive to all of them in a given order as fast as possible. Our most efficient method has proven to be robust and successful, since our robot won the competition using the final vision systems described in this paper.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/scherer11.pdf} } @article{Schroeder2011c, author = {Schr\"oder, Adrian and Klein, Kathrin and Winter, Stefan and Schwab, Matthias and Bonin, Michael and Zell, Andreas and Zanger, Ulrich M.}, title = {{Genomics of ADME gene expression: mapping expression quantitative trait loci relevant for absorption, distribution, metabolism and excretion of drugs in human liver}}, journal = {The Pharmacogenomics Journal}, year = {2011}, pages = {1473--1150}, month = sep, abstract = {Expression quantitative trait loci (eQTL) analysis is a powerful approach toward identifying genetic loci associated with quantitative changes in gene expression. We applied genome-wide association analysis to a data set of 4300\,000 single-nucleotide polymorphisms and 48 000 mRNA expression phenotypes obtained by Illumina microarray profiling of 149 human surgical liver samples obtained from Caucasian donors with detailed medical documentation. Of 1\,226 significant associations, only 200 were validated when comparing with a previously published similar study. Potential explanations for low replication rate include differences in microarray platforms, statistical modeling, covariates considered and origin and collection procedures of tissues. Focused analysis revealed a subset of 95 associations related to absorption, distribution, metabolism and excretion of drugs. Of these, 21 were true replications and 74 were newly discovered associations in enzymes, transporters, transcriptional regulators and other genes. This study extends our knowledge about the genetics of interindividual variability of gene expression with particular emphasis on pharmacogenomics.}, doi = {10.1038/tpj.2011.44}, keywords = {ADME, eQTL, gene expression, pharmacogenetics, quantitative trait loci, SNP}, pdf = {http://www.nature.com/tpj/journal/vaop/ncurrent/pdf/tpj201144a.pdf}, url = {http://dx.doi.org/10.1038/tpj.2011.44} } @techreport{Buechel2011a, author = {B\"uchel, Finja and Wrzodek, Clemens and Mittag, Florian and Dr\"ager, Andreas and Schr\"oder, Adrian and Zell, Andreas}, title = {{ProDGe: investigating protein-protein interactions at the domain level}}, institution = {Nature Precedings}, year = {2011}, month = aug, abstract = {An important goal of systems biology is the identification and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins interact via domains, thus it is important to know which domains a protein contains and which domains interact with each other. Here we present the Java\texttrademark{} program ProDGe (Protein Domain Gene), which visualizes existing and suggests novel domain-domain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe suggests novel protein interactions and assigns them to four confidence classes, depending on the reliability of the underlying domain interaction. Furthermore, ProDGe is able to identify potential homologous interaction partners in other species, which is particularly helpful when investigating poorly annotated species. We further evaluated and compared experimentally identified protein interactions from IntAct with domain interactions from DOMINE for six species and noticed that 31.13% of all IntAct protein interactions in all six species can be mapped to the actual interacting domains. ProDGe and a comprehensive documentation are freely available at \url{http://www.cogsys.cs.uni-tuebingen.de/software/ProDGe}.}, doi = {10.1038/npre.2011.6188.1}, keywords = {protein, domain, interaction, domain-domain interaction, interaction visualization, protein-protein interaction}, pdf = {http://precedings.nature.com/documents/6188/version/1/files/npre20116188-1.pdf}, url = {http://precedings.nature.com/documents/6188/version/1} } @phdthesis{vorst2011thesis, author = {Vorst, Philipp}, title = {Mapping, Localization, and Trajectory Estimation with Mobile Robots Using Long-Range Passive {RFID}}, school = {University of Tuebingen, T\"ubingen, Germany}, year = {2011}, month = aug, abstract = {This thesis addresses the use of radio-frequency identification (RFID) for three fundamental tasks in mobile robotics: mapping, self-localization, and trajectory estimation. These topics have widely been studied in recent years, because they are regarded as key ingredients to autonomous robots. In particular, we investigate the application of long-range passive RFID in the work at hand. This RFID standard is expected to play a major role in the automation of identification processes in industry and commerce. We present solutions to the automated inventory of RFID-tagged goods, which we interpret as mapping the locations of RFID transponders. In order to quickly provide the required model of the detection behavior of the RFID reader on board the mobile robot, we devise a semi-autonomous learning method for probabilistic sensor models. Moreover, we compare different techniques to self-localize in an RFID-tagged environment. In the last part, we show how the trajectory of the robot can be estimated in previously unknown surroundings by tailoring approaches from the field of simultaneous localization and mapping (SLAM).}, isbn = {978-3-8439-0060-7}, keywords = {radio-frequency identification (RFID), passive UHF RFID, mobile robot, self-localization, mapping, trajectory estimation, simultaneous localization and mapping, SLAM, sensor model, location fingerprinting}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/vorst/publications/Dissertation_Philipp_Vorst.pdf}, publisher = {Verlag Dr.~Hut}, series = {Robotik und Automation}, url = {http://www.dr.hut-verlag.de/978-3-8439-0060-7.html} } @phdthesis{hofmeistDiss, author = {Hofmeister, Marius}, title = {Self-Localization, Mapping and Coverage with Resource-Limited Mobile Robots}, school = {University of Tuebingen}, year = {2011}, address = {T\"ubingen, Germany}, month = {July}, isbn = {978-3-8325-2887-4}, publisher = {Logos Verlag Berlin GmbH, Comeniushof, Gubener Str. 47, 10243 Berlin}, } @article{Schroeder2011b, author = {Schr\"oder, Adrian and Wollnik, Johannes and Wrzodek, Clemens and Dr\"ager, Andreas and Bonin, Michael and Burk, Oliver and Thomas, Maria and Thasler, Wolfgang E. and Zanger, Ulrich M. and Zell, Andreas}, title = {Inferring statin-induced gene regulatory relationships in primary human hepatocytes}, journal = {Bioinformatics}, year = {2011}, volume = {27}, pages = {2473--2477}, number = {18}, month = jul, abstract = {Motivation: Statins are the most widely used cholesterol-lowering drugs. The primary target of statins is HMG-CoA reductase, a key enzyme in cholesterol synthesis. However, statins elicit pleitropic responses including beneficial as well as adverse effects in the liver or other organs. Today, the regulatory mechanisms that cause these pleiotropic effects are not sufficiently understood. Results: In this work, genome-wide RNA expression changes in primary human hepatocytes of six individuals were measured at up to six time points upon atorvastatin treatment. A computational analysis workflow was applied to reconstruct regulatory mechanisms based on these drug-response data and available knowledge about TF binding specificities, and protein-drug interactions. Several previously unknown transcription factors were predicted to be involved in atorvastatin-responsive gene expression. The novel relationships of nuclear receptors NR2C2 and PPARA on CYP3A4 were successfully validated in wet-lab experiments. Availability: Microarray data are available at the Gene Expression Omnibus (GEO) database at \url{http://www.ncbi.nlm.nih.gov/geo/}, under accession number GSE29868.}, doi = {10.1093/bioinformatics/btr416}, pdf = {http://bioinformatics.oxfordjournals.org/content/27/18/2473.full.pdf}, url = {http://bioinformatics.oxfordjournals.org/content/27/18/2473.abstract} } @article{Draeger2011b, author = {Dr\"ager, Andreas and Rodriguez, Nicolas and Dumousseau, Marine and D\"orr, Alexander and Wrzodek, Clemens and {Le Nov\`{e}re}, Nicolas and Zell, Andreas and Hucka, Michael}, title = {{JSBML: a flexible Java library for working with SBML}}, journal = {Bioinformatics}, year = {2011}, volume = {27}, pages = {2167--2168}, number = {15}, month = jun, abstract = {Summary: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations, and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java\texttrademark{} programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level~3 Version~1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end-user applications, as well as ease migration from a libSBML-based backend. Availability: Source code, binaries, and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website \url{http://sbml.org/Software/JSBML}.}, doi = {10.1093/bioinformatics/btr361}, pdf = {http://bioinformatics.oxfordjournals.org/content/27/15/2167.full.pdf}, url = {http://bioinformatics.oxfordjournals.org/content/27/15/2167} } @inproceedings{Schauwecker2011b, author = {Schauwecker, Konstantin and Morales, Sandino and Hermann, Simon and Klette, Reinhard}, title = {{A Comparative Study of Stereo-Matching Algorithms for Road-Modeling in the Presence of Windscreen Wipers}}, booktitle = {IEEE Intelligent Vehicles Symposium (IV)}, year = {2011}, pages = {7--12}, address = {Baden-Baden, Germany}, month = {June}, publisher = {IEEE}, abstract = {In this study we examine three road-modeling methods, which weevaluate on seven stereo matching algorithms. The road-modeling methods weconsider are a B-spline modeling technique based on region-growing and twoversions of the popular v-disparity approach. The used stereo algorithms arevariations or different parameterizations of belief propagation, graph cutand semi-global matching. We examine the performance of the possiblecombinations of modeling methods and stereo algorithms by comparing thedeviation towards a reference road profile. Two evaluation sequences areused, of which one features switched on windscreen wipers that are visiblein the the recorded imagery. Our findings are that the examined B-splinemodeling method provides the best results in most cases. In terms of themodeled distance, belief propagation is the most suitable stereo matchingmethod, which also performs best with the wiper sequence. Semi globalmatching achieves smaller model deviations, but with drastically reducedmodeled distances. }, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5940392} } @inproceedings{Schroeder2011a, author = {Schr\"oder, Adrian and Wrzodek, Clemens and Wollnik, Johannes and Dr\"ager, Andreas and Wanke, Dierk and Berendzen, Kenneth W. and Zell, Andreas}, title = {Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2011)}, year = {2011}, address = {New Orleans, USA}, month = jun, publisher = {IEEE}, abstract = {Higher organisms are able to respond to continuously changing external conditions by transducing cellular signals into specific regulatory programs, which control gene expression states of thousands of different genes. One of the central problems in understanding gene regulation is to decipher how combinations of transcription factors control sets of coexpressed genes under specific experimental conditions. Existing methods in this field mainly focus on sequence aspects and pattern recognition, e.g., by detecting \emph{cis}-regulatory modules (CRMs) based on gene expression profiling data. We propose a novel approach by combining experimental data with a priori knowledge of respective experimental conditions. These various sources of evidence are likewise considered using multi-objective evolutionary optimization. In this work, we present three objective functions that are especially designed for stimulus-response experiments and can be used to integrate a priori knowledge into the detection of gene regulatory modules. This method was tested and evaluated on whole-genome microarray measurements of drug-response in human hepatocytes.}, doi = {10.1109/CEC.2011.5949899}, isbn = {978-1-4244-7833-0}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/Schroeder2011cec.pdf}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5949899} } @article{Wrzodek2011, author = {Wrzodek, Clemens and Dr\"ager, Andreas and Zell, Andreas}, title = {{KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats}}, journal = {Bioinformatics}, year = {2011}, volume = {27}, pages = {2314--2315}, number = {16}, month = jun, abstract = {Summary: The KEGG PATHWAY database provides a widely used service for metabolic and non-metabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. Availability: KEGGtranslator is freely available as a Java\texttrademark{} Web Start application and for download at \url{http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/}. KGML files can be downloaded within the application.}, doi = {10.1093/bioinformatics/btr377}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/wrzodek/publications/2011-08-04-KEGGtranslator-with-color.pdf}, url = {http://bioinformatics.oxfordjournals.org/content/27/16/2314} } @inproceedings{hofmeistICRA, author = {Hofmeister, Marius and Kronfeld, Marcel and Zell, Andreas}, title = {Cooperative Visual Mapping in a Heterogeneous Team of Mobile Robots}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA)}, year = {2011}, pages = {1491--1496}, address = {Shanghai, China}, month = may, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/hofmeister2011icra.pdf} } @inproceedings{Schauwecker2011c, author = {Klette, Reinhard and Ahn, Je and Haeusler, Ralf and Herman, Simon and Huang, Jinsheng and Khan, Waqar and Manoharan, Sathiamoorthy and Morales, Sandino and Morris, John and Nicolescu, Radu and Ren, FeiXiang and Schauwecker, Konstantin and Yang, Xi}, title = {{Advance in Vision-Based Driver Assistance}}, booktitle = {Electric Technology and Civil Engineering (ICETCE)}, year = {2011}, pages = {987--990}, address = {Lushan, China}, month = {April}, publisher = {IEEE}, abstract = {Vision-based driver assistance is an active safety measure currently under development in various car companies and research institutes worldwide. The paper informs about related activities at The University of Auckland, focussing on stereo vision, performance evaluation, provided test data, and currently developed components. }, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5775884} } @phdthesis{Henneges2011, author = {Henneges, Carsten}, title = {Feature Selection and Data Mining for Proteomics and Metabolomics}, school = {University of Tuebingen}, year = {2011}, address = {T\"ubingen, Germany}, month = mar, abstract = {The past decades saw a rapid improvement in the technique of biological experiments. While the beginning was coined with long and complex experiments carried out by laboratory staff, automatic high-throughput methods emerged. Especially proteomics profited from advances in mass spectrometry to identify fragments from digested proteins. Mass spectrometry entered the novel field of metabolomics. Metabolomics investigates small molecules from metabolism for their role as disease markers. The goal here is to develop monitoring and screening techniques based on easily obtained body fluids. However, further methods, as IR spectroscopy, are waiting for their advent into metabolomics research. Connected to each area of research is the topic of data mining. Essentially, data mining can be subdivided into the tasks of feature selection and feature construction. Feature selection aims to select relevant features out of a larger pool. A selected combination may aid visualisation and thus understanding of a dataset as well as improve the prediction performance of learning algorithms. To this end, three general approaches exist: wrapper, filter and embedded methods. While wrappers employ an arbitrary learning algorithm for assessing the value of a feature combination, filters rely on statistical criteria. Most recently, embedded methods attracted research interest, wherein feature selection is integrated into a learning algorithm. Feature construction algorithms on the other hand reconstruct the subsignals of an additive superposition. The key approach thereby is matrix factorisation by constraints. Frequent constraints used for this purpose are statistical independence as well as non-negativity and sparsity, leading to problem specific algorithms. This book supports life science researchers with adapted data mining methods from both feature selection and feature construction for proteomics and metabolomics. We describe biomarker identification for breast cancer prediction using a SVM-based wrapper and develop faster wrapper algorithms using surrogate-based optimisation. Applying filters for ranking-specific feature selection, we also design a cost-efficient prediction system for proteotypic peptides. As an application, embedded methods are used to infer energetical interaction patterns in protein 3D structures. Finally, we develop a novel factorisation method for feature construction to decompose IR spectra within a metabolomics context.}, isbn = {978-3-8439-0122-2}, publisher = {Verlag Dr.~Hut,Sternstra{\ss}e 18, M\"unchen}, url = {http://www.dr.hut-verlag.de/978-3-8439-0122-2.html} } @article{Yangs2011, author = {Huimin Lu and Shaowu Yang and Hui Zhang and Zhiqiang Zheng}, title = {A robust omnidirectional vision sensor for soccer robots}, journal = {Mechatronics}, year = {2011}, volume = {21}, pages = {373-389}, number = {2}, month = mar, issn = {0303-2647}, publisher = {Elsevier}, url = {http://dx.doi.org/10.1016/j.mechatronics.2010.06.007} } @inproceedings{Schauwecker2011a, author = {Schauwecker, Konstantin and van den Hurk, Simon and Yuen, Wallace and W\"unsche, Burkhard}, title = {{Sketched Interaction Metaphors for Character Animation}}, booktitle = {International Conference on Computer Graphics Theory and Applications (GRAPP)}, year = {2011}, pages = {247--252}, address = {Vilamoura, Algarve, Portugal}, month = {March}, publisher = {Springer}, abstract = {The use of 3D virtual worlds is increasing rapidly and new tools are necessary to enable untrained users to create3D content and interact with it. In this paper we present and evaluate sketch-based interaction metaphorsfor specifying complex animations of 3D skeletally animated models. Sketched interactions include bone rotation,motion path translation, sequencing and synchronisation of animations, and an undo-functionality. Thesketches are drawn directly onto a model in a 3D view and are translated into time-dependent joint transformations.We present the design concepts, the implementation of a prototype, and a user study assessing theusability of our animation metaphors. The user study demonstrates that the animation metaphors are intuitive,with the exception of animation ordering. A large variety of animations were successfully created by users.More work is necessary to synchronise animations better. Overall our research demonstrates that sketchedbasedanimations can be useful for applications requiring rapid prototyping containing a limited number ofjoint animations. Examples are the programming of household robots and the creation of simple animatedscenes in education and social network applications. }, pdf = {http://www.cs.auckland.ac.nz/~burkhard/Publications/GRAPP2011_SchauweckerEtAl.pdf}, } @article{Eichner2011, author = {Johannes Eichner and Georg Zeller and Sascha Laubinger and Gunnar Raetsch}, title = {{Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays.}}, journal = {BMC Bioinformatics}, year = {2011}, volume = {12}, pages = {55}, number = {1}, month = feb, __markedentry = {[eichner]}, abstract = {ABSTRACT: BACKGROUND: Alternative splicing (AS) is a process which generates several distinct mRNA isoforms from the same gene by splicing different portions out of the precursor transcript. Due to the (patho-)physiological importance of AS, a complete inventory of AS is of great interest. While this is in reach for human and mammalian model organisms, our knowledge of AS in plants has remained more incomplete. Experimental approaches for monitoring AS are either based on transcript sequencing or rely on hybridization to DNA microarrays. Among the microarray platforms facilitating the discovery of AS events, tiling arrays are well-suited for identifying intron retention, the most prevalent type of AS in plants. However, analyzing tiling array data is challenging, because of high noise levels and limited probe coverage. RESULTS: In this work, we present a novel method to detect intron retentions (IR) and exon skips (ES) from tiling arrays. While statistical tests have typically been proposed for this purpose, our method instead utilizes support vector machines (SVMs) which are appreciated for their accuracy and robustness to noise. Existing EST and cDNA sequences served for supervised training and evaluation. Analyzing a large collection of publicly available microarray and sequence data for the model plant A. thaliana, we demonstrated that our method is more accurate than existing approaches. The method was applied in a genome-wide screen which resulted in the discovery of 1,355 IR events. A comparison of these IR events to the TAIR annotation and a large set of short-read RNA-seq data showed that 830 of the predicted IR events are novel and that 525 events (39\%) overlap with either the TAIR annotation or the IR events inferred from the RNA-seq data. CONCLUSIONS: The method developed in this work expands the scarce repertoire of analysis tools for the identification of alternative mRNA splicing from whole-genome tiling arrays. Our predictions are highly enriched with known AS events and complement the A. thaliana genome annotation with respect to AS. Since all predicted AS events can be precisely attributed to experimental conditions, our work provides a basis for follow-up studies focused on the elucidation of the regulatory mechanisms underlying tissue-specific and stress-dependent AS in plants.}, doi = {10.1186/1471-2105-12-55}, language = {eng}, medline-pst = {aheadofprint}, pii = {1471-2105-12-55}, pmid = {21324185}, url = {http://dx.doi.org/10.1186/1471-2105-12-55} } @article{Hoeppe2011, author = {Hoeppe, Sibylle and Schreiber, Thomas D. and Planatscher, Hannes and Zell, Andreas and Templin, Markus F. and Stoll, Dieter and Joos, Thomas O. and Poetz, Oliver}, title = {Targeting peptide termini, a novel immunoaffinity approach to reduce complexity in mass spectrometric protein identification}, journal = {Mol Cell Proteomics}, year = {2011}, volume = {10}, pages = {M110.002857}, number = {2}, month = feb, abstract = {Mass spectrometry and peptide-centric approaches are powerful techniques for the identification of differentially expressed proteins. Despite enormous improvements in MS technologies, sample preparation and efficient fractionation of target analytes are still major bottlenecks in MS-based protein analysis. The complexity of tryptically digested whole proteomes needs to be considerably reduced before low abundance proteins can be effectively analyzed using MS/MS. Sample preparation strategies that use peptide-specific antibodies are able to reduce the complexity of tryptic digests and lead to a substantial increase in throughput and sensitivity; however, the number of peptide-specific capture reagents is low, and consequently immunoaffinity-based approaches are only capable of detecting small sets of protein-derived peptides. In this proof-of-principle study, special anti-peptide antibodies were used to enrich peptides from a complex mixture. These antibodies recognize short amino acid sequences that are found directly at the termini of the peptides. The recognized epitopes consist of three or four amino acids only and include the terminally charged group of the peptide. Because of its limited length, antibodies recognizing the epitope will enrich not only one peptide but a whole class of peptides that share this terminal epitope. In this study, $\beta$-catenin-derived peptides were used to demonstrate that it is possible (i) to effectively generate antibodies that recognize short C-terminal peptide epitopes and (ii) to enrich and identify peptide classes from a complex mixture using these antibodies in an immunoaffinity MS approach. The expected $\beta$-catenin peptides and a set of 38 epitope-containing peptides were identified from trypsin-digested cell lysates. This might be a first step in the development of proteomics applications that are based on the use of peptide class-specific antibodies.}, doi = {10.1074/mcp.M110.002857}, institution = {NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany}, keywords = {Antibodies, chemistry; Cell Line; Epitopes, chemistry; Gene Library; HEK293 Cells; Humans; Mass Spectrometry, methods; Peptides, chemistry; Protein Binding; Protein Structure, Tertiary; Proteins, chemistry; Proteome; Proteomics, methods; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Trypsin, chemistry}, language = {eng}, medline-pst = {ppublish}, pdf = {http://www.mcponline.org/content/10/2/M110.002857.pdf}, pii = {M110.002857}, pmid = {20962300}, url = {http://dx.doi.org/10.1074/mcp.M110.002857} } @phdthesis{Draeger2011a, author = {Dr\"ager, Andreas}, title = {Computational Modeling of Biochemical Networks}, school = {University of Tuebingen}, year = {2011}, address = {T\"ubingen, Germany}, month = jan, abstract = {In recent years biology has shifted its focus from the mainly descriptive exploration of individual organisms, cells, or molecules towards a holistic investigation of the complex interactions within living systems. This progress is driven by the development of large-scale measurement techniques, e.g., the timely resolved simultaneous quantification of many cellular components. The exploration of these data sets requires the application of methods from other areas of natural science and the development of novel analysis methods. At this intersection systems biology aims to understand mutual interactions and influences between biological components. Control mechanisms and regulation of processes, which often show a nonlinear behavior, are to be described. Predicting the dynamics of complex interaction systems constitutes its main challenge. Computational modeling methods play a central role to attain this goal. Without loss of generality, we here focus on metabolic systems in preparation for an extension to gene-regulatory systems. Physico-chemical, in particular thermodynamic, constraints restrict the investigated systems and define the domain of plausible and valid models. Setting up such a mathematical description is not only complicated and highly error-prone, it also requires knowledge from many different fields and is therefore not easily applicable for non-experts. This thesis aims at the development of a method that performs the model construction steps to the widest extent automatically, reducing the number of necessary human interactions to a minimum but that still leads to thermodynamically feasible and correct model systems. To this end, it introduces a five-step modeling pipeline that ultimately leads to a mathematical description of a biochemical reaction system. We discuss how to automate each individual step and how to put these steps together: First, we create a topology of interconversion processes and mutual influences between reactive species encoded in the Systems Biology Markup Language (SBML) including semantic information. Second, a procedure is established that generates kinetic equations in a context-sensitive manner. The resulting model can then be combined with already existing models. Third, we estimate the values of all newly introduced parameters in each created rate law. This procedure requires that a time series of quantitative measurements of the reactive species within this system be available, because we calibrate the parameters with the aim that the model will fit these experimental data. The applicability and functioning of these approaches is demonstrated on a model of the valine and leucine biosynthesis in \emph{C.~glutamicum}. In a large-scale benchmark the results of seven modeling techniques are systematically compared when estimating their parameters with a multitude of nature-inspired heuristic optimization processes. This step is crucial for the development of an automatic modeling procedure because it highlights the strength and weaknesses of all these approaches. Fourth, an experimental validation of the resulting model is advisable. Fifth, a model report is generated automatically to document the model with all of its components. In an extension, this computer-aided modeling pipeline is further developed to a fully automatic procedure, the AMUSE algorithm (Automated Modeling Using Specialized Enzyme kinetics). The network topology in form of an SBML file and biological reference data, i.e., at least one time-series of participating metabolite concentrations and some relevant target fluxes, build its only required input. Based on latest estimation methods for standard reaction Gibbs energies, AMUSE determines a thermodynamically feasible, minimal equilibrium configuration of the system, identifies the key reactions and selects kinetic equations describing all reaction velocities. Furthermore, it estimates all remaining parameters with respect to given experimental data. For a better understanding, we begin with an introduction to fundamental modeling and generalized approaches for common rate equations. Subsequently, parameter estimation techniques are introduced and evaluated on the valine and leucine biosynthesis in \emph{C.~glutamicum}. Thereafter, standardization attempts in systems biology will be discussed that are required for the computer-aided modeling pipeline. This pipeline necessitates extending the existing standards. In particular, the development and implementation of JSBML, the Java library for SBML, has been conducted to simplify computation and manipulation of complex models. A discussion of possible further improvements and an extension of the suggested modeling pipeline to gene-regulatory networks completes this thesis.}, isbn = {978-3-86853-850-2}, keywords = {automated modeling, AMUSE algorithm, C. glutamicum, enzyme kinetics, evolutionary algorithms, heuristic optimization, JSBML, leucine biosynthesis, metabolic modeling, gene-regulatory network, parameter estimation, rate law, SBML, SBML2LaTeX, SBMLsqueezer, valine biosynthesis}, publisher = {Verlag Dr.~Hut, Sternstra{\ss}e 18, M\"unchen}, url = {http://www.dr.hut-verlag.de/978-3-86853-850-2.html} } @incollection{Franken2011, author = {Franken, Holger and Lehmann, Rainer and H\"aring, Hans-Ulrich and Fritsche, Andreas and Stefan, Norbert and Zell, Andreas}, title = {Wrapper- and Ensemble-Based Feature Subset Selection Methods for Biomarker Discovery in Targeted Metabolomics}, booktitle = {Pattern Recognition in Bioinformatics}, publisher = {Springer Berlin / Heidelberg}, year = {2011}, editor = {Loog, Marco and Wessels, Lodewyk and Reinders, Marcel and de Ridder, Dick}, volume = {7036}, series = {Lecture Notes in Computer Science}, pages = {121-132}, note = {10.1007/978-3-642-24855-9_11}, abstract = {The discovery of markers allowing for accurate classification of metabolically very similar proband groups constitutes a challenging problem. We apply several search heuristics combined with different classifier types to targeted metabolomics data to identify compound subsets that classify plasma samples of insulin sensitive and -resistant subjects, both suffering from non-alcoholic fatty liver disease. Additionally, we integrate these methods into an ensemble and screen selected subsets for common features. We investigate, which methods appear the most suitable for the task, and test feature subsets for robustness and reproducibility. Furthermore, we consider the predictive potential of different compound classes. We find that classifiers fail in discriminating the non-selected data accurately, but benefit considerably from feature subset selection. Especially, a Pareto-based multi-objective genetic algorithm detects highly discriminative subsets and outperforms widely used heuristics. When transferred to new data, feature sets assembled by the ensemble approach show greater robustness than those selected by single methods.}, affiliation = {Center for Bioinformatics (ZBIT), University of T\"ubingen, D-72076 T\"ubingen, Germany}, isbn = {978-3-642-24854-2}, keyword = {Computer Science}, url = {http://dx.doi.org/10.1007/978-3-642-24855-9_11} } @incollection{Hinselmann2011evostar, author = {Hinselmann, Georg and Jahn, Andreas and Fechner, Nikolas and Rosenbaum, Lars and Zell, Andreas}, title = {Approximation of Graph Kernel Similarities for Chemical Graphs by Kernel Principal Component Analysis}, booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics}, publisher = {Springer Berlin Heidelberg}, year = {2011}, editor = {Pizzuti, Clara and Ritchie, Marylyn D. and Giacobini, Mario}, volume = {6623}, series = {Lecture Notes in Computer Science}, pages = {123--134}, editors = {C. Pizzuti and M.D. Ritchie and M. Giacobini}, } @inproceedings{HinselmannESANN2011, author = {Georg Hinselmann and Andreas Jahn and Lars Rosenbaum and Andreas Zell}, title = {Fast Data Mining with Sparse Chemical Graph Fingerprints by Estimating the Probability of Unique Patterns}, booktitle = {Proceedings of 19th European Symposium on Artificial Neural Networks (ESANN 2011)}, year = {2011}, editor = {Michel Verleysen}, pages = {417-422}, address = {Bruges, Belgium}, } @article{Hinselmann2010a, author = {Hinselmann, Georg and Rosenbaum, Lars and Jahn, Andreas and Fechner, Nikolas and Ostermann, Claude and Zell, Andreas}, title = {Large-Scale Learning of Structure-Activity Relationships Using a Linear Support Vector Machine and Problem-specific Metrics}, journal = {Journal of Chemical Information and Modeling}, year = {2011}, volume = {52}, pages = {203--213}, issue = {2}, } @article{Hinselmann2010c, author = {Georg Hinselmann and Lars Rosenbaum and Andreas Jahn and Nikolas Fechner and Andreas Zell}, title = {jCompoundMapper: An Open Source Java Library and Command-Line Tool for Chemical Fingerprints}, journal = {Journal of Cheminformatics}, year = {2011}, volume = {3}, number = {3}, } @article{Jahn2011a, author = {Andreas Jahn and Georg Hinselmann and Lars Rosenbaum and Nikolas Fechner and Andreas Zell}, title = {Boltzmann-enhanced Flexible Atom-Pair Kernel with Dynamic Dimension Reduction}, journal = {Molecular Informatics}, year = {2011}, volume = {30}, pages = {307--315}, number = {4}, } @article{Jahn2011b, author = {Andreas Jahn and Lars Rosenbaum and Georg Hinselmann and Andreas Zell}, title = {{4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening}}, journal = {Journal of Cheminformatics}, year = {2011}, volume = {3}, number = {23}, } @inproceedings{khan11a, author = {Khan, Yasir Niaz and Komma, Philippe and Bohlmann, Karsten and Zell, Andreas}, title = {Grid-based Visual Terrain Classification for Outdoor Robots using Local Features}, booktitle = {IEEE Symposium on Computational Intelligence in Vehicles and Transportation Systems (CIVTS 2011)}, year = {2011}, pages = {16 - 22}, address = {Paris, France}, month = {apr}, abstract = {In this paper we present a comparison of multiple approaches to visual terrain classification for outdoor mobile robots based on local features. We compare the more traditional texture classification approaches, such as Local Binary Patterns, Local Ternary Patterns and a newer extension Local Adaptive Ternary Patterns, and also modify and test three non-traditional approaches called SURF, DAISY and CCH. We drove our robot under different weather and ground conditions and captured images of five different terrain types for our experiments. We did not filter out blurred images which are due to robot motion and other artifacts caused by rain, etc.We used Random Forests for classification, and cross-validation for the verification of our results. The results show that most of the approaches work well for terrain classification in a fast moving mobile robot, despite image blur and other artifacts induced due to extremely variant weather conditions.}, comment = {http://ieeexplore.ieee.org/search/freesrchabstract.jsp?tp=&arnumber=5949534&queryText%3DGrid-based+Visual+Terrain+Classification+for+Outdoor+Robots+using+Local+Features%26openedRefinements%3D*%26filter%3DAND%28NOT%284283010803%29%29%26searchField%3DSearch+All&abstractAccess=no&userType=inst}, doi = {10.1109/CIVTS.2011.5949534}, keywords = {CCH;DAISY;SURF;artifacts;blurred images filtering;local features;outdoor mobile robots;random forests;robot motion;texture classification;visual terrain classification;feature extraction;image restoration;image texture;mobile robots;pattern classification}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/khan2011civts.pdf} } @inproceedings{khan11b, author = {Khan, Yasir Niaz and Komma, Philippe and Zell, Andreas}, title = {High Resolution Visual Terrain Classification for Outdoor Robots}, booktitle = {Computer Vision Workshops (ICCV Workshops), 2011 IEEE International Conference on}, year = {2011}, pages = {1014 -1021}, address = {Barcelona, Spain}, month = {nov}, abstract = {In this paper we investigate SURF features for visual terrain classification for outdoor mobile robots. The image is divided into a grid and SURF features are calculated on the intersections of this grid. These features are then used to train a classifier that can differentiate between different terrain classes. Images of five different terrain types are taken using a single camera mounted on a mobile outdoor robot. We further introduce another descriptor, which is a modified form of the dense Daisy descriptor. Random forests are used for classification on each descriptor. Classification results of SURF and Daisy descriptors are compared with the results from traditional texture descriptors like LBP, LTP and LATP. It is shown that SURF features perform better than other descriptors at higher resolutions. Daisy features, although not better than SURF features, also perform better than the three texture descriptors at high resolution.}, doi = {10.1109/ICCVW.2011.6130362}, keywords = {SURF;artifacts;blurred images filtering;local features;outdoor mobile robots;random forests;robot motion;texture classification;visual terrain classification;feature extraction;image restoration;image texture;mobile robots;pattern classification}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2011/khan2011iccvworkshop.pdf} } @misc{MasselliWenzel2011, author = {Andreas Masselli and Karl Engelbert Wenzel and Andreas Zell}, title = {{Verfahren zur Bestimmung der relativen Lage eines Objektes im Raum sowie optisches Eingabesystem}}, year = {2011}, note = {Patent, DE 10 2011 075 253.6, Submitted 2011.05.04}, } @article{Rosenbaum2011a, author = {Lars Rosenbaum and Georg Hinselmann and Andreas Jahn and Andreas Zell}, title = {Interpreting linear support vector machine models with heat map atom and bond coloring}, journal = {Journal of Cheminformatics}, year = {2011}, volume = {3}, pages = {11}, } @article{Schattel2011, author = {Schattel, Verena and Hinselmann, Georg and Jahn, Andreas and Zell, Andreas and Laufer, Stefan}, title = {A Modeling and Benchmark Data Set for the Inhibition of c-Jun N-terminal Kinase-3}, journal = {Journal of Chemical Information and Modeling}, year = {2011}, volume = {51}, pages = {670-679}, numbwe = {3}, } @article{Ran_image_matching_2008, author = {Heng Wang and Ran Liu and Xingzhe Xie}, title = {{Study on New Image Angle Matching Method and Applications}}, journal = {Computer Engineering and Applications}, year = {2011}, pages = {208--211}, url = {http://www.cnki.com.cn/Article/CJFDTotal-JSGG201104060.htm} } @inproceedings{Schauwecker2010, author = {Schauwecker, Konstantin and Klette, Reinhard}, title = {{A Comparative Study of Two Vertical Road Modelling Techniques}}, booktitle = {ACCV Workshop: Computer Vision in Vehicle Technology}, year = {2010}, pages = {174--183}, address = {Queenstown, New Zealand}, month = {November}, publisher = {Springer}, abstract = {Binocular vision combined with stereo matching algorithms can be used in vehicles to gatherdata of the spatial proximity. To utilize this data we propose a new method for modeling thevertical road profile from a disparity map. This method is based on a region-growing technique,which iteratively performs a least-squares fit of a B-spline curve to a region of selectedpoints. We compare this technique to two variants of the $v$-disparity method using either anenvelope function or a planarity assumption. Our findings are that the proposed road-modelingtechnique outperforms both variants of the $v$-disparity technique, for which the planarityassumption is slightly better than the envelope version. }, url = {http://www.springerlink.com/content/gh26u84p44037834/} } @article{Schroeder2010, author = {Schr\"oder, Adrian and Eichner, Johannes and Supper, Jochen and Eichner, Jonas and Wanke, Dierk and Henneges, Carsten and Zell, Andreas}, title = {{Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2010}, volume = {5}, pages = {e13876}, number = {11}, month = nov, abstract = {Today, annotated amino acid sequences of more and more transcription factors (TFs) are readily available. Quantitative information about their DNA-binding specificities, however, are hard to obtain. Position frequency matrices (PFMs), the most widely used models to represent binding specificities, are experimentally characterized only for a small fraction of all TFs. Even for some of the most intensively studied eukaryotic organisms (i.e., human, rat and mouse), roughly one-sixth of all proteins with annotated DNA-binding domain have been characterized experimentally. Here, we present a new method based on support vector regression for predicting quantitative DNA-binding specificities of TFs in different eukaryotic species. This approach estimates a quantitative measure for the PFM similarity of two proteins, based on various features derived from their protein sequences. The method is trained and tested on a dataset containing 1 239 TFs with known DNA-binding specificity, and used to predict specific DNA target motifs for 645 TFs with high accuracy.}, doi = {10.1371/journal.pone.0013876}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/schroederTFBSPrediction.pdf}, publisher = {Public Library of Science}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0013876} } @inproceedings{komma10b, author = {Komma, Philippe and Zell, Andreas}, title = {Markov Random Field-based Clustering of Vibration Data}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2010)}, year = {2010}, pages = {1902-1908}, address = {Taipei, Taiwan}, month = oct, note = {Best Paper Award Nominee}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/komma2010iros-mrfcluster.pdf} } @inproceedings{Liu2010:3D, author = {Xingzhe Xie and Heng Wang and Ran Liu and Wen-qiang Xiang and Ming Jiang}, title = {3D Terrain Reconstruction for Patrol Robot Using Point Grey Research Stereo Vision Cameras}, booktitle = {Proceedings of the 2010 International Conference on Artificial Intelligence and Computational Intelligence (AICI '10)}, year = {2010}, volume = {1}, pages = {47--51}, address = {Sanya, China}, month = {October}, abstract = {This paper uses Bumblebee stereo vision system to reconstruct the 3D terrain for patrol robot. Firstly, with the selected points in the disparity image, the ground plane equation of the current frame is calculated by the RANSAC (Random Sample Consensus) algorithm, and then estimated and predicted by the Kalman filter. Secondly, the elevation image is obtained through the distance between the obstacle and the ground plane, which is calculated on basis of the formula from the point to the plane. Finally, the noise points in the elevation image are removed through erosion and dilation operations, and the location and size of obstacles are determined via the connected component analysis method. The actual test in substation environment verified the reliability of the system.}, acmid = {1917716}, days = {23-24}, doi = {http://dx.doi.org/10.1109/AICI.2010.17}, isbn = {978-0-7695-4225-6}, keywords = {patrol robot, RANSAC algorithm, Kalman filter, connected component analysis}, numpages = {5}, } @inproceedings{hofmeistIAV, author = {Hofmeister, Marius and Kronfeld, Marcel}, title = {Multi-robot Coverage Considering Line-of-sight Conditions}, booktitle = {7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV)}, year = {2010}, address = {Lecce, Italy}, month = sep, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/hofmeister2010iav.pdf} } @inproceedings{kanjanaw_IAV2010_1, author = {Kiattisin Kanjanawanishkul and Marius Hofmeister and Andreas Zell}, title = {Path Following with an Optimal Forward Velocity for a Mobile Robot}, booktitle = {7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV)}, year = {2010}, address = {Lecce, Italy}, month = sep, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/kanjanaw2010iav.pdf} } @inproceedings{kanjanaw_IAV2010_2, author = {Kiattisin Kanjanawanishkul and Andreas Zell}, title = {Distributed Role Assignment in Multi-robot Formation}, booktitle = {7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV)}, year = {2010}, address = {Lecce, Italy}, month = sep, abtract = {In this paper, we study the problem of distributed role assignment for multiple mobile robots. This problem arises when a mobile robot in the team must decide what role to take on in a desired formation configuration. In some applications, in which the center and orientation of a desired formation are not predetermined, the rotation and translation of the formation can be computed by using average consensus protocols. A conflict arises when the same role is assigned to more than one robot. This problem is resolved by using a negotiation strategy, while each assigned robot is traveling to the target position. Furthermore, dynamic consensus is used to measure the degree of task completion in this work. Once the consensus reaches a preset threshold, implying that robots should abandon the current task and start the next one. We verify our proposed framework through simulations on a team of nonholonomic mobile robots performing distributed formation switching.}, } @inproceedings{komma10a, author = {Komma, Philippe and Zell, Andreas}, title = {Clustering Vibration Data Using a Temporally Coherent {E}xpectation {M}aximization Approach}, booktitle = {7th Symposium on Intelligent Autonomous Vehicles (IAV 2010)}, year = {2010}, pages = {1-6}, address = {Lecce, Italy}, month = sep, } @inproceedings{Beck10, author = {Markus Beck and Jozsef Hecht-Mendez and Michael de Paly and Peter Bayer and Philipp Blum and Andreas Zell}, title = {Optimization of the Energy Extraction of a Shallow Geothermal System}, booktitle = {Proceedings of the IEEE Congress on Evolutionary Computation (CEC)}, year = {2010}, pages = {3622-3628}, address = {Barcelona, Spain}, month = jul, abstract = {Geothermal energy use from shallow groundwater systems is attractive for the supply of heat and hot water to buildings. It offers economic and environmental advantages over traditional fossil-fuel based technologies, in particular when large scale systems are well adapted to the always unique hydrogeological conditions. Computer based numerical simulations are used to examine the performance of multiple borehole heat exchangers installed in the ground. This paper demonstrates how evolutionary algorithms can be utilized to configure the elements of a geothermal system in an ideal way, and thus substantially enhance the energy extraction rate in comparison to standardized approaches. Differential evolution (DE), evolution strategies (ES) and particle swarm optimizers (PSO) are combined with a local search approach and compared with respect to their efficiency in the optimization of synthetic, real case oriented and static systems. First results are promising, especially for the PSO and the DE with the local search approach.}, doi = {10.1109/CEC.2010.5585921}, } @inbook{Draeger2010a, chapter = {Automating mathematical modeling of biochemical reaction networks}, pages = {159--205}, title = {Systems Biology for Signaling Networks}, publisher = {Springer-Verlag}, year = {2010}, editor = {Choi, Sangdun}, author = {Dr\"ager, Andreas and Schr\"oder, Adrian and Zell, Andreas}, volume = {1}, series = {Systems Biology}, month = jul, abstract = {In this chapter we introduce a five-step modeling pipeline that ultimately leads to a mathematical description of a biochemical reaction system. We discuss how to automate each single step and how to put these steps together: First, we have to create a topology of interconversion processes and mutual influences between reactive species. An automated modeling procedure requires an appropriate data format that encodes the model in a computer-readable form. A standard like the Systems Biology Markup Language (SBML) serves this purpose and allows us to add semantic information to each component of the model. Second, from such an annotated network the procedure SBMLsqueezer generates kinetic equations in a context sensitive manner. The resulting model can then be combined with already existing models. Third, we estimate the values of all newly introduced parameters in each created rate law. This procedure requires a time series of quantitative measurements of the reactive species within this system to be available, because we calibrate the parameters with the aim that the model will fit these experimental data. Fourth, an experimental validation of the resulting model is advisable. Finally, a model report should be generated to document the model with all of its components. For a better understanding, we start our consideration with an introduction into necessary standardization attempts in today's systems biology and generalized approaches for common rate equations before we discuss the computer-aided modeling, parameter estimation, and automatic report generation. We complete this chapter with a discussion on possible further improvements of our modeling pipeline.}, doi = {10.1007/978-1-4419-5797-9_7}, url = {http://www.springerlink.com/content/n77k80h76vj17806} } @inproceedings{kanjanaw_AIM2010, author = {Kanjanawanishkul, Kiattisin and Hofmeister, Marius and Zell, Marius}, title = {Experiments on Formation Switching for Mobile Robots}, booktitle = {IEEE/ASME International Conference on Advanced Intelligent Mechatronics (AIM 2010)}, year = {2010}, pages = {323--328}, address = {Montr{\'e}al, Canada}, month = {July}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/kanjanaw2010aim.pdf} } @mastersthesis{koch2010thesis, author = {Koch, Artur}, title = {Fast and Scalable {CPU}/{GPU} Collision Detection for Rigid and Deformable Surfaces}, school = {University of Tuebingen}, year = {2010}, type = {Diplomarbeit}, month = jul, abstract = {...}, url = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/koch/publications/koch2010diplomathesis.pdf} } @inproceedings{Kron10Niching, author = {Kronfeld, Marcel and Zell, Andreas}, title = {Towards Scalability in Niching Methods}, booktitle = {Proceedings of the IEEE Congress on Evolutionary Computation (CEC)}, year = {2010}, pages = {4409--4416}, address = {Barcelona, Spain}, month = jul, abstract = {The scaling properties of multimodal optimization methods have seldom been studied, and existing studies often concentrated on the idea that all local optima of a multimodal function can be found and their number can be estimated a priori. We argue that this approach is impractical for complex, high-dimensional target functions, and we formulate alternative criteria for scalable multimodal optimization methods. We suggest that a scalable niching method should return the more local optima the longer it is run, without relying on a fixed number of expected optima. This can be fulfilled by sequential and semi-sequential niching methods, several of which are presented and analyzed in that respect. Results show that, while sequential local search is very successful on simpler functions, a clustering-based particle swarm approach is most successful on multi-funnel functions, offering scalability even under deceptive multimodality, and denoting it a starting point towards effective scalable niching.}, isbn = {978-1-4244-6910-9}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Kron10Scaling.pdf} } @inproceedings{Lambeck2010, author = {Lambeck, Sandro and Dr\"ager, Andreas and Guthke, Reinhard}, title = {Network Inference by Considering Multiple Objectives: Insights from In Vivo Transcriptomic Data Generated by a Synthetic Network}, booktitle = {International Conference on Bioinformatics and Computational Biology, BIOCOMP 2010}, year = {2010}, editor = {Arabnia, Hamid R. and Tran, Quoc-Nam and Chang, Rui and He, Matthew and Marsh, Andy and Solo, Ashu M. G. and Yang, Jack Y.}, volume = {2}, pages = {734--742}, month = jul, publisher = {CSREA Press}, abstract = {This paper addresses the problem of finding gene regulatory networks for various data sets derived from the same underlying network, but challenged to different stimuli. To this end, we propose to adapt solutions of systems of non-linear difference equations by including multiple objectives. The model structure and parameter estimation, is facilitated by application of an hybrid Evolutionary Multi-Objective Algorithm. Furthermore, we compare the fit of the logistic and double logistic transfer function. The application is driven by data obtained from a recently published synthetic gene regulatory network, being especially designed for the assessment of network inference methods. Inferred networks were in high accordance with the designed structure and indicated the favor of a multi-objective approach including all available data. The double logistic transfer function outperformed the logistic transfer function to model saturation effects. Results also suggested that the protein-protein interaction should be integrated in the model of transcriptional regulation.}, isbn = {1-60132-134-1}, keywords = {Network Inference; Synthetic Biology; Multiple Objective Optimization}, url = {http://www.cs.uga.edu/~hra/2010-proceedings-final/biocomp/papers.pdf} } @inproceedings{DePaly10, author = {Michael de Paly and Niels Schuetze and Andreas Zell}, title = {Determining Crop-Production Functions using Multi-Objective Evolutionary Algorithms}, booktitle = {Proceedings of the IEEE Congress on Evolutionary Computation (CEC)}, year = {2010}, pages = {1870 - 1877}, address = {Barcelona, Spain}, month = jul, doi = {10.1109/CEC.2010.5586147}, } @inproceedings{Hofmeister2010CompEff, author = {Marius Hofmeister and Philipp Vorst and Andreas Zell}, title = {A Comparison of Efficient Global Image Features for Localizing Small Mobile Robots}, booktitle = {ISR/ROBOTIK 2010 (Proceedings of the joint conference of ISR 2010 (41st International Symposium on Robotics) and ROBOTIK 2010 (6th German Conference on Robotics))}, year = {2010}, pages = {143--150}, month = jun, publisher = {VDE Verlag}, abstract = {Global image features are well-suited for the visual self-localization of mobile robots. They are fast to compute, to compare and do not require much storage space. Especially when using small mobile robots with limited processing capabilities and low-resolution cameras, global features can be preferred to local features. In this paper, we compare the accuracy and computation times of different global image features when localizing small mobile robots. We test the methods under realistic conditions, taking illumination changes and translations into account. By employing a particle filter and reducing the image resolution, we speed up the localization process considerably.}, isbn = {978-3-8007-3273-9}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/hofmeister2010isr.pdf} } @inproceedings{jiang_hou2010, author = {Jin Hou and Dengsheng Zhang and Zeng Chen and Lixing Jiang and Huazhong Zhang and Xue Qin}, title = {Web Image Search by Automatic Image Annotation and Translation }, booktitle = {17th International Conference on Systems, Signals and Image Processing (IWSSIP'10)}, year = {2010}, address = {Rio de Janeiro, Brazil}, month = {June}, url = {http://www.creacteve.com.br/iwssip/nav/papers/paper_26.pdf} } @article{Planatscher2010, author = {Planatscher, Hannes and Supper, Jochen and Poetz, Oliver and Stoll, Dieter and Joos, Thomas and Templin, Markus and Zell, Andreas}, title = {Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry}, journal = {Algorithms for Molecular Biology}, year = {2010}, volume = {5}, pages = {28}, number = {1}, month = jun, abstract = {BACKGROUND: Mass spectrometry (MS) based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an efficient fractionation step to reduce the complexity of the biological samples, which are too complex to be analyzed directly with MS. Sample preparation strategies that reduce the complexity of tryptic digests by using immunoaffinity based methods have shown to lead to a substantial increase in throughput and sensitivity in the proteomic mass spectrometry approach. The limitation of using such immunoaffinity-based approaches is the availability of the appropriate peptide specific capture antibodies. Recent developments in these approaches, where subsets of peptides with short identical terminal sequences can be enriched using antibodies directed against short terminal epitopes, promise a significant gain in efficiency.RESULTS:We show that the minimal set of terminal epitopes for the coverage of a target protein list can be found by the formulation as a set cover problem, preceded by a filtering pipeline for the exclusion of peptides and target epitopes with undesirable properties.CONCLUSIONS:For small datasets (a few hundred proteins) it is possible to solve the problem to optimality with moderate computational effort using commercial or free solvers. Larger datasets, like full proteomes require the use of heuristics.}, doi = {10.1186/1748-7188-5-28}, isbn = {1748-7188}, url = {http://www.almob.org/content/5/1/28} } @inproceedings{vorst2010isr, author = {Philipp Vorst and Andreas Zell}, title = {A Comparison of Similarity Measures for Localization with Passive {RFID} Fingerprints}, booktitle = {ISR/ROBOTIK 2010 (Proceedings of the joint conference of ISR 2010 (41st International Symposium on Robotics) and ROBOTIK 2010 (6th German Conference on Robotics))}, year = {2010}, pages = {354--361}, month = jun, publisher = {VDE Verlag}, abstract = {We present a novel approach to self-localization with passive RFID fingerprints using vector space similarity measures and weighted k-nearest neighbors (WKNN). Embedded in a particle filter, our technique provides robust and accurate position estimates. This is shown through various experiments with a mobile robot. The formulation of the observation model guarantees applicability to any type of off-the-shelf RFID reader which counts RFID tag detections. Different similarity measures are investigated, and a new measure is proposed.}, isbn = {978-3-8007-3273-9}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/vorst2010isr.pdf} } @article{DePalyWRR10, author = {Peter Bayer and Michael de Paly and Claudius N. B\"urger}, title = {Optimization of high-reliability-based hydrological design problems by robust automatic sampling of critical model realizations}, journal = {Water Resources Research}, year = {2010}, volume = {46}, pages = {W05504}, number = {5}, month = may, abstract = {This study demonstrates the high efficiency of the so-called stack-ordering technique for optimizing a groundwater management problem under uncertain conditions. The uncertainty is expressed by multiple equally probable model representations, such as realizations of hydraulic conductivity. During optimization of a well-layout problem for contaminant control, a ranking mechanism is applied that extracts those realizations that appear most critical for the optimization problem. It is shown that this procedure works well for evolutionary optimization algorithms, which are to some extent robust against noisy objective functions. More precisely, differential evolution (DE) and the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) are applied. Stack ordering is comprehensively investigated for a plume management problem at a hypothetical template site based on parameter values measured at and on a geostatistical model developed for the Lauswiesen study site near T\"ubingen, Germany. The straightforward procedure yields computational savings above 90% in comparison to always evaluating the full set of realizations. This is confirmed by cross testing with four additional validation cases. The results show that both evolutionary algorithms obtain highly reliable near-optimal solutions. DE appears to be the better choice for cases with significant noise caused by small stack sizes. On the other hand, there seems to be a problem-specific threshold for the evaluation stack size above which the CMA-ES achieves solutions with both better fitness and higher reliability.}, doi = {10.1029/2009WR008081}, issn = {00431397}, keywords = {optimization groundwater management 1829 Hydrology: Groundwater hydrology 6309 Policy Sciences: Decision making under uncertainty 1805 Hydrology: Computational hydrology 6344 Policy Sciences: System operation and management}, publisher = {AGU}, url = {http://dx.doi.org/10.1029/2009WR008081} } @article{Jahn2010, author = {Jahn, Andreas and Hinselmann, Georg and Fechner, Nikolas and Henneges, Carsten and Zell, Andreas}, title = {Probabilistic Modeling of Conformational Space for 3D Machine Learning Approaches}, journal = {Molecular Informatics}, year = {2010}, volume = {29}, pages = {441--455}, number = {5}, month = may, abstract = {We present a new probabilistic encoding of the conformational space of a molecule that allows for the integration into common similarity calculations. The method uses distance profiles of flexible atom-pairs and computes generative models that describe the distance distribution in the conformational space. The generative models permit the use of probabilistic kernel functions and, therefore, our approach can be used to extend existing 3D molecular kernel functions, as applied in support vector machines, to build QSAR models. The resulting kernels are valid 4D kernel functions and reduce the dependency of the model quality on suitable conformations of the molecules. We showed in several experiments the robust performance of the 4D kernel function, which was extended by our approach, in comparison to the original 3D-based kernel function. The new method compares the conformational space of two molecules within one kernel evaluation. Hence, the number of kernel evaluations is significantly reduced in comparison to common kernel-based conformational space averaging techniques. Additionally, the performance gain of the extended model correlates with the flexibility of the data set and enables an a priori estimation of the model improvement.}, doi = {10.1002/minf.201000036}, } @inproceedings{Yangs2010, author = {Huimin Lu and Hui Zhang and Shaowu Yang and Zhiqiang Zheng}, title = {Camera parameters auto-adjusting technique for robust robot vision}, booktitle = {2010 IEEE International Conference on Robotics and Automation (ICRA 2010)}, year = {2010}, pages = {1518-1523 }, address = {Anchorage, Alaska, USA}, month = may, days = {3-7}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5509978} } @inproceedings{vorst2010icra, author = {Philipp Vorst and Andreas Zell}, title = {Fully Autonomous Trajectory Estimation with Long-Range Passive {RFID}}, booktitle = {2010 IEEE International Conference on Robotics and Automation (ICRA)}, year = {2010}, pages = {1867--1872}, address = {Anchorage, Alaska, USA}, month = may, publisher = {IEEE}, abstract = {We present a novel approach which enables a mobile robot to estimate its trajectory in an unknown environment with long-range passive radio-frequency identification (RFID). The estimation is based only on odometry and RFID measurements. The technique requires no prior observation model and makes no assumptions on the RFID setup. In particular, it is adaptive to the power level, the way the RFID antennas are mounted on the robot, and environmental characteristics, which have major impact on long-range RFID measurements. Tag positions need not be known in advance, and only the arbitrary, given infrastructure of RFID tags in the environment is utilized. By a series of experiments with a mobile robot, we show that trajectory estimation is achieved accurately and robustly.}, doi = {10.1109/ROBOT.2010.5509810}, isbn = {978-1-4244-5040-4}, issn = {1050-4729}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/vorst2010icra.pdf} } @article{Hoene2010, author = {Hoene, Miriam and Franken, Holger and Fritsche, Louise and Lehmann, Rainer and Pohl, Ann Kathrin and H\"aring, Hans-Ulrich and Zell, Andreas and Schleicher, Erwin D. and Weigert, Cora}, title = {Activation of the mitogen-activated protein kinase ({MAPK}) signalling pathway in the liver of mice is related to plasma glucose levels after acute exercise}, journal = {Diabetologia}, year = {2010}, volume = {53}, pages = {1131--1141}, number = {6}, month = mar, abstract = {AIMS/HYPOTHESIS: We aimed to identify, in the liver of mice, signal transduction pathways that show a pronounced regulation by acute exercise. We also aimed to elucidate the role of metabolic stress in this response. METHODS: C57Bl6 mice performed a 60 min run on a treadmill under non-exhaustive conditions. Hepatic RNA and protein lysates were prepared immediately after running and used for whole-genome-expression analysis, quantitative real-time PCR and immunoblotting. A subset of mice recovered for 3 h after the treadmill run. A further group of mice performed the treadmill run after having received a vitamin C- and vitamin E-enriched diet over 4 weeks. RESULTS: The highest number of genes differentially regulated by exercise in the liver was found in the mitogen-activated protein kinase (MAPK) signalling pathway, with a pronounced and transient upregulation of the transcription factors encoded by c-Fos (also known as Fos), c-Jun (also known as Jun), FosB (also known as Fosb) and JunB (also known as Junb) and phosphorylation of hepatic MAPK. Acute exercise also activated the p53 signalling pathway. A major role for oxidative stress is unlikely since the antioxidant-enriched diet did not prevent the activation of the MAPK pathway. In contrast, lower plasma glucose levels after running were related to enhanced levels of MAPK signalling proteins, similar to the upregulation of Igfbp1 and Pgc-1alpha (also known as Ppargc1a). In the working muscle the activation of the MAPK pathway was weak and not related to plasma glucose concentrations. CONCLUSIONS/INTERPRETATION: Metabolic stress evidenced as low plasma glucose levels appears to be an important determinant for the activation of the MAPK signalling pathway and the transcriptional response of the liver to acute exercise.}, doi = {10.1007/s00125-010-1666-3}, institution = {Division of Endocrinology, Diabetology, Angiology, Nephrology, Pathobiochemistry and Clinical Chemistry, Department of Internal Medicine, University Hospital of Tuebingen, Otfried-Mueller-Strasse 10, D-72076, Tuebingen, Germany.}, issn = {0012-186X}, language = {eng}, medline-pst = {aheadofprint}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Hoene2010.pdf}, pmid = {20195842}, publisher = {Springer}, url = {http://dx.doi.org/10.1007/s00125-010-1666-3} } @article{Kron10LocRAS, author = {Kronfeld, Marcel and Weiss, Christian and Zell, Andreas}, title = {Swarm-supported Outdoor Localization with Sparse Visual Data}, journal = {Robotics and Autonomous Systems. Selected papers from the 2007 European Conference on Mobile Robots (ECMR 2007)}, year = {2010}, volume = {58}, pages = {166-173}, number = {2}, month = feb, abstract = {The localization of mobile systems with video data is a challenging field in robotic vision research. Apart from support technologies like GPS, a self-sufficient visual system is desirable. We introduce a new heuristic approach to outdoor localization in a scenario with sparse visual data and without odometry readings. Localization is interpreted as an optimization problem, and a swarm-based optimization method is adapted and applied, remaining independent of the specific visual feature type. The new method obtains similar or better localization results in our experiments while requiring only two-thirds of the number of image comparisons, indicating an all-over speed-up by 25%.}, doi = {10.1016/j.robot.2009.09.012}, keywords = {Outdoor robotics; Robot vision; Visual localization; Swarm intelligence; Particle swarm optimization}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/Kron09SwarmSupp.pdf}, url = {http://www.sciencedirect.com/science/article/B6V16-4X908T5-3/2/559434e23a220afad0b33d51ed559198} } @article{Bertsch2010, author = {Bertsch, Andreas and Jung, Stephan and Zerck, Alexandra and Pfeifer, Nico and Nahnsen, Sven and Henneges, Carsten and Nordheim, Alfred and Kohlbacher, Oliver}, title = {Optimal de novo Design of MRM Experiments for Rapid Assay Development in Targeted Proteomics}, journal = {Journal of Proteome Research}, year = {2010}, volume = {9}, pages = {2696-2704}, number = {5}, note = {PMID: 20201589}, doi = {10.1021/pr1001803}, eprint = {http://pubs.acs.org/doi/pdf/10.1021/pr1001803}, url = {http://pubs.acs.org/doi/abs/10.1021/pr1001803} } @article{Fechner2010b, author = {Fechner, Nikolas and Hinselmann, Georg and Jahn, Andreas and Rosenbaum, Lars and Zell,Andreas}, title = {A {F}ree-{W}ilson-like approach to analyze {QSAR} models based on graph decomposition kernels}, journal = {Molecular Informatics}, year = {2010}, volume = {29}, pages = {491-497}, doi = {10.1002/minf.201000053}, url = {http://www3.interscience.wiley.com/journal/123567123/abstract} } @inbook{Fechner2010a, chapter = {Molecular Descriptors}, pages = {89-143}, title = {Handbook of Chemoinformatics Algorithms}, publisher = {Chapman \& Hall/CRC Mathematical \& Computational Biology}, year = {2010}, editor = {Jean-Loup Faulon and Andreas Bender}, author = {Nikolas Fechner and Georg Hinselmann and J\"org Kurt Wegner}, } @article{Fechner2010, author = {Fechner, Nikolas and Jahn, Andreas and Hinselmann, Georg and Zell, Andreas}, title = {Estimation of the applicability domain of kernel-based machine learning models for virtual screening}, journal = {Journal of Cheminformatics}, year = {2010}, volume = {2}, pages = {2}, number = {1}, abstract = {BACKGROUND:The virtual screening of large compound databases is an important application of structural-activity relationship models. Due to the high structural diversity of these data sets, it is impossible for machine learning based QSAR models, which rely on a specific training set, to give reliable results for all compounds. Thus, it is important to consider the subset of the chemical space in which the model is applicable. The approaches to this problem that have been published so far mostly use vectorial descriptor representations to define this domain of applicability of the model. Unfortunately, these cannot be extended easily to structured kernel-based machine learning models. For this reason, we propose three approaches to estimate the domain of applicability of a kernel-based QSAR model.RESULTS:We evaluated three kernel-based applicability domain estimations using three different structured kernels on three virtual screening tasks. Each experiment consisted of the training of a kernel-based QSAR model using support vector regression and the ranking of a disjoint screening data set according to the predicted activity. For each prediction, the applicability of the model for the respective compound is quantitatively described using a score obtained by an applicability domain formulation. The suitability of the applicability domain estimation is evaluated by comparing the model performance on the subsets of the screening data sets obtained by different thresholds for the applicability scores. This comparison indicates that it is possible to separate the part of the chemspace, in which the model gives reliable predictions, from the part consisting of structures too dissimilar to the training set to apply the model successfully. A closer inspection reveals that the virtual screening performance of the model is considerably improved if half of the molecules, those with the lowest applicability scores, are omitted from the screening.CONCLUSION:The proposed applicability domain formulations for kernel-based QSAR models can successfully identify compounds for which no reliable predictions can be expected from the model. The resulting reduction of the search space and the elimination of some of the active compounds should not be considered as a drawback, because the results indicate that, in most cases, these omitted ligands would not be found by the model anyway.}, doi = {10.1186/1758-2946-2-2}, issn = {1758-2946}, url = {http://www.jcheminf.com/content/2/1/2} } @article{21078178, author = {Henneges, Carsten and Laskov, Pavel and Darmawan, Endang and Backhaus, Juergen and Kammerer, Bernd and Zell, Andreas}, title = {A factorization method for the classification of infrared spectra}, journal = {BMC Bioinformatics}, year = {2010}, volume = {11}, pages = {561}, number = {1}, abstract = {BACKGROUND:Bioinformatics data analysis often deals with additive mixtures of signals for which only class labels are known. Then, the overall goal is to estimate class related signals for data mining purposes. A convenient application is metabolic monitoring of patients using infrared spectroscopy. Within an infrared spectrum each single compound contributes quantitatively to the measurement.RESULTS:In this work, we propose a novel factorization technique for additive signal factorization that allows learning from classified samples. We define a composed loss function for this task and analytically derive a closed form equation such that training a model reduces to searching for an optimal threshold vector. Our experiments, carried out on synthetic and clinical data, show a sensitivity of up to 0.958 and specificity of up to 0.841 for a 15-class problem of disease classification. Using class and regression information in parallel, our algorithm outperforms linear SVM for training cases having many classes and few data.CONCLUSIONS:The presented factorization method provides a simple and generative model and, therefore, represents a first step towards predictive factorization methods.}, doi = {10.1186/1471-2105-11-561}, issn = {1471-2105}, pubmedid = {21078178}, url = {http://www.biomedcentral.com/1471-2105/11/561} } @article{Hinselmann2010, author = {Georg Hinselmann and Nikolas Fechner and Andreas Jahn and Matthias Eckert and Andreas Zell}, title = {Graph kernels for chemical compounds using topological and three-dimensional local atom pair environments}, journal = {Neurocomputing}, year = {2010}, volume = {74}, pages = {219-229}, number = {1-3}, doi = {10.1016/j.neucom.2010.03.008}, issn = {0925-2312}, keywords = {Graph Kernel}, url = {http://www.sciencedirect.com/science/article/B6V10-4YP8TKR-2/2/4b8b4c3246c074e37b2964d79794f335} } @article{komma10c, author = {Komma, Philippe and Zell, Andreas}, title = {Posterior Probability Estimation Techniques Embedded in a Bayes Filter for Vibration-Based Terrain Classification}, journal = {Springer Tracts in Advanced Robotics}, year = {2010}, volume = {62}, pages = {79-89}, } @inproceedings{Kron10EvA2, author = {Kronfeld, Marcel and Planatscher, Hannes and Zell, Andreas}, title = {The {EvA2} Optimization Framework}, booktitle = {Learning and Intelligent Optimization Conference, Special Session on Software for Optimization (LION-SWOP)}, year = {2010}, editor = {Blum, Christian and Battiti, Roberto}, number = {6073}, series = {Lecture Notes in Computer Science, LNCS}, pages = {247-250}, address = {Venice, Italy}, month = jan, publisher = {Springer Verlag}, abstract = {We present EvA2, a comprehensive metaheuristic optimization framework with emphasis on Evolutionary Algorithms implemented in Java. It presents a modular structure of interfaces and abstract classes for the implementation of optimization problems. End users may choose among several layers of abstraction for an entrance point meeting their requirements on both ease of use and access to extensive functionality. The EvA2 framework has been applied successfully in several academic as well as industrial cooperations and is extended continuously. It is freely available under an open source license (LGPL).}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Kron10EvA2Short.pdf} } @inproceedings{Kron10GPPSO, author = {Kronfeld, Marcel and Zell, Andreas}, title = {Gaussian Process assisted Particle Swarm Optimization}, booktitle = {Learning and Intelligent Optimization Conference (LION IV)}, year = {2010}, editor = {Blum, Christian and Battiti, Roberto}, number = {6073}, series = {Lecture Notes in Computer Science, LNCS}, pages = {139-153}, address = {Venice, Italy}, month = jan, publisher = {Springer Verlag}, abstract = {Real-world optimization problems often are non-convex, non-differentiable and highly multimodal, which is why stochastic, population-based metaheuristics are frequently applied. If the optimization problem is also computationally very expensive, only relatively few function evaluations can be afforded. We develop a model-assisted optimization approach as a coupling of Gaussian Process modeling, a regression technique from machine learning, with the Particle Swarm Optimization metaheuristic. It uses earlier function evaluations to predict areas of improvement and exploits the model information in the heuristic search. Under the assumption of a costly target function, it is shown that model-assistance improves the performance across a set of standard benchmark functions. In return, it is possible to reduce the number of target function evaluations to reach a certain fitness level to speed up the search.}, } @article{PabstKS10, author = {Simon Pabst and Artur Koch and Wolfgang Stra{\ss}er}, title = {Fast and Scalable {CPU}/{GPU} Collision Detection for Rigid and Deformable Surfaces}, journal = {Computer Graphics Forum}, year = {2010}, volume = {29}, pages = {1605-1612}, number = {5}, abstract = {We present a new hybrid CPU/GPU collision detection technique for rigid and deformable objects based on spatial subdivision. Our approach efficiently exploits the massive computational capabilities of modern CPUs and GPUs commonly found in off-the-shelf computer systems. The algorithm is specifically tailored to be highly scalable on both the CPU and the GPU sides. We can compute discrete and continuous external and self-collisions of non-penetrating rigid and deformable objects consisting of many tens of thousands of triangles in few milliseconds on a modern PC. Our approach is orders of magnitude faster than earlier CPU-based approaches and up to twice as fast as the most recent GPU-based techniques.}, doi = {10.1111/j.1467-8659.2010.01769.x}, pdf = {http://www.gris.uni-tuebingen.de/people/staff/spabst/pdf/hashing-SGP10.pdf}, } @article{DePaly10HydroInf, author = {Niels Schuetze and Michael de Paly and Uri Shamir}, title = {Novel simulation-based algorithms for optimal open-loop and closed-loop}, journal = {Journal of Hydroinformatics}, year = {2010}, abstract = {The scarcity of water compared with the abundance of land constitutes the main drawback within agricultural production. Besides the improvement of irrigation techniques a task of primary importance is solving the problem of intra-seasonal irrigation scheduling under limited seasonal water supply. An efficient scheduling algorithm has to take into account the crops' response to water stress at different stages throughout the growing season. Furthermore, for large scale planning tools compact presentations of the relationship between irrigation practices and grain yield, such as crop water production functions, are often used which also rely on an optimal scheduling of the considered irrigation systems. In this study, two new optimization algorithms for single-crop intra-seasonal scheduling of deficit irrigation systems are introduced which are able to operate with general crop growth simulation models. First, a tailored evolutionary optimization technique (EA) searches for optimal schedules over a whole growing season within an open-loop optimization framework. Second, a neuro-dynamic programming technique (NDP) is used for determining optimal irrigation policy. In this paper, different management schemes are considered and crop-yield functions generated with both the EA and the NDP optimization algorithms compared.}, doi = {10.2166/hydro.2011.073}, url = {http://www.iwaponline.com/jh/up/jh2011073.htm} } @inproceedings{weiss2010icmla, author = {Ulrich Weiss and Peter Biber and Stefan Laible and Karsten Bohlmann and Andreas Zell}, title = {Plant Species Classification Using a 3D LIDAR Sensor and Machine Learning}, booktitle = {Machine Learning and Applications (ICMLA), 2010 Ninth International Conference on}, year = {2010}, pages = {339--345}, address = {Washington, D.C., USA}, month = {dec.}, organization = {IEEE Computer Society}, publisher = {IEEE}, abstract = {In the domain of agricultural robotics, one major application is crop scouting, e.g., for the task of weed control. For this task a key enabler is a robust detection and classification of the plant and species. Automatically distinguishing between plant species is a challenging task, because some species look very similar. It is also difficult to translate the symbolic high level description of the appearances and the differences between the plants used by humans, into a formal, computer understandable form. Also it is not possible to reliably detect structures, like leaves and branches in 3D data provided by our sensor. One approach to solve this problem is to learn how to classify the species by using a set of example plants and machine learning methods. In this paper we are introducing a method for distinguishing plant species using a 3D LIDAR sensor and supervised learning. For that we have developed a set of size and rotation invariant features and evaluated experimentally which are the most descriptive ones. Besides these features we have also compared different learning methods using the toolbox Weka. It turned out that the best methods for our application are simple logistic regression functions, support vector machines and neural networks. In our experiments we used six different plant species, typically available at common nurseries, and about 20 examples of each species. In the laboratory we were able to identify over 98% of these plants correctly.}, doi = {10.1109/ICMLA.2010.57}, keywords = {3D LIDAR sensor;Weka;agricultural robotics;crop scouting;logistic regression;machine learning;neural networks;plant species classification;supervised learning;support vector machines;agriculture;biology computing;botany;learning (artificial intelligence);neural nets;optical radar;robots;support vector machines;}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/weiss2010icmla.pdf} } @article{wenzel2010c, author = {Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell}, title = {{Automatic Take Off, Tracking and Landing of a Miniature UAV on a Moving Carrier Vehicle}}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2010}, volume = {61}, pages = {221-238}, abstract = {We present a system consisting of a miniature unmanned aerial vehicle (UAV) and a small carrier vehicle, in which the UAV is capable of autonomously starting from the moving ground vehicle, tracking it at a constant distance and landing on a platform on the carrier in motion. Our visual tracking approach differs from other methods by using low-cost, lightweight commodity consumer hardware. As main sensor we use a Wii remote infrared (IR) camera, which allows robust tracking of a pattern of IR lights in conditions without direct sunlight. The system does not need to communicate with the ground vehicle and works with an onboard 8-bit microcontroller. Nevertheless the position and orientation relative to the IR pattern is estimated at a frequency of approximately 50 Hz. This enables the UAV to fly fully autonomously, performing flight control, self-stabilisation and visual tracking of the ground vehicle. We present experiments in which our UAV performs autonomous flights with a moving ground carrier describing a circular path and where the carrier is rotating. The system provides small errors and allows for safe, autonomous indoor flights.}, affiliation = {Department of Computer Science, University of Tuebingen, Sand 1, 72076 T\"ubingen, Germany}, doi = {10.1007/s10846-010-9473-0}, editor = {Kimon P. Valavanis}, issn = {0921-0296}, issue = {1}, keyword = {Engineering}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Wenzel2010uav.pdf} } @inproceedings{wenzel2010a, author = {Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell}, title = {{Automatic Take Off, Tracking and Landing of a Miniature UAV on a Moving Carrier Vehicle}}, booktitle = {Proceedings of UAV'10 3rd International Symposium on Unmanned Aerial Vehicles}, year = {2010}, pages = {1-18}, address = {Dubai, UAE}, publisher = {Kimon P. Valavanis}, abstract = {We present a system consisting of a miniature unmanned aerial vehicle (UAV) and a small carrier vehicle, in which the UAV is capable of autonomously starting from the moving ground vehicle, tracking it at a constant distance and landing on a platform on the carrier in motion. Our visual tracking approach differs from other methods by using low-cost, light-weight commodity consumer hardware. As main sensor we use a Wii remote infrared (IR) camera, which allows robust tracking of a pattern of IR lights in conditions without direct sunlight. The system does not need to communicate with the ground vehicle and works with an onboard 8-bit microcontroller. Nevertheless the position and orientation relative to the IR pattern is estimated at a frequency of approximately 50 Hz. This enables the UAV to fly fully autonomously, performing flight control, self-stabilisation and visual tracking of the ground vehicle.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Wenzel2010uav.pdf} } @inproceedings{Wenzel2010b, author = {Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell}, title = {{A Quadrocopter Hovering above a Person Wearing a Modified Cap}}, booktitle = {Proceedings of International Micro Air Vehicle Conference and Flight Competition}, year = {2010}, pages = {1-7}, address = {Braunschweig, Germany}, publisher = {DGON}, abstract = {We here describe an application of a quadrocopter hovering stably above a person wearing a cap with 4 infrared LEDs. The application has originally been developed in the context of wearable computing. Our ``wearable helicopter'' hovers above the user. In further work, the system could send a birds-eye view of the area to the operator, while the robot follows autonomously. The entire aerial robot works autonomously, all processing is done onboard. We use a miniature quadrocopter with an inertial measurement unit and a low-cost Wii remote camera, i.e., commodity consumer hardware. This proof of concept gives an insight into flight control and some experiments.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Wenzel2010imav.pdf} } @article{Wrzodek2010, author = {Wrzodek, Clemens and Schr\"oder, Adrian and Dr\"ager, Andreas and Wanke, Dierk and Berendzen, Kenneth W. and Kronfeld, Marcel and Harter, Klaus and Zell, Andreas}, title = {{ModuleMaster}: A new tool to decipher transcriptional regulatory networks}, journal = {Biosystems}, year = {2010}, volume = {99}, pages = {79--81}, number = {1}, month = jan, abstract = {In this article we present ModuleMaster, a novel application for finding \emph{cis}-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the program includes all necessary data and algorithms to perform every step to find CRMs. This workbench possesses an easy-to-use graphical user interface, together with job-processing and command-line options, making ModuleMaster a sophisticated program for large-scale batch processing. The detected CRMs can be visualized and evaluated in various ways, i.e., generating GraphML- and R-based whole regulatory network visualizations or generating SBML files for subsequent analytical processing and dynamic modeling. Availability: ModuleMaster is freely available to academics as a webstart application and for download at \url{http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/}, including comprehensive documentation.}, comment = {http://www.cogsys.cs.uni-tuebingen.de/software/ModuleMaster/}, doi = {10.1016/j.biosystems.2009.09.005}, issn = {0303-2647}, keywords = {Gene regulation, Cis-regulatory modules, Regulatory sequence analysis, Matrix scan, Transcription factors}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/wrzodek2010_ModuleMaster.pdf}, publisher = {Elsevier}, url = {http://dx.doi.org/10.1016/j.biosystems.2009.09.005} } @inproceedings{Wenzel2009b, author = {Karl Engelbert Wenzel and Andreas Zell}, title = {{Automatic Take Off, Hovering and Landing Control for Miniature Helicopters with Low-Cost Onboard Hardware}}, booktitle = {Autonome Mobile Systeme 2009}, year = {2009}, pages = {73-80}, address = {Karlsruhe, Germany}, month = {December 3-4}, publisher = {KIT}, abstract = {This paper details experiments for autonomous take off, hovering above a landing place and autonomous landing. Our visual tracking approach differs from other methods by using an inexpensive Wii remote camera, i.e., commodity consumer hardware. All processing is done with an onboard microcontroller and the system does not require stationary sensors. The only requirements are a stationary pattern of four infrared spots at the start and landing site and a roll and pitch attitude estimation of sufficient quality, provided by an separate inertial measurement unit.}, isbn = {978-3642102837}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/wenzel2009_WiiStartLand.pdf} } @inproceedings{hofmeister2009tiny, author = {Marius Hofmeister and Sara Erhard and Andreas Zell}, title = {Visual Self-Localization with Tiny Images}, booktitle = {Autonome Mobile Systeme 2009 - 21. Fachgespr\"ach}, year = {2009}, editor = {R\"udiger Dillmann and J\"urgen Beyerer and Christoph Stiller}, pages = {177--184}, address = {Karlsruhe, Germany}, month = dec, publisher = {Springer-Verlag}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/hofmeister2009ams_tinyImages.pdf} } @inproceedings{kanjanaw_AMS2009, author = {Kiattisin Kanjanawanishkul and Marius Hofmeister and Andreas Zell}, title = {Coordinated Path Following for Mobile Robots}, booktitle = {Autonome Mobile Systeme 2009 - 21. Fachgespr\"ach}, year = {2009}, editor = {R\"udiger Dillmann and J\"urgen Beyerer and Christoph Stiller}, pages = {185-192}, address = {Karlsruhe, Germany}, month = dec, publisher = {Springer-Verlag}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/kanjanaw2009ams.pdf} } @inproceedings{jiang2009, author = {Lixing Jiang and Jin Hou and Zeng Chen and Dengsheng Zhang}, title = {Automatic image annotation based on decision tree machine learning}, booktitle = {IEEE International Conference on Cyber-Enabled Distributed Computing and Knowledge Discovery (CyberC'09)}, year = {2009}, pages = {170-175 }, address = {Zhangijajie, China}, month = {October}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5342168&abstractAccess=no&userType=inst} } @inproceedings{vorst2009iros, author = {Philipp Vorst and Andreas Zell}, title = {Particle Filter-based Trajectory Estimation with Passive {UHF} {RFID} Fingerprints in Unknown Environments}, booktitle = {Proceedings of the 2009 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2009)}, year = {2009}, pages = {395--401}, address = {St. Louis, Missouri, USA}, month = oct, abstract = {In this paper we present a novel approach to estimating the trajectory of a robot by means of inexpensive passive RFID tags and odometry in unknown environments. We show how trajectory estimation, a prerequisite of mapping RFID transponder positions without a reference positioning system, can be achieved using a particle filter. The presented technique is based on a non-parametric model of spatial relationships between RFID measurements. It overcomes the noisy nature of RFID measurements and the absence of distance and bearing information. The accuracy of our method is investigated in a series of experiments with a mobile robot.}, citeseerurl = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/vorst/publications/vorst2009iros.html}, doi = {10.1109/IROS.2009.5354627}, ee = {http://dx.doi.org/10.1109/IROS.2009.5354627}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/vorst2009iros-traj-estimation.pdf} } @inproceedings{bohlmann2009ecmr, author = {Karsten Bohlmann and Peter Biber and Andreas Zell}, title = { Using Geographical Data and Sonar to Improve {GPS} Localization for Mobile Robots}, booktitle = {4th European Conference on Mobile Robots (ECMR 2009)}, year = {2009}, pages = {55--60}, address = {Mlini/Dubrovnik, Croatia}, month = sep, abstract = {Internet technology and the availability of large public knowledge bases should enable future autonomous systems to drastically improve their perceptual and cognitive capabilities with only inexpensive sensors. In this paper we investigate this aspect with respect to robot self-localization. We present a method to improve GPS-based localization of mobile robots using geographic data from a public database. From a cadastral map a basic map of a robot's working area is automatically created. A mobile robot is equipped with a low-cost GPS receiver and ultrasonic sensors. Then, a particle filter is used to fuse GPS position values and odometry data and to match sonar scan data with the a priori geodata map. The map is also updated with previously unknown environment features. The algorithm was tested in an outdoor environment with uneven terrain. Experimental results show considerable improvements in position estimation compared to using GPS alone. }, affiliation = {Chair of Cognitive Systems, University of Tuebingen, Department of Computer Science, Sand 1, 72076 Tuebingen, Germany}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/bohlmann2009ecmr-geographical-data.pdf} } @inproceedings{kanjanaw_ECMR2009, author = {Kiattisin Kanjanawanishkul and Marius Hofmeister and Andreas Zell}, title = {Smooth Reference Tracking of a Mobile Robot using Nonlinear Model Predictive Control}, booktitle = {4th European Conference on Mobile Robots (ECMR)}, year = {2009}, pages = {161-166}, address = {Mlini/Dubrovnik, Croatia}, month = sep, publisher = {KoREMA, Zagreb}, isbn = {978-953-6037-54-4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/kanjanaw2009ecmr.pdf} } @inproceedings{Kron09NichingGCB, author = {Kronfeld, Marcel and Dr\"ager, Andreas and Aschoff, Moritz and Zell, Andreas}, title = {{On the Benefits of Multimodal Optimization for Metabolic Network Modeling}}, booktitle = {German Conference on Bioinformatics (GCB 2009)}, year = {2009}, editor = {Grosse, Ivo and Neumann, Steffen and Posch, Stefan and Schreiber, Falk and Stadler, Peter}, volume = {P-157}, number = {978-3-88579-251-2}, series = {Lecture Notes in Informatics}, pages = {191--200}, address = {Halle (Saale), Germany}, month = sep, publisher = {German Informatics Society}, abstract = {The calibration of complex models of biological systems requires numerical simulation and optimization procedures to infer undetermined parameters and fit measured data. The optimization step typically employs heuristic global optimization algorithms, but due to measurement noise and the many degrees of freedom, it is not guaranteed that the identified single optimum is also the most meaningful parameter set. Multimodal optimization allows for identifying multiple optima in parallel. We consider high-dimensional benchmark functions and a realistic metabolic network model from systems biology to compare evolutionary and swarm-based multimodal methods. We show that an extended swarm based niching algorithm is able to find a considerable set of solutions in parallel, which have significantly more explanatory power. As an outline of the information gain, the variations in the set of high-quality solutions are contrasted to a state-of-the-art global sensitivity analysis.}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/Kron09NichingFinal.pdf}, url = {http://www.gcb2009.de/program.php} } @inproceedings{rohweder2009ecmr, author = {Karsten Rohweder and Philipp Vorst and Andreas Zell}, title = {Improved Mapping of {RFID} Tags by Fusion with Spatial Structure}, booktitle = {Proceedings of the 4th European Conference on Mobile Robots (ECMR 2009)}, year = {2009}, editor = {Ivan Petrovi\'c and Achim J. Lilienthal}, pages = {247--252}, address = {Mlini/Dubrovnik, Croatia}, month = sep, publisher = {KoREMA, Zagreb, Croatia}, abstract = {This paper shows how to exploit knowledge about the spatial structure of an environment in order to obtain more accurate position estimates of passive RFID tags. Such labels are increasingly used as electronic product codes and are originally aimed at identifying goods. Estimating the positions of labeled products, however, is difficult because passive tags only reveal their presence and neither bearings nor distances to them. Previous related work showed that tag detection rates yield decent tag position estimates. Our method combines these solely RFID-based methods with structural information. Indoor experiments with a mobile robot show increased accuracy as compared to mapping purely based on RFID measurements.}, isbn = {978-953-6037-54-4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/rohweder2009ecmr-mapping-rfid.pdf} } @article{jahn2009optimal, author = {Jahn, Andreas and Hinselmann, Georg and Fechner, Nikolas and Zell, Andreas}, title = {Optimal Assignment Methods for Ligand-Based Virtual Screening}, journal = {Journal of Cheminformatics}, year = {2009}, volume = {1}, number = {14}, month = aug, doi = {10.1186/1758-2946-1-14}, pdf = {http://www.jcheminf.com/content/pdf/1758-2946-1-14.pdf}, url = {http://www.jcheminf.com/content/1/1/14} } @mastersthesis{Tscherneck2009a, author = {Tscherneck, Stephanie}, title = {{Aufbau einer integrierten Wissensbasis zur quantitativen Modellierung von Proteininteraktionen}}, school = {Universtity of Applied Sciences Wildau (UASW)}, year = {2009}, type = {Masterthesis}, address = {Bahnhofstr. 1, 15745 Wildau (Germany)}, month = aug, abstract = {{\"Offentliche, biologische Online-Datenbanken erm\"oglichen schnelle Antworten auf Einzelabfragen. Komplexe Abfragen erfordern hingegen lange Wartezeiten. Eine lokale Installationen der Datenbanken w\"urde diesem Problem entgegen wirken. Bestandteil dieser Arbeit ist die Schaffung eines Prototypen der integrativen Interaktions-Wissensbasis WINTER KB (Wildau INTERaction Knowledge Base). Hierf\"ur wird \"offentliches und propriet\"ares Wissen in einer lokalen, relationalen Datenbank zusammengefasst. PubMed, UniProt/SwissProt, IntAct, MINT,Entrez Gene, NCBI Taxonomy, Gene Ontology sowie die propriet\"are Datenbank IPA finden ihre Verwendung. Mit Hilfe der darin enthaltenden Daten k\"onnen DGL-Systeme f"ur Konzentrationsverl\"aufe "uber die neu entwickelte Weboberfl\"ache erstellt werden. Des Weiteren kann die \emph{Mutual Information} zwischen den Zufallsvariablen Protein, Hub und Funktion errechnet werden. Erwartungsgem\"a{\ss} ist die Mutual Information der integrierten propriet\"aren Ingenuity\textregistered-Daten deutlich h\"oher als die der integrierten \"offentlichen Daten aus IntAct, MINT und UniProt/SwissProt.}}, } @inproceedings{komma09d, author = {Komma, Philippe and Zell, Andreas}, title = {Posterior Probability Estimation Techniques Embedded in a {B}ayes Filter for Vibration-based Terrain Classification}, booktitle = {7th International Conference on Field and Service Robots (FSR 2009)}, year = {2009}, pages = {1-10}, address = {MIT, Cambridge, Massachusetts, USA}, month = jul, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/komma2009fsr-prob_est.pdf} } @inproceedings{vorst2009icar, author = {Philipp Vorst and Bin Yang and Andreas Zell}, title = {Loop Closure and Trajectory Estimation with Long-Range Passive {RFID} in Densely Tagged Environments}, booktitle = {14th International Conference on Advanced Robotics (ICAR 2009)}, year = {2009}, pages = {1--6}, address = {Munich, Germany}, month = {June 22-26}, abstract = {In more and more commercial scenarios, radio frequency identification (RFID) is used to tag assets on a large scale. These given tag infrastructures offer themselves for the navigation of autonomous transport vehicles and service robots. In this paper we investigate loop closure for graph-based simultaneous localization and mapping (SLAM) and trajectory estimation in environments with such dense RFID infrastructures: We compare different methods of inferring that a place has been revisited, examine their robustness, and show how the trajectory of the robot can be reconstructed. Given this trajectory, a robot is able to map transponder positions or to localize itself with RFID and odometry alone and without a reference localization system. The accuracy of our approach is shown through a series of experiments with a mobile robot.}, isbn = {978-1-4244-4855-5}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/vorst2009icar-loop-closure.pdf} } @article{Supper2009, author = {Supper, Jochen and Spangenberg, Luc\'{i}a and Planatscher, Hannes and Dr\"ager, Andreas and Schr\"oder, Adrian and Zell, Andreas}, title = {{BowTieBuilder: modeling signal transduction pathways}}, journal = {BMC Systems Biology}, year = {2009}, volume = {3}, pages = {67}, number = {1}, month = jun, abstract = {Background: Sensory proteins react to changing environmental conditions by transducing signals into the cell. These signals are integrated into core proteins that activate downstream target proteins such as transcription factors (TFs). This structure is referred to as a bow tie, and allows cells to respond appropriately to complex environmental conditions. Understanding this cellular processing of information, from sensory proteins (e.g., cell-surface proteins) to target proteins (e.g., TFs) is important, yet for many processes the signaling pathways remain unknown. Results: Here, we present BowTieBuilder for inferring signal transduction pathways from multiple source and target proteins. Given protein-protein interaction (PPI) data signaling pathways are assembled without knowledge of the intermediate signaling proteins while maximizing the overall probability of the pathway. To assess the inference quality, BowTieBuilder and three alternative heuristics are applied to several pathways, and the resulting pathways are compared to reference pathways taken from KEGG. In addition, BowTieBuilder is used to infer a signaling pathway of the innate immune response in humans and a signaling pathway that potentially regulates an underlying gene regulatory network. Conclusions: We show that BowTieBuilder, given multiple source and/or target proteins, infers pathways with satisfactory recall and precision rates and detects the core proteins of each pathway.}, doi = {10.1186/1752-0509-3-67}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-3-67.pdf}, url = {http://www.biomedcentral.com/1752-0509/3/67} } @inproceedings{kanjanaw_ICRA2009, author = {Kanjanawanishkul, Kiattisin and Zell, Andreas}, title = {Path Following for an Omnidirectional Mobile Robot Based on Model Predictive Control}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA 2009)}, year = {2009}, pages = {3341-3346}, address = {Kobe, Japan}, month = {May 12-17}, publisher = {IEEE}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/kanjanaw2009icra.pdf} } @inproceedings{komma09b, author = {Komma, Philippe and Weiss, Christian and Zell, Andreas}, title = {Adaptive {B}ayesian Filtering for Vibration-Based Terrain Classification}, booktitle = {IEEE/RSJ International Conference on Robotics and Automation (ICRA 2009)}, year = {2009}, pages = {3307-3313}, address = {Kobe, Japan}, month = may, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/komma2009icra_bayes.pdf} } @inproceedings{Tscherneck2009b, author = {Tscherneck, Stephanie and Strunk, Sarah and Schmidt, Christian and Hammer, Paul and Amberg, Ronny and Wang, Chong and Gillert, Rainer and Krause, Antje and Petznick, Gabriele and Beyerlein, Peter}, title = {{On the Mutual Information Between Interaction Perplexity and Function of Proteins}}, booktitle = {IEEE International Workshop on Genomic Signal Processing and Statistics}, year = {2009}, pages = {1--4}, address = {Minneapolis, MN, USA}, month = may, organization = {IEEE}, abstract = {We are exploring a novel information theory based approach to analyse the relation of the number of protein interactions (interaction perplexity) and protein function. The interaction perplexity is translated into a smooth sigmoid function, indicating if the protein is a hub candidate or not (hub likelihood). The overall mutual information between the hub likelihood and the protein function exhibits a clear maximum at an interaction perplexity of 21. Moreover the conditional probability of observing a certain protein function given the hub likelihood shows discriminative power. In addition our findings support that the mutual information between hub likelihood and protein function depends upon the cell compartment under investigation, it's maximum ranging up to 29\,\% of the achievable information value at interaction perplexities, ranging from 15 to 50.}, doi = {10.1109/GENSIPS.2009.5174359}, isbn = {978-1-4244-4761-9}, url = {http://dx.doi.org/10.1109/GENSIPS.2009.5174359} } @article{Draeger2009b, author = {Dr\"ager, Andreas and Planatscher, Hannes and Wouamba, Dieudonn{\'e} Motsou and Schr\"oder, Adrian and Hucka, Michael and Endler, Lukas and Golebiewski, Martin and M\"uller, Wolfgang and Zell, Andreas}, title = {{SBML2\LaTeX: Conversion of SBML files into human-readable reports}}, journal = {Bioinformatics}, year = {2009}, volume = {25}, pages = {1455--1456}, number = {11}, month = apr, abstract = {SUMMARY: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g., unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2\LaTeX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, \LaTeX{} and PDF, and provides many settings for customization. AVAILABILITY: Source code, documentation and a web service are freely available at \url{http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX}.}, doi = {10.1093/bioinformatics/btp170}, pdf = {http://bioinformatics.oxfordjournals.org/cgi/reprint/25/11/1455.pdf}, url = {http://dx.doi.org/10.1093/bioinformatics/btp170} } @inproceedings{2009_34, author = {Hinselmann, Georg and Jahn, Andreas and Fechner, Nikolas and Zell, Andreas}, title = {Chronic Rat Toxicity Prediction of Chemical Compounds Using Kernel Machines}, booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: 7th European Conference (EvoBio 2009)}, year = {2009}, volume = {5483}, pages = {25-36}, address = {T\"ubingen, Germany}, month = apr, publisher = {Springer}, url = {http://www.springerlink.com/content/1830j78741430154/?p=75793a94ffac4731856613ab7511d24c&pi=2} } @inproceedings{komma09c, author = {Komma, Philippe and Zell, Andreas}, title = {Towards Real-Time and Memory Efficient Predictions of Valve States in Diesel Engines}, booktitle = {IEEE Workshop on Computational Intelligence in Vehicles and Vehicular Systems (CIVVS 2009)}, year = {2009}, pages = {8-15}, address = {Nashville, TN, USA}, month = apr, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/komma2009civvs-valve.pdf} } @inproceedings{Liu2009:Stereo, author = {Ran Liu and Hua Zhang and Manlu Liu and Xianfeng Xia and Tianlian Hu}, title = {Stereo Cameras Self-Calibration Based on SIFT}, booktitle = {Proceedings of the 2009 International Conference on Measuring Technology and Mechatronics Automation (ICMTMA '09)}, year = {2009}, volume = {1}, pages = {352--355}, address = {Zhangjiajie, Hunan}, month = {April}, abstract = {At present, a new algorithm of feature matching-SIFT has become a hot topic in the feature matching field, whose matching ability is strong, and could process the matching problems with translation, rotation and affine transformation among different images, and to a certain extent is with more stable feature matching ability for images which are captured from random different angles.In this paper, single camera is first calibrated using plane chessboard based on OpenCV,in order to overcome shortcomings in traditional and previous self-calibration methods, SIFT algorithm is proposed to calibrate stereo cameras after two cameras intrinsic parameters are calibrated. Fundamentalmatrix is gained through several matching points in two images using SIFT feature matching method, combined with intrinsic parameters, we can compute essential matrix. Translation matrix and the rotation matrix of stereo cameras can be resolved through SVD of essential matrix known as Huang- Faugeras constrains. Experiment results show that our method can calibrate relationship of stereo cameras accurately, and be able to calibrate two cameras in any circumstances. The algorithm has strong adaptability and robustness, but the expense time needs to be further improved.}, acmid = {1606062}, days = {11-12}, doi = {http://dx.doi.org/10.1109/ICMTMA.2009.338}, isbn = {978-0-7695-3583-8}, keywords = {SIFT, Self-calibration, OpenCV, SVD, Huang- Faugeras' constrains}, numpages = {4}, } @inproceedings{kanjanaw_ROBOCOMM2009, author = {Kiattisin Kanjanawanishkul}, title = {Formation Control of Omnidirectional Mobile Robot using Distributed Model Predictive Control}, booktitle = {Proceedings of Second International Conference on Robot Communication and Coordination (ROBOCOMM-2009)}, year = {2009}, address = {Odense, Denmark}, month = {March 31-April 2}, abstract = {This paper presents experimental results of formation control problems of omnidirectional mobile robots using distributed nonlinear model predictive control (NMPC). Two main objectives are (i) to maintain a desired flexible formation pattern and (ii) to follow a reference path. Both pose errors and formation errors are included into a local objective function, which is minimized at each update time. In the formation control, the curvilinear abscissa s has been used as a coupling term with neighboring robots. The strategy in such a way that the exchange of the most recent optimal state trajectory between coupled subsystems has been employed. The distinct features of NMPC are that constraints can be explicitly accommodated, as well as nonlinear and time-varying systems can be easily handled. Experiments with three omnidirectional mobile robots are presented to illustrate the validity of our proposed method.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/kanjanaw2009robocomm.pdf} } @article{2009_12, author = {Fechner, Nikolas and Jahn, Andreas and Hinselmann, Georg and Zell, Andreas}, title = {Atomic local neighborhood flexibility incorporation into a structured similarity measure for QSAR}, journal = {Journal of Chemical Information and Modeling}, year = {2009}, volume = {49}, pages = {549-560}, number = {3}, month = mar, abstract = {In this work, we introduce a new method to regard the geometry in a structural similarity measure by approximating the conformational space of a molecule. Our idea is to break down the molecular conformation into the local conformations of neighbor atoms with respect to core atoms. This local geometry can be implicitly accessed by the trajectories of the neighboring atoms, which are emerge by rotatable bonds. In our approach, the physicochemical atomic similarity, which can be used in structured similarity measures, is augmented by a local flexibility similarity, which gives a rough estimate of the similarity of the local conformational space. We incorporated this new type of encoding the flexibility into the optimal assignment molecular similarity approach, which can be used as a pseudokernel in support vector machines. The impact of the local flexibility was evaluated on several published QSAR data sets. This lead to an improvement of the model quality on 9 out of 10 data sets compared to the unmodified optimal assignment kernel.}, keywords = {Models, Molecular *Molecular Structure Quantitative Structure-Activity Relationship}, } @inproceedings{komma09a, author = {Komma, Philippe and Weiss, Christian and Zell, Andreas}, title = {Improved Vibration based Terrain Classification Using Temporal Coherence}, booktitle = {40th International Symposium on Robotics (ISR)}, year = {2009}, pages = {359-364}, address = {Barcelona, Spain}, month = mar, } @inproceedings{2009_238, author = {John Shutty and Wolfgang Wenzel and Philippe Komma}, title = {Control Strategy Optimization for Hybrid {EGR} Engines}, booktitle = {9. Internationales Stuttgarter Symposium 2009 - Automobil- und Motorentechnik}, year = {2009}, address = {Stuttgart, Germany}, month = mar, } @article{Draeger2009a, author = {Dr\"ager, Andreas and Kronfeld, Marcel and Ziller, Michael J. and Supper, Jochen and Planatscher, Hannes and Magnus, J{\o}rgen B. and Oldiges, Marco and Kohlbacher, Oliver and Zell, Andreas}, title = {{Modeling metabolic networks in \emph{C.~glutamicum}: a comparison of rate laws in combination with various parameter optimization strategies}}, journal = {BMC Systems Biology}, year = {2009}, volume = {3}, pages = {5}, number = {5}, month = jan, abstract = {Background: To understand the dynamic behavior of cellular systems, mathematical modeling is often necessary and comprises three steps: (1) experimental measurement of participating molecules, (2) assignment of rate laws to each reaction, and (3) parameter calibration with respect to the measurements. In each of these steps the modeler is confronted with a plethora of alternative approaches, e.g., the selection of approximative rate laws in step two as specific equations are often unknown, or the choice of an estimation procedure with its specific settings in step three. This overall process with its numerous choices and the mutual influence between them makes it hard to single out the best modeling approach for a given problem. Results: We investigate the modeling process using multiple kinetic equations together with various parameter optimization methods for a well-characterized example network, the biosynthesis of valine and leucine in \emph{C.~glutamicum}. For this purpose, we derive seven dynamic models based on generalized mass action, Michaelis-Menten and convenience kinetics as well as the stochastic Langevin equation. In addition, we introduce two modeling approaches for feedback inhibition to the mass action kinetics. The parameters of each model are estimated using eight optimization strategies. To determine the most promising modeling approaches together with the best optimization algorithms, we carry out a two-step benchmark: (1) coarse-grained comparison of the algorithms on all models and (2) fine-grained tuning of the best optimization algorithms and models. To analyze the space of the best parameters found for each model, we apply clustering, variance, and correlation analysis. Conclusion: A mixed model based on the convenience rate law and the Michaelis-Menten equation, in which all reactions are assumed to be reversible, is the most suitable deterministic modeling approach followed by a reversible generalized mass action kinetics model. A Langevin model is advisable to take stochastic effects into account. To estimate the model parameters, three algorithms are particularly useful: For first attempts the settings-free Tribes algorithm yields valuable results. Particle swarm optimization and differential evolution provide significantly better results with appropriate settings.}, doi = {10.1186/1752-0509-3-5}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-3-5.pdf}, url = {http://www.biomedcentral.com/1752-0509/3/5} } @inproceedings{voduc2009, author = {My Vo Duc and Nitin Kumar Tripathi}, title = {The Integration of Support Vector Mahcine and 2-D Wavelet Analysis for face detection}, booktitle = {IFToMM International Symposium on Robotics and Mechatronics}, year = {2009}, } @inproceedings{Erhard2009c, author = {Sara Erhard and Karl Engelbert Wenzel and Andreas Zell}, title = {Flyphone: {V}isual {S}elf-{L}ocalisation {U}sing a {M}obile {P}hone as {O}nboard {I}mage {P}rocessor on a {Q}uadrocopter}, booktitle = {Proceedings of UAV'09 2nd International Symposium on Unmanned Aerial Vehicles}, year = {2009}, pages = {451--465}, address = {Reno, Nevada, USA}, abstract = {An unmanned aerial vehicle (UAV) needs to orient itself in its operating environment to fly autonomously. Localisation methods based on visual data are independent of erroneous GPS measurements or imprecise inertial sensors. In our approach, a quadrocopter first etablishes an image database of the environment. Afterwards, the quadrocopter is able to locate itself by comparing a current image taken of the environment with earlier images in the database. Therefore, characteristic image features are extracted which can be compared efficiently. We analyse three feature extraction methods and five feature similarity measures. The evaluation is based on two datasets recorded under real conditions. The computations are performed on a Nokia N95 mobile phone, which is mounted on the quadrocopter. This lightweight, yet powerful device offers an integrated camera and serves as central processing unit. The mobile phone proved to be a good choice for visual localisation on a quadrocopter.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/erhard2009_Flyphone.pdf} } @article{Erhard2009j, author = {Sara Erhard and Karl Engelbert Wenzel and Andreas Zell}, title = {Flyphone: {V}isual {S}elf-{L}ocalisation {U}sing a {M}obile {P}hone as {O}nboard {I}mage {P}rocessor on a {Q}uadrocopter}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2009}, volume = {57}, pages = {451-465}, abstract = {An unmanned aerial vehicle (UAV) needs to orient itself in its operating environment to fly autonomously. Localisation methods based on visual data are independent of erroneous GPS measurements or imprecise inertial sensors. In our approach, a quadrocopter first etablishes an image database of the environment. Afterwards, the quadrocopter is able to locate itself by comparing a current image taken of the environment with earlier images in the database. Therefore, characteristic image features are extracted which can be compared efficiently. We analyse three feature extraction methods and five feature similarity measures. The evaluation is based on two datasets recorded under real conditions. The computations are performed on a Nokia N95 mobile phone, which is mounted on the quadrocopter. This lightweight, yet powerful device offers an integrated camera and serves as central processing unit. The mobile phone proved to be a good choice for visual localisation on a quadrocopter.}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/erhard2009_Flyphone.pdf} } @article{2009_15, author = {Henneges, Carsten and Bullinger, D. and Fux, R. and Friese, N. and Seeger, H. and Neubauer, H. and Laufer, S. and Gleiter, C. H. and Schwab, M. and Zell, Andreas and Kammerer, B.}, title = {Prediction of breast cancer by profiling of urinary RNA metabolites using Support Vector Machine-based feature selection}, journal = {BMC Cancer}, year = {2009}, volume = {9}, number = {104}, abstract = {BACKGROUND: Breast cancer belongs to the most frequent and severe cancer types in human. Since excretion of modified nucleosides from increased RNA metabolism has been proposed as a potential target in pathogenesis of breast cancer, the aim of the present study was to elucidate the predictability of breast cancer by means of urinary excreted nucleosides. METHODS: We analyzed urine samples from 85 breast cancer women and respective healthy controls to assess the metabolic profiles of nucleosides by a comprehensive bioinformatic approach. All included nucleosides/ribosylated metabolites were isolated by \emph{cis}-diol specific affinity chromatography and measured with liquid chromatography ion trap mass spectrometry (LC-ITMS). A valid set of urinary metabolites was selected by exclusion of all candidates with poor linearity and/or reproducibility in the analytical setting. The bioinformatic tool of Oscillating Search Algorithm for Feature Selection (OSAF) was applied to iteratively improve features for training of Support Vector Machines (SVM) to better predict breast cancer. RESULTS: After identification of 51 nucleosides/ribosylated metabolites in the urine of breast cancer women and/or controls by LC- ITMS coupling, a valid set of 35 candidates was selected for subsequent computational analyses. OSAF resulted in 44 pairwise ratios of metabolite features by iterative optimization. Based on this approach ultimately estimates for sensitivity and specificity of 83.5% and 90.6% were obtained for best prediction of breast cancer. The classification performance was dominated by metabolite pairs with SAH which highlights its importance for RNA methylation in cancer pathogenesis. CONCLUSION: Extensive RNA-pathway analysis based on mass spectrometric analysis of metabolites and subsequent bioinformatic feature selection allowed for the identification of significant metabolic features related to breast cancer pathogenesis. The combination of mass spectrometric analysis and subsequent SVM-based feature selection represents a promising tool for the development of a non-invasive prediction system.}, url = {http://www.biomedcentral.com/1471-2407/9/104} } @article{2009_76, author = {Henneges, Carsten and Hinselmann, Georg and Jung, S and Madlung, J and Sch\"utz, W and Nordheim, A and Zell, Andreas}, title = {Ranking Methods for the Prediction of Frequent Top Scoring Peptides from Proteomics Data}, journal = {Journal of Proteomics \& Bioinformatics}, year = {2009}, volume = {2}, pages = {226-235}, number = {5}, url = {http://www.omicsonline.com/ArchiveJPB/2009/May/03/JPB2.226.php} } @inproceedings{Henneges2009, author = {Henneges, C. and Huster, S. and Zell, A.}, title = {An artificial t cell immune system for predicting MHC-II binding peptides}, booktitle = {IEEE Symposium on Artificial Life. ALife '09.}, year = {2009}, pages = {163 -170}, month = {32009-april2}, doi = {10.1109/ALIFE.2009.4937708}, keywords = {MHC-II binding peptides;T lymphocytes;artificial T cell immune system;biological immune system;immunization;machine learning;natural immune systems;artificial immune systems;learning (artificial intelligence);pattern classification;}, } @inproceedings{2009_229, author = {Hofmeister, Marius and Liebsch, Maria and Zell, Andreas}, title = {Visual Self-Localization for Small Mobile Robots with Weighted Gradient Orientation Histograms}, booktitle = {40th International Symposium on Robotics (ISR)}, year = {2009}, pages = {87--91}, address = {Barcelona, Spain}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/hofmeister2009isr_vselflocalization.pdf} } @inproceedings{2009_236, author = {de Paly, Michael and Zell, Andreas}, title = {Optimal Irrigation Scheduling with Evolutionary Algorithms}, booktitle = {Lecture Notes in Computer Science (EvoWorkshops 2009)}, year = {2009}, volume = {5484}, pages = {142-151}, address = {T\"ubingen, Germany}, publisher = {Springer-Verlag Berlin Heidelberg}, url = {http://www.springerlink.com/content/8006865n7706l8qw/} } @article{Wenzel2009aj, author = {Karl Engelbert Wenzel and Paul Rosset and Andreas Zell}, title = {{Low-Cost Visual Tracking of a Landing Place and Hovering Flight Control with a Microcontroller}}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2009}, volume = {57}, pages = {297-311}, abstract = {The growth of civil and military use has recently promoted the development of unmanned miniature aerial vehicles dedicated to surveillance tasks. These flying vehicles are often capable of carrying only a few dozen grammes of payload. To achieve autonomy for this kind of aircraft novel sensors are required, which need to cope with strictly limited onboard processing power. One of the key aspects in autonomous behaviour is target tracking. Our visual tracking approach differs from other methods by not using expensive cameras but a Wii remote camera, i.e. commodity consumer hardware. The system works without stationary sensors and all processing is done with an onboard microcontroller. The only assumptions are a good roll and pitch attitude estimation, provided by an inertial measurement unit and a stationary pattern of four infrared spots on the target or the landing spot. This paper details experiments for hovering above a landing place, but tracking a slowly moving target is also possible.}, address = {Reno, USA}, editor = {Kimon P. Valavanis}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/wenzel2009_uav_wiitracking.pdf} } @inproceedings{Wenzel2009ap, author = {Karl Engelbert Wenzel and Paul Rosset and Andreas Zell}, title = {{Low-Cost Visual Tracking of a Landing Place and Hovering Flight Control with a Microcontroller}}, booktitle = {Proceedings of UAV'09 2nd International Symposium on Unmanned Aerial Vehicles}, year = {2009}, pages = {1-15}, address = {Reno, USA}, publisher = {Kimon P. Valavanis}, abstract = {The growth of civil and military use has recently promoted the development of unmanned miniature aerial vehicles dedicated to surveillance tasks. These flying vehicles are often capable of carrying only a few dozen grammes of payload. To achieve autonomy for this kind of aircraft novel sensors are required, which need to cope with strictly limited onboard processing power. One of the key aspects in autonomous behaviour is target tracking. Our visual tracking approach differs from other methods by not using expensive cameras but a Wii remote camera, i.e. commodity consumer hardware. The system works without stationary sensors and all processing is done with an onboard microcontroller. The only assumptions are a good roll and pitch attitude estimation, provided by an inertial measurement unit and a stationary pattern of four infrared spots on the target or the landing spot. This paper details experiments for hovering above a landing place, but tracking a slowly moving target is also possible.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/wenzel2009_uav_wiitracking.pdf} } @mastersthesis{Wrzodek2008, author = {Wrzodek, Clemens}, title = {Modeling transcriptional regulatory networks by integrating expression data and promoter analysis}, school = {University of Tuebingen}, year = {2008}, type = {Diplomarbeit}, month = nov, abstract = {Die Genexpression ist ein sehr wichtiger Prozess, welcher f\"ur die Auspr\"agung des Verhaltens einer Zelle auf irgendeinen Reiz hin verantwortlich ist. W\"are dieser Prozess komplett vorhersagbar, so k\"onnte zum Beispiel in der Medizin die Wirkung eines Medikamentes deutlich besser abgesch\"atzt werden. F\"ur solch eine Vorhersage ist es wichtig, die Regulation der Genexpression zu verstehen. Diese wird auf transkriptioneller Ebene durch Transkriptionsfaktoren gesteuert, welche spezifisch an kurze, sogenannte Motive auf der DNA in der N\"ahe des Gens binden. Es ist bekannt, dass Transkriptionsfaktoren h\"aufig die Genexpression von mehreren Genen regulieren, welche mit hoher Wahrscheinlichkeit funktional verwandt sind. Weiterhin ist bekannt, dass die Regulation der Expression von Genen nicht durch einzelne, sondern durch mehrere Transkriptionsfaktoren bestimmt wird, welche alle in einem kurzen Abschnitt auf der DNA binden und zusammen ein sogenanntes \emph{cis}-regulatorisches Modul (CRM) bilden. In dieser Arbeit wird eine neue Methode vorgestellt, welche CRMs nicht nur aufgrund des Vorhandenseins von Bindemotiven, sondern auch unter Beachtung experimentell gemessener Genexpressionsdaten (in Form eines sogenannten Microarray-Experiments) detektieren kann. Damit ist es m\"oglich, bisher unbekannte Funktionen von Genen pr\"aziser als mit bisherigen Ans\"atzen vorherzusagen. Diese Methode wird auf Datens\"atzen aus Homo sapiens, Saccharomyces cerevisiae und Arabidopsis thaliana angewendet. Die Ergebnisse werden auf ihre Plausibilit\"at hin \"uberpr\"uft und validiert. Es wird gezeigt, dass insbesondere durch die Hinzunahme von experimentell ermittelten Expressionsdaten die Vorhersage von CRMs deutlich verbessert werden konnte, im Vergleich zu Methoden, welche lediglich die DNA-Sequenzen betrachten. Diese neue Methode wurde in ein Java Programm implementiert, welches \"offentlich zug\"anglich gemacht wird und frei benutzbar ist.}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/diplomarbeiten/Diplomarbeit_Clemens_Wrzodek.pdf}, } @inproceedings{kanjanaw_SMC2008, author = {Kanjanawanishkul, Kiattisin and Zell, Andreas}, title = {Distributed Model Predictive Control for Coordinated Path Following Control of Omnidirectional Mobile Robots}, booktitle = {IEEE International Conference on Systems, Man, and Cybernetics (SMC 2008)}, year = {2008}, pages = {3120-3125}, address = {Singapore}, month = {October 12-15}, publisher = {IEEE}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/kanjanaw2008smc.pdf} } @inproceedings{kanjanaw_IROS2008, author = {Kanjanawanishkul, Kiattisin and Zell, Andreas}, title = {A model-predictive approach to formation control of omnidirectional mobile robots}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2008)}, year = {2008}, pages = {2771-2776}, address = {Nice, France}, month = {September 22-26}, publisher = {IEEE}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/kanjanaw2008iros.pdf} } @inproceedings{vorst2008iros, author = {Philipp Vorst and Sebastian Schneegans and Bin Yang and Andreas Zell}, title = {Self-Localization with {RFID} Snapshots in Densely Tagged Environments}, booktitle = {Proceedings of the 2008 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2008)}, year = {2008}, pages = {1353--1358}, address = {Nice, France}, month = {September 22-26}, abstract = {In this paper we show that, despite some disadvantageous properties of radio frequency identification (RFID), it is possible to localize a mobile robot quite accurately in environments which are densely tagged. We therefore employ a recently presented probabilistic fingerprinting technique called RFID snapshots. This method interprets short series of RFID measurements as feature vectors and is able to position a mobile robot after a training phase. It requires no explicit sensor model and is capable of exploiting given tag infrastructures, e.g., provided by supermarket shelves containing labeled products.}, citeseerurl = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/vorst/publications/vorst2008iros.html}, doi = {10.1109/IROS.2008.4650715}, ee = {http://dx.doi.org/10.1109/IROS.2008.4650715}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/vorst2008iros_snapshots.pdf} } @inproceedings{Gundelach08, author = {Volker Gundelach and Michael de Paly and Dieter Eisenburger}, title = {Recognition of patterns from geological structures in radar signals with the neuronal network simulator JNNS}, booktitle = {Ultra-Wideband, 2008. ICUWB 2008. IEEE International Conference on}, year = {2008}, volume = {3}, pages = {167 -170}, month = {September}, abstract = {Aim of GPR measurements is not only to detect the spatial position of reflecting structures, but also to classify its geological reason. The reflection coefficient of a radar signal depends on the reflecting material. Numerous propeties of the recorded signal can be used to assign a reflection with geology. Necessary is the knowledge about unique parameters for a classification and the validation of the results in a known environment. Data from well explored salt mines allows this validation. Neuronal networks are a good tool to optimize parameter sets or patterns regarding to its relevance for an assignment. A neuronal network consists of simple units which transmit information weighted and directed to the next level. The connections between the units are characterized by activation functions which vary during learning processes. By validating a parameter set it is possible to connect an input level with an output level and creating an associative pattern without knowing the deterministic rules between them. Which parameters of a radar signal are relevant to get a result with this method is the topic of this paper. The neuronal network simulator JNNS used here was developed at the university Stuttgart.}, doi = {10.1109/ICUWB.2008.4653442}, keywords = {JNNS;geological structures;ground-penetrating radar;learning processes;neuronal network simulator;pattern recognition;radar signals;reflection coefficient;Java;digital simulation;geology;ground penetrating radar;learning (artificial intelligence);neural nets;pattern recognition;}, } @inproceedings{Kron08DynLocAnts, author = {Kronfeld, Marcel and Weiss, Christian and Zell, Andreas}, title = {A Dynamic Swarm for Visual Location Tracking}, booktitle = {6th International Conference on Ant Colony Optimization and Swarm Intelligence ({ANTS} 2008)}, year = {2008}, pages = {203--210}, address = {Brussels, Belgium}, month = sep, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/Kron08DynLoc.pdf} } @article{Holland2008, author = {Holland, Richard C.~G. and Down, Thomas and Pocock, Matthew and Prli\'{c}, Andreas and Huen, David and James, Keith and Foisy, Sylvain and Dr\"ager, Andreas and Yates, Andy and Heuer, Michael and Schreiber, Mark J.}, title = {{BioJava: an open-source framework for bioinformatics}}, journal = {Bioinformatics}, year = {2008}, volume = {24}, pages = {2096--2097}, number = {18}, month = aug, abstract = {Motivation: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats, and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language. Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (\url{http://www.biojava.org}). BioJava requires Java 1.5 or higher. Contact: \url{mailto:andreas.prlic@gmail.com} All queries should be directed to the BioJava mailing lists. Details are available at (\url{http://biojava.org/wiki/BioJava:MailingLists}). Supplementary Information: Full documentation can be found at the BioJava website}, doi = {10.1093/bioinformatics/btn397}, pdf = {http://bioinformatics.oxfordjournals.org/content/24/18/2096.full.pdf}, url = {http://bioinformatics.oxfordjournals.org/content/24/18/2096.abstract} } @inproceedings{kanjanaw_IAS2008, author = {Kanjanawanishkul, Kiattisin and Li, Xiang and Zell, Andreas}, title = {Nonlinear Model Predictive Control of Omnidirectional Mobile Robot Formations}, booktitle = {10th International Conference on Intelligent Autonomous Systems (IAS 2008)}, year = {2008}, editor = {Dillmann, R\"udiger and Burgard, Wolfram}, pages = {41-48}, address = {Baden-Baden, Germany}, month = {July 23-25}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/Li_Kiat_IAS2008.pdf} } @inproceedings{Li_IAS2008, author = {Xiang Li and Kiattisin Kanjanawanishkul and Andreas Zell}, title = {Nonlinear Model Predictive Control of an Omnidirectional Mobile Robot}, booktitle = {10th International Conference on Intelligent Autonomous Systems (IAS 2008)}, year = {2008}, pages = {92-99}, address = {Baden-Baden, Germany}, month = {July 23-25}, publisher = {IOS Press}, abstract = {This paper focuses on motion control problems of an omnidirectional robot based on the Nonlinear Model Predictive Control (NMPC) method. Although NMPC has been studied in many mobile robots applications due to the advantages of taking the robot constraints into account and increasing the robot performance with future information, the high computational requirement makes NMPC difficult to be utilized in the real systems with fast sampling time. In order to reduce the computational effort, many works either eliminate the computations which are necessary to keep the control stability, or linearize the nonlinear models only with local stability. Lots of research only presents the simulation results with NMPC. The main contributions of this paper are not only to analyze and design NMPC controllers with guaranteed stability to nonlinear kinematic models, but also to show the feasibility of NMPC with a real fast moving omnidirectional robot.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/LiIAS2008.pdf} } @inproceedings{ambisense2008integrated-scenario-rfid-systech, author = {Timo Schairer and Christian Weiss and Philipp Vorst and J\"urgen Sommer and Christian Hoene and Wolfgang Rosenstiel and Wolfgang Stra{\ss}er and Andreas Zell and Georg Carle and Patrick Schneider and Anette Weisbecker}, title = {Integrated Scenario for Machine-Aided Inventory Using Ambient Sensors}, booktitle = {4th European Workshop on RFID Systems and Technologies (RFID SysTech 2008)}, year = {2008}, number = {209}, series = {ITG-Fachbericht}, address = {Freiburg, Germany}, month = {June 10-11}, publisher = {VDE Verlag}, citeseerurl = {http://www.vde-verlag.de/data/buecher.php?action=bookdetail&vertriebsnr=453106&rubrik=ITG-Fachberichte&overview=overview&sort=ERSCHDATUM&direction=DESC&pg=1}, isbn = {978-3-8007-3106-0}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/ambisense2008integrated-scenario-rfid-systech.pdf} } @inproceedings{ambisense2008positioning-rfid-systech, author = {Philipp Vorst and J\"urgen Sommer and Christian Hoene and Patrick Schneider and Christian Weiss and Timo Schairer and Wolfgang Rosenstiel and Andreas Zell and Georg Carle}, title = {Indoor Positioning via Three Different {RF} Technologies}, booktitle = {4th European Workshop on RFID Systems and Technologies (RFID SysTech 2008)}, year = {2008}, number = {209}, series = {ITG-Fachbericht}, address = {Freiburg, Germany}, month = {June 10-11}, publisher = {VDE Verlag}, citeseerurl = {http://www.vde-verlag.de/data/buecher.php?action=bookdetail&vertriebsnr=453106&rubrik=ITG-Fachberichte&overview=overview&sort=ERSCHDATUM&direction=DESC&pg=1}, isbn = {978-3-8007-3106-0}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/ambisense2008positioning-rfid-systech.pdf} } @article{Draeger2008, author = {Dr\"ager, Andreas and Hassis, Nadine and Supper, Jochen and Schr\"oder, Adrian and Zell, Andreas}, title = {{SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks}}, journal = {BMC Systems Biology}, year = {2008}, volume = {2}, pages = {39}, number = {1}, month = apr, abstract = {Background: The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language). This effort is accompanied by the ongoing development of the human-readable diagrammatic representation SBGN (Systems Biology Graphical Notation). The graphical SBML editor CellDesigner allows direct translation of SBGN into SBML, and vice versa. For the assignment of kinetic rate laws, however, this process is not straightforward, as it often requires manual assembly and specific knowledge of kinetic equations. Results: SBMLsqueezer facilitates exactly this modeling step via automated equation generation, overcoming the highly error-prone and cumbersome process of manually assigning kinetic equations. For each reaction the kinetic equation is derived from the stoichiometry, the participating species (e.g., proteins, mRNA or simple molecules) as well as the regulatory relations (activation, inhibition or other modulations) of the SBGN diagram. Such information allows distinctions between, for example, translation, phosphorylation or state transitions. The types of kinetics considered are numerous, for instance generalized mass-action, Hill, convenience and several Michaelis-Menten-based kinetics, each including activation and inhibition. These kinetics allow SBMLsqueezer to cover metabolic, gene regulatory, signal transduction and mixed networks. Whenever multiple kinetics are applicable to one reaction, parameter settings allow for user-defined specifications. After invoking SBMLsqueezer, the kinetic formulas are generated and assigned to the model, which can then be simulated in CellDesigner or with external ODE solvers. Furthermore, the equations can be exported to SBML, \LaTeX{} or plain text format. Conclusion: SBMLsqueezer considers the annotation of all participating reactants, products and regulators when generating rate laws for reactions. Thus, for each reaction, only applicable kinetic formulas are considered. This modeling scheme creates kinetics in accordance with the diagrammatic representation. In contrast most previously published tools have relied on the stoichiometry and generic modulators of a reaction, thus ignoring and potentially conflicting with the information expressed through the process diagram. Additional material and the source code can be found at the project homepage (URL found in the Availability and requirements section).}, doi = {10.1186/1752-0509-2-39}, pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-2-39.pdf}, url = {http://www.biomedcentral.com/1752-0509/2/39} } @incollection{2008_79, author = {Wanke, Dierk and Kilian, Joachim and Supper, Jochen and Berendzen, Kenneth W. and Zell, Andreas and Harter, Klaus}, title = {The analysis of gene expression and \emph{cis}-regulatory elements in large microarray expression datasets}, booktitle = {{Quantum Bio-Informatics: From Quantum Information to Bio-Informatics}}, publisher = {World Scientific Pub Co Inc.}, year = {2008}, volume = {21}, number = {XXI}, pages = {294--314}, month = mar, abstract = {A challenging task for biologists and bioinformatic scientists is the analysis of gene expression mediated by \emph{cis}-regulatory elements (CREs). Regulatory DNA sequences harbor essential information to control specific gene expression and integrate information derived from signaling cascades. By the means of microarrays, the abundance of several thousand transcripts can be monitored simultaneously. This data can be used to model the flow of information from incoming signals via CREs that orchestrate gene expression, which may converge on downstream CREs. In the last few years, many large, directly comparable microarray datasets have been performed in the AtGenExpress project with the plant model organism \emph{Arabidopsis thaliana}. Each of these datasets constitutes an invaluable information resource for the study of plant developmental processes, physiological responses or interaction with its environment. Moreover, there is an increasing number of multidimensional expression datasets, for which suitable analysis programs that can keep track of all dimensions are still missing. Additional limitations of microarray analysis include overcoming a ``smoothing effect" on the relative gene expression when a large number of expression profile datasets are combined for comparison. Ultimately, the investigation of CREs possibly involved in regulating transcription is best aided by using specific gene clusters and determining linkage between gene expression, CRE position, orientation and number.}, isbn = {981279316X}, journal = {Quantum Bio-Informatics: From Quantum Information to Bio-Informatics}, keywords = {Multidimensional gene expression datasets, microarray expression profiles, cis-regulatory elements, transcriptional regulation, Arabidopsis thaliana, AtGenExpress}, url = {http://www.worldscibooks.com/physics/6756.html} } @inproceedings{vorst2008sensor-model-learning, author = {Philipp Vorst and Andreas Zell}, title = {Semi-Autonomous Learning of an {RFID} Sensor Model for Mobile Robot Self-localization}, booktitle = {European Robotics Symposium 2008}, year = {2008}, editor = {Bruno Siciliano and Oussama Khatib and Frans Groen}, volume = {44/2008}, series = {Springer Tracts in Advanced Robotics}, pages = {273--282}, month = feb, publisher = {Springer Berlin/Heidelberg}, abstract = {In this paper, we present a method of learning a probabilistic RFID reader model with a mobile robot in a semi-automatic fashion. RFID and position data, recorded during an exploration phase, are used to learn the probability of detecting an RFID tag, for which we investigate two non-parametric probability density estimation techniques. The trained model is finally used to localize the robot via a particle filter-based approach and optimized with respect to the resulting localization error. Experiments have shown that the learned models perform comparably well as a grid-based model learned from measurements in a stationary setup, but can be obtained easier.}, comment = {1610-7438 (Print) 1610-742X (Online)}, doi = {10.1007/978-3-540-78317-6}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/vorst2008rfid-sensor-model.pdf} } @article{2008_88, author = {Beigi, Majid and Zell, Andreas}, title = {A kernel-based method for local pattern extraction in random process signals}, journal = {Neurocomputing}, year = {2008}, volume = {71}, pages = {1238--1247}, url = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V10-4RR8YPB-3&_user=1634476&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000054037&_version=1&_urlVersion=0&_userid=1634476&md5=c8de9382aeb1d55d88177c40265cc454} } @inproceedings{2008_89, author = {Beigi, Majid and Zell, Andreas}, title = {A boosting approach for object classification in biosonar based robot navigation}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA2008)}, year = {2008}, pages = {3270-3275}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/BeigiICRA2008.pdf} } @inproceedings{2008_90, author = {Beigi, Majid and Zell, Andreas}, title = {{FIR}-based classifiers for animal behavior classification}, booktitle = {International Joint Conference on Neural Networks (IJCNN2008)}, year = {2008}, pages = {977-983}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/publikationen/2008/BeigiIJCNN2008.pdf} } @article{2008_45, author = {Bullinger, D. and Fr\"ohlich, Holger and Klaus, F. and Neubauer, H. and Frickenschmidt, A. and Henneges, Carsten and Zell, Andreas and Laufer, S. and Gleiter, C. H. and Liebich, H. and Kammerer, B.}, title = {Bioinformatical evaluation of modified nucleosides as biomedical markers in diagnosis of breast cancer}, journal = {Analytica Chimica Acta}, year = {2008}, volume = {618}, pages = {29-34}, number = {1}, abstract = {It is known that patients suffering from cancer diseases excrete increased amounts of modified nucleosides with their urine. Especially methylated nucleosides have been proposed to be potential tumor markers for early diagnosis of cancer. For determination of nucleosides in randomly collected urine samples, the nucleosides were extracted using affinity chromatography and then analyzed via reversed phase high-performance liquid chromatography (HPLC) with UV-detection. Eleven nucleosides were quantified in urine samples from 51 breast cancer patients and 65 healthy women. The measured concentrations were used to train a Support Vector Machine (SVM) and a k-nearest-neighbor classifier (k-NN) to discriminate between healthy control subjects and patients suffering from breast cancer. Evaluations of the learned models by computing the leave-one-out error and the prediction error on an independent test set of 29 subjects (15 healthy, 14 breast cancer patients) showed that by using the eleven nucleosides, the occurrence of breast cancer could be forecasted with 86% specificity and 94% sensitivity when using an SVM and 86% for both specificity and sensitivity with the k-NN model. (C) 2008 Elsevier B.V. All rights reserved.}, url = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF4-4SDGR56-1&_user= 1634476&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000054037&_version=1&_u rlVersion=0&_userid=1634476&md5=2ed1e7b9969bf4f5226fa1f88844b665} } @inproceedings{Mittag2008_2, author = {Georg Buscher and Andreas Dengel and Ludger van Elst and Florian Mittag}, title = {Generating and Using Gaze-Based Document Annotations}, booktitle = {Proceedings and Extended Abstracts of the Conference on Human Factors in Computing Systems}, year = {2008}, pages = {3045-3050}, publisher = {ACM}, abstract = {In this paper we describe a prototypical system that is able to generate document annotations based on eye movement data. Document parts can be annotated as being read or skimmed. We further explain ideas how such gaze-based document annotations could enhance document-centered office work in the future.}, pdf = {http://www.ra.cs.uni-tuebingen.de/mitarb/mittag/publications/mittag2008chi_gazeannotations.pdf}, } @article{2008_48, author = {Frickenschmidt, A. and Fr\"ohlich, Holger and Bullinger, D. and Zell, Andreas and Laufer, S. and Gleiter, C. H. and Liebich, H. and Kammerer, B.}, title = {Metabonomics in cancer diagnosis: mass spectrometry-based profiling of urinary nucleosides from breast cancer patients}, journal = {Biomarkers}, year = {2008}, volume = {13}, pages = {435-449}, number = {4}, abstract = {Modified nucleosides are formed post-transcriptionally in RNA. In cancer disease, the cell turnover and thus RNA metabolism is increased, yielding higher concentrations of excreted modified nucleosides. In the presented study, urinary ribonucleosides were used to differentiate between breast cancer patients and healthy volunteers. The nucleosides were extracted from urine samples using affinity chromatography and subsequently analyzed via liquid chromatography ion trap mass spectrometry (LC-IT-MS). The peak areas were related to the internal standard isoguanosine and to the urinary creatinine level. For bioinformatic pattern recognition we used the support vector machine. We examined 113 urine samples from breast cancer patients (stage Tis-T4) and 99 control samples from healthy volunteers. We achieved a sensitivity of 87.67% and a specificity of 89.90% when including 31 nucleosides. The medical metabonomics concept based on the urinary nucleoside profile reveals a significantly improved classification compared with currently applied breast cancer biomarkers such as CA15-3.}, comment = {Times Cited: 1}, url = {http://www.informaworld.com/smpp/content~content=a791845894~db=all~jumptype=rss } } @inproceedings{Haering08, author = {H\"{a}ring, Tim and de Paly, Michael and Henneges, Carsten and Hochschild, Volker}, title = {Modelling Tsunami Vulnerability. The development of a Tsunami Inundation Model with Machine Learning Tools.}, booktitle = {Digital Earth Summit on Geoinformatics 2008: Tools for Global Change Research}, year = {2008}, pages = {182-187}, address = {Heidelberg, Germany}, publisher = {Wichmann}, } @manual{EvA2ShortDoc08, title = {{EvA2} Short Documentation}, author = {Kronfeld, Marcel}, organization = {Center for Bioinformatics Tuebingen, University of Tuebingen}, address = {Sand 1, 72076 T\"ubingen, Germany}, edition = {2008}, year = {2008}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/software/EvA2/EvA2Doc/EvA2Doc.pdf}, url = {http://www.cogsys.cs.uni-tuebingen.de/software/EvA2/shortdoc.html} } @inproceedings{2008_84, author = {Li, Xiang and Zell, Andreas}, title = {Nonlinear predictive control of an omnidirectional robot dribbling a rolling ball}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA'08)}, year = {2008}, pages = {1678-1683}, address = {Pasadena, California}, publisher = {IEEE}, } @inproceedings{Mittag2008_1, author = {Thomas Roth-Berghofer and Florian Mittag}, title = {{ReduxExp}: A Justification-based Explanation-Support Server.}, booktitle = {Research and Development in Intelligent Systems XXV. Twenty-eighth SGAI International Conference on Artificial Intelligence (AI-2008), November 9-11, Cambridge, United Kingdom}, year = {2008}, editor = {Miltos Petridis and Frans Coenen and Max Bramer}, publisher = {Springer Verlag, London, UK}, abstract = {Trust in any decision depends on many factors. One way of improving trust is by explaining why a certain decision has been made and how certain actions in the context of a decision have been performed. In order to provide such explanations information systems need a mechanism for recording decisions and actions. The open-source server ReduxExp is such a system. This paper describes the architecture of ReduxExp and first experiences with the system.}, isbn = {1848821700}, keywords = {Explanation}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/mittag/publications/mittag2008sgai_reduxexp.pdf}, } @inproceedings{2008_77, author = {Weiss, Christian and Tamimi, Hashem and Zell, Andreas}, title = {A combination of vision-and vibration-based terrain classification}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2008)}, year = {2008}, pages = {2204-2209}, address = {Nice, France}, } @inproceedings{2008_78, author = {Weiss, Christian and Zell, Andreas}, title = {Novelty Detection and Online Learning for Vibration-based Terrain Classification}, booktitle = {10th International Conference on Intelligent Autonomous Systems (IAS 2008)}, year = {2008}, pages = {16-25}, address = {Baden-Baden, Germany}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2008/weiss2008ias.pdf} } @inproceedings{Ran_pathplanning_2008, author = {Hua Zhang and Manlu Liu and Ran Liu and Tianlian Hu}, title = {{Path Planning of Robot in Three-dimensional Grid Environment based on Genetic Algorithms}}, booktitle = {Proceedings of the World Congress on Intelligent Control and Automation (WCICA 2008)}, year = {2008}, pages = {1010--1014}, days = {June 25-June 27}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=4593059&abstractAccess=no&userType=inst} } @article{Ran_barcode_2008, author = {Hua Zhang and Bo Qiu and Yatao Wang and Ran Liu}, title = {{Design and Application of 2D Barcode in Inspection Robots}}, journal = {Journal of Huazhong University of Science and Technology}, year = {2008}, url = {http://en.cnki.com.cn/Article_en/CJFDTOTAL-HZLG2008S1072.htm} } @inproceedings{2007_96, author = {Tamimi, Hashem and Weiss, Christian and Zell, Andreas}, title = {Appearance-Based Robot Localization Using Wavelets-PCA}, booktitle = {Autonome Mobile Systeme 2007: 20. Fachgespr\"ach Kaiserslautern}, year = {2007}, editor = {Brauer, W. and Karsten Berns and Tobias Luksch and Brauer, W. and Berns, K. and Luksch, T.}, series = {Informatik aktuell}, pages = {36-42}, month = oct, abstract = {This paper presents an efficient image based feature extraction approach to solve the robot localization problem. The approach has two stages: in the first stage, the image is transformed to the wavelet domain using the fast wavelet transform. In the second stage, Principal Component Analysis (PCA) is applied to the wavelet coefficients in order to further reduce the feature dimension by selecting the significant feature elements. The experiments show that the proposed approach is superior to the PCA-based approach and the wavelet-based approach. The main advantages of wavelets-PCA are the efficiency in extracting the features and the robustness against illumination changes.}, } @inproceedings{schneegans2007rfid-snapshots, author = {Sebastian Schneegans and Philipp Vorst and Andreas Zell}, title = {Using {RFID} Snapshots for Mobile Robot Self-Localization}, booktitle = {Proceedings of the 3rd European Conference on Mobile Robots (ECMR 2007)}, year = {2007}, pages = {241--246}, address = {Freiburg, Germany}, month = {September 19-21}, abstract = {In recent years, radio frequency identification (RFID) has found its way into the field of mobile robot navigation. On the one hand, the technology promises to contribute solutions to common problems in self-localization and mapping such as the data association problem. On the other hand, questions like how to cope with poor or even missing range and bearing information remain open. In this paper, we present a novel method which tackles these challenges: Inspired by vision-based self-localization approaches, it utilizes RFID snapshots for the estimation of the robot pose. Our experiments show that the new technique enables a robot to successfully localize itself in an indoor environment. The accuracy is comparable to the one of a previous approach using an explicit model of detection probabilities. Our method, however, requires fewer iterations of the underlying particle filter in order to converge to the approximate robot pose.}, citeseerurl = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.72.9869}, keywords = {RFID, mobile robot, self-localization, particle filter}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/schneegans07ecmr.pdf} } @inproceedings{Draeger2007b, author = {Dr\"ager, Andreas and Kronfeld, Marcel and Supper, Jochen and Planatscher, Hannes and Magnus, J{\o}rgen B. and Oldiges, Marco and Zell, Andreas}, title = {{Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in \emph{C.~glutamicum}}}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2007)}, year = {2007}, editor = {Srinivasan, Dipti and Wang, Lipo}, pages = {896--903}, address = {Singapore}, month = sep, organization = {IEEE Computational Intelligence Society}, publisher = {IEEE Press}, abstract = {An important problem in systems biology is parameter estimation for biochemical system models. Our work concentrates on the metabolic subnetwork of the valine and leucine biosynthesis in \emph{Corynebacterium glutamicum}, an anaerobic actinobacterium of high biotechnological importance. Using data of an in vivo experiment measuring 13 metabolites during a glucose stimulus-response experiment we investigate the performance of various Evolutionary Algorithms on the parameter inference problem in biochemical modeling. Due to the inconclusive information on the reversibility of the reactions in the pathway, we develop both a reversible and an irreversible differential equation model based on the recent convenience kinetics approach. As the reversible model allows better approximation on the whole, we use it to analyze the impact of different settings on four especially promising EAs. We show that Particle Swarm Optimization as well as Differential Evolution are useful methods for parameter estimation on convenience kinetics models outperforming Genetic Algorithm and Evolution Strategy approaches and nearly reaching the quality of independent spline approximations on the raw data.}, doi = {10.1109/CEC.2007.4424565}, isbn = {1-4244-1340-0}, keywords = {systems biology, mathematical modeling, benchmark, evolutionary algorithms, valine and leucine biosynthesis, Corynebacterium glutamicum, convenience kinetics}, notes = {CEC 2007 - A joint meeting of the IEEE, the EPS, and the IET. IEEE Catalog Number: 07TH8963C}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/Draeger2007b.pdf}, url = {http://dx.doi.org/10.1109/CEC.2007.4424565} } @inproceedings{Draeger2007a, author = {Dr\"ager, Andreas and Supper, Jochen and Planatscher, Hannes and Magnus, J{\o}rgen B. and Oldiges, Marco and Zell, Andreas}, title = {{Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in \emph{Corynebacterium glutamicum}}}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2007)}, year = {2007}, editor = {Srinivasan, Dipti and Wang, Lipo}, pages = {620--627}, address = {Singapore}, month = sep, organization = {IEEE Computational Intelligence Society}, publisher = {IEEE Press}, abstract = {Parameter estimation for biochemical model systems has become an important problem in systems biology. Here we focus on the metabolic subnetwork of the valine and leucine biosynthesis in \emph{C.~glutamicum}. Due to the lack of indisputable information regarding reversibility of the reactions in the pathway we derived two alternative ordinary differential equation models based on the formalisms of the generalized mass-action rate law. We introduced two alternative modeling approaches for feedback inhibition and evaluated the applicability of six optimization procedures (multi start Hill Climber, binary and real valued Genetic Algorithm, standard and covariance matrix adaption Evolution Strategy as well as Simulated Annealing) to the problem of parameter fitting. The model considering irreversible reactions performed worse and was therefore rejected from further analysis. We benchmarked the impact of different mutation and crossover operators as well as the influence of the population size on the remaining system and the two best optimization procedures namely binary Genetic Algorithm and the Evolution Strategy. The GA performed best on average and found the best total result based on the relative squared error.}, doi = {10.1109/CEC.2007.4424528}, isbn = {1-4244-1340-0}, keywords = {systems biology, mathematical modeling, benchmark, Evolutionary Algorithms, valine and leucine biosynthesis, Corynebacterium glutamicum, generalized mass-action kinetics}, notes = {CEC 2007 - A joint meeting of the IEEE, the EPS, and the IET, Dr\"ager, Andreas and Supper, Jochen and Planatscher, Hannes and Magnus, J{\o}rgen B. and Oldiges, Marco and Zell, Andreas IEEE Catalog Number: 07TH8963C}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/Draeger2007a.pdf}, url = {http://dx.doi.org/10.1109/CEC.2007.4424528} } @inproceedings{2007_92, author = {Weiss, Christian and Masselli, Andreas and Zell, Andreas}, title = {Fast Vision-based Localization for Outdoor Robots Using a Combination of Global Image Features}, booktitle = {6th Symposium on Intelligent Autonomous Vehicles (IAV 2007)}, year = {2007}, address = {Toulouse, France}, month = sep, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/weiss07iav.pdf} } @mastersthesis{Tscherneck2007a, author = {Tscherneck, Stephanie}, title = {{Identifizierung und Charakterisierung der Prophagen Repressor Bindungsstellen auf den Genomen PY54 und phiKO2}}, school = {University of Applied Sciences Wildau (UASW)}, year = {2007}, type = {Bachelorthesis}, address = {Bahnhofstr. 1, 15745 Wildau (Germany)}, month = aug, abstract = {following soon}, } @article{Hofmeister2007, author = {Marius Hofmeister}, title = {{BMF} im {P}raxiseinsatz. {E}ntwicklung einer {I}ntegrationsschnittstelle f\"ur {C}ontent-{M}anagement-{S}yteme}, journal = {Fachzeitschrift f\"ur Fernsehen, Film und elektronische Medien (FKT)}, year = {2007}, pages = {230-237}, number = {5}, month = may, url = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/hofmeister/publications/hofmeister_fktg.pdf} } @inproceedings{beigi2007novel, author = {Majid Beigi and Andreas Zell}, title = {A novel kernel-based method for local pattern extraction in random process signals}, booktitle = {Proc. 15th European Symposium on Artificial Neural Networks (ESANN 2007)}, year = {2007}, pages = {265-270}, address = {Bruges, Belgium}, month = apr, ee = {http://www.dice.ucl.ac.be/Proceedings/esann/esannpdf/es2007-32.pdf}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/BeigiESANN2007.pdf} } @inproceedings{komma07, author = {Komma, Philippe and Fischer, Jan and Duffner, Frank and Bartz, Dirk}, title = {Lossless Volume Data Compression Schemes}, booktitle = {Simulation and Visualization 2007 (SimVis 2007)}, year = {2007}, pages = {169-182}, address = {Magdeburg, Germany}, month = mar, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/komma2007simvis-lossless.pdf} } @inproceedings{2007_91, author = {Weiss, Christian and Masselli, Andreas and Tamimi, Hashem and Zell, Andreas}, title = {Fast Outdoor Robot Localization Using Integral Invariants}, booktitle = {5th International Conference on Computer Vision Systems (ICVS 2007)}, year = {2007}, pages = {21-24}, address = {Bielefeld, Germany}, month = mar, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/weiss07icvs.pdf} } @inproceedings{2007_107, author = {Beigi, Majid and Wang, Maosen and Zell, Andreas}, title = {Time-resolved spectrum kernel for biosonar target classification}, booktitle = {Fourth IASTED International Conference on Signal Processing, Pattern Recognition, and Applications (SPPRA 2007)}, year = {2007}, pages = {126--131}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/BeigiSpKernel2007.pdf} } @inproceedings{2007_108, author = {Beigi, Majid and Zell, Andreas}, title = {Object Detection in Biosonar Based Robot Navigation}, booktitle = {Proceedings of the ICRA 2007 Workshop: Planning,Perception and Navigation for Intelligent Vehicles}, year = {2007}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/BeigiICRA2007.pdf} } @inproceedings{2007_4, author = {Beigi, Majid and Zell, Andreas}, title = {Synthetic protein sequence oversampling method for classification and remote homology detection in imbalanced protein data}, booktitle = {International Conference on Bioinformatics Research and Development (BIRD 2007)}, year = {2007}, volume = {4414}, series = {LNBI}, pages = {263-277}, address = {Berlin, Germany}, publisher = {Springer}, abstract = {Many classifiers are designed with the assumption of well-balanced datasets. But in real problems, like protein classification and remote homology detection, when using binary classifiers like support vector machine (SVM) and kernel methods, we are facing imbalanced data in which we have a low number of protein sequences as positive data (minor class) compared with negative data (major class). A widely used solution to that issue in protein classification is using a different error cost or decision threshold for positive and negative data to control the sensitivity of the classifiers. Our experiments show that when the datasets are highly imbalanced, and especially with overlapped datasets, the efficiency and stability of that method decreases. This paper shows that a combination of the above method and our suggested oversampling method for protein sequences can increase the sensitivity and also stability of the classifier. Synthetic Protein Sequence Oversampling (SPSO) method involves creating synthetic protein sequences of the minor class, considering the distribution of that class and also of the major class, and it operates in data space instead of feature space. We used G-protein-coupled receptors families as real data to classify them at subfamily and sub-subfamily levels (having low number of sequences) and could get better accuracy and Matthew's correlation coefficient than other previously published method. We also made artificial data with different distributions and overlappings of minor and major classes to measure the efficiency of our method. The method was evaluated by the area under the Receiver Operating Curve (ROC).}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/BeigiBird2007.pdf} } @inproceedings{2007_106, author = {Heinemann, Patrick and Haase, J\"urgen and Zell, Andreas}, title = {A Novel Approach to Efficient {Monte-Carlo} Localization in {RoboCup}}, booktitle = {RoboCup 2006: Robot Soccer World Cup X}, year = {2007}, volume = {4434/2009}, series = {Lecture Notes in Computer Science}, pages = {322-329}, publisher = {Springer}, abstract = {Recently, efficient self-localization methods have been developed, among which probabilistic Monte-Carlo localization (MCL) is one of the most popular. However, standard MCL algorithms need at least 100 samples to compute an acceptable position estimation. This paper presents a novel approach to MCL that uses an adaptive number of samples that drops down to a single sample if the pose estimation is sufficiently accurate. Experiments show that the method remains in this efficient single sample tracking mode for more than 90% of the cycles.}, doi = {10.1007/978-3-540-74024-7_29}, isbn = {978-3-540-74023-0}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/heinemann07novel.pdf} } @inproceedings{2007_105, author = {Heinemann, Patrick and Sehnke, Frank and Streichert, Felix and Zell, Andreas}, title = {Towards a Calibration-Free Robot: The {ACT} Algorithm for Automatic Online Color Training}, booktitle = {RoboCup 2006: Robot Soccer World Cup X}, year = {2007}, editor = {G. Lakemeyer and E. Sklar and D. G. Sorrenti and T. Takahashi}, volume = {4434}, series = {Lecture Notes in Computer Science}, pages = {363-370}, publisher = {Springer}, abstract = {Many approaches for object detection based on color coding were published in the RoboCup domain. They are tuned to the typical RoboCup scenario of constant lighting using a static subdivision of the color space. However, such algorithms will soon be of limited use, when playing under changing and finally natural lighting. This paper presents an algorithm for automatic color training, which is able to robustly adapt to different lighting situations online. Using the ACT algorithm a robot is able to play a RoboCup match while the illumination of the field varies.}, doi = {10.1007/978-3-540-74024-7_34}, isbn = {978-3-540-74023-0}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/heinemann07towards.pdf} } @inproceedings{Kron07Loc, author = {Kronfeld, Marcel and Weiss, Christian and Zell, Andreas}, title = {Swarm-supported Outdoor Localization with Sparse Visual Data}, booktitle = {3rd European Conference on Mobile Robots (ECMR 2007)}, year = {2007}, pages = {259--264}, address = {Freiburg, Germany}, abstract = {The localization of mobile systems with video data is a challenging field in robotic vision research. Apart from artificial environmental support technologies like GPS localization, a selfsufficient visual system is desirable. In this work, we introduce a new heuristic approach to outdoor localization in a scenario where no odometry readings are available. In an earlier work, we employed SIFT features and a common particle filter method in the scenario. A modification of Particle Swarm Optimization, a popular optimization technique especially in dynamically changing environments, is developed and fit to the localization problem, including self-adaptive mechanisms. The new method obtains similar or better localization results in our experiments, while requiring a fraction of SIFT comparisons of the standard method, indicating an all-over speed-up by 25%.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/Kron07SwarmSuppFinal.pdf} } @inproceedings{2007_101, author = {Li, Xiang and Wang, Maosen and Zell, Andreas}, title = {Dribbling Control of Omnidirectional Soccer Robots}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA'07)}, year = {2007}, pages = {2623-2628}, address = {Roma, Italy}, publisher = {IEEE}, abstract = {This paper focuses on the dribbling control problem of an omnidirectional mobile robot. Because the movement of the dribbled object must be considered, dribbling control is more challenging than normal mobile robot motion control. A new feedback control algorithm, which steers a reference point to follow the desired movement and keeps the ball near to this point simultaneously, is proposed. To dribble a rolling ball along a given path, the robot should provide the ball with appropriate force by consecutive pushing operations when they travel in an environment with obstacles. Based on the analysis of the forces acting on the ball with respect to the mobile robot coordinate system, a constraint for robot movement in the dribbling process is also introduced. The simulation and real-world experiments address the performance of this control algorithm.}, doi = {10.1109/ROBOT.2007.363861}, isbn = {1-4244-0601-3}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/li07ICRA.pdf} } @inproceedings{2007_103, author = {Li, Xiang and Zell, Andreas}, title = {{H} Infinity Filtering for a Mobile Robot Tracking a Free Rolling Ball}, booktitle = {RoboCup 2006: Robot Soccer World Cup X}, year = {2007}, editor = {Gerhard Lakemeyer and Elizabeth Sklar and Domenico G. Sorrenti and Tomoichi Takahashi}, volume = {4434}, pages = {296-303}, publisher = {Springer}, doi = {10.1007/978-3-540-74024-7_26}, ee = {http://dx.doi.org/10.1007/978-3-540-74024-7_26}, isbn = {978-3-540-74023-0}, journal = {Lecture Notes in Computer Science}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/li06Hinfinity.pdf} } @inproceedings{2007_102, author = {Li, Xiang and Zell, Andreas}, title = {Motion control of an omnidirectional mobile robot}, booktitle = {Proceedings of the 4th International Conference on Informatics in Control, Automation and Robotics, ICINCO'07)}, year = {2007}, volume = {24}, series = {Lecture Notes in Electrical Engineering}, pages = {181-193}, address = {Angers, France}, publisher = {Springer}, abstract = {This paper focuses on the motion control problem of an omnidirectional mobile robot. A new control method based on the inverse input-output linearized kinematic model is proposed. As the actuator saturation and actuator dynamics have important impacts on the robot performance, this control law takes into account these two aspects and guarantees the stability of the closed-loop control system. Real-world experiments with an omnidirectional middle-size RoboCup robot verify the performance of this proposed control algorithm.}, doi = {10.1007/978-3-540-85640-5_14}, isbn = {978-3-540-85639-9}, issn = {1876-1100}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/li07ICINCO.pdf} } @article{Schmitz07, author = {Schmitz, Gerd H. and W\"ohling, Thomas and de Paly, Michael and Sch\"utze, Niels}, title = {Gain-P: A New Strategy To Increase Furrow Irrigation Efficiency}, journal = {Arabian Journal for Science and Engineering}, year = {2007}, volume = {32}, pages = {103-116}, number = {1}, } @article{2007_38, author = {Strauch, Martin and Supper, Jochen and Spieth, Christian and Wanke, Dierk and Kilian, Joachim and Harter, Klaus and Zell, Andreas}, title = {A Two-Step Clustering for 3-D Gene Expression Data Reveals the Main Features of the Arabidopsis Stress Response}, journal = {Journal of Integrative Bioinformatics}, year = {2007}, volume = {4}, number = {1}, abstract = {We developed an integrative approach for discovering gene modules, i.e. genes that are tightly correlated under several experimental conditions and applied it to a threedimensional Arabidopsis thaliana microarray dataset. The dataset consists of approximately 23000 genes responding to 9 abiotic stress conditions at 6-9 different points in time. Our approach aims at finding relatively small and dense modules lending themselves to a specific biological interpretation. In order to detect gene modules within this dataset, we employ a two-step clustering process. In the first step, a k-means clustering on one condition is performed, which is subsequently used in the second step as a seed for the clustering of the remaining conditions. To validate the significance of the obtained modules, we performed a permutation analysis and determined a null hypothesis to compare the module scores against, providing a p-value for each module. Significant modules were mapped to the Gene Ontology (GO) in order to determine the participating biological processes. As a result, we isolated modules showing high significance with respect to the p-values obtained by permutation analysis and GO mapping. In these modules we identified a number of genes that are either part of a general stress response with similar characteristics under different conditions (coherent modules), or part of a more specific stress response to a single stress condition (single response modules). We also found genes clustering within several conditions, which are, however, not part of a coherent module. These genes have a distinct temporal response under each condition. We call the modules they are contained in individual response modules (IR).}, doi = {10.2390/biecoll-jib-2007-54}, url = {http://journal.imbio.de/articles/pdf/jib-54.pdf} } @phdthesis{Streichert07, author = {Felix Streichert}, title = {Evolutionary Algorithms in Multi-Modal and Multi-Objective Environments}, school = {University of T\"ubingen}, year = {2007}, address = {T\"ubingen, Germany}, isbn = {978-3-8325-1552-2}, } @article{2007_97, author = {Sung, Alexander and Kl\"opper, Florian and Mitterer, Alexander and Wachtmeister, Georg and Zell, Andreas}, title = {{Modellbasierte Online-Optimierung in der Simulation und am Motorenpr\"ufstand}}, journal = {MTZ-Motortechnische Zeitschrift}, year = {2007}, volume = {68}, pages = {42-49}, number = {1}, issn = {0024-8525 10814}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/OnlineOpti_BMW_m01-07-09.pdf} } @inproceedings{2007_98, author = {Sung, Alexander and Zell, Andreas and Kl\"opper, Florian and Vogel, Alexander}, title = {Target Value Prediction For Online Optimization At Engine Test Beds}, booktitle = {4th International Conference on Informatics in Control, Automation and Robotics (ICINCO'07)}, year = {2007}, pages = {108-115}, address = {Angers, France}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/TargetValuePrediction.pdf} } @inproceedings{Supper2007, author = {Supper, Jochen and Fr\"ohlich, Holger and Spieth, Christian and Dr\"ager, Andreas and Zell, Andreas}, title = {Inferring Gene Regulatory Networks by Machine Learning Methods}, booktitle = {Proceedings of the 5\textsuperscript{th} Asia-Pacific Bioinformatics Conference (APBC 2007)}, year = {2007}, editor = {Sankoff, David and Wang, Lusheng and Chin, Francis}, volume = {5}, series = {Series on Advances in Bioinformatics and Computational Biology}, pages = {247--256}, address = {57 Shelton Street, Govent Garden, London WC2H 9HE, UK}, month = jan, publisher = {Imperial College Press}, abstract = {The ability to measure the transcriptional response after a stimulus has drawn much attention to the underlying gene regulatory networks. Several machine learning related methods, such as Bayesian networks and decision trees, have been proposed to deal with this difficult problem, but rarely a systematic comparison between different algorithms has been performed. In this work, we critically evaluate the application of multiple linear regression, SVMs, decision trees and Bayesian networks to reconstruct the budding yeast cell cycle network. The performance of these methods is assessed by comparing the topology of the reconstructed models to a validation network. This validation network is defined \emph{a priori} and each interaction is specified by at least one publication. We also investigate the quality of the network reconstruction if a varying amount of gene regulatory dependencies is provided \emph{a priori}.}, doi = {10.1142/9781860947995_0027}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/SupperAPBC2007_GRNs.pdf}, url = {http://dx.doi.org/10.1142/9781860947995_0027} } @inproceedings{2007_40, author = {Supper, Jochen and Fr\"ohlich, Holger and Zell, Andreas}, title = {Gene Regulatory Network Inference via Regression Based Topological Refinement}, booktitle = {Asia-Pacific Bioinformatics Conference (APBC 2007)}, year = {2007}, editor = {David Sankoff and Lusheng Wang and Francis Chin}, volume = {5}, series = {Advances in Bioinformatics and Computational Biology}, pages = {267-276}, address = {Hong Kong, China}, month = jan, publisher = {Imperial College Press}, isbn = {978-1-86094-783-4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/SupperAPBC2007_TopologicalRefinement.pdf} } @inproceedings{2007_39, author = {Supper, Jochen and Spieth, Christian and Zell, Andreas}, title = {Reconstructing Linear Gene Regulatory Networks}, booktitle = {Proceedings of the 5th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2007)}, year = {2007}, editor = {Elena Marchiori and Jason H. Moore and Jagath C. Rajapakse}, volume = {4447}, series = {Lecture Notes in Computer Science}, pages = {270-279}, address = {Valencia, Spain}, publisher = {Springer}, isbn = {978-3-540-71782-9}, } @article{2007_5, author = {Supper, Jochen and Strauch, Martin and Wanke, Dierk and Harter, Klaus and Zell, Andreas}, title = {{EDISA}: extracting biclusters from multiple time-series of gene expression profiles}, journal = {BMC Bioinformatics}, year = {2007}, volume = {8}, pages = {334}, number = {1}, abstract = {Background: Cells dynamically adapt their gene expression patterns in response to various stimuli. This response is orchestrated into a number of gene expression modules consisting of co-regulated genes. A growing pool of publicly available microarray datasets allows the identification of modules by monitoring expression changes over time. These time-series datasets can be searched for gene expression modules by one of the many clustering methods published to date. For an integrative analysis, several time-series datasets can be joined into a three-dimensional gene-condition-time dataset, to which standard clustering or biclustering methods are, however, not applicable. We thus devise a probabilistic clustering algorithm for gene-condition-time datasets. Results: In this work, we present the EDISA (Extended Dimension Iterative Signature Algorithm), a novel probabilistic clustering approach for 3D gene-condition-time datasets. Based on mathematical definitions of gene expression modules, the EDISA samples initial modules from the dataset which are then refined by removing genes and conditions until they comply with the module definition. A subsequent extension step ensures gene and condition maximality. We applied the algorithm to a synthetic dataset and were able to successfully recover the implanted modules over a range of background noise intensities. Analysis of microarray datasets has lead us to define three biologically relevant module types: 1) We found modules with independent response profiles to be the most prevalent ones. These modules comprise genes which are co-regulated under several conditions, yet with a different response pattern under each condition. 2) Coherent modules with similar responses under all conditions occurred frequently, too, and were often contained within these modules. 3) A third module type, which covers a response specific to a single condition was also detected, but rarely. All of these modules are essentially different types of biclusters. Conclusion: We successfully applied the EDISA to different 3D datasets. While previous studies were mostly aimed at detecting coherent modules only, our results show that coherent responses are often part of a more general module type with independent response profiles under different conditions. Our approach thus allows for a more comprehensive view of the gene expression response. After subsequent analysis of the resulting modules, the EDISA helped to shed light on the global organization of transcriptional control. An implementation of the algorithm is available at \url{http://www-ra.informatik.uni-tuebingen.de/software/IAGEN/}.}, doi = {10.1186/1471-2105-8-334}, issn = {1471-2105}, url = {http://www.biomedcentral.com/1471-2105/8/334} } @inproceedings{2007_93, author = {Weiss, Christian and Fechner, Nikolas and Stark, Matthias and Zell, Andreas}, title = {Comparison of Different Approaches to Vibration-based Terrain Classification}, booktitle = {3rd European Conference on Mobile Robots (ECMR 2007)}, year = {2007}, pages = {7-12}, address = {Freiburg, Germany}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/weiss07ecmr.pdf} } @inproceedings{2007_95, author = {Weiss, Christian and Stark, Matthias and Zell, Andreas}, title = {{SVMs} for Vibration-based Terrain Classification}, booktitle = {Proc. Autonome Mobile Systeme (AMS)}, year = {2007}, pages = {1--7}, address = {Kaiserslautern, Germany}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/weiss07ams.pdf} } @inproceedings{2007_94, author = {Weiss, Christian and Tamimi, Hashem and Masselli, Andreas and Zell, Andreas}, title = {A hybrid approach for vision-based outdoor robot localization using global and local image features}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2007)}, year = {2007}, pages = {1047-1052}, address = {San Diego, CA, USA}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2007/weiss07iros.pdf} } @inproceedings{2006_43, author = {Beigi, Majid and Zell, Andreas}, title = {A Novel Method for Classifying Subfamilies and Sub-subfamilies of G-Protein Coupled Receptors}, booktitle = {Biological and Medical Data Analysis: 7th International Symposium, ISBMDA 2006}, year = {2006}, volume = {4345}, series = {LNBI}, pages = {25-36}, address = {Thessaloniki, Greece}, month = dec, publisher = {Springer}, abstract = {G-protein coupled receptors (GPCRs) are a large superfamily of integral membrane proteins that transduce signals across the cell membrane. Because of that important property and other physiological roles undertaken by the GPCR family, they have been an important target of therapeutic drugs. The function of many GPCRs is not known and accurate classification of GPCRs can help us to predict their function. In this study we suggest a kernel based method to classify them at the subfamily and sub-subfamily level. To enhance the accuracy and sensitivity of classifiers at the sub-subfamily level that we were facing with a low number of sequences (imbalanced data), we used our new synthetic protein sequence oversampling (SPSO) algorithm and could gain an overall accuracy and Matthew's correlation coefficient (MCC) of 98.4% and 0.98 for class A, nearly 100% and 1 for class B and 96.95% and 0.91 for class C, respectively, at the subfamily level and overall accuracy and MCC of 97.93%, and 0.95 at the sub-subfamily level. The results shows that Our oversampling technique can be used for other applications of protein classification with the problem of imbalanced data.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/BeigiGPCR2006.pdf} } @inproceedings{2006_44, author = {Beigi, Majid and Zell, Andreas}, title = {{SPSO}: Synthetic Protein Sequence Oversampling for Imbalanced Protein Data and Remote Homology Detection}, booktitle = {Biological and Medical Data Analysis: 7th International Symposium, ISBMDA 2006}, year = {2006}, volume = {4345}, series = {LNBI}, pages = {104-115}, address = {Thessaloniki, Greece}, month = dec, publisher = {Springer}, abstract = {Many classifiers are designed with the assumption of well-balanced datasets. But in real problems, like protein classification and remote homology detection, when using binary classifiers like support vector machine (SVM) and kernel methods, we are facing imbalanced data in which we have a low number of protein sequences as positive data (minor class) compared with negative data (major class). A widely used solution to that issue in protein classification is using a different error cost or decision threshold for positive and negative data to control the sensitivity of the classifiers. Our experiments show that when the datasets are highly imbalanced, and especially with overlapped datasets, the efficiency and stability of that method decreases. This paper shows that a combination of the above method and our suggested oversampling method for protein sequences can increase the sensitivity and also stability of the classifier. Our method of oversampling involves creating synthetic protein sequences of the minor class, considering the distribution of that class and also of the major class, and it operates in data space instead of feature space. This method is very useful in remote homology detection, and we used real and artificial data with different distributions and overlappings of minor and major classes to measure the efficiency of our method. The method was evaluated by the area under the Receiver Operating Curve (ROC).}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/BeigiSpso2006.pdf} } @inproceedings{cerco, author = {Simon Rieche and Klaus Wehrle and Leo Petrak and Clemens Wrzodek}, title = {Cerco: Supporting Range Queries with a Hierarchically Structured Peer-to-Peer System}, booktitle = {Proceedings of 31st IEEE Conference on Local Computer Networks (LCN 2006)}, year = {2006}, address = {Tampa, Florida, USA}, month = {November}, abstract = {Structured Peer-to-Peer systems are designed for a highly scalable, self organizing, and efficient lookup for data. The key space of the so-called Distributed Hash Tables (DHTs) is partitioned and each partition with its keys and values is assigned to a node in the DHT. For data retrieval however, the very nature of hash tables allows only exact pattern matches. We propose Cerco, a simple solution for the problem of range queries by employing a hierarchically structured P2P approach based on the principles of Distributed Hash Tables. We show that a dynamic hierarchy of DHTs with on-demand classification of items can positively influence the response time of queries while maintaining lookup correctness.}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/WrzodekCerco.pdf}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4116490&arnumber=4116594&count=192&index=90} } @article{2005_122, author = {Tamimi, Hashem and Andreasson, Henrik and Treptow, Andr\'{e} and Duckett, Tom and Zell, Andreas}, title = {Localization of Mobile Robots with Omnidirectional Vision Using Particle Filter and Iterative {SIFT}}, journal = {Robotics and Autonomous Systems}, year = {2006}, volume = {54}, pages = {758-765}, number = {9}, month = sep, note = {Selected papers from the 2nd European Conference on Mobile Robots (ECMR '05), Ancona, Italy}, abstract = {The Scale Invariant Feature Transform, SIFT, has been successfully applied to robot localization. Still, the number of features extracted with this approach is immense, especially when dealing with omnidirectional vision. In this work, we propose a new approach that reduces the number of features generated by SIFT as well as their extraction and matching time. With the help of a Particle Filter, we demonstrate that we can still localize the mobile robot accurately with a lower number of features.}, doi = {10.1016/j.robot.2006.04.018}, issn = {0921-8890}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/tamimi05-ecmr.pdf} } @inproceedings{2006_49, author = {Fr\"ohlich, Holger and Speer, Nora and Spieth, Christian and Zell, Andreas}, title = {Kernel Based Functional Gene Grouping}, booktitle = {International Joint Conference on Neural Networks (IJCNN 2006)}, year = {2006}, pages = {6886-6891}, address = {Vancouver, Canada}, publisher = {IEEE Press}, } @inproceedings{2006_116, author = {Heinemann, Patrick and Becker, Hannes and Haase, J\"urgen and Zell, Andreas}, title = {The Attempto T\"ubingen Robot Soccer Team 2006}, booktitle = {Robot Soccer World Cup X}, year = {2006}, volume = {4434}, series = {Lecture Notes in Computer Science}, publisher = {Springer}, note = {CD supplement}, abstract = {This paper describes the Attempto T\"ubingen Robot Soccer Team 2006. After radical changes in the software and hardware we present a team of six new omnidirectional robots in 2006 together with promising innovative algorithms. Apart from the ability to play at changing illumination we present effective methods of ball interception and efficient path planning around dynamically moving objects using sophisticated tracking algorithms. This paper introduces the robot hardware and some of these algorithms.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/heinemann07attempto.pdf} } @article{2006_112, author = {Heinemann, Patrick and Becker, Hannes and Zell, Andreas}, title = {Improved path planning in highly dynamic environments based on time variant potential fields}, journal = {VDI BERICHTE}, year = {2006}, volume = {1956}, pages = {177-178}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/heinemann06improved.pdf} } @inproceedings{2006_115, author = {Heinemann, Patrick and Haase, J\"urgen and Zell, Andreas}, title = {A Combined Monte-Carlo Localization and Tracking Algorithm for RoboCup}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS '06)}, year = {2006}, pages = {1535-1540}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/heinemann06combined.pdf} } @inproceedings{2006_114, author = {Heinemann, Patrick and Sehnke, Frank and Streichert, Felix and Zell, Andreas}, title = {An Automatic Approach to Online Color Training in {RoboCup} Environments}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS '06)}, year = {2006}, pages = {4880-4885}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/heinemann06automatica.pdf} } @inproceedings{2006_113, author = {Heinemann, Patrick and Streichert, Felix and Sehnke, Frank and Zell, Andreas}, title = {Automatic Calibration of Camera to World Mapping in RoboCup using Evolutionary Algorithms}, booktitle = {IEEE International Congress on Evolutionary Computing (CEC 2006)}, year = {2006}, pages = {4459-4466}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/heinemann06automatic.pdf} } @inproceedings{2006_117, author = {Li, Xiang and Zell, Andreas}, title = {Path Following Control for a Mobile Robot Pushing a Ball}, booktitle = {IFAC Symposium on Robot Control (SYROCO 2006)}, year = {2006}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/li06push.pdf} } @inproceedings{Schuetze06, author = {Sch\"{u}tze, Niels and W\"{o}hling, Thomas and de Paly, Michael and Schmitz, Gerd}, title = {Global optimization of deficit irrigation systems using evolutionary algorithms}, booktitle = {Proceedings of the XVI International Conference on Computational Methods in Water Resources}, year = {2006}, address = {Copenhagen, Denmark}, } @inproceedings{2006_spieth06comparing, author = {Spieth, Christian and Hassis, Nadine and Streichert, Felix and Supper, Jochen and Speer, Nora and Beyreuther, Klaus and Zell, Andreas}, title = {Comparing Mathematical Models on the Problem of Network Inference}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO 2006)}, year = {2006}, series = {Lecture Notes in Computer Science}, pages = {305-306}, address = {Seattle, USA}, publisher = {Springer}, abstract = {In this paper we address the problem of finding gene regulatory networks from experimental DNA microarray data. We focus on the evaluation of the performance of different mathematical models on the inference problem. They are used to model the underlying dynamic system of artificial regulatory networks. The dynamics of the artificial systems represent different basic types of behavior, dimensionality and mathematical properties. They are all created with three commonly used approaches, namely linear weight matrices, H-systems, and S-systems. Due to the complexity of the inference problem, some researchers suggested evolutionary algorithms for this purpose. However, in many publications only one algorithm is used without any comparison to other optimization methods. Thus, we introduce a framework to systematically apply evolutionary algorithms for further comparative analysis.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/spieth06models.pdf} } @article{2006_62, author = {Spieth, Christian and Supper, Jochen and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {{JCell} - a Java-based framework for inferring regulatory networks from time series data}, journal = {Bioinformatics}, year = {2006}, volume = {22}, pages = {2051-2052}, number = {16}, abstract = {Motivation: JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers.}, url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/16/2051?etoc} } @inproceedings{2006_109, author = {Spieth, Christian and Worzischek, Rene and Streichert, Felix}, title = {Comparing evolutionary algorithms on the problem of network inference}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO 2006)}, year = {2006}, pages = {305-306}, address = {Seattle, USA}, publisher = {ACM New York, NY, USA}, abstract = {In this paper, we address the problem of finding gene regulatory networks from experimental DNA microarray data. We focus on the evaluation of the performance of different evolutionary algorithms on the inference problem. These algorithms are used to evolve an underlying quantitative mathematical model. The dynamics of the regulatory system are modeled with two commonly used approaches, namely linear weight matrices and S-systems and a novel formulation, namely H-systems. Due to the complexity of the inference problem, some researchers suggested evolutionary algorithms for this purpose. However, in many publications only one algorithm is used without any comparison to other optimization methods. Thus, we introduce a framework to systematically apply evolutionary algorithms and different types of mutation and crossover operators to the inference problem for further comparative analysis.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/spieth06eas.pdf} } @article{2006_110, author = {Gudrun Szalay and Silke Meiners and Antje Voigt and J\"org Lauber and Christian Spieth and Nora Speer and Martina Sauter and Ulrike Kuckelkorn and Andreas Zell and Karin Klingel and Karl Stangl and Reinhard Kandolf}, title = {Ongoing coxsackievirus myocarditis is associated with increased formation and activity of myocardial immunoproteasomes}, journal = {American Journal of Pathology}, year = {2006}, volume = {168}, pages = {1542-1552}, number = {5}, } @inproceedings{2006_262, author = {Tamimi, Hashem and Halawani, Alaa and Burkhardt, Hans and Zell, Andreas}, title = {Appearance-based Localization of Mobile Robots using Local Integral Invariants}, booktitle = {Proceedings of the 9th International Conference on Intelligent Autonomous Systems (IAS-9)}, year = {2006}, editor = {Tamio Arai and Rolf Pfeifer and Tucker R. Balch and Hiroshi Yokoi}, pages = {181-188}, address = {Tokyo, Japan}, publisher = {IOS Press}, isbn = {1-58603-595-9}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/tamimi06-ias9.pdf} } @phdthesis{2006_69, author = {Wegner, J\"org K.}, title = {Data Mining und Graph Mining auf molekularen Graphen - Cheminformatik und molekulare Kodierungen f\"ur ADME/Tox-QSAR-Analysen}, school = {University of Tuebingen, Germany}, year = {2006}, university = {University of Tuebingen} } @inproceedings{2006_111, author = {Weiss, Christian and Fr\"ohlich, Holger and Zell, Andreas}, title = {Vibration-based terrain classification using support vector machines}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2006)}, year = {2006}, pages = {4429-4434}, address = {Beijing, China}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2006/weiss06.pdf} } @mastersthesis{Wrzodek2006, author = {Wrzodek, Clemens}, title = {Range queries in hierarchically structured peer-to-peer systems}, school = {University of Tuebingen}, year = {2006}, type = {Studienarbeit}, } @mastersthesis{Draeger2005, author = {Dr\"ager, Andreas}, title = {{Automatische und vergleichende Analyse bakterieller Genome mit Schwerpunkt auf \emph{Ralstonia}/\emph{Cupriavidus}-Arten sowie verwandten Proteobakerien}}, school = {Martin-Luther-Universit\"at Halle-Wittenberg}, year = {2005}, type = {Diplomarbeit}, address = {von-Seckendorff-Platz 1, 06120 Halle (Saale)}, month = dec, abstract = {Knowledge generation by comparative genomics become more and more meaningful due to the increased availability of genomic sequence data. This thesis compares the genomes of $\beta$-proteobacteria, a taxonomic group of bacteria showing a high degree of diversity. Sequenced species of this group inhabit various ecological niches. Therefore, they need special features to surviving toxic heavy metal concentrations, to act as pathogens of plants or animals or to degrade organic substances, which are normally difficult to break down. These characteristic features are mediated by special proteins, leading to the question, if characteristic proteins can be detected automatically by comparing the sequences of related proteins of different species. By comparison of highly conserved proteins with essential life functions in a taxonomic context a measurement should be developed to normalize later on comparison of these specialized proteins. The taxonomic context of different bacterial species can be derived from comparisons of the highly conserved genes for the 16 S rRNA, which is involved in the protein synthesis of bacteria. To perform those comparisons different algorithms have been released. For global alignments the Needleman-Wunsch algorithm or a special Hidden Markov Model can be used. Local alignments can be done by the Smith-Waterman algorithm or its heuristic approximation BLAST. Global alignments compare whole sequences, whereas local alignments find longest conserved regions in two sequences. Proteins contain functional regions (domains) surrounded by less important regions, so that these can be compared by local alignments. The complete 16 S rRNA sequence is essential for its functionality, so that for taxonomic analysis global alignments are needed. To evaluate the quality of alignments different substitutions matrices like BLOSUM, PAM, NUC contain scores for the substitution of a symbol with another one. The sum of these scores is the score of the alignment. Several online database servers like NCBI, RDP, EMBL, JGI, SwissProt, Tigr and many others provide genomic and proteomic sequence data of different species. These databases grow at an exponential rate, because new techniques of sequencing proteins and genetic elements in high throughput analysis are used and data can be uploaded by individual authors, laboratories or other scientific institutions. However, to use these data to perform comparative local analysis, an efficient way of storage has to be found. Problems of data storage occur due to the different naming conventions of species, genes, proteins and other biological data. To maintain the data consistently without redundancy, a database server was installed using MySQL. As a relation scheme BioSQL was used. To integrate downloaded data into the local database different pre-processing steps (data cleaning) were necessary. A client program to compare the locally stored data was implemented in Java, using the open source library BioJava. The resulting database application also provides interactive visualizations of the data in the database such as the taxonomic tree and genetic annotations. It contains a graphical user interface to interact with BioSQL without knowledge of databases. In addition, different file formats of biological sequence data can be converted into each other. With a special dialog global and local sequence alignments can be performed interactively. The BioJava library had to be extended to provide the full functionality of that program. This application was used on a selection of essential proteins (involved in DNA transcription and translation) of 15 $\beta$-proteobacteria and 7 $\gamma$-proteobacteria and non essential proteins (involved in heavy metal resistance) and the 16 S rRNA genes. All comparisons are relative to the well investigated species \emph{Escherichia coli} K12. Plotting the protein similarity against the taxonomic neighborhood shows an almost linear increase for essential proteins with taxonomic nearness. The other proteins show higher variability. This leads to the conclusion that proteins with special features are less conserved than highly essential proteins, so that these can be detected from the taxonomic context by normalization with essential proteins.}, pdf = {https://nirvana.informatik.uni-halle.de/~molitor/Diplomarbeiten/2005/draeger_andreas.pdf}, } @inproceedings{2005_19, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Sinzger, Christian and Eberhard, Kathrin and Zell, Andreas}, title = {Predicting Single Genes Related to Immune-Relevant Processes}, booktitle = {IEEE Symposium on Computational Intelligence and Computational Biology}, year = {2005}, pages = {461-468}, address = {San Diego, USA}, month = nov, publisher = {IEEE Press}, abstract = {In this paper we address the problem of predicting gene activities by finding gene regulatory dependencies in experimental DNA microarray data. Only few approaches to infer the dependencies of complete gene interconnectivity networks can be found in the literature. Due to the limited number of available data, the inferring problem is under-determined and ambiguous. Therefore, we introduce a new algorithm to infer relationships only between selected genes and the unknown gene network. This method is able to predict gene activation by mathematical modeling of the network and its simulation. The parameters of the mathematical model are determined by optimization with evolutionary algorithms. In this paper we will show that our approach is able to correctly predict gene responses in immune related regulatory processes and correctly identify some of the true genomic relationships of these genes.}, isbn = {0-7803-9387-2}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05single.pdf} } @inproceedings{2005_20, author = {Spieth, Christian and Streichert, Felix and Supper, Jochen and Speer, Nora and Zell, Andreas}, title = {Feedback Memetic Algorithms for Modelling Gene Regulatory Networks}, booktitle = {IEEE Symposium on Computational Intelligence and Computational Biology}, year = {2005}, pages = {61-67}, address = {San Diego, USA}, month = nov, publisher = {IEEE Press}, abstract = {In this paper we address the problem of finding gene regulatory networks from experimental DNA microarray data. We focus on the evaluation of the performance of memetic algorithms on the inference problem. These algorithms are used to evolve an underlying quantitative mathematical model. The dynamics of the regulatory system are modeled with two commonly used approaches, namely linear weight matrices and S-systems. Due to the complexity of the inference problem, some researchers suggested evolutionary algorithms for this purpose. We introduce memetic enhancements to this optimization process to infer the parameters of sparsely connected nonlinear systems from the observed data. Due to the limited number of available data, the inferring problem is underdetermined and ambiguous. Further on, the problem often is multimodal and therefore appropriate optimization strategies become necessary. We propose a memetic method, which separates the overall inference problem into two subproblems to find the correct network: first, the search for a valid topology, and secondly, the optimization of the parameters of the mathematical model. The performance and the properties of the proposed methods are evaluated and compared to standard algorithms found in the literature.}, isbn = {0-7803-9387-2}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05feedback.pdf} } @article{2005_18, author = {Stefan, Norbert and Machicao, Fausto and Staiger, Harald and Machann, J. and Schick, F. and Tschritter, Otto and Spieth, Christian and Weigert, Cora and Fritsche, Andreas and Stumvoll, M. and H\"aring, Hans-Ulrich}, title = {Polymorphisms in the gene encoding adiponectin receptor 1 are associated with insulin resistance and high liver fat}, journal = {Diabetologia}, year = {2005}, volume = {48}, pages = {2282-2291}, number = {11}, month = nov, abstract = {AIMS/HYPOTHESIS: The adipokine adiponectin has insulin-sensitising, anti-atherogenic and anti-inflammatory properties. Recently, the genes for mouse and human adiponectin receptor-1 (ADIPOR1) and -2 (ADIPOR2) have been cloned. The aim of this study was to investigate whether genetic variants of the genes encoding ADIPOR1 and ADIPOR2 play a role in human metabolism. MATERIALS AND METHODS: We screened ADIPOR1 and ADIPOR2 for polymorphisms and determined their association with glucose metabolism, lipid metabolism, an atherogenic lipid profile and inflammatory markers in 502 non-diabetic subjects. A subgroup participated in a longitudinal study; these subjects received diet counselling and increased their physical activity. RESULTS: We identified six variants of ADIPOR1 and seven variants of ADIPOR2. A single-nucleotide polymorphism (SNP) in the putative promoter region 8503 bp upstream of the translational start codon (-8503 G/A) of ADIPOR1 (frequency of allele A=0.31) was in almost complete linkage disequilibrium with another SNP (-1927 T/C) in intron 1. Subjects carrying the -8503 A and -1927 C alleles had lower insulin sensitivity, as estimated from a 75 g OGTT (p=0.04) and determined during a euglycaemic clamp (n=295, p=0.04); they also had higher HbA(1)c levels (p=0.02) and, although the difference was not statistically significant, higher liver fat (n=85, determined by proton magnetic resonance spectroscopy, p=0.056) (all p values are adjusted for age, sex and percentage of body fat). In the longitudinal study (n=45), the -8503 A and -1927 C alleles were associated with lower insulin sensitivity (p=0.03) and higher liver fat (p=0.02) at follow-up compared with the -8503 G and -1927 T alleles, independently of basal measurements, sex and baseline and follow-up percentage of body fat. CONCLUSIONS/INTERPRETATION: The present findings suggest that the -8503 G/A SNP in the promoter or the -1927 T/C SNP in intron 1 of ADIPOR1 may affect insulin sensitivity and liver fat in humans.}, doi = {10.1007/s00125-005-1948-3}, keywords = {Adipose Tissue/pathology Adult Body Fat Distribution Cross-Sectional Studies Diabetes Mellitus, Type 2/*genetics/pathology Female Gene Frequency Genetic Predisposition to Disease Germany Humans Insulin Resistance/*genetics Introns Lipids/chemistry Liver/*pathology Longitudinal Studies Male Middle Aged *Polymorphism, Single Nucleotide Promoter Regions, Genetic Receptors, Adiponectin Receptors, Cell Surface/*genetics}, } @inproceedings{2005_22, author = {Supper, Jochen and Spieth, Christian and Zell, Andreas}, title = {Reverse Engineering Non-Linear Gene Regulatory Networks Based on the Bacteriophage lambda cI Circuit}, booktitle = {Proceedings of the 2005 IEEE Symposium on Computational Intelligence and Computational Biology (CIBCB '05)}, year = {2005}, pages = {325-332}, address = {San Diego, USA}, month = nov, publisher = {IEEE}, abstract = {The ability to measure the transcriptional response of cells has drawn much attention to the underlying transcriptional networks. To untangle the network, numerous models with corresponding reverse engineering methods have been applied. In this work, we propose a non-linear model with adjustable degrees of complexity. The corresponding reverse engineering method uses a probabilistic scheme to reduce the reconstruction problem to subnetworks. Adequate models for gene regulatory networks must be anchored on sufficient biological knowledge. Here, the cI auto-inhibition circuit (cI circuit) is used to validate our reverse engineering method. Simulations of the cI circuit are used for the reconstruction, whereas a simplified cI circuit model assists the modeling phase. Several levels of complexity are evaluated, subsequently the reconstructed models show different properties. As a result, we reconstruct an abstract model, capturing the dynamic behavior of the cI circuit to a high degree.}, doi = {10.1109/CIBCB.2005.1594936}, isbn = {0-7803-9387-2}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/Supper05reveng.pdf} } @inproceedings{2005_123, author = {Tamimi, Hashem and Zell, Andreas}, title = {Global Robot localization using Iterative Scale Invariant Feature Transform}, booktitle = {36th International Symposium Robotics (ISR 2005)}, year = {2005}, volume = {36}, pages = {142-149}, address = {Tokyo, Japan}, month = nov, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/tamimi05-isr2.pdf} } @inproceedings{2005_124, author = {Tamimi, Hashem and Zell, Andreas}, title = {Using Scale Space Image Histograms for Global Localization of Mobile Robots}, booktitle = {36th International Symposium Robotics (ISR 2005)}, year = {2005}, volume = {36}, pages = {143-150}, address = {Tokyo, Japan}, month = nov, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/tamimi05-isr1.pdf} } @inproceedings{2005_25, author = {Speer, Nora and Spieth, Christian and Zell, Andreas}, title = {Spectral Clustering Gene Ontology Terms to Group Genes by Function}, booktitle = {Algorithms in Bioinformatics, 5th InternationalWorkshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings}, year = {2005}, editor = {Rita Casadio and Gene Myers}, volume = {3692}, series = {Lecture Note in Computer Science}, pages = {1-12}, address = {Palma, Spain}, month = oct, publisher = {Springer}, abstract = {With the invention of biotechnological high throughput methods like DNA microarrays, biologists are capable of producing huge amounts of data. During the analysis of such data the need for a grouping of the genes according to their biological function arises. In this paper, we propose a method that provides such a grouping. As functional information, we use Gene Ontology terms. Our method clusters all GO terms present in a data set using a Spectral Clustering method. Then, mapping the genes back to their annotation, genes can be associated to one or more clusters of defined biological processes. We show that our Spectral Clustering method is capable of finding clusters with high inner cluster similarity.}, doi = {10.1007/11557067_1}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/speer05-wabi.pdf} } @inproceedings{2005_23, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Inferring Regulatory Systems with Noisy Pathway Information}, booktitle = {Proceedings of the German Conference on Bioinformatics (GCB 2005)}, year = {2005}, volume = {71}, series = {LNI}, pages = {193-203}, address = {Hamburg, Germany}, month = oct, publisher = {GI}, isbn = {3-88579-400-4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05inferring.pdf} } @inproceedings{Streichert05Hybrid, author = {Felix Streichert and Holger Ulmer and Andreas Zell}, title = {Hybrid Representations for Composition Optimization and Parallelizing MOEAs}, booktitle = {Practical Approaches to Multi-Objective Optimization}, year = {2005}, editor = {J\"urgen Branke and Kalyanmoy Deb and Kaisa Miettinen and Ralph E. Steuer}, number = {04461}, series = {Dagstuhl Seminar Proceedings}, month = aug, publisher = {Internationales Begegnungs- und Forschungszentrum (IBFI), Schloss Dagstuhl, Germany}, abstract = {In many real-world optimization problems sparse solution vectors are often preferred. Unfortunately, evolutionary algorithms can have problems to eliminate certain components completely, especially in multi-modal or neutral search spaces. A simple extension of the real-valued representation enables evolutionary algorithms to solve these types of optimization problems more efficiently. In case of multi-objective optimization some of these compositional optimization problems show most peculiar structures on the Pareto front. Here, the Pareto front is often non-convex and consists of multiple local segments. This feature invites parallelization based on the 'divide and conquer' principle, since subdivision into multiple local multi-objective optimization problems seems to be feasible. Therefore, we introduce a new parallelization scheme for multi-objective evolutionary algorithms based on clustering.}, url = {http://drops.dagstuhl.de/opus/volltexte/2005/251} } @inproceedings{2005_121, author = {Wang, Maosen and Tamimi, Hashem and Zell, Andreas}, title = {{Robot Navigation Using Biosonar for Natural Landmark Tracking}}, booktitle = {IEEE International Symposium on Computational Intelligence in Robotics and Automation (CIRA 2005)}, year = {2005}, pages = {3--7}, address = {Espoo, Finland}, month = jun, publisher = {IEEE Press}, abstract = {A biosonar based mobile robot navigation system is presented for the natural landmark classification using acoustic image matching. The aim of this approach is to take advantage of the perceived properties of bats' prey and landmark identification mechanisms for mobile robots' tracking of natural landmarks. Recognizing natural landmarks like trees through sequential echolocation and acoustic image analyzing allows mobile robot to update its location in the natural environment. In this work, a working implementation of the biosonar system on a mobile robot is shown. It collects sequential echoes to produce acoustic images through digital signal processing (DSP), then compresses images with discrete cosine transform or pyramid algorithm. Fast normalized cross correlation (FNCC) and kernel principal component analysis (KPCA) are respectively used to make the final classification. Experimental result indicates that a mobile robot can achieve the ability of natural landmark classification only based on biomemetic sonar, the topological congruency of the relational structure with cross correlation in acoustic images is reliable in time domain, while the kernel principle component analysis based classification is robust in frequency domain and demands fewer echolocation for landmark classification.}, doi = {10.1109/CIRA.2005.1554246}, isbn = {0-7803-9355-4}, keywords = {image classification, mobile robots, path planning, robot vision, sonar detection, sonar target recognition, sonar tracking}, url = {http://dx.doi.org/10.1109/CIRA.2005.1554246} } @inproceedings{2005_261, author = {Wang, Maosen and Zell, Andreas}, title = {{Sequential sensing with Biosonar for natural landmark classification}}, booktitle = {Safety, Security and Rescue Robotics, Workshop, 2005 IEEE International}, year = {2005}, pages = {137--142}, address = {Kobe, Japan}, month = jun, publisher = {IEEE Press}, abstract = {Echolocating bats can make nocturnal flights in acoustically cluttered environments with the use of echolocation. Their ability to evaluate targets in complete darkness provides mobile robots an opportunity to learn target detection, classification and identification with similar biomimetic platforms. In this work, natural landmark classification with a binaural system, a sequential sensing strategy and a frequency after reconstruction algorithm were developed and tested. The aim of the work is to overcome some inherent shortcomings of airborne sonar and take advantage of bats' perceived properties for mobile robots' navigation in natural environments. Experimental results suggest considerable improvements in classification accuracy can be achieved by the use of this sequential classification method.}, doi = {10.1109/SSRR.2005.1501230}, isbn = {0-7803-8945-x}, keywords = {mobile robots, mobile robots, navigation, remote sensing, signal reconstruction, sonar detection}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/wang_1006.pdf}, url = {http://dx.doi.org/10.1109/SSRR.2005.1501230} } @inproceedings{Kron05GI, author = {Bronni, Jan and Hofmann, Stefanie and Kronfeld, Marcel and Monger, Andreas}, title = {{Eine strategieorientierte, modulare Simulationsumgebung f\"ur mobile Ad-Hoc-Szenarien}}, booktitle = {Informatiktage 2005}, year = {2005}, address = {Bonn, Germany}, month = apr, publisher = {Gesellschaft f\"ur Informatik (GI)}, } @techreport{2005_70, author = {Streichert, Felix and Ulmer, Holger}, title = {{JavaEvA}: a {Java} based framework for Evolutionary Algorithms}, institution = {Center for Bioinformatics Tuebingen (ZBIT) of the Eberhard Karls University, Tuebingen, Germany}, year = {2005}, number = {WSI-2005-06}, month = apr, abstract = {The package JavaEvA (a Java implementation of Evolutionary Algorithms) is a general modular framework with an inherent client server structure to solve practical optimization problems. This package was especially designed to test and develop new approaches for Evolutionary Algorithms and to utilize them in real-world applications. JavaEvA already provides implementations of the most common Evolutionary Algorithms, like Genetic Algorithms, CHC Adaptive Search, Population Based Incremental Learning, Evolution Strategies, Model-Assisted Evolution Strategies, Genetic Programming and Grammatical Evolution. In addition the modular framework of JavaEvA allows everyone to add their own optimization modules to meet their specific requirements. The JavaEvA package uses a generic GUI framework that allows GUI access to any member of a class if get and set methods are provided and an editor is defined for the given data type. This approach allows very fast development cycles, since hardly any additional effort is necessary for implementing GUI elements, while still at the same time user specific GUI elements can be developed and integrated to increase usability. Since we cannot anticipate specific optimization problem and requirements, it is necessary for users to define their optimization problem. Therefore, we provide an additional framework and explain how one can include JavaEvA in an existing Java project or how one can implement ones own optimization problem and optimize it by using JavaEvA. This gives users total control of the optimization algorithms used.}, url = {http://w210.ub.uni-tuebingen.de/dbt/volltexte/2005/1702/} } @inproceedings{2005_33, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Multi-Objective Model Optimization for Inferring Gene Regulatory Networks}, booktitle = {Conference on Evolutionary Multi-Criterion Optimization (EMO 2005)}, year = {2005}, editor = {Carlos A. Coello Coello and Arturo Hern{\'a}ndez Aguirre and Eckart Zitzler}, volume = {3410}, series = {Lecture Notes in Computer Science}, pages = {607-620}, address = {Guanajuato, Mexico}, month = mar, publisher = {Springer}, isbn = {3-540-24983-4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05multiobjective.pdf} } @inproceedings{2005_118, author = {Streichert, Felix and Ulmer, Holger and Zell, Andreas}, title = {Parallelization of multi-objective evolutionary algorithms using clustering algorithms}, booktitle = {Conference on Evolutionary Multi-Criterion Optimization (EMO 2005)}, year = {2005}, editor = {Carlos A. Coello Coello and Arturo Hern{\'a}ndez Aguirre and Eckart Zitzler}, volume = {3410}, series = {Lecture Notes in Computer Science}, pages = {92--107}, address = {Guanajuato, Mexico}, month = mar, publisher = {Springer}, isbn = {3-540-24983-4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/streichert05parallelization.pdf} } @inproceedings{2005_125, author = {Tamimi, Hashem and Halawani, Alaa and Burkhardt, Hans and Zell, Andreas}, title = {Using Descriptive Image Features for Global Localization of Mobile Robots}, booktitle = {19th Autonomous Mobile Systems (AMS 2005)}, year = {2005}, series = {Informatik aktuell}, pages = {139-145}, address = {Stuttgart, Germany}, month = mar, publisher = {Springer}, abstract = {In this paper descriptive visual features based on integral invariants are proposed to solve the global localization of indoor mobile robots. These descriptive features are locally extracted by applying a set of non-linear kernel functions around a set ofinterest points in the image. To investigate the approach thoroughly, we use a set of Images taken by re-assigning the robot Position many times near a set of reference locations. Also, the presence of Illumination variations is encountered many times inthe Images. Compared to a wellknown approach, our approach has better localization rate with moderate computational overhead.}, doi = {10.1007/3-540-30292-1_18}, isbn = {978-3-540-30291-9}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/tamimi05-ams.pdf} } @article{2005_7, author = {Wegner, J\"org K. and Sieker, Florian and Zell, Andreas}, title = {Relevance of feature selection for clustering molecules}, journal = {Abstracts of Papers American Chemical Society (229th National Meeting of the American-Chemical-Society)}, year = {2005}, volume = {229}, pages = {U612}, number = {Part 1}, month = mar, abstract = {We present an extensive study to classify and cluster four different activity classes (5HT1A antagonists, thrombin inhibitors, MAO inhibitors and H2 antagonists) by using four different feature selection algorithms, ten different classification algorithms and three clustering algorithms. We show that depending on the used number of features the generalization ability of the results varies dramatically for clustering compounds. The number of features used was based on the previous feature selection results. The classification rates ranges from 85% up to 97%, which are much better than the clustering confusion matrix results. Finally, we conclude the work with presenting a new approch avoiding the feature selection dilemma.}, address = {San Diego, CA, USA}, } @article{2005_6, author = {Wegner, J\"org K. and Zell, Andreas}, title = {Difference in vector based and graph based coding for {ADME} prediction}, journal = {Abstracts of Papers American Chemical Society (229th National Meeting of the American-Chemical-Society)}, year = {2005}, volume = {229}, pages = {U608}, number = {Part 1}, month = mar, abstract = {We present an extensive study to build classification and regression models using five different ADMET data sets (HIA, LogP, LogS, BBB, and two toxicological data sets causing cancer in rats and mice). We compare especially the relevance of vector based coding for molecules using descriptors and fingerprints and a coordinate-free coding working directly on the molecular structures avoiding a temporary abstract vector representation. We see that the vector coding can be used for large data sets by loosing accuracy and the coordinate-free approach avoids the feature selection problem, but is only applicable for smaller data sets. Furthermore we discuss shortly the underlying space and time complexities.}, address = {San Diego, CA, USA}, } @article{2005_27, author = {Fr\"ohlich, Holger and Wegner, J\"org K. and Sieker, Florian and Zell, Andreas}, title = {Kernel Functions for Attributed Molecular Graphs - A New Similarity Based Approach To {ADME} Prediction in Classification and Regression}, journal = {QSAR \& Combinatorial Science}, year = {2005}, volume = {25}, pages = {317-326}, number = {4}, abstract = {Kernel methods, like the well-known Support Vector Machine (SVM), have received growing attention in recent years for designing QSAR models that have a high predictive strength. One of the key concepts of SVMs is the usage of a so-called kernel function, which can be thought of as a special similarity measure. In this paper we consider kernels for molecular structures, which are based on a graph representation of chemical compounds. The similarity score is calculated by computing an optimal assignment of the atoms from one molecule to those of another one, including information on specific chemical properties, membership to a substructure (e.g., aromatic ring, carbonyl group, etc.) and neighborhood for each atom. We show that by using this kernel we can achieve a generalization performance comparable to a classical model with a few descriptors, which are a-priori known to be relevant for the problem, and significantly better results than with and without performing an automatic descriptor selection. For this purpose we investigate ADME classification and regression datasets for predicting bioavailability (Yoshida), Human Intestinal Absorption (HIA), Blood-Brain-Barrier (BBB) penetration and a dataset consisting of four different inhibitor classes (SOL). We further explore the effect of combining our kernel with a problem-dependent descriptor set. We also demonstrate the usefulness of an extension of our method to a reduced graph representation of molecules, in which certain structural features, like, e.g., rings, donors or acceptors, are represented as a single node in the molecular graph.}, doi = {10.1002/qsar.200510135}, issn = {1611020X}, publisher = {Wiley}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/froehlich05QSAR&CombSci.pdf} } @inproceedings{2005_28, author = {Fr\"ohlich, Holger and Wegner, J\"org K. and Sieker, Florian and Zell, Andreas}, title = {Optimal Assignment Kernels For Attributed Molecular Graphs}, booktitle = {International Conference on Machine Learning (ICML 2005)}, year = {2005}, pages = {252-232}, address = {Bonn, Germany}, publisher = {ACM Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/froehlich05OAKernels.pdf} } @inproceedings{2005_29, author = {Fr\"ohlich, Holger and Wegner, J\"org K. and Zell, Andreas}, title = {Assignment Kernels For Chemical Compounds}, booktitle = {International Joint Conference on Neural Networks (IJCNN 2005)}, year = {2005}, pages = {913-918}, address = {Montreal, Canada}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/froehlich05ChemKernels.pdf} } @inproceedings{2005_31, author = {Fr\"ohlich, Holger and Wegner, J\"org K. and Zell, Andreas}, title = {Efficient Parameter Selection for Support Vector Machines in Classification and Regression via Model-Based Global Optimization}, booktitle = {International Joint Conference on Neural Networks (IJCNN 2005)}, year = {2005}, pages = {1431-1438}, address = {Montreal, Canada}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/froehlich05ParamSelSVM.pdf} } @inproceedings{2005_127, author = {Heinemann, Patrick and Haase, J\"urgen and Zell, Andreas}, title = {{Verbesserte Effizienz der Monte-Carlo-Lokalisierung im RoboCup}}, booktitle = {Autonome Mobile Systeme: 19. Fachgespr\"ach Stuttgart, 8./9. Dezember 2005}, year = {2005}, pages = {19-24}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/heinemann05verbesserte.pdf } } @inproceedings{2005_260, author = {Heinemann, Patrick and Treptow, Andr\'{e} and Zell, Andreas}, title = {The {Attempto} {T\"ubingen} Robot Soccer Team}, booktitle = {RoboCup-2004: Robot Soccer World Cup VIII}, year = {2005}, editor = {Nardi, D. and Riedmiller, M. and Sammut, C. and Santos-Victor, J}, volume = {3276 (CD supplement)}, series = {Lecture Notes in Computer Science}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/heinemann05attempto.pdf} } @inproceedings{2005_119, author = {Lilienthal, Achim and Streichert, Felix and Zell, Andreas}, title = {Model-based shape analysis of gas concentration gridmaps for improved gas source localisation}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA 2005)}, year = {2005}, pages = {3575-3580}, address = {Barcelona, Spain}, publisher = {IEEE}, } @inproceedings{Schuetze05, author = {Sch\"{u}tze, Niels and de Paly, Michael and W\"{o}hling, Thomas and Schmitz, Gerd}, title = {Global optimisation of deficit irrigation systems using evolutionary algorithms and neural networks}, booktitle = {Proceedings of the ICID 21st European Regional Conference 2005, Integrated Land and Water Resources Management Towards Sustainable Rural Development}, year = {2005}, address = {Frankfurt (Oder), Germany and Slubice, Poland}, } @inproceedings{2005_21, author = {Speer, Nora and Fr\"ohlich, Holger and Spieth, Christian and Zell, Andreas}, title = {Functional Distances for Genes Based on {GO} Feature Maps and their Application to Clustering}, booktitle = {IEEE Symposium on Computational Intelligence and Computational Biology}, year = {2005}, pages = {142-149}, address = {San Diego, USA}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/Speer05goclust.pdf} } @inproceedings{2005_32, author = {Speer, Nora and Fr\"ohlich, Holger and Spieth, Christian and Zell, Andreas}, title = {Functional Grouping of Genes Using Spectral Clustering and Gene Ontology}, booktitle = {International Joint Conference on Neural Networks (IJCNN 2005)}, year = {2005}, pages = {298-303}, address = {Montreal, Canada}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/speer05-ijcnn.pdf} } @inproceedings{2005_26, author = {Speer, Nora and Spieth, Christian and Zell, Andreas}, title = {Biological Cluster Validity Indices Based on the Gene Ontology}, booktitle = {Advances in Intelligent Data Analysis VI, 6th International Symposium on Intelligent Data Analysis, IDA 2005, Madrid, Spain, September 8-10, 2005, Proceedings}, year = {2005}, editor = {A. Fazel Famili and Joost N. Kok and Jos{\'e} Mar\'{\i}a Pe{\~n}a and Arno Siebes and A. J. Feelders}, volume = {3646}, series = {Lecture Notes in Computer Science}, pages = {429-439}, address = {Madrid, Spain}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/speer05-ida.pdf} } @inproceedings{2005_30, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Identifying Valid Solutions for the Inference of Regulatory Networks}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO 2005)}, year = {2005}, pages = {469-471}, address = {Washington, USA}, publisher = {ACM Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05identifying.pdf} } @inproceedings{Spieth2005ClusteringApproach, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Clustering-based Approach to Identify Solutions for the Inference of Regulatory Networks}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2005)}, year = {2005}, pages = {660-667}, address = {Edinburgh, UK}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/spieth05clustering.pdf} } @article{2005_17, author = {Tschritter, Otto and Machicao, Fausto and Stefan, Norbert and Sch\"afer, Silke and Weigert, Cora and Staiger, Harald and Spieth, Christian and H\"aring, Hans-Ulrich and Fritsche, Andreas}, title = {A new variant in the human {Kv1.3} gene is associated with low insulin sensitivity and impaired glucose tolerance}, journal = {Journal of Clinical Endocrinology \& Metabolism}, year = {2005}, volume = {91}, pages = {654-658}, number = {2}, abstract = {CONTEXT: The voltage-gated potassium channel Kv1.3 (KCNA3) is expressed in a variety of tissues including liver and skeletal muscle. In animal models, knockout of Kv1.3 has been found to improve insulin sensitivity and glucose tolerance. OBJECTIVE: We examined whether mutations in the Kv1.3 gene exist in humans and whether they are associated with alterations of glucose homeostasis. DESIGN AND SETTING: We conducted a genotype-phenotype association study at a university hospital. PARTICIPANTS AND METHODS: In 50 nondiabetic subjects, we screened approximately 4.5 kb of chromosome 1 comprising the single exon, the promoter/5'-untranslated region, and the 3'-untranslated region of the human Kv1.3 gene for mutations by direct sequencing. Subsequently, all identified single-nucleotide polymorphisms were analyzed in 552 nondiabetic subjects who underwent an oral glucose tolerance test (OGTT). Of these, 304 had undergone an additional hyperinsulinemic euglycemic clamp. MAIN OUTCOME MEASURES: We assessed postprandial blood glucose during OGTT and insulin sensitivity measured by hyperinsulinemic euglycemic clamp. RESULTS: We identified five single-nucleotide polymorphisms in the promoter region (T-548C, G-697T, A-845G, T-1645C, and G-2069A) with allelic frequencies of the minor allele of 26, 23, 9, 41, and 16%, respectively. The -1645C allele was associated with higher plasma glucose concentrations in the 2-h OGTT (P = 0.03) even after adjustment for sex, age, and body mass index (P = 0.002). In addition, it was associated with lower insulin sensitivity (P = 0.01, adjusted for sex, age, and body mass index). Functional in vitro analysis using EMSA showed differential transcription factor binding to the T-1645C polymorphism. CONCLUSIONS: We show that a variant in the promoter of the Kv1.3 gene is associated with impaired glucose tolerance and lower insulin sensitivity. Therefore, the Kv1.3 channel represents a candidate gene for type 2 diabetes.}, keywords = {3' Untranslated Regions/chemistry/genetics 5' Untranslated Regions/chemistry/genetics Adult Blood Glucose/metabolism DNA/chemistry/genetics Electrophoretic Mobility Shift Assay Female Glucose Intolerance/*genetics/physiopathology Glucose Tolerance Test Humans Insulin Resistance/*genetics/physiology Kv1.3 Potassium Channel/*genetics/physiology Male Polymerase Chain Reaction Polymorphism, Single Nucleotide Promoter Regions, Genetic/genetics/physiology Sequence Analysis, DNA}, } @inproceedings{2005_126, author = {Weiss, Christian and Zell, Andreas}, title = {Automatic Generation of Indoor {VR}-Models by a Mobile Robot with a Laser Range Finder and a Color Camera}, booktitle = {Autonome Mobile Systeme (AMS 2005)}, year = {2005}, pages = {107-113}, address = {Stuttgart, Germany}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2005/weiss05ams.pdf} } @article{2004_142, author = {Wang, Maosen and Zell, Andreas}, title = {Classification of natural landmark with biosonar}, journal = {Journal of the Acoustical Society of America}, year = {2004}, volume = {116}, pages = {2640}, number = {4}, month = oct, abstract = {Echolocating bats can make nocturnal flights in acoustically cluttered environments with the use of echolocation. Their marvelous ability to evaluate natural targets in complete darkness provides us an opportunity to learn target detection, classification, and identification with similar biomimetic platforms. In this work, natural landmark classification with a binaural system, a sequential sensing strategy, and a frequency after reconstruction algorithm are adopted to provide sequential acoustic images for target classification. Experimental results suggest that considerable improvements in classification accuracy can be achieved by the use of this sequential classification method.}, url = {http://link.aip.org/link/?JASMAN/116/2640/1} } @inproceedings{2004_138, author = {Tamimi, Hashem and Zell, Andreas}, title = {Vision based Localization of Mobile Robots using Kernel approaches}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2004)}, year = {2004}, volume = {4}, pages = {1-6}, address = {Sendai, Japan}, month = sep, abstract = {The aim of this article is to present the potential of Kernel Principal Component Analysis (Kernel PCA) in the field of vision based robot localization. Using Kernel PCA we can extract features from the visual scene of a mobile robot. The analysis is applied only to local features so as to guarantee better computational performance as well as translation invariance. Compared with the classical Principal Component Analysis (PCA), Kernel PCA results show superiority in localization and robustness in presence of noisy scenes. The key success of the kernel PCA is the use of fractional power polynomial kernels.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/tamimi04-iros04.pdf} } @inproceedings{2004_58, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Optimizing Topology and Parameters of Gene Regulatory Network Models from Time-Series Experiments}, booktitle = {Genetic and Evolutionary Computation (GECCO 2004)}, year = {2004}, volume = {3102}, pages = {461-470}, address = {Seattle, USA}, month = jun, publisher = {Springer}, abstract = {In this paper we address the problem of finding gene regulatory networks from experimental DNA microarray data. Different approaches to infer the dependencies of gene regulatory networks by identifying parameters of mathematical models like complex S-systems or simple Random Boolean Networks can be found in literature. Due to the complexity of the inference problem some researchers suggested Evolutionary Algorithms for this purpose. We introduce enhancements to the Evolutionary Algorithm optimization process to infer the parameters of the non-linear system given by the observed data more reliably and precisely. Due to the limited number of available data the inferring problem is under-determined and ambiguous. Further on, the problem often is multi-modal and therefore appropriate optimization strategies become necessary. We propose a new method, which evolves the topology as well as the parameters of the mathematical model to find the correct network.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/spieth04optimizing.pdf} } @inproceedings{2004_63, author = {Streichert, Felix and Planatscher, Hannes and Spieth, Christian and Ulmer, Holger and Zell, Andreas}, title = {Comparing Genetic Programming and Evolution Strategies on Inferring Gene Regulatory Networks}, booktitle = {Genetic and Evolutionary Computation (GECCO 2004)}, year = {2004}, volume = {3102}, series = {Lecture Notes in Computer Science}, pages = {471-480}, address = {Seattle, USA}, month = jun, publisher = {Springer}, abstract = {In recent years several strategies for inferring gene regulatory networks from observed time series data of gene expression have been suggested based on Evolutionary Algorithms. But often only few problem instances are investigated and the proposed strategies are rarely compared to alternative strategies. In this paper we compare Evolution Strategies and Genetic Programming with respect to their performance on multiple problem instances with varying parameters. We show that single problem instances are not sufficient to prove the effectiveness of a given strategy and that the Genetic Programming approach is less prone to varying instances than the Evolution Strategy.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/streichert04comparing.pdf} } @inproceedings{2004_130, author = {Mojaev, Alexander and Zell, Andreas}, title = {Tracking Control and Adaptive Local Navigation for Nonholonomic Mobile Robot}, booktitle = {Intelligent Autonomous Systems (IAS-8)}, year = {2004}, pages = {521--528}, address = {Amsterdam, Netherlands}, month = mar, publisher = {IOS Press}, abstract = {A reactive tracking control law and a flexible local navigation method for non-holonomic mobile vehicles are presented. The tracking controller enables noise tolerant trajectory following and collision avoidance with a feedback control loop through raw sensor data (laser scanner, sonars, IR). The controller needs no knowledge about absolute robot coordinates. Based on the tracking control a local navigation method is described, which allows collision avoidance and flexible path search in a changing environment.}, } @article{2004_131, author = {Wegner, J\"org K. and Fr\"ohlich, Holger and Zell, Andreas}, title = {{Feature selection for Descriptor based Classification Models. 1. Theory and GA-SEC Algorithm}}, journal = {Journal of Chemical Information and Computer Science (JCICS)}, year = {2004}, volume = {44}, pages = {921--930}, number = {3}, month = feb, abstract = {The paper describes different aspects of classification models based on molecular data sets with the focus on feature selection methods. Especially model quality and avoiding a high variance on unseen data (overfitting) will be discussed with respect to the feature selection problem. We present several standard approaches and modifications of our Genetic Algorithm based on the Shannon Entropy Cliques (GA-SEC) algorithm and the extension for classification problems using boosting.}, doi = {10.1021/ci0342324}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/Wegner2004.pdf}, url = {http://dx.doi.org/10.1021/ci0342324} } @article{2004_65, author = {Wegner, J\"org K. and Fr\"ohlich, Holger and Zell, Andreas}, title = {{Feature selection for Descriptor based Classification Models. 2. Human intestinal absorption (HIA)}}, journal = {Journal of Chemical Information and Computer Science (JCICS)}, year = {2004}, volume = {44}, pages = {931--939}, number = {3}, month = feb, abstract = {We show that the topological polar surface area (TPSA) descriptor and the radial distribution function (RDF) applied to electronic and steric atom properties, like the conjugated electrotopological state (CETS), are the most relevant features/descriptors for predicting the human intestinal absorption (HIA) out of a large set of 2934 features/descriptors. A HIA data set with 196 molecules with measured HIA values and 2934 features/descriptors were calculated using JOELib and MOE. We used an adaptive boosting algorithm to solve the binary classification problem (AdaBoost.M1) and Genetic Algorithms based on Shannon Entropy Cliques (GA-SEC) variants as hybrid feature selection algorithms. The selection of relevant features was applied with respect to the generalization ability of the classification model, avoiding a high variance for unseen molecules (overfitting).}, doi = {10.1021/ci034233w}, pdf = {http://www.cogsys.uni-tuebingen.de/publikationen/2004/Wegner2004b.pdf}, url = {http://dx.doi.org/10.1021/ci034233w} } @article{2004_128, author = {Bohn, E and M\"uller, S and Lauber, J and Geffers, R and Speer, Nora and Spieth, Christian and Krejci, J and Manncke, B and Buer, J and Zell, Andreas}, title = {Gene expression patterns of epithelial cells modulated by pathogenicity factors of Yersinia enterocolitica}, journal = {Cellular Microbiology}, year = {2004}, volume = {6}, pages = {129-141}, number = {2}, } @article{2004_51, author = {Fr\"ohlich, Holger and Wegner, J\"org K. and Zell, Andreas}, title = {Towards Optimal Descriptor Subset Selection with Support Vector Machines in Classification and Regression}, journal = {QSAR \& Combinatorial Science}, year = {2004}, volume = {23}, pages = {311-318}, number = {5}, url = {http://dx.doi.org/10.1002/qsar.200410011} } @inproceedings{2004_52, author = {Fr\"ohlich, Holger and Zell, Andreas}, title = {Feature Subset Selection for Support Vector Machines by Incremental Regularized Risk Minimization}, booktitle = {IEEE International Joint Conference on Neural Networks}, year = {2004}, volume = {3}, pages = {2041-2046}, address = {Budapest, Hungary}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/froehlich04_ijcnn.pdf} } @article{2004_143, author = {Heinemann, Patrick and Plagge, Michael and Treptow, Andr\'{e} and Zell, Andreas}, title = {Tracking Dynamic Objects in a RoboCup Environment - The Attempto T\"ubingen Robot Soccer Team}, journal = {RoboCup-2003: Robot Soccer World Cup VII, Lecture Notes in Computer Science (CD-Supplement). Springer Verlag}, year = {2004}, volume = {3020}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/heinemann04tracking.pdf} } @incollection{2004_144, author = {Heinemann, Patrick and R\"uckstie{\ss}, T and Zell, Andreas}, title = {Fast and Accurate Environment Modelling using Omnidirectional Vision}, booktitle = {Dynamic Perception: Workshop of the {GI} section "Computer Vision"}, publisher = {Akademische Verlagsgesellschaft AKA}, year = {2004}, editor = {Uwe J. Ilg and Heinrich H. B\"ulthoff and Hanspeter A. Mallot}, volume = {1}, pages = {9-14}, journal = {Dynamic Perception}, organization = {Eberhard Karls University Tuebingen, Max Planck Institute for Biological Cybernetics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/heinemann04fast.pdf} } @inproceedings{2004_139, author = {Lilienthal, Achim and Ulmer, Holger and Fr\"ohlich, Holger and St\"utzle, Andreas and Werner, Felix and Zell, Andreas}, title = {Gas Source Declaration with a Mobile Robot}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA 2004)}, year = {2004}, volume = {2}, address = {New Orleans, USA}, publisher = {IEEE}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/lilien04-icra2004_col.pdf} } @inproceedings{2004_137, author = {Mojaev, Alexander and Zell, Andreas}, title = {Real-Time Face Tracking using Discriminator Technique on Standard PC Hardware}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2004)}, year = {2004}, volume = {2}, pages = {1335--1339}, address = {Sendai, Japan}, } @inproceedings{Schuetze04, author = {Sch\"{u}tze, Niels and W\"{o}hling, Thomas and de Paly, Michael and Schmitz, Gerd}, title = {Meeting challenges of the Blue Revolution: increasing irrigation efficiency with soft-computing optimisation methods}, booktitle = {Workshop on Integrated Water Research and Water Management}, year = {2004}, pages = {92-95}, address = {Altmorschen (Kassel), Germany}, } @article{2004_54, author = {Schmollinger, M. and Fischer, Igor and Nerz, C. and Pinkenburg, S. and Gotz, F. and Kaufmann, Michael and Lange, Klaus J. and Reuter, R. and Rosenstiel, Wolfgang and Zell, Andreas}, title = {{ParSeq}: searching motifs with structural and biochemical properties}, journal = {Bioinformatics}, year = {2004}, volume = {20}, pages = {1459-1461}, number = {9}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/fischer04parseq.pdf} } @inproceedings{2004_55, author = {Speer, Nora and Spieth, Christian and Zell, Andreas}, title = {A Memetic Clustering Algorithm for the Functional Partition of Genes Based on the Gene Ontology}, booktitle = {IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology}, year = {2004}, pages = {252-259}, address = {San Diego, USA}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/speer04-cibcb2004.pdf} } @inproceedings{2004_56, author = {Speer, Nora and Spieth, Christian and Zell, Andreas}, title = {A Memetic Co-Clustering Algorithm for Gene Expression Profiles and Biological Annotation}, booktitle = {IEEE Congress on Evolutionary Computation}, year = {2004}, volume = {2}, pages = {1631-1638}, address = {Portland, USA}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/speer04-cec2004_col.pdf} } @inproceedings{2004_59, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {A Memetic Inference Method for Gene Regulatory Networks Based on S-Systems}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2004)}, year = {2004}, volume = {1}, pages = {152-157}, address = {Portland, USA}, publisher = {IEEE Press}, abstract = {In this paper we address the problem of finding gene regulatory networks from experimental DNA microarray data. As underlying mathematical model we used S-Systems, a quantitative model, which recently has found increased attention in the literature. Due to the complexity of the inference problem some researchers suggested Evolutionary Algorithms for this purpose. We introduce enhancements to this optimization process to infer the parameters of sparsely connected non-linear systems given by the observed data more reliably and precisely. Due to the limited number of available data the inferring problem is under-determined and ambiguous. Further on, the problem often is multi-modal and therefore appropriate optimization strategies become necessary. In this paper we propose a new method, which evolves the topology as well as the parameters of the mathematical model to find the correct network. This method is compared to standard algorithms found in the literature.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/spieth04optimizing.pdf} } @inproceedings{2004_60, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Utilizing an Island Model for EA to Preserve Solution Diversity for Inferring Gene Regulatory Networks}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2004)}, year = {2004}, volume = {1}, pages = {146-151}, address = {Portland, USA}, publisher = {IEEE Press}, abstract = {In this paper we address the problem of finding gene regulatory networks from artificial data sets of DNA microarray experiments. Some researchers suggested Evolutionary Algorithms for this purpose. We suggest to use an enhancement for Evolutionary Algorithms to infer the parameters of the non-linear system given by the observed data more reliably and precisely. At present, we use S-Systems because they are a general mathematical model for simulating the complex interactions of gene regulatory networks. Due to the limited number of available data, the inferring problem is highly under-determined and ambiguous. Further on, the problem often is highly multi-modal and therefore appropriate optimization strategies become necessary. We propose to use an island model to maintain diversity in the EA population to prevent premature convergence and to raise the probability of finding the global optimum.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/spieth04island.pdf} } @inproceedings{2004_61, author = {Spieth, Christian and Streichert, Felix and Speer, Nora and Zell, Andreas}, title = {Iteratively Inferring Gene Regulatory Networks with Virtual Knockout Experiments}, booktitle = {European Workshop on Evolutionary Bioinformatics (evoBIO)}, year = {2004}, volume = {3005}, series = {Lecture Notes in Computer Science}, pages = {102-111}, address = {Coimbra, Portugal}, publisher = {Springer}, abstract = {In this paper we address the problem of finding gene regulatory networks from experimental DNA microarray data. We introduce enhancements to an Evolutionary Algorithm optimization process to infer the parameters of the non-linear system given by the observed data more reliably and precisely. Due to the limited number of available data the inferring problem is under-determined and ambiguous. Further on, the problem often is multi-modal and therefore appropriate optimization strategies become necessary. Therefore, we propose a new method, which will suggest necessary additional biological experiments to remove the ambiguities.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/spieth04iteratively.pdf} } @inproceedings{2004_135, author = {Streichert, Felix and Spieth, Christian and Ulmer, Holger and Zell, Andreas}, title = {How to evolve the Head-Tail Pattern from Reaction-Diffusion Systems}, booktitle = {NASA/DoD Conference on Evolvable Hardware}, year = {2004}, pages = {261-268}, address = {Seattle, WA, USA}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/streichert04howtoevolve.pdf} } @inproceedings{2004_133, author = {Streichert, Felix and Ulmer, Holger and Zell, Andreas}, title = {Evaluating a Hybrid Encoding and Three Crossover Operators on the Constrained Portfolio Selection Problem}, booktitle = {Evolutionary Computation (CEC 2004)}, year = {2004}, volume = {1}, pages = {932-939}, address = {Portland, OR, USA}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/streichert04evaluating.pdf} } @inproceedings{2004_136, author = {Streichert, Felix and Ulmer, Holger and Zell, Andreas}, title = {Comparing Discrete and Continuous Genotypes on the Constrained Portfolio Selection Problem}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO 2004)}, year = {2004}, volume = {2}, series = {Lecture Notes in Computer Science}, pages = {1239-1250}, address = {Seattle, WA, USA}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/streichert04comparingdiscrete.pdf} } @inproceedings{2004_140, author = {Treptow, Andr\'{e} and Zell, Andreas}, title = {Combining Adaboost Learning and Evolutionary Search to select Features for Real-Time Object Detection}, booktitle = {IEEE Congress on Evolutionary Computation (CEC 2004)}, year = {2004}, volume = {2}, pages = {2107-2113}, address = {IEEE Congress on Evolutionary Computation (CEC 2004)}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/treptow/publications/treptow04-cec.pdf } } @article{2004_141, author = {Treptow, Andr\'{e} and Zell, Andreas}, title = {Real-Time Object Tracking for Soccer-Robots without Color Information}, journal = {Robotics and Autonomous Systems}, year = {2004}, volume = {48}, pages = {41-48}, number = {1}, } @inbook{ulmer04MAES, chapter = {Model Assisted Evolution Strategies}, pages = {333--358}, title = {Knowledge Incorporation in Evolutionary Computation}, publisher = {Springer}, year = {2004}, editor = {Jin, Yaochu}, author = {Holger Ulmer and Felix Streichert and Andreas Zell}, volume = {167}, series = {Studies in Fuzziness and Soft Computing Series}, isbn = {978-3-540-22902-5}, } @inproceedings{2004_134, author = {Ulmer, Holger and Streichert, Felix and Zell, Andreas}, title = {Evolution Strategies with Controlled Model Assistance}, booktitle = {Congress on Evolutionary Computation (CEC 2004)}, year = {2004}, volume = {2}, pages = {1569-1576}, address = {Portland, OR, USA}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2004/ulmer04evolution.pdf} } @inproceedings{Tamimi2003AMS, author = {Tamimi, Hashem and Zell, Andreas}, title = {Vision-based Global Localization of a Mobile Robot using Wavelet Features}, booktitle = {Proceedings of the 18th Autonomous Mobile Systems (AMS)}, year = {2003}, pages = {32-41}, month = dec, } @inproceedings{Streichert03CBN, author = {Streichert, Felix and Stein, Gunnar and Ulmer, Holger and Zell, Andreas}, title = {A Clustering Based Niching {EA} for Multimodal Search Spaces}, booktitle = {Evolution Artificielle 6th International Conference (EA 2003)}, year = {2003}, volume = {2936}, series = {Lecture Notes in Computer Science}, pages = {293-304}, address = {Marseille, France}, month = oct, publisher = {Springer}, abstract = {We propose a new niching method for Evolutionary Algorithms which is able to identify and track global and local optima in a multimodal search space. To prevent the loss of diversity we replace the global selection pressure within a single population by local selection of a multi-population strategy. The sub-populations representing species specialized on niches are dynamically identified using standard clustering algorithms on a primordial population. With this multi-population strategy we are able to preserve diversity within the population and to identify global/local optima directly without further post-processing.}, doi = {10.1007/b96080}, isbn = {3-540-21523-9}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/streichert03clustering.pdf}, url = {http://dx.doi.org/10.1007/b96080} } @mastersthesis{Draeger2003, author = {Dr\"ager, Andreas}, title = {{Suche h\"aufiger Proteinfragmente unter Ber\"ucksichtigung von Mutationen und L\"ucken}}, school = {Martin-Luther-Universit\"at Halle-Wittenberg}, year = {2003}, type = {Projektarbeit}, address = {von-Seckendorff-Platz 1, 06120 Halle (Saale)}, month = aug, abstract = {Bei Analysen biologischer Daten stellt die Suche nach h\"aufigen Teilsequenzen in Proteinsequenzen eine wichtige Fragestellung dar. In dieser Arbeit wird ein Algorithmus beschrieben, der aus gegebenen Proteinsequenzen alle h\"aufigen Muster fester L\"ange herausfindet. Es werden dabei nicht nur echte Teilsequenzen betrachtet, sondern auch allgemeinere Muster, bei denen einzelne Zeichen variieren d\"urfen. Dieses Vorgehen wird im Folgenden vorgestellt, und unter verschiedenen Aspekten durchgef\"uhrte Laufzeitmessungen werden pr\"asentiert.}, } @inproceedings{2003_158, author = {Wandel, Michael R. and Lilienthal, Achim and Duckett, Tom and Weimar, Udo and Zell, Andreas}, title = {{Gas Distribution in Unventilated Indoor Environments Inspected by a Mobile Robot}}, booktitle = {Proceedings of the IEEE International Conference on Advanced Robotics (ICAR 2003)}, year = {2003}, pages = {507--512}, address = {Coimbra, Portugal}, month = jul, publisher = {IEEE Press}, abstract = {Gas source localisation with robots is usually performed in environments with a strong, unidirectional airflow created by artificial ventilation. This tends to create a strong, well defined analyte plume and enables upwind searching. By contrast, this paper presents experiments conducted in unventilated rooms. Here, the measured concentrations also indicate an analyte plume with, however, different properties concerning its shape, width, concentration profile and stability over time. In the results presented in this paper, two very different mobile robotic systems for odour sensing were investigated in different environments, and the similarities as well as differences in the analyte gas distributions measured are discussed.}, doi = {10.1.1.2.2483}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/wandel03-icar2003_col.pdf} } @inproceedings{Abolm2003Disc, author = {Abolmaali, Badreddin F. and Zell, Andreas and Vogl, T. J. and Abolmaali, N. D.}, title = {Discovering new lead structures for {Gd}-based contrast agents using the Compressed Feature Matrix}, booktitle = {European Congress of Radiology 13}, year = {2003}, address = {Wien, Austria}, note = {Suppl.: 234}, } @inproceedings{Abolm2003Neue, author = {Abolmaali, N. D. and Zell, Andreas and Vogl, T. J. and Abolmaali, Badreddin F.}, title = {{Neue Leitstrukturen f\"ur Gadolinium-basierte Kontrastmittel}}, booktitle = {84. Deutscher R\"ontgenkongress}, year = {2003}, publisher = {Thieme}, note = {R\"oFo 175}, abstract = {Ziele: Suche nach Verbindungen mit potenziellen Gd-Bindungsstellen mittels der Compressed Feature Matrix (CFM) zur Entwicklung neuer Gd-basierter MR-Kontrastmittel (Gd-KM). Material: F\"ur die Suche nach Leitstrukturen f\"ur Gd-KM wurden \"uber 250000 Molek\"ule (MW:500-900Da) aus kommerziellen Datenbanken untersucht. Auswahlkriterium war die m\"oglichst gro{\ss}e \"Ubereinstimmung mit einem Pharmakophormodell, das auf der Basis von 6 bekannten Gd-Kontrastmitteln erstellt wurde. Zur Berechnung dieses Modells sowie zur \"Ahnlichkeitsbewertung der untersuchten Strukturen wurde die Software COFEA verwendet. Kern dieses Programms ist ein neuer molekularer Deskriptor, die CFM. Ergebnisse: Die 16 ermittelten Verbindungen geh\"oren zu drei verschiedenen strukturellen Klassen, die sowohl neue zyklische und lineare, als auch verzweigte Gd-Bindungsstellen aufweisen. Die Zentren der 4 zyklischen Verbindungen (MW:604-913Da) enthalten 2 N- und 3 bzw. 4 O-Atome, w\"ahrend die unterschiedlichen Grundger\"uste der zehn linearen Komponenten (MW:503-728Da) 4 bzw. 5 N-Atome besitzen. Die beiden verzweigten Strukturen (MW:577-644Da) enthalten 5 bzw. 6 N-Atome, die f\"ur eine m\"ogliche Bindung von Gd3+ infrage kommen. Neben den polaren Gruppen der jeweiligen Zentren enthalten die Verbindungen zwischen 4 und 10 weitere polare oder geladene Gruppen. Schlussfolgerungen: Aufgrund der M\"oglichkeit zur Erstellung von Pharmakophormodellen ist die CFM besonders geeignet f\"ur die Suche nach neuen Leitstrukturen von Gd-KM. Zur Weiterentwicklung zu Kontrastmitteln mit spezifischen Eigenschaften werden unterschiedliche strukturelle Varianten erzeugt.}, page = {283}, } @article{2003_1, author = {Abolmaali, S. F. Badreddin and Ostermann, Claude and Zell, Andreas}, title = {The Compressed Feature Matrix - a novel descriptor for adaptive similarity search}, journal = {Journal of Molecular Modeling}, year = {2003}, volume = {9}, pages = {66-75}, number = {1}, abstract = {The Compressed Feature Matrix (CFM) is a new molecular descriptor for adaptive similarity searching. Depending on the requirements, it is based on a distance or geometry matrix. Thus, the CFM permits topological and three-dimensional comparisons of molecules. In contrast to the common distance matrix, the CFM is based on features instead of atoms. Each kind of these features may be weighted separately, depending on its (estimated) contribution to the biological effect of the molecule. In this work, we show that the CFM allows us to adapt similarity evaluations to particular ligands as well as to classification requirements. The CFM method is analyzed regarding correctness, adaptivity and speed. Applying the basic setting of feature weights, the similarity evaluations using the CFM on the one hand and the Tanimoto coefficient together with MACCS Keys on the other yield similar results. However, in contrast to the latter method, the CFM even permits us to focus on small parts of molecules to serve as a basis for similarity. Accordingly, we have achieved striking results not only by readjusting the feature weights with regard to the scaffold but also to the side chain of the respective target. The results of the latter run turned out to be rather independent of the molecular scaffold. Hence, the CFM is suitable not only for common similarity evaluation, but also for techniques such as lead or scaffold hopping.}, doi = {10.1007/s00894-002-0110-0}, publisher = {Springer}, url = {http://dx.doi.org/10.1007/s00894-002-0110-0} } @article{2003_9, author = {Abolmaali, S. F. B. and Wegner, J\"org K. and Zell, Andreas}, title = {The Compressed Feature Matrix - a fast method for feature based substructure search}, journal = {Journal of Molecular Modeling}, year = {2003}, volume = {9}, pages = {235-241}, number = {4}, abstract = {The compressed feature matrix (CFM) is a feature based molecular descriptor for the fast processing of pharmacochemical applications such as adaptive similarity search, pharmacophore development and substructure search. Depending on the particular purpose, the descriptor may be generated upon either topological or Euclidean molecular data. To assure a variable utilizability, the assignment of the structural patterns to feature types is arbitrarily determined by the user. This step is based on a graph algorithm for substructure search, which resembles the common substructure descriptors. While these merely allow a screening for the predefined patterns, the CFM permits a real substructure/subgraph search, presuming that all desired elements of the query substructure are described by the selected feature set. In this work, the CFM based substructure search is evaluated with regard to both the different outputs resulting from varying feature sets and the search speed. As a benchmark we use the programmable atom typer (PATTY) graph algorithm. When comparing the two methods, the CFM based matrix algorithm is up to several hundred times faster than PATTY and when using the CFM as a basis for substructure screening, the search speed is accelerated by three orders of magnitude. Thus, the CFM based substructure search complies with the requirements for interactive usage, even for the evaluation of several hundred thousand compounds. The concept of the CFM is implemented in the software COFEA.}, doi = {10.1007/s00894-003-0126-0}, publisher = {Springer}, url = {http://dx.doi.org/10.1007/s00894-003-0126-0} } @inproceedings{2003_146, author = {Fischer, Igor}, title = {Similarity-based neural networks for applications in computational molecular biology}, booktitle = {Advances in Intelligent Data Analysis V (Proc. 5th International Symposium on Intelligent Data Analysis)}, year = {2003}, volume = {2811}, series = {Lecture Notes in Computer Science}, pages = {208-218}, publisher = {Springer}, abstract = {This paper presents an alternative to distance-based neural networks. A distance measure is the underlying property on which many neural models rely, for example self-organizing maps or neural gas. However, a distance measure implies some requirements on the data which are not always easy to satisfy in practice. This paper shows that a weaker measure, the similarity measure, is sufficient in many cases. As an example, similarity-based networks for strings are presented. Although a metric can also be defined on strings, similarity is the established measure in string-intensive research, like computational molecular biology. Similarity-based neural networks process data based on the same criteria as other tools for analyzing DNA or amino-acid sequences.}, doi = {10.1007/b13240}, isbn = {978-3-540-40813-0}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/fischer-IDA.pdf} } @article{2003_246, author = {J\"urgens, Clemens and Ulmer, Holger and Wiest, Simon and Schiefer, Ulrich and Zell, Andreas}, title = {Darstellung perimetrischer Befunde auf mobilen kabellosen Ger\"aten mit dynamisch generierten Grafiken}, journal = {Informatik, Biometrie und Epidemiologie in Medizin und Biologie}, year = {2003}, volume = {34}, number = {3}, } @inproceedings{2003_159, author = {Lilienthal, Achim and Reimann, D and Zell, Andreas}, title = {Gas Source Tracing With a Mobile Robot Using an Adapted Moth Strategy}, booktitle = {18. AMS (Autonome Mobile Systeme)}, year = {2003}, editor = {Dillman, R. and W\"orn, H. and Gockel, T.}, pages = {150-160}, address = {Karlsruhe, Germany}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/lilien03-ams2003b_col.pdf} } @inproceedings{2003_157, author = {Mojaev, Alexander and Zell, Andreas}, title = {Real-Time Scale Invariant Object and Face Tracking using Gabor Wavelet Templates}, booktitle = {18. AMS (Autonome Mobile Systeme)}, year = {2003}, editor = {Dillman, R. and W\"orn, H. and Gockel, T.}, pages = {12--20}, address = {Karlsruhe, Germany}, publisher = {Springer}, } @article{2003_129, author = {Mojaev, Alexander and Zell, Andreas}, title = {Image Decomposition and Tracking with Gabor Wavelets}, journal = {Machine Intelligence and Robotics Control}, year = {2003}, volume = {5}, pages = {113--119}, number = {3}, abstract = {This paper explores the use of the Gabor wavelet representation of an image for robust object tracking in robot vision (object grasping, gesture recognition and face tracking in human-robot interaction). For image decomposition we developed a fast non-iterative transform algorithm, in which the original image is processed with a 2D Gabor wavelet filter bank. We used the positions of the local extrema (low-level object features) in the filter responses to calculate a set of Gabor wavelet coefficients. That guarantees on the one hand a low redundancy of the resulting representation and on the other hand an automatic detection of the significant features in the image. To prove the quality of the object representation the image can be reconstructed from the descriptor. It was shown that such descriptors can be used for real-time scale invariant object tracking by gradient following or template adaptation. Tracking control was realized by a scale factor discriminator control technique and convolution based 2D cross-correlation. Our experiments revealed that this method enables real-time object or face tracking in a wide scale range and provides robustness against high frequency camera vibrations, from which cameras on mobile vehicles suffer.}, keywords = {Image Decomposition, Gabor Wavelets, Face Tracking}, url = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/mojaev/documents/miroc2003.pdf} } @inproceedings{2003_156, author = {Mojaev, Alexander and Zell, Andreas}, title = {Real-Time Object and Face Tracking with Gabor Wavelets}, booktitle = {11th IEEE International Conference on Advanced Robotics (ICAR 2003)}, year = {2003}, volume = {2}, pages = {1178--1183}, address = {Coimbra, Portugal}, } @inproceedings{2003_16, author = {Speer, Nora and Merz, Peter and Spieth, Christian and Zell, Andreas}, title = {Clustering Gene Expression Data with Memetic Algorithms based on Minimum Spanning Trees}, booktitle = {Congress on Evolutionary Computation (CEC 2003)}, year = {2003}, volume = {3}, pages = {1848-1855}, address = {Canberra, Australia}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/speer03-cec2003.pdf} } @inproceedings{2003_150, author = {Streichert, Felix and Spieth, Christian and Ulmer, Holger and Zell, Andreas}, title = {Evolving the Ability of Limited Growth and Self-Repair for Artificial Embryos}, booktitle = {7th European Conference on Artificial Life (ECAL)}, year = {2003}, volume = {2801}, series = {Lecture Notes in Artificial Intelligence}, pages = {289-298}, address = {Dortmund, Germany}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/streichert03evolving.pdf} } @inproceedings{Streichert03clustGecco, author = {Streichert, Felix and Stein, Gunnar and Ulmer, Holger and Zell, Andreas}, title = {A Clustering Based Niching Method for Evolutionary Algorithms}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO 2003)}, year = {2003}, editor = {E. Cant{\'u}-Paz and J. A. Foster and K. Deb and D. Davis and R. Roy and U.-M. O'Reilly and H.-G. Beyer and R. Standish and G. Kendall and S. Wilson and M. Harman and J. Wegener and D. Dasgupta and M. A. Potter and A. C. Schultz and K. Dowsland and N. Jonoska and J. Miller}, volume = {1}, series = {Lecture Notes in Computer Science}, pages = {644-645}, address = {Chicago, IL, USA}, publisher = {Springer}, details = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/streichert03aclustering.html}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/streichert03aclustering.pdf}, } @inproceedings{2003_152, author = {Streichert, Felix and Ulmer, Holger and Zell, Andreas}, title = {Evolutionary Algorithms and the Cardinality Constrained Portfolio Selection Problem}, booktitle = {Operations Research Proceedings 2003}, year = {2003}, pages = {253-260}, address = {Heidelberg, Germany}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/streichert03evolutionary.pdf} } @inproceedings{2003_155, author = {Treptow, Andr\'{e} and Masselli, Andreas and Zell, Andreas}, title = {Real-Time Object Tracking for Soccer-Robots without Color Information}, booktitle = {European Conference on Mobile Robotics (ECMR 2003)}, year = {2003}, pages = {33-38}, address = {Radziejowice, Poland}, url = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/treptow/publications/treptow03-ecmr.pdf} } @inproceedings{2003_148, author = {Ulmer, Holger and Streichert, Felix and Zell, Andreas}, title = {Model-Assisted Steady-State Evolution Strategies}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO 2003)}, year = {2003}, volume = {1}, series = {Lecture Notes in Computer Science}, pages = {610-621}, address = {Chicago, IL, USA}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/ulmer03modelassisted.pdf} } @inproceedings{2003_151, author = {Ulmer, Holger and Streichert, Felix and Zell, Andreas}, title = {Optimization by Gaussian Processes Assisted Evolution Strategies}, booktitle = {Selected Papers of the International Conference on Operations Research (OR 2003)}, year = {2003}, pages = {435-442}, address = {Heidelberg, Germany}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/ulmer03optimization.pdf} } @inproceedings{2003_154, author = {Ulmer, Holger and Streichert, Felix and Zell, Andreas}, title = {Evolution Strategies assisted by Gaussian Processes with improved Pre-Selection Criterion}, booktitle = {2003 Congress on Evolutionary Computation (CEC 2003)}, year = {2003}, volume = {1}, pages = {692-699}, publisher = {IEEE Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2003/ulmer03evolution.pdf} } @article{2003_10, author = {Wegner, J\"org K. and Zell, Andreas}, title = {Prediction of aqueous solubility and partition coefficient optimized by a genetic algorithm based descriptor selection method}, journal = {Journal of Chemical Information and Computer Sciences (JCICS)}, year = {2003}, volume = {43}, pages = {1077-1084}, number = {3}, abstract = {The paper describes a fast and flexible descriptor selection method using a genetic algorithm variant (GA-SEC). The relevance of the descriptors will be measured using Shannon entropy (SE) and differential Shannon entropy (DSE), which have very sparse memory requirements and allow the processing of huge data sets. A small quantity of the most important descriptors will be used automatically to build a value prediction model. The most important descriptors are not a linear combination of other descriptors, but transparent, pure descriptors. We used an artificial neural network (ANN) model to predict the aqueous solubility logS and the octanol/water partition coefficient logP. The logS data set was divided into a training set of 1016 compounds and a test set of 253 compounds. A correlation coefficient of 0.93 and an empirical standard deviation of 0.54 were achieved. The logP data set was divided into a training set of 1853 compounds and a test set of 138 compounds. A correlation coefficient of 0.92 and an empirical standard deviation of 0.44 were achieved.}, url = {http://dx.doi.org/10.1021/ci034006u} } @inproceedings{2003_145, author = {Wiest, Simon and Zell, Andreas}, title = {Automatic Audio Thumbnail Positioning Using Self-Similarity}, booktitle = {4th European Workshop on Image Analysis for Multimedia Interactive Services (WIAMIS)}, year = {2003}, editor = {Izquierdo, Ebroul}, pages = {302-305}, publisher = {World Scientific}, } @inproceedings{2002_162, author = {Kn\"odler, Kosmas and Poland, Jan and Zell, Andreas and Mitterer, Alexander}, title = {Memetic Algorithms for Combinatorial Optimization Problems in the Calibration of Modern Combustion Engines}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO-2002)}, year = {2002}, editor = {E. Cant{\'u}-Paz and K. Mathias and R. Roy and D. Davis and R. Poli and K. Balakrishnan and V. Honavar and G. Rudolph and J. Wegener and L. Bull and M. A. Potter and A. C. Schultz and J. F. Miller and E. Burke and N. Jonoska and W. B. Langdon}, pages = {687}, month = jul, publisher = {Morgan Kaufmann Publishers Inc. San Francisco, CA, USA}, } @inproceedings{2002_161, author = {Koch, Thomas E and Zell, Andreas}, title = {{MOCS}: Multi-Objective Clustering Selection Evolutionary Algorithm}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO-2002)}, year = {2002}, editor = {E. Cant{\'u}-Paz and K. Mathias and R. Roy and D. Davis and R. Poli and K. Balakrishnan and V. Honavar and G. Rudolph and J. Wegener and L. Bull and M. A. Potter and A. C. Schultz and J. F. Miller and E. Burke and N. Jonoska and W. B. Langdon}, pages = {423-430}, month = jul, publisher = {Morgan Kaufmann Publishers Inc. San Francisco, CA, USA}, } @inproceedings{2002_168, author = {Huhse, Jutta and Villmann, Thomas and Merz, Peter and Zell, Andreas}, title = {Evolution Strategy with Neighborhood Attraction Using a Neural Gas Approach}, booktitle = {7th International Conference on Parallel Problem Solving from Nature (PPSN VII)}, year = {2002}, series = {Lecture Notes in Computer Science}, pages = {391-400}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2002/huhse_ppsnvii.ps.gz} } @inproceedings{2002_164, author = {Huhse, Jutta and Villmann, Thomas and Zell, Andreas}, title = {Investigation of the Neighborhood Attraction Evolutionary Algorithm Based on Neural Gas}, booktitle = {Proceedings of the 6th International Conference on Neural Networks and Soft Computing}, year = {2002}, editor = {Rutkowski, L. and Kacprzyk, J.}, pages = {340-346}, address = {Zakopane, Poland}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/huhse_icnnsc.ps.gz} } @article{2002_165, author = {J\"urgens, Clemens and Schiefer, Ulrich and Burth, Roland and Zell, Andreas}, title = {Interpolation of Perimetric Test Grids using Neural Networks}, journal = {Perimetry Update 2002/2003}, year = {2002}, volume = {2003}, pages = {13--19}, } @article{2002_247, author = {J\"urgens, Clemens and Wiest, Simon and Schiefer, Ulrich and Burth, Roland and Zell, Andreas}, title = {Darstellung perimetrischer Befunde auf mobilen Ausgabeger\"aten}, journal = {Ophthalmologe}, year = {2002}, volume = {99}, pages = {Suppl. 1}, number = {1}, } @article{2002_248, author = {J\"urgens, Clemens and Wiest, Simon and Schiefer, Ulrich and Burth, Roland and Zell, Andreas}, title = {Displaying perimetric records on mobile wireless devices}, journal = {Graefe's Archive for Clinical and Experimental Ophthalmology}, year = {2002}, volume = {240}, pages = {Suppl. 1}, number = {1}, } @article{2002_249, author = {J\"urgens, Clemens and Wiest, Simon and Schiefer, Ulrich and Burth, Roland and Zell, Andreas}, title = {Automated classification of perimetric records on mobile wireless devices}, journal = {European Journal of Medical Research}, year = {2002}, volume = {7}, pages = {Suppl. 1}, number = {36}, } @inproceedings{khan02, author = {Yasir Niaz Khan and Syed Atif Mehdi}, title = {Sign Language Recognition using Sensor Gloves}, booktitle = {9th International Conference on Neural Information Processing}, year = {2002}, volume = {5}, pages = {2204 - 2206}, abstract = {This paper examines the possibility of recognizing sign language gestures using sensor gloves. Previously sensor gloves are used in games or in applications with custom gestures. This paper explores their use in Sign Language recognition. This is done by implementing a project called "Talking Hands", and studying the results. The project uses a sensor glove to capture the signs of American Sign Language performed by a user and translates them into sentences of English language. Artificial neural networks are used to recognize the sensor values coming from the sensor glove. These values are then categorized in 24 alphabets of English language and two punctuation symbols introduced by the author. So, mute people can write complete sentences using this application.}, doi = {10.1109/ICONIP.2002.1201884}, keywords = {American Sign language, Neural Network, sensor gloves, language recognition, deaf}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1201884} } @article{2002_160, author = {Kn\"odler, Kosmas and Poland, Jan and Mitterer, Alexander and Zell, Andreas}, title = {Memory Economy for Electronic Control Units: Compression of Conventional Look-up Tables}, journal = {Recent Advances in Simulation, Computational Methods and Soft Computing}, year = {2002}, pages = {234--239}, abstract = {The operation of modern technical systems is often controlled by electronic units. In the automotive sector lattice-like look-up tables are a common representation of non-linear multi-dimensional parameter functions of actuators. Regardless of the strongly restricted memory capacity of automotive electronic control units, manufacturers need to introduce additional functionalities to meet the new specifications. With an increasing number of adjustable actuators the number of parameters and thus the memory requirement within the control unit grows enormously. This work introduces a method based on evolutionary and classical optimization algorithms which reduces the memory requirement for 2-dimensional look-up tables.}, publisher = {WSEAS Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2002/knoedler_EC2002.pdf} } @article{2002_167, author = {Lilienthal, Achim and Zell, Andreas and Wandel, Michael R. and Weimar, Udo}, title = {{Detektion und Lokalisierung einer Geruchsquelle mit einem autonomen mobilen Roboter}}, journal = {Robotik 2002}, year = {2002}, volume = {VDI-Bericht Nr. 1679}, pages = {689--694}, comment = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2002/lilien02-robotik2002_presentation.pdf}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2002/lilien02-robotik2002_col.pdf} } @inproceedings{2002_163, author = {Poland, Jan and Zell, Andreas}, title = {Different Criteria for Active Learning in Neural Networks: A Comparative Study}, booktitle = {10th European Symposium on Artificial Neural Networks (ESANN 2002)}, year = {2002}, editor = {Verleysen, M.}, pages = {119--124}, address = {Evere, Belgium}, publisher = {D-Facto}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2002/poland_query.pdf} } @inproceedings{2002_166, author = {Wiest, Simon and Zell, Andreas}, title = {EduBeans: Efficient development of interactive instructional exhibits leveraging a multi-layered, component based framework}, booktitle = {World Conference on Educational Multimedia, Hypermedia \& Telecommunication (ED-MEDIA)}, year = {2002}, editor = {Montgomerie, C and Viteli, J}, pages = {2056-2057}, } @inproceedings{2001_173, author = {Wandel, Michael R. and Weimar, Udo and Lilienthal, Achim and Zell, Andreas}, title = {{Leakage Localisation with a Mobile Robot Carrying Chemical Sensors}}, booktitle = {The 8\textsuperscript{th} IEEE International Conference on Electronics, Circuits, and Systems (ICECS 2001)}, year = {2001}, volume = {3}, pages = {1247--1250}, address = {Malta}, month = sep, publisher = {IEEE Press}, abstract = {On the way to developing an electronic watchman one more sense, i.e. gas sensing facilities, are added to an autonomous mobile robot. For the gas detection, up to eight metal oxide sensors are operated using a commercial sensor system. The robot is able to move and navigate autonomously. The geometric information is extracted from laser range finder data. This input is used to build up an internal map while driving. Using the new sensor the localisation of a gas source in unventilated in-house environments is performed. First experiments in a one-dimensional case show a very good correlation between the peak and the gas source. The one-dimensional concentration profile is repeatedly recorded and stable for at least two hours. The two-dimensional experiments exhibit a circulation of the air within the room due to temperature and hence density effects. The latter is limiting the available recording time for the two-dimensional mapping.}, doi = {10.1109/ICECS.2001.957441}, isbn = {0-7803-7057-0}, keywords = {electric sensing devices , gas sensors , mobile robots , sensor fusion}, url = {http://dx.doi.org/10.1109/ICECS.2001.957441} } @inproceedings{2001_251, author = {Kn\"odler, Kosmas and Poland, Jan and Zell, Andreas and Mitterer, Alexander}, title = {Genetic Algorithms Solve Combinatorial Optimization Problems in the Calibration of Combustion Engines}, booktitle = {Optimization in Industry III}, year = {2001}, pages = {45-56}, address = {Barga, Toskana, Italy}, month = jun, publisher = {Springer, London}, } @inproceedings{2001_250, author = {Koch, Thomas E and Zell, Andreas}, title = {Optimal Positioning of Clamps for Workpiece Adjustment using Multi-Criteria Evolutionary Computation}, booktitle = {Optimization in Industry III}, year = {2001}, address = {Barga, Toskana, Italy}, month = jun, publisher = {Springer, London}, } @inproceedings{2001_169, author = {Kn\"odler, Kosmas and Poland, Jan and Mitterer, Alexander and Zell, Andreas}, title = {Optimizing Data Measurements at Test Beds Using Multi-Step Genetic Algorithms}, booktitle = {Advances in Fuzzy Systems and Evolutionary Computation - Proceedings of the 2nd WSES International Conference on Evolutionary Computation}, year = {2001}, editor = {Mastorakis, N.}, pages = {277-282}, month = feb, abstract = {Series of measurements should be planned carefully in order to reduce the costs and to allow an efficient execution at measuring devices. For this planning process, we present a multi-step optimization method using genetic algorithms. As a concrete application, we arrange a set of Design of Experiment measuring points appearing during the calibration of combustion engines in an optimal way.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/knoedler_pap.pdf} } @article{2001_177, author = {Cheng, Guo-Jian and Zell, Andreas}, title = {Externally Growing Cell Structures for Data Evaluation of Chemical Gas Sensors}, journal = {Neural Computing \& Applications}, year = {2001}, volume = {10}, pages = {89-97}, number = {1}, } @inproceedings{2001_176, author = {Huhse, Jutta and Zell, Andreas}, title = {Evolution Strategy with Neighborhood Attraction - A Robust Evolution Strategy}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO-2001)}, year = {2001}, editor = {Spector, Lee}, pages = {1026-1033}, publisher = {Morgan Kaufmann, San Francisco/CA}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/huhse_gecco2001.pdf} } @inproceedings{2001_174, author = {Huhse, Jutta and Zell, Andreas}, title = {Investigating the Influence of the Neighborhood Attraction Factor to Evolution Strategies with Neighborhood Attraction}, booktitle = {9th European Symposium on Artificial Neural Networks (ESANN-2001)}, year = {2001}, editor = {Verleysen, Michel}, pages = {179-184}, address = {Evere, Belgium}, publisher = {D-Facto}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/huhse_esann2001.ps.gz} } @article{2001_252, author = {J\"urgens, Clemens and Koch, Thomas and Burth, Roland and Schiefer, Ulrich and Zell, Andreas}, title = {Scotoma classification with artificial neural networks}, journal = {Graefe's Archive for Clinical and Experimental Ophthalmology}, year = {2001}, volume = {239}, pages = {Suppl. 1}, number = {1}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/juergens_dog_e.pdf} } @article{2001_175, author = {J\"urgens, Clemens and Koch, Thomas E and Burth, Roland and Schiefer, Ulrich and Zell, Andreas}, title = {Classification of perimetric results and reduction of number of test locations using artificial neural networks}, journal = {Investigative Ophthalmology \& Visual Science}, year = {2001}, volume = {42}, pages = {846}, number = {4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/juergens_arvo.pdf} } @inproceedings{2001_182, author = {Lilienthal, Achim and Wandel, Michael R. and Weimar, Udo and Zell, Andreas}, title = {{Experiences Using Gas Sensors on an Autonomous Mobile Robot}}, booktitle = {EUROBOT 2001}, year = {2001}, pages = {1--8}, address = {Lund, Sweden}, publisher = {IEEE Computer Press}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/lilien01-eurobot2001_col.pdf} } @inproceedings{2001_172, author = {Lilienthal, Achim and Zell, Andreas and Wandel, Michael R. and Weimar, Udo}, title = {{Sensing Odour Sources in Indoor Environments Without a Constant Airflow by a Mobile Robot}}, booktitle = {Frontiers of Robotics \& Automation in the new Millennium (ICRA 2001)}, year = {2001}, volume = {4}, pages = {4005--4010}, address = {Seoul, South Korea}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/lilien01-icra2001_col.pdf} } @inproceedings{2001_183, author = {Mojaev, Alexander and Zell, Andreas}, title = {{Aufbau topologischer Karten und schnelle globale Bahnplanung f\"ur mobile Roboter}}, booktitle = {Autonome Mobile Systeme (AMS)}, year = {2001}, pages = {164-70}, address = {Stuttgart, Germany}, note = {(in German)}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/documents/ams01tp.ps.gz} } @article{2001_181, author = {Poland, Jan and Kn\"odler, Kosmas and Mitterer, Alexander and Fleischhauer, T and Zuber-Goos, F and Zell, Andreas}, title = {Evolutionary Search for Smooth Maps in Motor Control Unit Calibration}, journal = {Stochastic Algorithms: Foundations and Applications}, year = {2001}, pages = {107-116}, editor = {K. Steinh\"ofel}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/poland_kfglaettung.pdf} } @inproceedings{2001_171, author = {Poland, Jan and Kn\"odler, Kosmas and Zell, Andreas}, title = {On the Efficient Construction of Rectangular Grids from Given Data Points}, booktitle = {Applications of Evolutionary Computing, EvoWorkshops 2001: EvoCOP, EvoFlight, EvoIASP, EvoLearn, and EvoSTIM, Como, Italy, April 18-20, 2001, Proceedings}, year = {2001}, editor = {Egbert J. W. Boers and Jens Gottlieb and Pier Luca Lanzi and Robert E. Smith and Stefano Cagnoni and Emma Hart and G\"unther R. Raidl and H. Tijink}, volume = {2037}, series = {Lecture Notes in Computer Science}, pages = {110-119}, abstract = {Many combinatorial optimization problems provide their data in an input space with a given dimension. Genetic algorithms for those problems can benefit by using this natural dimension for the encoding of the individuals rather than a traditional one-dimensional bit string. This is true in particular if each data point of the problem corresponds to a bit or a group of bits of the chromosome.We develop different methods for constructing a rectangular grid of near-optimal dimension for given data points, providing a natural encoding of the individuals. Our algorithms are tested with some large TSP instances.}, doi = {10.1007/3-540-45365-2_12}, isbn = {978-3-540-41920-4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/poland_ndpoints.pdf} } @inproceedings{2001_170, author = {Poland, Jan and Mitterer, Alexander and Kn\"odler, Kosmas and Zell, Andreas}, title = {Genetic Algorithms Can Improve the Construction of {D}-optimal Experimental Designs}, booktitle = {Advances in Fuzzy Systems and Evolutionary Computation}, year = {2001}, pages = {227--231}, abstract = {We study the benefits of Genetic Algorithms, in particular the crossover operator, in constructing experimental designs that are D-optimal. To this purpose, we use standard Monte Carlo algorithms such as DETMAX and k-exchange as the mutation operator in a Genetic Algorithm. Compared to the heuristics, our algorithms are slower but yield better results.}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/poland_doe.pdf} } @inproceedings{2001_179, author = {Poland, Jan and Zell, Andreas}, title = {Main Vector Adaptation: A {CMA} Variant with Linear Time and Space Complexity}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO - 2001)}, year = {2001}, editor = {Spector, L.}, pages = {1050--1055}, publisher = {Morgan Kaufmann}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/poland_mvaes.pdf} } @inproceedings{2001_180, author = {Wiest, Simon and Zell, Andreas}, title = {Improving Web Based Training Using an XML Content Base}, booktitle = {World Conference on Educational Multimedia, Hypermedia \& Telecommunication (ED-MEDIA)}, year = {2001}, editor = {Montgomerie, C and Viteli, J}, pages = {2045-2050}, address = {Tampere, Finland}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2001/wiest_edmedia2001.pdf} } @inproceedings{2001_178, author = {Wiest, Simon and Zell, Andreas}, title = {XML in Web-Based Training: Workflow and Opportunities}, booktitle = {Computer-Based Learning in Science (CBLIS) 2001}, year = {2001}, volume = {1}, address = {Brno, Czech Republic}, } @inproceedings{2000_193, author = {Wakunda, J\"urgen and Zell, Andreas}, title = {Median-selection for parallel steady-state evolution strategies}, booktitle = {Parallel Problem Solving from Nature - PPSN VI}, year = {2000}, editor = {Marc Schoenauer and Kalyanmoy Deb and G\"unther Rudolph and Xin Yao and Evelyne Lutton and Juan Julian Merelo and Hans-Paul Schwefel}, volume = {1917}, pages = {405-414}, address = {Paris, France}, month = sep, publisher = {Springer Berlin}, journal = {Lecture Notes in Computer Science}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/steadymedian_ppsnvi.ps.gz} } @inproceedings{2000_191, author = {Koch, Thomas E and Scheer, Volker and Wakunda, J\"urgen and Zell, Andreas}, title = {A parallel, hybrid meta-optimization for finding better parameters of an evolution strategy in real world optimization problems}, booktitle = {Proceedings of the 2000 Genetic and Evolutionary Computation Conference Workshop Program}, year = {2000}, editor = {A. Wu}, pages = {17--19}, address = {Las Vegas, Nevada}, month = jul, } @inproceedings{2000_189, author = {Fischer, Igor and Wiest, Simon and Zell, Andreas}, title = {An example of generating Internet-based course material}, booktitle = {Proceedings of the 22nd Intl. Conf. Information Technology Interfaces ITI}, year = {2000}, editor = {D. Kalpic and V. Dobric}, pages = {229--234}, address = {Pula, Croatia}, month = jun, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/iti2000.pdf} } @inproceedings{2000_46, author = {Cheng, Guojian and Zell, Andreas}, title = {Double Growing Neural Gas for Disease Diagnosis}, booktitle = {Proceedings of the Artificial Neural Networks in Medicine and Biology Conference (ANNIMAB-1)}, year = {2000}, editor = {H. Malmgren and M. Borga and L. Niklasson}, pages = {309-314}, address = {Goteborg, Schweden}, month = may, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/dgng_annimab1.ps.gz} } @inproceedings{2000_184, author = {Fischer, Igor and Zell, Andreas}, title = {Visualization of neural networks using Java applets}, booktitle = {Innovations in Education for Electrical and Information Engineering (EIE), Proceedings of the 11th annual conference of the EAEEIE}, year = {2000}, editor = {M. Hoffmann}, pages = {71--76}, address = {Ulm, Germany}, month = apr, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/NN-applets.ps.gz} } @inproceedings{2000_186, author = {Cheng, Guojian and Zell, Andreas}, title = {Externally growing cell structures for pattern classification}, booktitle = {Proceedings of the Second ICSC Symposium on Neural Computation - NC'2000}, year = {2000}, editor = {H. Bothe and R. Rojas}, pages = {233-239}, publisher = {ICSC Academic Press, Canada/Switzerland}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/egcs_nc2000.ps.gz} } @inproceedings{2000_192, author = {Feyrer, Stefan and Zell, Andreas}, title = {Robust real-time pursuit of persons with a mobile robot using multisensor fusion}, booktitle = {6th International Conference on Intelligent Autonomous Systems (IAS-6)}, year = {2000}, pages = {710-715}, address = {Venice, Italy}, journal = {Intelligent Autonomous Systems 6}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/feyrer_IAS_2000.ps.gz} } @article{2000_253, author = {Feyrer, Stefan and Zell, Andreas}, title = {{Auf dem Weg zum pers\"onlichen Assistenten - Multisensorielle Personendetektion zur Realisierung von robustem Folgeverhalten f\"ur einen mobilen Serviceroboter}}, journal = {Robotik 2000 - Leistungsstand, Anwendungen, Visionen, Trends}, year = {2000}, volume = {VDI Berichte 1552}, pages = {465-470}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/feyrer_ROBOTIK_2000.ps.gz} } @inproceedings{2000_188, author = {Fischer, Igor and Zell, Andreas}, title = {String averages and self-organizing maps for strings}, booktitle = {Proceedings of the Second ICSC Symposium on Neural Computation - NC'2000}, year = {2000}, editor = {H. Bothe and R. Rojas}, pages = {208-215}, publisher = {ICSC Academic Press, Canada/Switzerland}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/stringSOM.ps.gz} } @inproceedings{2000_194, author = {Fischer, Igor and Zell, Andreas}, title = {A simple management tool for medium-sized Web sites}, booktitle = {Eighth International Conference on Digital Documents and Electronic Publishing (DDEP00)}, year = {2000}, editor = {Br\"uggemann-Klein, A. and King, P. R.}, series = {Lecture Notes in Computer Science}, pages = {77-90}, address = {Munich, Germany}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/pages2site.pdf} } @inproceedings{2000_195, author = {Fischer, Igor and Zell, Andreas}, title = {Processing Symbolic Data With Self-Organizing Maps}, booktitle = {Workshop SOAVE '2000 - Selbstorganisation von Adaptivem Verhalten}, year = {2000}, editor = {H.-M. Gro{\ss} and K. Debes and H.-J. B\"ohme}, volume = {10}, number = {643}, series = {VDI Reihe}, pages = {96--105}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/SOAVE2000.pdf} } @inproceedings{2000_187, author = {Huhse, Jutta and Zell, Andreas}, title = {Evolution strategy with neighborhood attraction}, booktitle = {Proceedings of the Second ICSC Symposium on Neural Computation - NC'2000}, year = {2000}, editor = {H. Bothe and R. Rojas}, pages = {363-369}, publisher = {ICSC Academic Press, Canada/Switzerland}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/paper_EN.ps.gz} } @article{2000_196, author = {Achim Lilienthal and Andreas Zell}, title = {{Ein autonomer mobiler Roboter mit elektronischer Nase}}, journal = {Informatik Aktuell}, year = {2000}, pages = {201--209}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/lilien00-ams2000_col.pdf} } @inproceedings{2000_190, author = {Wakunda, J\"urgen and Zell, Andreas}, title = {A new selection scheme for steady-state evolution strategies}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference}, year = {2000}, editor = {Darell Whitley and David Goldberg and Erick Cant\'u-Paz and Lee Spector and Ian Parmee and Hans-Georg Beyer}, pages = {794-801}, address = {Las Vegas, Nevada}, publisher = {Morgan Kaufmann, San Francisco, CA}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2000/steadymedian_gecco2000.ps.gz} } @inproceedings{1999_208, author = {Feyrer, Stefan and Schimmel, Oliver and Zell, Andreas}, title = {Dreidimensionale Umgebungsmodellierung durch monokulare Exploration mit einem mobilen Roboter}, booktitle = {Autonome Mobile Systeme 1999, 15. Fachgespr\"ach}, year = {1999}, series = {Informatik aktuell}, pages = {366-375}, month = nov, publisher = {Springer}, isbn = {3-540-66732-6}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1999/feyrer_AMS_99.ps.gz} } @inproceedings{1999_203, author = {Franz, Matthias O. and Neumann, Titus R. and Plagge, Michael and Mallot, Hanspeter A. and Zell, Andreas}, title = {Can fly tangential neurons be used to estimate self-motion?}, booktitle = {Proceedings of the 9th International Conference on Artificial Neural Networks (ICANN 1999)}, year = {1999}, editor = {D. Willshaw and A. Murray}, volume = {2}, pages = {994-999}, month = sep, publisher = {Institution of Electrical Engineers (IEE)}, abstract = {The so-called tangential neurons in the fly brain are sensitive to the typical optic flow patterns generated during self-motion. This suggests a possible involvement in the self-motion estimation process. In this study, the authors examine whether a simplified matched filter model of these neurons can be used to estimate self-motion from the optic flow. They present a theory for the construction of an optimal matched filter incorporating both the noise properties of the motion signal, and prior knowledge about the distance distribution of the environment. Tests on a mobile robot demonstrate that the matched filter approach works for real time camera input and the noisy motion fields computed by Reichardt motion detectors}, doi = {10.1049/cp:19991242}, isbn = {0-85296-721-7}, } @article{1999_209, author = {Cheng, Guojian and Zell, Andreas}, title = {Multiple growing cell structures}, journal = {Neural Network World}, year = {1999}, volume = {9}, pages = {425-452}, number = {5}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1999/mgcs_nnw.ps.gz} } @inproceedings{1999_198, author = {Ebner, Marc}, title = {Evolving an environment model for robot localization}, booktitle = {Lecture Notes in Computer Science}, year = {1999}, pages = {184-192}, } @article{1999_204, author = {Ebner, Marc}, title = {On the search space of genetic programming and its relation to nature's search space}, journal = {Trees}, year = {1999}, volume = {1}, pages = {5}, } @inproceedings{1999_199, author = {Ebner, Marc and Zell, Andreas}, title = {Evolving a task specific image operator}, booktitle = {Lecture Notes in Computer Science}, year = {1999}, pages = {74-89}, } @inproceedings{1999_201, author = {Ebner, Marc and Zell, Andreas}, title = {Evolving a behavior-based control architecture-From simulations to the real world}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 1999)}, year = {1999}, pages = {1009--1014}, address = {Orlando, Florida, USA}, month = {jul}, publisher = {Morgan Kaufmann}, } @article{1999_197, author = {Feyrer, Stefan and Zell, Andreas}, title = {Personentracking mit einer mobilen Roboterplattform unter Verwendung eines multimodalen Detektionsansatzes}, journal = {KI}, year = {1999}, volume = {13}, pages = {7-12}, number = {1}, publisher = {arenDTaP Desktop Publishing}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1999/feyrer_KI_99.ps.gz} } @inproceedings{1999_205, author = {Feyrer, Stefan and Zell, Andreas}, title = {Tracking and pursuing persons with a mobile robot}, booktitle = {RATFG-RTS '99: Proceedings of the International Workshop on Recognition, Analysis, and Tracking of Faces and Gestures in Real-Time Systems}, year = {1999}, pages = {83-88}, publisher = {IEEE Computer Society}, abstract = {In this paper we address the problem of detecting, tracking, and pursuing persons with a mobile robot in real-time. Our system consists of two cooperatively interacting parts: A visual gaze holding process using an active stereo vision system and a component controlling the trajectory of the robot. The detection process is based on an approach which combines color, motion, and contour information. Additionally, facial features and depth information are integrated to increase the robustness of detection. For navigation a potential field method is used taking into account the path of the person going ahead as well as a local environment map built by means of laser range sensor data. Consequently, stationary and dynamic obstacles can be avoided during the process of pursuit. The system is able to operate at approximately human walking rates}, doi = {10.1109/RATFG.1999.799228}, isbn = {0-7695-0378-0}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1999/feyrer_ICCV_99.ps.gz} } @inproceedings{1999_206, author = {Feyrer, Stefan and Zell, Andreas}, title = {Detection, Tracking, and Pursuit of Humans with an Autonomous Mobile Robot}, booktitle = {International Conference on Intelligent Robots and Systems 1999 (IROS '99)}, year = {1999}, pages = {864-869}, address = {Kyongju, Korea}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1999/feyrer_IROS_99.ps.gz} } @article{1999_200, author = {Koch, Thomas E. and M\"uller, Ralph and Schneider, Franz and Zell, Andreas}, title = {{Positionierung von Spannmitteln zur Werkst\"uckfixierung mittels Evolution\"arer Algorithmen}}, journal = {Automatisierungstechnische Praxis atp}, year = {1999}, volume = {41}, pages = {32-39}, number = {9}, publisher = {R. Oldenbourg Verlag}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1999/koch_atp_9909.ps.gz} } @article{1999_207, author = {Mojaev, Alexander and Zell, Andreas and Rechnerarchitektur, A}, title = {Robuste reaktive Bahnregelung und Kollisionsvermeidung eines autonomen mobilen Roboters}, journal = {Informatik Aktuell}, year = {1999}, pages = {284-292}, } @inproceedings{1999_202, author = {Plagge, Michael and G\"unther, Richard and Ihlenburg, J\"orn and Jung, Dirk and Zell, Andreas}, title = {The attempto robocup robot team}, booktitle = {Lecture Notes in Computer Science}, year = {1999}, pages = {424-433}, } @inproceedings{1998_255, author = {Ebner, Marc and Zell, Andreas}, title = {Visual navigation using ego-motion information}, booktitle = {Workshop Dynamische Perzeption}, year = {1998}, editor = {Stefan Posch and Helge Ritter}, pages = {55--62}, month = jun, publisher = {Infix-Verlag}, } @inproceedings{1998_212, author = {Feyrer, Stefan and Zell, Andreas}, title = {{Ein integrierter Ansatz zur Lokalisierung von Personen in Bildfolgen}}, booktitle = {Workshop Dynamische Perzeption}, year = {1998}, editor = {Stefan Posch and Helge Ritter}, pages = {183--190}, month = jun, publisher = {Infix-Verlag}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1998/feyrer_DP_98.ps.gz} } @inproceedings{1998_211, author = {Ebner, Marc}, title = {On the Evolution of Interest Operators using Genetic Programming}, booktitle = {Late Breaking Papers at EuroGP'98: the First European Workshop on Genetic Programming}, year = {1998}, editor = {Riccardo Poli and W. B. Langdon and Marc Schoenauer and Terry Fogarty and Wolfgang Banzhaf}, pages = {6-10}, address = {Birmingham, UK}, journal = {COGNITIVE SCIENCE RESEARCH PAPERS-UNIVERSITY OF BIRMINGHAM CSRP}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1998/gpmoravec.ps.gz} } @inproceedings{1998_210, author = {Ebner, Marc}, title = {Extraction of moving objects with a moving mobile robot}, booktitle = {3rd {IFAC} Symposium on Intelligent Autonomous Vehicles}, year = {1998}, editor = {Miguel Angel Salichs and Aarne Halme}, pages = {749-754}, } @inproceedings{1998_216, author = {Ebner, Marc}, title = {Evolution of a control architecture for a mobile robot}, booktitle = {Second International Conference on Evolvable Systems: From Biology to Hardware}, year = {1998}, editor = {Moshe Sipper and Daniel Mange and Andr\'es P\'erez-Uribe}, pages = {303-310}, address = {Lausanne, Switzerland}, publisher = {Springer-Verlag}, journal = {Lecture Notes in Computer Science}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1998/gprealrob.ps.gz} } @inproceedings{1998_218, author = {Feyrer, Stefan and Zell, Andreas}, title = {{Videobasierte Erkennung von Personen und hindernisvermeidendes Folgeverhalten mit einem mobilen Serviceroboter}}, booktitle = {Autonome Mobile Systeme}, year = {1998}, editor = {Heinz W\"orn and R\"udiger Dillmann and Dominik Henrich}, pages = {75-84}, publisher = {Springer-Verlag, Berlin, Heidelberg}, note = {German}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1998/feyrer_AMS_98.ps.gz} } @inproceedings{1998_213, author = {Leonhardi, Alexander and Reissenberger, Wolfgang and Schmelmer, Tim and Weicker, Karsten and Weicker, Nicole}, title = {Development of problem-specific evolutionary algorithms}, booktitle = {Parallel Problem Solving from Nature - {PPSN} V}, year = {1998}, editor = {Agnoston E. Eiben and Thomas B\"ack and Marc Schoenauer and Hans-Paul Schwefel}, pages = {388-397}, } @inproceedings{1998_217, author = {Mojaev, Alexander and Zell, Andreas}, title = {{Sonardaten-Integration f\"ur autonome mobile Roboter}}, booktitle = {20. DAGM-Symposium Mustererkennung}, year = {1998}, editor = {Paul Levi and R.-J.Ahlers and F.May and M.Schanz}, pages = {556--565}, address = {Stuttgart, Germany}, journal = {Mustererkennung}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1998/dagm98si.ps.gz} } @inproceedings{1998_219, author = {Mojaev, Alexander and Zell, Andreas}, title = {{Online-Positionskorrektur f\"ur mobile Roboter durch Korrelation lokaler Gitterkarten}}, booktitle = {Autonome Mobile Systeme}, year = {1998}, editor = {Heinz W\"orn and R\"udiger Dillmann and Dominik Henrich}, pages = {93--99}, publisher = {Springer-Verlag, Berlin, Heidelberg}, journal = {Informatik Aktuell}, } @inproceedings{1998_254, author = {Ott, Hartmut and Wakunda, J\"urgen and Zell, Andreas}, title = {{Evolution\"are Algorithmen f\"ur die Positionsoptimierung von Vakuumspannern zur Holzwerkst\"uckfixierung}}, booktitle = {Soft Computing in Produktion und Materialwirtschaft}, year = {1998}, editor = {J. Kuhl and V. Nissen and M. Tietze}, pages = {87--101}, publisher = {Cuvillier Verlag, G\"ottingen}, isbn = {3-89712-134-4}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1998/SympSoftComp.ps.gz} } @inproceedings{1998_215, author = {Plagge, Michael and Diebold, Boris and G\"unther, Richard and Ihlenburg, J and Jung, Dirk and Zahedi, Keyan and Zell, Andreas}, title = {Design and Evaluation of the T-Team of the University of Tuebingen for {RoboCup}'98}, booktitle = {{RoboCup}}, year = {1998}, editor = {Minoru Asada and Hiroaki Kitano}, volume = {1604}, pages = {464-472}, journal = {Lecture Notes In Computer Science}, } @inproceedings{1998_214, author = {Weicker, Karsten and Weicker, Nicole}, title = {Locality vs. randomness - dependence of operator quality on the search state}, booktitle = {Proceedings of the Fifth Workshop on Foundations of Genetic Algorithms (FOGA 5)}, year = {1998}, editor = {Wolfgang Banzhaf and Colin R. Reeves}, pages = {147-163}, address = {Leiden, The Netherlands}, publisher = {Morgan Kaufmann}, } @inproceedings{wakunda1997EvA, author = {Wakunda, J\"urgen and Zell, Andreas}, title = {{EvA: A Tool for Optimization with Evolutionary Algorithms}}, booktitle = {23\textsuperscript{rd} EUROMICRO Conference '97 New Frontiers of Information Technology}, year = {1997}, volume = {0}, pages = {644--651}, address = {Los Alamitos, CA, USA}, month = sep, publisher = {IEEE Computer Society}, abstract = {We describe the EvA software package which consists of parallel (and sequential) implementations of genetic algorithms (GAs) and evolution strategies (ESs) and a common graphical user interface. We concentrate on the descriptions of the two distributed implementations of GAs and ESs which are of most interest for the future. We present comparisons of different kinds of genetic algorithms and evolution strategies that include implementations of distributed algorithms on the Intel Paragon, a large MIMD computer, and massively parallel algorithms on a 16384 processor MasPar MP-1, a large SIMD computer. The results show that parallelization of evolution strategies not only achieves a speedup in execution time of the algorithm, but also a higher probability of convergence and an increase of quality of the achieved solutions. In the benchmark functions we tested, the distributed ESs have a better performance than the distributed GAs.}, doi = {http://www.computer.org/portal/web/csdl/doi/10.1109/EURMIC.1997.617395}, isbn = {0-8186-8129-2}, issn = {1089-6503}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1997/Wakunda1997.pdf}, url = {http://doi.ieeecomputersociety.org/10.1109/EURMIC.1997.617395} } @inbook{1997_221, chapter = {28}, pages = {343-360}, title = {Application of a neural network for pattern recognition of pesticides in water samples by different immunochemical techniques}, publisher = {American Chemical Society}, year = {1997}, editor = {Aga, D. S. and Thurman, E. M.}, author = {Wittman, C and Schmid, RD and L\"offler, S and Zell, Andreas}, month = may, doi = {10.1021/bk-1997-0657.ch028}, } @article{1997_224, author = {Ebner, Marc}, title = {Evolution of hierarchical translation-invariant feature detectors with an application to character recognition}, journal = {Informatik Aktuell}, year = {1997}, pages = {456-463}, } @inproceedings{1997_225, author = {Ebner, Marc}, title = {On the evolution of edge detectors for robot vision using genetic programming}, year = {1997}, pages = {127--134}, } @inproceedings{1997_223, author = {Feyrer, Stefan and Schimmel, O and Zell, Andreas}, title = {{Adaptive farbbasierte Objektverfolgung mit dem mobilen Roboter ROBIN}}, year = {1997}, volume = {97}, pages = {176-185}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1997/feyrer_SOAVE_97_1.ps.gz} } @article{1997_220, author = {Seemann, J and Rapp, FR and Zell, Andreas and Gauglitz, G}, title = {Classical and modern algorithms for the evaluation of data from sensor-arrays}, journal = {Fresenius'Journal of Analytical Chemistry}, year = {1997}, volume = {359}, pages = {100-106}, number = {1}, } @inproceedings{1997_257, author = {Zell, Andreas and Feyrer, Stefan and Ebner, Marc and Mojaev, Alexander and Schimmel, O and Langenbacher, K}, title = {{Systemarchitektur der autonomen mobilen Roboter Robin und Colin der Universit\"at T\"ubingen}}, booktitle = {Workshop SOAVE 97 - Selbstorganisation von Adaptivem Verhalten 1997}, year = {1997}, editor = {Gro{\ss}, Horst-Michael}, pages = {151-155}, publisher = {VDI Verlag}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/1997/feyrer_SOAVE_97_2.ps.gz} } @inproceedings{1997_256, author = {Zell, Andreas and Hirche, Johannes and Jung, Dirk and Scheer, Volker}, title = {Erfahrungen mit einer Gruppe mobiler Kleinroboter in einem Roboterpraktikum}, booktitle = {1. Workshop Kognitive Robotik, 21. Deutsche Jahrestagung f\"ur K\"unstliche Intelligenz}, year = {1997}, address = {Freiburg, Germany}, note = {In German}, } @inproceedings{1996_228, author = {Iglesias-Rozas, Jos\'{e} Rafael and Brodbeck, A and Zell, Andreas}, title = {Classification of Oligodendrogliomas Using Neural Networks}, booktitle = {Proceedings of the 20th Annual Conference of the Gesellschaft fur Klassifikation e.V.}, year = {1996}, editor = {Klar, R\"udiger and Opitz, Otto}, pages = {434--440}, address = {Freiburg, Germany}, month = mar, publisher = {Springer Verlag}, } @article{1996_226, author = {Bauknecht, Henri and Zell, Andreas and Bayer, Harold and Levi, Paul and Wagener, Markus and Sadowski, Jens and Gasteiger, Johann}, title = {Locating Biologically Active Compounds in Medium-Sized Heterogeneous Datasets by Topological Autocorrelation Vectors: Dopamine and Benzodiazepine Agonists}, journal = {J. Chem. Inf. Comput. Sci}, year = {1996}, volume = {36}, pages = {1205-1213}, number = {6}, } @inproceedings{1996_258, author = {Siemens, H and Zell, Andreas and Sadowski, Jens and Wagener, Markus and Gasteiger, Johann}, title = {{Neuronale Netze zur Wirkstoffsuche in Strukturdatenbanken}}, booktitle = {Workshop Klassifizierung und Vorhersage von Molek\"uleigenschaften}, year = {1996}, address = {T\"ubingen, Germany}, } @inproceedings{1996_227, author = {Zell, Andreas and Baumann, R}, title = {Distributed Genetic Algorithms on the Intel Paragon, a large MIMD Computer}, booktitle = {5th Annual Conference on Evolutionary Programming}, year = {1996}, editor = {Fogel, L J and Angeline, P J and B\"ack, T}, pages = {385--394}, address = {San Diego, CA, USA}, publisher = {MIT Press}, } @inbook{1995_311, chapter = {{\"Ahnlichkeitsanalyse biologisch aktiver Molek\"ule mit durch Autokorrelationsvektoren trainierten selbstorganisierenden Karten}}, pages = {153-167}, title = {Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism}, publisher = {Wiley}, year = {1995}, editor = {Dietmar Schomburg and Uta Lessel}, author = {Bauknecht, Henri and Zell, Andreas and Bayer, Harold and Levi, Paul and Wagener, Markus and Sadowski, Jens and Gasteiger, Johann}, address = {Braunschweig, Germany}, month = dec, doi = {10.1002/9783527615193.ch12}, isbn = {9783527615193}, keywords = {SIMD, selbstorganisierende Karten, PETRA, Gesamtladung, Atompolarisierbarkeit}, url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527615193.ch12/pdf} } @techreport{1995_315, author = {Zell, Andreas and Mamier, G\"unter and Vogt, Michael and Mache, Niels}, title = {{Der Stuttgarter Neuronale Netze Simulator}}, year = {1995}, month = oct, } @inproceedings{1995_317, author = {Gasteiger, Johann and Sadowski, Jens and Wagener, Markus and Levi, Paul and Zell, Andreas and Bauknecht, Henri and Will, T. and Klebe, G. and Mietzner, T. and Weber, F. and Barnickel, G. and Anzali, S. and Krug, M.}, title = {\"Ahnlichkeitsanalyse biologisch aktiver Verbindungen unter Einsatz genetischer Algorithmen und neuronaler Netze}, booktitle = {Statusseminar des BMBF Bioinformatik}, year = {1995}, editor = {Wolf, G. and Schmidt, R. and van der Meer, M.}, pages = {79-103}, address = {Braunschweig, Germany}, } @inproceedings{1995_318, author = {Hatzigeorgiou, Artemis and Herrmann, F. and Reczko, M. and Suhai, S. and Reich, J.G. and Hanke, J. and Mache, Niels and Zell, Andreas and Levi, Paul}, title = {{Verbundprojekt NEUROGEN: Neuronale und Genetische Algorithmen auf Parallelrechnern in der Genomforschung}}, booktitle = {Statusseminar des BMBF Bioinformatik}, year = {1995}, editor = {Wolf, G. and Schmidt, R. and van der Meer, M.}, pages = {195-220}, address = {Braunschweig, Germany}, } @inproceedings{1995_310, author = {Kett, B. and Fritz, H. and Zell, Andreas}, title = {Autonomous Neural Longitudinal Vehicle Control Trained on Human Driving Examples}, booktitle = {28th International Symposium on Automotive Technology and Automation}, year = {1995}, address = {Stuttgart, Germany}, } @inproceedings{1995_312, author = {Kett, B. and Fritz, H. and Zell, Andreas}, title = {Autonomous Neural Car Distance Control Trained on Human Driving Patterns}, booktitle = {International Conference on Artificial Neural Networks, Industrial Conference}, year = {1995}, address = {Paris, France}, } @inproceedings{1995_316, author = {Oberdorfer, M. and Zell, Andreas and Levi, Paul}, title = {NEUROPA: Ein paralleles System zum neuronalen Einparken eines autonomen mobilen Roboters}, booktitle = {Autonome Mobile Systeme 1995}, year = {1995}, editor = {Dillmann, R. and Rembold, U. and L\"uth, T.}, series = {Informatik Aktuell}, pages = {182-93}, publisher = {Springer}, } @article{1995_309, author = {Reczko, M. and Hatzigeorgiou, Artemis and Mache, Niels and Zell, Andreas}, title = {A Parallel Neural Network Simulator on the Connection Machine CM-5}, journal = {Computer Applications in the Bioscience}, year = {1995}, volume = {11}, pages = {309-315}, number = {3}, } @incollection{1995_313, author = {Sommerau, M. and Mamier, G\"unter and Zell, Andreas and Vogt, Michael and Levi, Paul}, title = {Fast Face Localization and Tracking with Model-Based Time Synchronization of a Head System}, booktitle = {Mustererkennung}, publisher = {Springer-Verlag}, year = {1995}, editor = {Sagerer, G. and Posch, Stefan and Kummert, F.}, pages = {516--523}, } @article{1995_314, author = {Zell, Andreas and Mamier, G\"unter and Mache, Niels}, title = {Neuronale Netze auf Massiv Parallelen Rechnersystemen: MasPar MP-1, Intel Paragon und Adaptive Solutions CNAPS}, journal = {GI-ITG Mitteilungen, Gesellschaft f\"ur Informatik, Parallel-Algorithmen und Rechnerstrukturen}, year = {1995}, volume = {14}, pages = {58-67}, issn = {0177-0454}, } @inproceedings{1994_301, author = {Zell, Andreas and Mache, Niels and Bayer, Harold}, title = {Effiziente Simulation Neuronaler Netze auf dem Neurocomputer Adaptive Solutions CNAPS}, booktitle = {ASIM-94, Fortschritte der Simulationstechnik}, year = {1994}, editor = {G. Kampe and M. Zeitz}, month = oct, publisher = {Vieweg}, } @inproceedings{1994_303, author = {Bauknecht, Henri and Zell, Andreas and Bayer, Harold and Levi, Paul and Wagener, Markus and Sadowski, Jens and Gasteiger, Johann}, title = {\"Ahnlichkeitsanalyse biologisch aktiver Molek\"ule mit selbstorganisierenden Karten}, booktitle = {Bioinformatik 94}, year = {1994}, address = {Jena, Germany}, month = sep, } @inproceedings{1994_298, author = {Zell, Andreas and H\"ubner, Ralf}, title = {Low-Cost 3D-Visualization of Neural Networks}, booktitle = {IPA/IAO-Forum Virtual Reality '94, Anwendungen und Trends}, year = {1994}, series = {IPA-IAO - Forschung und Praxis}, address = {Stuttgart, Germany}, month = feb, publisher = {Springer}, editors = {Hans J. Warnecke and Hans-J\"org Bullinger}, isbn = {978-3540577683}, } @incollection{1993_288, author = {Zell, Andreas and Mache, Niels and H\"ubner, Ralf and Mamier, G\"unter and Vogt, Michael and Schmalzl, Michael and Herrmann, Kai-Uwe}, title = {{SNNS} (Stuttgart Neural Network Simulator)}, booktitle = {Neural Network Simulation Environments}, publisher = {Kluwer Academic Publishers, Norwell, MA, USA}, year = {1994}, editor = {Skrzypek, Josef}, volume = {254}, series = {The Springer International Series in Engineering and Computer Science}, month = feb, note = {Chapter 9}, isbn = {978-0-7923-9415-0}, } @inproceedings{1994_306, author = {Mache, N. and Zell, Andreas and Levi, P. and Hatzigeorgiou, A. and Wieland, D. and Reczko, M. and Suhai, S.}, title = {Erkennung von Promotoren und kodierenden Bereichen in eukaryontischen genomischen Sequenzen mit neuronalen Netzen}, booktitle = {Bioinformatik}, year = {1994}, pages = {70-74}, address = {Jena, Germany}, } @phdthesis{1994_307, author = {Zell, Andreas}, title = {Simulation Neuronaler Netze}, school = {Universit\"at Stuttgart}, year = {1994}, type = {Habilitationsschrift}, } @inproceedings{1994_304, author = {Zell, Andreas and Bauknecht, Henri and Bayer, Harold and Levi, Paul}, title = {{Selbstorganisierende Oberfl\"achen auf Parallelrechnern zur \"Ahnlichkeitsanalyse biologisch aktiver Molek\"ule}}, booktitle = {Tagungsband Bioinformatik}, year = {1994}, pages = {215--217}, address = {Jena, Germany}, publisher = {Universit\"at Jena}, } @inproceedings{1994_300, author = {Zell, Andreas and Bayer, Harold and Bauknecht, Henri}, title = {Self-Organizing Surfaces and Volumes - An Extension of the Self-Organizing Map}, booktitle = {IEEE World Congress on Computational Intelligence}, year = {1994}, pages = {269--274}, address = {Orlando, Florida, USA}, publisher = {IEEE Press}, } @inproceedings{1994_302, author = {Zell, Andreas and Bayer, Harold and Bauknecht, Henri}, title = {Similarity Analysis of Molecules with Self-Organizing Surfaces An Extension of the Self-Organizing Map}, booktitle = {IEEE World Congress on Computational Intelligence}, year = {1994}, pages = {719--724}, address = {Orlando, Florida, USA}, publisher = {IEEE Press}, } @inproceedings{1994_305, author = {Zell, Andreas and Brodbeck, A. and Bayer, Harold and Levi, Paul and Brenner, J. and Suhr, D. and H\"ulser, D.}, title = {{Klassifikation durchflusszytometrischer Daten mit Neuronalen Netzen auf Hochleistungsrechnern}}, booktitle = {Bioinformatik}, year = {1994}, pages = {112-22}, address = {Jena, Germany}, } @inproceedings{1994_308, author = {Zell, Andreas and Mamier, G\"unter and Vogt, Michael and Mache, Niels and H\"ubner, Ralf}, title = {Der Stuttgarter Neuronale Netze Simulator}, booktitle = {Konnektionismus und Neuronale Netze, Beitr\"age zur Herbstschule HeKoNN-94}, year = {1994}, series = {GMD-Studien}, pages = {81-97}, address = {M\"unster/Westfalen, Germany}, } @inproceedings{1994_299, author = {Zell, Andreas and Schmalzl, Michael}, title = {Dynamic {LVQ} - A Fast Neural Network Learning Algorithm}, booktitle = {International Conference on Artificial Neural Networks}, year = {1994}, editor = {Marinaro, M. and Morasso, P. G.}, pages = {1095-8}, address = {Sorrento, Italy}, publisher = {Springer}, } @inproceedings{1993_294, author = {Brahim, K. and Zell, Andreas}, title = {{ANFIS-SNNS: Adaptive Network Fuzzy Inference System im Stuttgarter Neuronale Netze Simulator}}, booktitle = {Fuzzy-Systeme'93, Deutsche Informatik-Akademie}, year = {1993}, pages = {1--2}, address = {Braunschweig, Germany}, month = oct, } @incollection{1993_296, author = {Schmalzl, Michael and Zell, Andreas}, title = {{Dynamisches LVQ - Ein schnelles Lernverfahren zur Musterklassifikation mit neuronalen Netzen}}, booktitle = {Workshop Simulation Neuronaler Netze mit SNNS (SNNS-93)}, year = {1993}, volume = {10/93}, address = {Stuttgart, Germany}, month = sep, institution = {Universit\"at Stuttgart, Institut f\"ur Parallele und Verteilte H\"ochstleistungsrechner, Bildverstehen}, } @incollection{1993_295, author = {Zell, Andreas}, title = {Benchmarking Neural Networks on Parallel Computers}, booktitle = {Workshop Simulation Neuronaler Netze mit SNNS}, year = {1993}, pages = {1--2}, address = {Stuttgart, Germany}, month = sep, institution = {University of Stuttgart, Institute of Parallel and Distributed High-Performance Systems, Applied Computer Science Image Understanding}, } @inproceedings{1993_292, author = {Zell, Andreas and Mache, Niels and H\"uttel, Markus and Vogt, Michael}, title = {Simulation Neuronaler Netze auf Massiv Parallelen Rechnern}, booktitle = {GI-Jahrestagung}, year = {1993}, editor = {Reichel, Horst}, series = {Informatik Aktuell}, pages = {495-502}, address = {Dresden}, month = {September/October}, publisher = {Springer}, isbn = {3-540-57192-2}, } @inproceedings{1993_289, author = {Zell, Andreas and Mache, Niels and H\"uttel, Markus and Vogt, Michael}, title = {Performance Aspects Of Mapping Neural Networks Onto A Massively Parallel {SIMD}-Computer}, booktitle = {Applications of Artificial Neural Networks IV}, year = {1993}, editor = {Steven K. Rogers}, volume = {1965}, series = {Proc. SPIE}, pages = {364-374}, month = apr, publisher = {Society of Photo-Optical Instrumentation Engineers (SPIE)}, abstract = {In this paper we present and compare three different massively parallel implementations of multilayer feedforward neural networks on a MasPar MP-1216, a parallel SIMD computer with 16,384 processors. For multilayer feedforward networks we have obtained sustained rates of up to 348 MCPS and 129 MCUPS with backpropagation, a high mark for general purpose SIMD computers. After a brief introduction to SNNS, the paper first focuses on the problems of mapping neural networks to parallel hardware. Different aspects of parallelism are presented. Two combinations of unit and training pattern parallelism were implemented as well as link and training pattern parallelism. We describe the implementation problems in obtaining high propagation rates on a SIMD machine and problems with the resulting learning algorithms in general.}, } @inproceedings{1993_291, author = {Zell, Andreas and Mache, Niels and H\"uttel, Markus and Vogt, Michael}, title = {Massive Parallelism in Neural Network Simulation}, booktitle = {AAAI Spring Symposium Series, Symposium Innovative Applications of Massive Parallelism}, year = {1993}, pages = {234-241}, month = mar, publisher = {AAAI}, } @inproceedings{1993_290, author = {Zell, Andreas and Mache, Niels and Vogt, Michael and H\"uttel, Markus}, title = {Problems of Massive Parallelism in Neural Network Simulation}, booktitle = {IEEE International Conference on Neural Networks}, year = {1993}, volume = {3}, pages = {1890-1895}, address = {San Francisco, California, USA}, month = mar, abstract = {Different massively parallel implementations of multilayer feedforward neural networks are presented and compared on a MasPar MP-1216, a parallel single instruction, multiple data (SIMD) computer with 16384 processors. For multilayer feedforward networks, sustained rates of up to 348 M CPS and 129 M CUPS with backpropagation are obtained, a high mark for general purpose SIMD computers. Emphasis is placed on the problems of mapping neural networks to parallel hardware, on implementation problems in obtaining high propagation rates on a SIMD machine, and on problems with the resulting learning algorithms}, doi = {10.1109/ICNN.1993.298845}, isbn = {0-7803-0999-5}, } @inproceedings{1993_297, author = {Brahim, K. and Zell, Andreas}, title = {{ANFIS-SNNS: Adaptive Network Fuzzy Inference System im Stuttgarter Neuronale Netze Simulator}}, booktitle = {Workshop Simulation Neuronaler Netze mit SNNS}, year = {1993}, address = {Stuttgart, Germany}, } @inproceedings{1993_287, author = {Zell, Andreas and H\"ubner, Ralf and Korb, Thomas and Mache, Niels and Mamier, G\"unter and Schmalzl, Michael and Sommer, Tilman and Vogt, Michael}, title = {{SNNS}: An Efficient Simulator for Neural Nets}, booktitle = {MASCOTS '93: Proceedings of the International Workshop on Modeling, Analysis, and Simulation On Computer and Telecommunication Systems}, year = {1993}, editor = {Herbert D. Schwetman and Jean C. Walrand and Kallol Kumar Bagchi and Doug DeGroot}, pages = {343-346}, address = {San Diego, California, USA}, month = jan, publisher = {Society for Computer Simulation International}, isbn = {1-56555-018-8}, } @inproceedings{1993_293, author = {Zell, Andreas and Mamier, G\"unter and Mache, Niels and H\"uttel, Markus}, title = {{Simulation Neuronaler Netze auf SIMD- und MIMD-Parallelrechnern}}, booktitle = {8. Symposium Simulationstechnik}, year = {1993}, editor = {Sydow, A.}, pages = {529-534}, address = {Berlin, Germany}, publisher = {Vieweg}, } @inproceedings{1992_286, author = {Zell, Andreas and Mache, Niels and Bayer, Harold and H\"ubner, Ralf and Vogt, Michael}, title = {Efficient Parallel Simulation of Neural Networks}, booktitle = {Statusseminar Neuroinformatik}, year = {1992}, address = {Schloss Maurach (Bodensee), Germany}, month = oct, publisher = {BMFT}, } @inproceedings{1992_282, author = {Bayer, Harold and Br\"aunl, T. and Engelhardt, S. and Zell, Andreas}, title = {Data Parallel Research at the University of Stuttgart}, booktitle = {Data Parallel Research Initiative (DPRI) Symposium}, year = {1992}, address = {Boston, USA}, } @techreport{1992_284, author = {Zell, Andreas}, title = {Workshop Simulation Neuronaler Netze mit SNNS}, institution = {Universit\"at Stuttgart, Fakult\"at Informatik}, year = {1992}, } @techreport{1992_283, author = {Zell, Andreas and Mache, Niels and H\"ubner, Ralf and Vogt, Michael and Mamier, G\"unter and Schmalzl, Michael and Sommer, Tilman}, title = {{SNNS} User Manual, Version 2.0}, institution = {Universit\"at Stuttgart, Fakult\"at Informatik}, year = {1992}, number = {3/92}, address = {Stuttgart, Germany}, } @inproceedings{1992_285, author = {Zell, Andreas and Mache, Niels and Sommer, Tilman and H\"ubner, Ralf and Mamier, G\"unter and Vogt, Michael and Schmalzl, Michael and Hatzigeorgiou, Artemis and Herrmann, Kai-Uwe and H\"uttel, Markus}, title = {SNNS (Stuttgart Neural Network Simulator)}, booktitle = {Workshop Simulation Neuronaler Netze mit SNNS}, year = {1992}, editor = {Zell, Andreas}, pages = {1-22}, publisher = {Universit\"at Stuttgart, Institut f\"ur Parallele und Verteilte H\"ochstleistungsrechner (IPVR)}, note = {tech. report 10/92}, } @inproceedings{1991_278, author = {Zell, Andreas and Mache, Niels and Sommer, Tilman and Korb, Thomas}, title = {The {SNNS} Neural Network Simulator}, booktitle = {Mustererkennung 1991, 13. DAGM-Symposium}, year = {1991}, editor = {Bernd Radig}, volume = {290}, series = {Informatik-Fachberichte}, pages = {454-461}, address = {M\"unchen, Germany}, month = oct, publisher = {Springer}, isbn = {3-540-54597-2}, } @inproceedings{1991_281, author = {Zell, Andreas and Mache, Niels and Sommer, Tilman and Korb, Thomas}, title = {Design of the {SNNS} Neural Network Simulator}, booktitle = {Proc. 7th Austrian Conference on Artificial Intelligence, \"OGAI-91}, year = {1991}, editor = {Hermann Kaindl}, volume = {287}, series = {Informatik-Fachberichte}, pages = {93-102}, address = {Wien, Austria}, month = sep, publisher = {Springer}, } @inproceedings{1991_280, author = {Zell, Andreas and Mache, Niels and Sommer, Tilman and Korb, Thomas}, title = {The {SNNS} Neural Network Simulator}, booktitle = {GWAI-91, 15. Fachtagung f\"ur K\"unstliche Intelligenz}, year = {1991}, volume = {285}, series = {Informatik-Fachberichte}, pages = {254-263}, address = {Bonn, Germany}, month = sep, publisher = {Springer}, isbn = {3-540-54558-1}, } @inproceedings{1991_271, author = {Adrian M\"uller and Andreas Zell}, title = {Connectionist Natural Language Parsing with {BrainC}}, booktitle = {Applications of Artificial Neural Networks II (SPIE's 1991 Aerospace Sensing International Symposium)}, year = {1991}, editor = {Steven K. Rogers}, volume = {1469}, series = {Proceedings of SPIE}, pages = {188--196}, month = aug, publisher = {SPIE}, abstract = {A close examination of pure neural parsers shows that they either could not guarantee the correctness of their derivations or had to hard-code seriality into the structure of the net. The authors therefore decided to use a hybrid architecture, consisting of a serial parsing algorithm and a trainable net. The system fulfills the following design goals: (1) parsing of sentences without length restriction, (2) soundness and completeness for any context-free language, and (3) learning the applicability of parsing rules with a neural network to increase the efficiency of the whole system. BrainC (backtracktacking and backpropagation in C) combines the well- known shift-reduce parsing technique with backtracking with a backpropagation network to learn and represent typical structures of the trained natural language grammars. The system has been implemented as a subsystem of the Rochester Connectionist Simulator (RCS) on SUN workstations and was tested with several grammars for English and German. The design of the system and then the results are discussed.}, doi = {10.1117/12.44957}, isbn = {9780819405784}, } @inproceedings{1991_274, author = {Zell, Andreas and Mache, Niels and Sommer, Tilman and Korb, Thomas}, title = {Recent Developments of the {SNNS} Neural Network Simulator}, booktitle = {Applications of Artificial Neural Networks II (SPIE's 1991 Aerospace Sensing International Symposium)}, year = {1991}, editor = {Steven K. Rogers}, volume = {1469}, series = {Proceedings of SPIE}, pages = {708-718}, month = aug, publisher = {SPIE}, abstract = {A neural network simulator for Unix workstations, SNNS, under development at the Universitat Stuttgart, Germany, is described. The network simulation environment is a tool to generate, train, test, and visualize artificial neural networks. The simulator consists of three major components: a simulator kernel that operates on the internal representation of the neural networks, a graphical user interface based on X-Windows to interactively construct and change small neural nets, and a compiler to generate the internal representation of large neural networks from a high-level network description language.}, doi = {10.1117/12.45009}, isbn = {9780819405784}, } @techreport{1991_273, author = {Zell, Andreas and Becker, Wolfgang}, title = {{Kooperatives Planen unabh\"angiger Agenten}}, institution = {Universit\"at Stuttgart}, year = {1991}, month = apr, } @inproceedings{1991_272, author = {Adrian M{\"}uller and Andreas Zell}, title = {Natural Language Parsing in a Hybrid Connectionist-Symbolic Architecture}, booktitle = {Applications of Artificial Neural Networks II (SPIE's 1991 Aerospace Sensing International Symposium)}, year = {1991}, editor = {Mohan M. Trivedi}, volume = {1468}, series = {Proceedings of SPIE}, pages = {875--881}, month = mar, publisher = {SPIE}, abstract = {Most connectionist parsers either cannot guarantee the correctness of their derivations or have to simulate a serial flow of control. In the first case, users have to restrict the tasks (e.g. parse less complex or shorter sentences) of the parser or they need to believe in the soundness of the result. In the second case, the resulting network has lost most of its attractivity because seriality needs to be hard-coded into the structure of the net. We here present a hybrid symbolic connectionist parser, which was designed to fulfill the following goals: (1) parsing of sentences without length restriction, (2) soundness and completeness for any context-free grammar, and (3) learning the applicability of parsing rules with a neural network. Our hybrid architecture consists of a serial parsing algorithm and a trainable net. BrainC (Backtracking and Backpropagation in C) combines the well known shift-reduce parsing technique with backtracking with a backpropagation network to learn and represent the typical properties of the trained natural language grammars. The system has been implemented as a subsystem of the Rochester Connectionist Simulator (RCS) on SUN- Workstations and was tested with several grammars for English and German. We discuss how BrainC reached its design goals and what results we observed.}, doi = {10.1117/12.45526}, isbn = {9780819405777}, } @techreport{1991_277, author = {Becker, Wolfgang and Zell, Andreas}, title = {Cooperative Planning of Independent Agents}, institution = {Universit\"at Stuttgart, Fakult\"at Informatik}, year = {1991}, number = {5/91}, } @techreport{1991_275, author = {Zell, Andreas and Korb, Thomas and Mache, Niels and Sommer, Tilman}, title = {{SNNS Benutzerhandbuch}}, institution = {Universit\"at Stuttgart, Fakult\"at Informatik, Germany}, year = {1991}, number = {1/91}, } @techreport{1991_276, author = {Zell, Andreas and Korb, Thomas and Mache, Niels and Sommer, Tilman}, title = {{SNNS Nessus-Handbuch}}, institution = {Universit\"at Stuttgart, Fakult\"at Informatik, Germany}, year = {1991}, number = {3/91}, } @inproceedings{1991_279, author = {Zimmerer, Peter and Zell, Andreas}, title = {{Translations- und rotationsinvariante Erkennung von Werkst\"ucken mit neuronalen Netzen}}, booktitle = {13. DAGM Symposium Mustererkennung}, year = {1991}, volume = {290}, series = {Informatik-Fachberichte}, pages = {51-58}, address = {M\"unchen, Germany}, publisher = {Springer}, isbn = {3-540-54597-2}, } @inproceedings{1990_270, author = {Zell, Andreas and Korb, Thomas and Sommer, Tilman and Bayer, Rolf}, title = {A Neural Network Simulation Environment}, booktitle = {SPIE's 1990 Aerospace Sensing International Symposium}, year = {1990}, pages = {535-44}, address = {Orlando, Florida, USA}, } @inproceedings{1989_269, author = {Zell, Andreas and Korb, Thomas and Sommer, Tilman and Bayer, Rolf}, title = {{NetSim: Ein Simulator f\"ur Neuronale Netze}}, booktitle = {13th German Workshop on Artificial Intelligence}, year = {1989}, volume = {216}, series = {Informatik Fachberichte}, pages = {134--143}, address = {Eringerfeld, Germany}, month = sep, publisher = {Springer}, note = {In German}, isbn = {3-540-51743-X}, } @inproceedings{1989_267, author = {Korb, Thomas and Zell, Andreas}, title = {A Declarative Neural Network Description Language}, booktitle = {Fifteenth {EUROMICRO} Symposium on Microprocessing and Microprogramming}, year = {1989}, volume = {27}, number = {1-5}, series = {Microprocessing and Microprogramming}, pages = {181-188}, address = {North Holland}, month = aug, } @inproceedings{1989_264, author = {Zell, Andreas and Br\"aunl, Thomas}, title = {Iterative Deepening Prolog}, booktitle = {Frontiers in Artificial Intelligence and Applications (Proceedings of the Second Scandinavian Conference on Artificial Intelligence)}, year = {1989}, pages = {919--929}, address = {Amsterdam, The Netherlands}, month = jun, publisher = {IOS Press}, isbn = {90-5199-017-0}, location = {Tampere, Finland}, } @inproceedings{1989_265, author = {Zell, Andreas}, title = {{Zeitbeschr\"anktes Logisches Programmieren}}, booktitle = {5.~\"Osterreichische Artificial Intelligence-Tagung}, year = {1989}, editor = {Retti, J. and Leidlmair, K.}, pages = {96-105}, address = {Igls, Tirol, Austria}, publisher = {Springer}, note = {In German}, } @phdthesis{1989_268, author = {Zell, Andreas}, title = {{Metaebenen-Architekturen logischer Programme}}, school = {Universit\"at Stuttgart}, year = {1989}, note = {In German}, } @inproceedings{1989_266, author = {Zell, Andreas and Br\"aunl, Thomas}, title = {An Alternative Prolog Search Strategy}, booktitle = {2nd International Conference on Industrial and Engineering Applications of Artificial Intelligence and Expert Systems (IEA/AIE)}, year = {1989}, pages = {722--728}, address = {Tullahoma, Tennessee, USA}, publisher = {ACM}, doi = {http://doi.acm.org/10.1145/67312.67339}, isbn = {0-89791-320-5}, } @inproceedings{1988_263, author = {Zell, Andreas}, title = {Time Constrained Logic Programming}, booktitle = {Fifth Israeli Symposium on Artificial Intelligence, Vision and Pattern Recognition}, year = {1988}, pages = {301--314}, address = {Tel Aviv, Israel}, }