Dräger, Andreas and Kronfeld, Marcel and Supper, Jochen and Planatscher, Hannes and Magnus, Jørgen B. and Oldiges, Marco and Zell, Andreas

Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in C. glutamicum

IEEE Congress on Evolutionary Computation (CEC 2007), Singapore, IEEE Press, 2007, pp. 896-903


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 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.


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BibTeX

@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}
}