NDLI: Comparing various evolutionary algorithms on the parameter optimization of the valine and leucine biosynthesis in corynebacterium glutamicum

Content Provider	IEEE Xplore Digital Library
Author	Drager, A. Supper, J. Planatscher, H. Magnus, J.B. Oldiges, M. Zell, A.
Copyright Year	2007
Description	Author affiliation: Center for Bioinformatics Tubingen (ZBIT), Tubingen (Drager, A.; Supper, J.; Planatscher, H.)
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 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.
Starting Page	620
Ending Page	627
File Size	387616
Page Count	8
File Format	PDF
ISBN	9781424413393
DOI	10.1109/CEC.2007.4424528
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-09-25
Publisher Place	Singapore
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Amino acids Evolutionary computation Biological system modeling Genetic algorithms Evolution (biology) Parameter estimation Systems biology Differential equations Feedback Covariance matrix
Content Type	Text
Resource Type	Article

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