Name
Title | ||
|---|---|---|
Benchmarking evolutionary algorithms on convenience kinetics models of the valine and leucine biosynthesis in C. glutamicum |
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. |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1109/CEC.2007.4424565 | IEEE Congress on Evolutionary Computation |
Keywords | Field | DocType |
biochemistry,differential equations,evolutionary computation,parameter estimation,corynebacterium glutamicum,anaerobic actinobacterium,benchmarking,biochemical modeling,biochemical system models,convenience kinetics models,differential evolution,evolution strategy,evolutionary algorithms,genetic algorithm,glucose stimulus-response experiment,independent spline approximations,irreversible differential equation model,leucine biosynthesis,metabolic subnetwork,metabolites,parameter inference problem,particle swarm optimization,systems biology,valine biosynthesis,kinetics,differential equation,system modeling,evolutionary algorithm,difference set,system biology | Particle swarm optimization,Corynebacterium glutamicum,Mathematical optimization,Evolutionary algorithm,Computer science,Systems biology,Evolutionary computation,Differential evolution,Evolution strategy,Genetic algorithm | Conference |
ISBN | Citations | PageRank |
978-1-4244-1340-9 | 3 | 0.49 |
References | Authors | |
6 | 7 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Andreas Dräger | 1 | 292 | 22.16 |
| Marcel Kronfeld | 2 | 74 | 6.67 |
| Jochen Supper | 3 | 106 | 8.69 |
| Hannes Planatscher | 4 | 76 | 5.90 |
| Jørgen B. Magnus | 5 | 29 | 2.45 |
| Marco Oldiges | 6 | 38 | 2.82 |
| Andreas Zell | 7 | 1419 | 137.58 |