Name
Abstract | ||
|---|---|---|
Motivation: The modeling of system dynamics of genetic networks, metabolic networks or signal transduction cascades from time-course data is formulated as a reverse-problem. Previous studies focused on the estimation of only network structures, and they were ineffective in inferring a network structure with feedback loops. We previously proposed a method to predict not only the network structure but also its dynamics using a Genetic Algorithm (GA) and an S-system formalism. However, it could predict only a small number of parameters and could rarely obtain essential structures. In this work, we propose a unified extension of the basic method. Notable improvements are as follows: (1) an additional term in its evaluation function that aims at eliminating futile parameters; (2) a crossover method called Simplex Crossover (SPX) to improve its optimization ability; and (3) a gradual optimization strategy to increase the number of predictable parameters. Results: The proposed method is implemented as a C program called PEACE1 (Predictor by Evolutionary Algorithms and Canonical Equations 1). Its performance was compared with the basic method. The comparison showed that: (1) the convergence rate increased about 5-fold; (2) the optimization speed was raised about 1.5-fold; and (3) the number of predictable parameters was increased about 5-fold. Moreover, we successfully inferred the dynamics of a small genetic network constructed with 60 parameters for 5 network variables and feedback loops using only time-course data of gene expression. |
Year | DOI | Venue |
|---|---|---|
2003 | 10.1093/bioinformatics/btg027 | BIOINFORMATICS |
Keywords | Field | DocType |
signal transduction,convergence rate,evolutionary algorithm,gene expression,system dynamics,metabolic network,genetic algorithm,feedback loop | Small number,Crossover,Evolutionary algorithm,Computer science,Evaluation function,Simplex,System dynamics,Rate of convergence,Bioinformatics,Genetic algorithm | Journal |
Volume | Issue | ISSN |
19 | 5.0 | 1367-4803 |
Citations | PageRank | References |
176 | 12.33 | 10 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Shinichi Kikuchi | 1 | 211 | 15.30 |
| D Tominaga | 2 | 305 | 38.88 |
| Masanori Arita | 3 | 484 | 46.91 |
| Katsutoshi Takahashi | 4 | 179 | 14.14 |
| Masaru Tomita | 5 | 1009 | 180.20 |