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ABSTRACT
From gene expression profiles, it is desirable to rebuild cellular dynamic regulation networks to discover more delicate and substantial functions in molecular biology, biochemistry, bioengineering and pharmaceutics. S-system model is suitable to characterize biochemical network systems and capable to analyze the regulatory system dynamics. However, inference of an S-system model of N-gene genetic networks has 2N(N+1) parameters in a set of non-linear differential equations to be optimized. This paper proposes an intelligent two-stage evolutionary algorithm (iTEA) to efficiently infer the S-system models of genetic networks from time-series data of gene expression. To cope with curse of dimensionality, the proposed algorithm consists of two stages where each uses a divide-and-conquer strategy. The optimization problem is first decomposed into N subproblems having 2(N+1) parameters each. At the first stage, each subproblem is solved using a novel intelligent genetic algorithm (IGA) with intelligent crossover based on orthogonal experimental design (OED). At the second stage, the obtained N solutions to the N subproblems are combined and refined using an OED-based simulated annealing algorithm for handling noisy gene expression profiles. The effectiveness of iTEA is evaluated using simulated expression patterns with and without noise running on a single-processor PC. It is shown that 1) IGA is efficient enough to solve subproblems; 2) IGA is significantly superior to the existing method SPXGA; and 3) iTEA performs well in inferring S-system models for dynamic pathway identification.
INDEX TERMS
Divide-and-conquer, Evolutionary algorithm, Genetic network, Orthogonal experimental design, Pathway identification, S-system model
CITATION
Shinn-Ying Ho, Fu-Chieh Yu, Chih-Hung Hsieh, Hui-Ling Huang, "An Intelligent Two-Stage Evolutionary Algorithm for Dynamic Pathway Identification From Gene Expression Profiles", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. , pp. 648-704, October-December 2007, doi:10.1109/tcbb.2007.1051
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