Evolutionary divide-and-conquer approach to inferring S-system models of genetic networks

Abstract

This paper proposes an efficient evolutionary divide-and-conquer approach (EDACA) to inferring S-system models of genetic networks from time-series data of gene expression. Inference of an S-system model has 2N(N+l) parameters to be optimized where N is the number of genes in a genetic network. To cope with higher dimensionality, the proposed approach 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). The intelligent crossover divides two parents into n pairs of parameter groups, economically identifies the potentially better one of two groups of each pair, and systematically obtains a potentially good approximation to the best one of all 2(n) combinations using at most 2n function evaluations. At the second stage, the obtained N solutions to the N subproblems are combined and refined using an OED-based simulated annealing algorithm (OSA) for handling noisy gene expression data. The effectiveness of EDACA is evaluated using simulated expression patterns with/without noise running on a single-CPU PC. It is shown that: 1) IGA is efficient enough to solve subproblems; 2) IGA is significantly superior to. the existing method of using GA with simplex crossover; and 3) EDACA performs well in inferring S-system models of genetic networks from small-noise gene expression data.