Effective parameter estimation for S-system models using LPMs and evolutionary algorithms

Abstract

An S-system model is considered as an ideal model for describing genetic networks. As one of effective techniques for inferring S-system models of genetic networks, the problem decomposition strategy has been proposed. This strategy defines the inference of a genetic network consisting of N genes as N subproblems, each of which is a 2(N+1)-dimensional function optimization problem. When we try to infer large-scale genetic networks consisting of many genes, however, it is not always easy for function optimization algorithms to solve 2(N + 1)-dimensional problems. In this study, we thus propose a new technique that transforms the 2(N + 1)-dimensional S-system parameter estimation problems into (N+2)-dimensional problems. The proposed technique reduces the search dimensions of the problems by solving linear programming problems. The transformed problems are then optimized using evolutionary algorithms. Finally, through numerical experiments on an artificial genetic network inference problem, we show that the proposed dimension reduction approach is more than 3 times faster than the problem decomposition approach.