Winner-Take-All Memetic Differential Evolution for Genetic Interaction: Parameter Identification
Shinq-Jen Wu, Cheng-Tao Wu · 2013
The emerging large-scale biological tools (e.g., micro array) challenge biologists to realize the connectivity of genes and/or proteins at the system level (global view). Having advantages in good generalization and showing the direct interaction of genes and/or proteins, the S-system becomes one of the popular models, which is able to capture the dynamic behavior of the biological system. Differential evolution (DE) and its variants have recently applied to solve various optimization problems in engineering fields. However, the exploitative and explorative abilities are insufficient. In this study, we propose a winner-take-all memetic differential evolution scheme to infer the parameters of the S-type gene regulatory networks. This method was tested with a genetic-branch pathway and a twenty-gene network. The learning was implemented in a wide search space ([0, 100] for rate constants and [-100, 100] for kinetic orders) with a bad initial start (All parameters were randomly initialized at the neighborhood of 80). Simulation results show high-accuracy solutions are obtained.