Inferring causal networks using fuzzy cognitive maps and evolutionary algorithms with application to gene regulatory network reconstruction

Abstract

Fuzzy cognitive maps have been widely used as abstract models for complex networks. Traditional ways to construct fuzzy cognitive maps rely on domain knowledge. In this paper, we propose to use fuzzy cognitive map learning algorithms to discover domain knowledge in the form of causal networks from data. More specifically, we propose to infer gene regulatory networks from gene expression data. Furthermore, a new efficient fuzzy cognitive map learning algorithm based on a decomposed genetic algorithm is developed to learn large scale networks. In the proposed algorithm, the simulation error is used as the objective function, while the model error is expected to be minimized. Experiments are performed to explore the feasibility of this approach. The high accuracy of the generated models and the approximate correlation between simulation errors and model errors suggest that it is possible to discover causal networks using fuzzy cognitive map learning. We also compared the proposed algorithm with ant colony optimization, differential evolution, and particle swarm optimization in a decomposed framework. Comparison results reveal the advantage of the decomposed genetic algorithm on datasets with small data volumes, large network scales, or the presence of noise.