A Preference-Based Evolutionary Biobjective Approach for Learning Large-Scale Fuzzy Cognitive Maps: An Application to Gene Regulatory Network Reconstruction

Learning large-scale fuzzy cognitive maps (FCMs) with the sparse attribute automatically from time series without prior knowledge remains a challenging problem. Most existing automated learning methods were applied to learn small-scale FCMs, and the learned FCMs are much denser than the maps constructed by human experts. Learning FCMs is the procedure of judging whether there are connecting edges and determining the weights of connecting edges. Thus, we transform the problem of learning FCMs into a biobjective optimization problem with two objects of minimizing the measure error and the number of nonzero entries, respectively. To solve this optimization problem, a preference-based iterative thresholding evolutionary biobjective optimization algorithm for learning FCMs is proposed. The strategy focuses on the knee area of the Pareto front (PF) with preference on the solutions near the true sparsity. Moreover, an initialization operator based on random forest is proposed to increase the speed of convergence toward the PF. The experiments on large-scale synthetic data with varying sizes and densities and the application to the gene regulatory network reconstruction problem have been conducted to demonstrate that our proposal matches or exceeds the existing state-of-the-art FCM learning approaches in most cases in terms of four measures, namely, Data_Error, Out_of_Sample_Error, Model Error, and SS_Mean. The Data_Error obtained by the proposed method can achieve 3.07E-06 even when the number of nodes reaches 200. We also demonstrate the effectiveness of the proposed initialization operator and the preference-based strategy, which can result in a fast convergence speed and higher accuracy.