A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive...

Inferring gene regulatory networks (GRNs) is vital to understand the complex cellular processes and reveal the regulatory mechanisms among genes. Although various methods have been developed, more accurate algorithms which can control the sparseness of GRNs still need to be developed. In this work, we model GRNs by fuzzy cognitive maps (FCMs), and a node in an FCM means a gene. Then, a new sparse and decomposed particle swarm optimization, termed as SDPSO_FCM-GRN, is proposed to train FCMs, which employs the least absolute shrinkage and selection operator (Lasso) to control the network sparseness with a decomposed strategy. In the experiments, the performance of SDPSO_FCM-GRN is validated on synthetic data and the well-known benchmark DREAM3 and DREAM4. The results show that SDPSO_FCM-GRN can well control the sparseness of GRNs, and infer directed GRNs with high accuracy and efficiency.