EnGRNT: Inference of gene regulatory networks using ensemble methods and topological feature extraction

Abstract The development of computational methods to predict gene regulatory networks (GRNs) from gene expression data is a challenging task. Many machine learning methods have been developed, including supervised, unsupervised, and semi-supervised to infer gene regulatory networks. Most of these methods ignore the class imbalance problem which can lead to decreasing the accuracy of predicting regulatory interactions in the network. Therefore, developing an effective method considering imbalanced data is a challenging task. In this paper, we propose EnGRNT approach to infer GRNs with high accuracy that uses ensemble-based methods. The proposed approach, as well as the gene expression data, considers the topological features of GRN. We applied our approach to the simulated Escherichia coli dataset. Experimental results demonstrate that the appropriateness of the inference method relies on the size and type of expression profiles in microarray data. Except for multifactorial experimental conditions, the proposed approach outperforms unsupervised methods. The obtained results recommend the application of EnGRNT on the imbalanced datasets.