SIGRN: Inferring Gene Regulatory Network with Soft Introspective Variational Autoencoders

Gene regulatory networks (GRNs) exhibit the complex regulatory relationships among genes, which are essential for understanding developmental biology and uncovering the fundamental aspects of various biological phenomena. It is an effective and economical way to infer GRNs from single-cell RNA sequencing (scRNA-seq) with computational methods. Recent researches have been done on the problem by using variational autoencoder (VAE) and structural equation model (SEM). Due to the shortcoming of VAE generating poor-quality data, in this paper, a soft introspective adversarial gene regulatory network unsupervised inference model, called SIGRN, is proposed by introducing adversarial mechanism in building a variational autoencoder model. SIGRN applies “soft” introspective adversarial mode to avoid training additional neural networks and adding additional training parameters. It demonstrates superior inference accuracy across most benchmark datasets when compared to nine leading-edge methods. In addition, method SIGRN also achieves better performance on representing cells and generating scRNA-seq data in most datasets. All of which have been verified via substantial experiments. The SIGRN method shows promise for generating scRNA-seq data and inferring GRNs.