Graph attention network with convolutional layer for predicting gene regulations from single-cell ribonucleic acid sequence data

Abstract

Reconstructing gene regulatory networks (GRNs) is an important task to reveal the regulatory relationship between genes and understand the mechanism of intracellular gene expression regulation. With the development of single-cell ribonucleic acid sequencing (scRNA-seq) technology, researchers begin to attempt to infer GRN within cells. In this paper, we propose graph attention network with convolutional layer (GATCL) to infer the latent interactions between transcription factors (TFs) and target genes in GRN. Firstly, GATCL uses graph attention network (GAT), which can effectively extract information about genes and TFs. Secondly, we combine multi-head attention layer with one-head attention layer and propose a new method of using convolution instead of weight matrix. Thirdly, we use the exponential linear unit (ELU) activation function to replace the leaky rectified linear unit (LReLU) commonly used in GAT, which further improves the accuracy of GATCL. The AUROC of our method on seven scRNA-seq datasets with four types of ground-truth networks reached an average of 0.827, which is higher than other state-of-the-art models. GATCL applies a supervised deep learning algorithm to solve the problems existing in the inference of GRN from scRNA-seq in the engineering field, and the effectiveness of this method is verified by a large number of experiments.