Single-cell RNA-sequencing data clustering using variational graph attention auto-encoder with self-supervised leaning

The emergence of single-cell RNA-seq (scRNA-seq) technology makes it possible to capture their differences at the cellular level, which contributes to studying cell heterogeneity. By extracting, amplifying and sequencing the genome at the individual cell level, scRNA-seq can be used to identify unknown or rare cell types as well as genes differentially expressed in specific cell types under different conditions using clustering for downstream analysis of scRNA-seq. Many clustering algorithms have been developed with much progress. However, scRNA-seq often appears with characteristics of high dimensions, sparsity and even the case of dropout events', which make the performance of scRNA-seq data clustering unsatisfactory. To circumvent the problem, a new deep learning framework, termed variational graph attention auto-encoder (VGAAE), is constructed for scRNA-seq data clustering. In the proposed VGAAE, a multi-head attention mechanism is introduced to learn more robust low-dimensional representations for the original scRNA-seq data and then self-supervised learning is also recommended to refine the clusters, whose number can be automatically determined using Jaccard index. Experiments have been conducted on different datasets and results show that VGAAE outperforms some other state-of-the-art clustering methods.