sigRGCN: A Robust Residual Graph Convolutional Network for scRNA-Seq Data Clustering

Zhenqiu Shu, Min Xia, Kaiwen Tan, Zhengtao Yu, Xiaojun Wu

Abstract: Clustering is a crucial step in single-cell RNA sequencing (scRNA-seq) data analysis, facilitating the discovery of new cell types and the grouping of similar cells. Recently, graph convolutional networks (GCNs) have gained prominence in scRNA-seq data clustering because they effectively learn cell representations by capturing the relationship between cells. However, GCNs are sensitive to noise in scRNA-seq data and are prone to over-smoothing, resulting in the loss of cell-specific information. To overcome these challenges, we propose sigRGCN, a robust residual graph convolutional network for scRNA-seq data clustering. Specifically, we first construct a disturbed cell graph by injecting noise into a cell graph constructed from scRNA-seq data. Then, we design a graph structure optimization graph convolutional network to eliminate the impact of noise in the disturbed cell graph. It significantly improves the robustness of the proposed model in real scRNA-seq data clustering tasks. After that, we utilize a $L$-layers residual graph convolutional network to alleviate the over-smoothing problem. It allows our model to effectively capture higher-order relationships between cells, leading to better cell representations. Finally, we employ a self-supervised manner to optimize our model. The experimental results on nine real scRNA-seq datasets show that our proposed model demonstrates competitive performance in real clustering tasks.

External IDs:dblp:journals/tcbb/ShuXTYW25