Single-Cell Clustering via Dual-Graph Alignment

In recent years, the field of single-cell RNA sequencing has seen a surge in the development of clustering methods. These methods enable the identification of cell subpopulations, thereby facilitating the understanding of tumor microenvironments. Despite their utility, most existing clustering algorithms primarily focus on the attribute information provided by the cell matrix or the network structure between cells, often neglecting the network between genes. This oversight could lead to loss of information and clustering results that lack clinical significance. To address this limitation, we develop an advanced single-cell clustering model incorporating dual-graph alignment, which integrates gene network information into the clustering process based on self-supervised and unsupervised optimization. Specifically, we designed a graph-based autoencoder enhanced by an attention mechanism to effectively capture relationships between cells. Moreover, we performed the node2vec method on Protein-Protein Interaction (PPI) networks to derive the gene network structure and maintained this structure throughout the clustering process. Our proposed method has been demonstrated to be effective through experimental results, showcasing its ability to optimize clustering outcomes while preserving the original associations between cells and genes. This research contributes to obtaining accurate cell subpopulations and generates clustering results that more closely resemble real-world biological scenarios. It provides better insights into the characteristics and distribution of diseased cells, ultimately building a foundation for early disease diagnosis and treatment.