A Single-Cell Clustering Algorithm Based on Structure Perturbation Non-Negative Matrix Factorization

The advent of single-cell RNA sequencing (scRNA-seq) has facilitated the acquisition of high-resolution data regarding cell heterogeneity across various tissues. A fundamental and critical step in the analysis of scRNA-seq data is cell type identification. An appropriate graph construction strategy can reflect the topological structure between cells and allows for detailed exploration of the relationships between cells and genes. Given the sparsity of scRNA-seq data and the pronounced noise generated by shallow sequencing, choosing an appropriate graph construction strategy has become a significant challenge. In this paper, we propose a single-cell clustering method, named Sc-PNNMF, based on structural perturbation of nonnegative matrix factorization. Sc-PNNMF employs a structural perturbation algorithm to optimize the gene expression matrix. The optimized matrix guides the matrix factorization process, effectively overcoming the impact of data sparsity and significant noise in gene expression data on the graph construction strategy. We compared the clustering abilities of Sc-PNNMF with five other methods on ten real datasets.