Accurate identification of single-cell types via correntropy-based Sparse PCA combining hypergraph and fusion similarity

Juan Wang, Tai-Ge Wang, Shasha Yuan and Feng Li

Journal of Applied Statistics, 2025, vol. 52, issue 2, 356-380

Abstract: The advent of single-cell RNA sequencing (scRNA-seq) technology enables researchers to gain deep insights into cellular heterogeneity. However, the high dimensionality and noise of scRNA-seq data pose significant challenges to clustering. Therefore, we propose a new single-cell type identification method, called CHLSPCA, to address these challenges. In this model, we innovatively combine correntropy with PCA to address the noise and outliers inherent in scRNA-seq data. Meanwhile, we integrate the hypergraph into the model to extract more valuable information from the local structure of the original data. Subsequently, to capture crucial similarity information not considered by the PCA model, we employ the Gaussian kernel function and the Euclidean metric to mine the similarity information between cells, and incorporate this information into the model as the similarity constraint. Furthermore, the principal components (PCs) of PCA are very dense. A new sparse constraint is introduced into the model to gain sparse PCs. Finally, based on the principal direction matrix learned from CHLSPCA, we conduct extensive downstream analyses on real scRNA-seq datasets. The experimental results show that CHLSPCA performs better than many popular clustering methods and is expected to promote the understanding of cellular heterogeneity in scRNA-seq data analysis and support biomedical research.

Date: 2025
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DOI: 10.1080/02664763.2024.2369955

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