SEAL: Semantic-Aware Contrastive Learning for scRNA-Seq Clustering

The development of single-cell RNA sequencing (scRNA-seq) technology has enabled the exploration of biological processes at the cellular level. A critical task in scRNA-seq data analysis is the unsupervised clustering of cells to distinguish different cell types. While various clustering methods have been successfully developed for scRNA-seq data, they still face limitations, particularly in terms of unstable clustering performance. This is often due to their inability to fully capture the intrinsic properties of cells, especially in the presence of high dropout rates and noise in the data. In this work, we propose a SEmantic-Aware contrastive Learning (SEAL) approach for scRNA-seq clustering. Specifically, we randomly mask the gene expression of each cell to generate two different augmentations of the cell data, and then apply semantic-aware contrastive learning to capture semantically invariant representations across these augmentations by leveraging semantic information from generated pseudo-labels. Experimental results demonstrate that our method effectively learns biologically meaningful representations and accurately identifies cell types.