An optimized graph-based structure for single-cell RNA-seq cell-type classification based on non-linear dimension reduction

Abstract

Abstract Background It is now possible to analyze cellular heterogeneity at the single-cell level thanks to the rapid developments in single-cell sequencing technologies. The clustering of cells is a fundamental and common step in heterogeneity analysis. Even so, accurate cell clustering remains a challenge due to the high levels of noise, the high dimensions, and the high sparsity of data. Results Here, we present SCEA, a clustering approach for scRNA-seq data. Using two consecutive units, an encoder based on MLP and a graph attention auto-encoder, to obtain cell embedding and gene embedding, SCEA can simultaneously achieve cell low-dimensional representation and clustering performing various examinations to obtain the optimal value for each parameter, the presented result is in its most optimal form. To evaluate the performance of SCEA, we performed it on several real scRNA-seq datasets for clustering and visualization analysis. Conclusions The experimental results show that SCEA generally outperforms several popular single-cell analysis methods. As a result of using all available datasets, SCEA, in average, improves clustering accuracy by 4.4% in ARI Parameters over the well-known method scGAC. Also, the accuracy improvement of 11.65% is achieved by SCEA, compared to the Seurat model.