MulCNN: An efficient and accurate deep learning method based on gene embedding for cell type identification in single-cell RNA-seq data

Advancements in single-cell sequencing research have revolutionized our understanding of cellular heterogeneity and functional diversity through the analysis of single-cell transcriptomes and genomes. A crucial step in single-cell RNA sequencing (scRNA-seq) analysis is identifying cell types. However, scRNA-seq data are often high dimensional and sparse, and manual cell type identification can be time-consuming, subjective, and lack reproducibility. Consequently, analyzing scRNA-seq data remains a computational challenge. With the increasing availability of well-annotated scRNA-seq datasets, advanced methods are emerging to aid in cell type identification by leveraging this information. Deep learning neural networks have great potential for analyzing single-cell data. This paper proposes MulCNN, a multi-level convolutional neural network that uses a unique cell type-specific gene expression feature extraction method. This method extracts critical features through multi-scale convolution while filtering noise. Extensive testing using datasets from various species and comparisons with popular classification methods show that MulCNN has outstanding performance and offers a new and scalable direction for scRNA-seq analysis.