Single-cell RNA sequencing data analysis utilizing multi-type graph neural networks

Single-cell RNA sequencing (scRNA-seq) is the sequencing technology of a single cell whose expression reflects the overall characteristics of the individual cell, facilitating the research of problems at the cellular level. However, the problems of scRNA-seq such as dimensionality reduction processing of massive data, technical noise in data, and visualization of single-cell type clustering cause great difficulties for analyzing and processing scRNA-seq data. In this paper, we propose a new single-cell data analysis model using denoising autoencoder and multi-type graph neural networks (scDMG), which learns cell–cell topology information and latent representation of scRNA-seq data. scDMG introduces the zero-inflated negative binomial (ZINB) model into a denoising autoencoder (DAE) to perform dimensionality reduction and denoising on the raw data. scDMG integrates multiple-type graph neural networks as the encoder to further train the preprocessed data, which better deals with various types of scRNA-seq datasets, resolves dropout events in scRNA-seq data, and enables preliminary classification of scRNA-seq data. By employing TSNE and PCA algorithms for the trained data and invoking Louvain algorithm, scDMG has better dimensionality reduction and clustering optimization. Compared with other mainstream scRNA-seq clustering algorithms, scDMG outperforms other state-of-the-art methods in various clustering performance metrics and shows better scalability, shorter runtime, and great clustering results. © 2024 Elsevier Ltd