Single-cell RNA-seq data clustering by deep information fusion

Abstract

Abstract Determining cell types by single-cell transcriptomics data is fundamental for downstream analysis. However, cell clustering and data imputation still face the computation challenges, due to the high dropout rate, sparsity and dimensionality of single-cell data. Although some deep learning based solutions have been proposed to handle these challenges, they still can not leverage gene attribute information and cell topology in a sensible way to explore the consistent clustering. In this paper, we present scDeepFC, a deep information fusion-based single-cell data clustering method for cell clustering and data imputation. Specifically, scDeepFC uses a deep auto-encoder (DAE) network and a deep graph convolution network to embed high-dimensional gene attribute information and high-order cell–cell topological information into different low-dimensional representations, and then fuses them to generate a more comprehensive and accurate consensus representation via a deep information fusion network. In addition, scDeepFC integrates the zero-inflated negative binomial (ZINB) into DAE to model the dropout events. By jointly optimizing the ZINB loss and cell graph reconstruction loss, scDeepFC generates a salient embedding representation for clustering cells and imputing missing data. Extensive experiments on real single-cell datasets prove that scDeepFC outperforms other popular single-cell analysis methods. Both the gene attribute and cell topology information can improve the cell clustering.