DISC: A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning

Abstract

Dropouts distort gene expression and misclassify cell types in single-cell transcriptome. Although imputation may improve gene expression and downstream analysis to some degree, it also inevitably introduces false signals. We develop DISC, a novel deep learning network with semi-supervised learning to infer gene structure and expression obscured by dropouts. Compared with seven state-of-the-art imputation approaches on ten real-world datasets, we show that DISC consistently outperforms the other approaches. Its applicability, scalability, and reliability make DISC a promising approach to recover gene expression, enhance gene and cell structures, and improve cell type identification for sparse scRNA-seq data.