Enhancing Single-Cell RNA-Seq Data Completeness With a Graph Learning Framework

Single cell RNA sequencing (scRNA-seq) is a powerful tool to capture gene expression snapshots in individual cells. However, a low amount of RNA in the individual cells results in dropout events, which introduce huge zero counts in the single cell expression matrix. We have developed VAImpute, a variational graph autoencoder based imputation technique that learns the inherent distribution of a large network/graph constructed from the scRNA-seq data leveraging copula correlation ($Ccor$) among cells/genes. The trained model is utilized to predict the dropouts events by computing the probability of all non-edges (cell-gene) in the network. We devise an algorithm to impute the missing expression values of the detected dropouts. The performance of the proposed model is assessed on both simulated and real scRNA-seq datasets, comparing it to established single-cell imputation methods. VAImpute yields significant improvements to detect dropouts, thereby achieving superior performance in cell clustering, detecting rare cells, and differential expression.