scGNN: scRNA-seq Dropout Imputation via Induced Hierarchical Cell Similarity Graph

Abstract: Single-cell RNA sequencing provides tremendous insights to understand biological systems. However, the noise from dropout can corrupt the downstream biological analysis. Hence, it is desirable to impute the dropouts accurately. In this work, we propose a simple and powerful dropout imputation method (scGNN) by applying a bottlenecked Graph Convolutional Neural Network on an induced hierarchical cell similarity graph. We show scGNN has competitive performance against state-of-the-art baselines across three datasets and can improve downstream analysis.