AdImpute: An Imputation Method for Single-Cell RNA-Seq Data Based on Semi-Supervised Autoencoders

Front Genet. 2021 Sep 8;12:739677. doi: 10.3389/fgene.2021.739677. eCollection 2021.

Abstract

Motivation: The emergence of single-cell RNA sequencing (scRNA-seq) technology has paved the way for measuring RNA levels at single-cell resolution to study precise biological functions. However, the presence of a large number of missing values in its data will affect downstream analysis. This paper presents AdImpute: an imputation method based on semi-supervised autoencoders. The method uses another imputation method (DrImpute is used as an example) to fill the results as imputation weights of the autoencoder, and applies the cost function with imputation weights to learn the latent information in the data to achieve more accurate imputation. Results: As shown in clustering experiments with the simulated data sets and the real data sets, AdImpute is more accurate than other four publicly available scRNA-seq imputation methods, and minimally modifies the biologically silent genes. Overall, AdImpute is an accurate and robust imputation method.

Keywords: autoencoder; imputation method; missing value filling; scRNA-seq; semi-supervised learning.