DeepImpute: an accurate, fast and scalable deep neural network method to impute single-cell RNA-Seq data

Abstract

BackgroundSingle-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. However, a significant problem of current scRNA-seq data is the large fractions of missing values or “dropouts” in gene counts. Incorrect handling of dropouts may affect downstream bioinformatics analysis. As the number of scRNA-seq datasets grows drastically, it is crucial to have accurate and efficient imputation methods to handle these dropouts.MethodsWe present DeepImpute, a deep neural network based imputation algorithm. The architecture of DeepImpute efficiently uses dropout layers and loss functions to learn patterns in the data, allowing for accurate imputation.ResultsOverall DeepImpute yields better accuracy than other publicly available scRNA-Seq imputation methods on experimental data, as measured by mean squared error or Pearson’s correlation coefficient. Moreover, its efficient implementation provides significantly higher performance over the other methods as dataset size increases. Additionally, as a machine learning method, DeepImpute allows to use a subset of data to train the model and save even more computing time, without much sacrifice on the prediction accuracy.ConclusionsDeepImpute is an accurate, fast and scalable imputation tool that is suited to handle the ever increasing volume of scRNA-seq data. The package is freely available at https://github.com/lanagarmire/DeepImpute