Semi-supervised Deep Learning for Cell Type Identification from Single-Cell Transcriptomic Data.

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Abstract

Cell type identification from single-cell transcriptomic data is a common goal of single-cell RNA sequencing (scRNAseq) data analysis. Deep neural networks have been employed to identify cell types from scRNAseq data with high performance. However, it requires a large mount of individual cells with accurate and unbiased annotated types to train the identification models. Unfortunately, labeling the scRNAseq data is cumbersome and time-consuming as it involves manual inspection of marker genes. To overcome this challenge, we propose a semi-supervised learning model “SemiRNet” to use unlabeled scRNAseq cells and a limited amount of labeled scRNAseq cells to implement cell identification. The proposed model is based on recurrent convolutional neural networks (RCNN), which includes a shared network, a supervised network and an unsupervised network. The proposed model is evaluated on two large scale single-cell transcriptomic datasets. It is observed that the proposed model is able to achieve encouraging performance by learning on the very limited amount of labeled scRNAseq cells together with a large number of unlabeled scRNAseq cells.