Deep feature extraction of single-cell transcriptomes by generative adversarial network

Single-cell RNA-sequencing (scRNA-seq) offers the opportunity to dissect heterogeneous cellular compositions and interrogate the cell-type-specific gene expression patterns across diverse conditions. However, batch effects such as laboratory conditions and individual-variability hinder their usage in cross-condition designs.

McGill University researchers have developed a single-cell Generative Adversarial Network (scGAN) to simultaneously acquire patterns from raw data while minimizing the confounding effect driven by technical artifacts or other factors inherent to the data. Specifically, scGAN models the data likelihood of the raw scRNA-seq counts by projecting each cell onto a latent embedding. Meanwhile, scGAN attempts to minimize the correlation between the latent embeddings and the batch labels across all cells. The researchers demonstrate scGAN on three public scRNA-seq datasets and show that this method confers superior performance over the state-of-the-art methods in forming clusters of known cell types and identifying known psychiatric genes that are associated with major depressive disorder.

Single-cell Generative Adversarial Network (scGAN)


The variational autoencoder (VAE) component of the scGAN model consists of the Encoder and Decoder networks. The Encoder projects each single-cell gene expression profile onto a low dimensional embedding. The Decoder takes the embedding as input and predicts the sufficient statistics of the Negative Binomial data likelihood of the scRNA-seq counts. The Discriminator, being trained adversarially alongside the Encoder network, predicts the batch effects using as input the Encoder’s embedding. Encoder, Decoder and the Discriminator are all parametric neural networks with learnable parameters.

Availability – The scGAN code and the information for the public scRNA-seq datasets are available at

Bahrami M, Maitra M, Nagy C, Turecki G, Rabiee HR, Li Y. (2020) Deep feature extraction of single-cell transcriptomes by generative adversarial network. Bioinformatics [Epub ahead of print]. [abstract]

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