Semisupervised Generative Autoencoder for Single-Cell Data

J Comput Biol. 2020 Aug;27(8):1190-1203. doi: 10.1089/cmb.2019.0337. Epub 2019 Dec 2.


Single-cell transcriptomics offers a tool to study the diversity of cell phenotypes through snapshots of the abundance of mRNA in individual cells. Often there is additional information available besides the single-cell gene expression counts, such as bulk transcriptome data from the same tissue, or quantification of surface protein levels from the same cells. In this study, we propose models based on the Bayesian deep learning approach, where protein quantification, available as CITE-seq counts, from the same cells is used to constrain the learning process, thus forming a SemI-SUpervised generative Autoencoder (SISUA) model. The generative model is based on the deep variational autoencoder (VAE) neural network architecture.

Keywords: autoencoder; deep learning; generative; protein; semisupervised; single-cell; variational.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bayes Theorem
  • Computational Biology / methods*
  • Neural Networks, Computer
  • Single-Cell Analysis / methods*
  • Transcriptome / genetics*