Supervised Adversarial Alignment of Single-Cell RNA-seq Data

Songwei Ge, Haohan Wang, Amir Alavi, Eric Xing, Ziv Bar-Joseph

Research output: Chapter in Book/Report/Conference proceedingConference contribution


Dimensionality reduction is an important first step in the analysis of single cell RNA-seq (scRNA-seq) data. In addition to enabling the visualization of the profiled cells, such representations are used by many downstream analyses methods ranging from pseudo-time reconstruction to clustering to alignment of scRNA-seq data from different experiments, platforms, and labs. Both supervised and unsupervised methods have been proposed to reduce the dimension of scRNA-seq. However, all methods to date are sensitive to batch effects. When batches correlate with cell types, as is often the case, their impact can lead to representations that are batch rather than cell type specific. To overcome this we developed a domain adversarial neural network model for learning a reduced dimension representation of scRNA-seq data. The adversarial model tries to simultaneously optimize two objectives. The first is the accuracy of cell type assignment and the second is the inability to distinguish the batch (domain). We tested the method by using the resulting representation to align several different datasets. As we show, by overcoming batch effects our method was able to correctly separate cell types, improving on several prior methods suggested for this task. Analysis of the top features used by the network indicates that by taking the batch impact into account, the reduced representation is much better able to focus on key genes for each cell type.

Original languageEnglish (US)
Title of host publicationResearch in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings
EditorsRussell Schwartz
PublisherSpringer Netherlands
Number of pages16
ISBN (Print)9783030452568
StatePublished - 2020
Externally publishedYes
Event24th Annual Conference on Research in Computational Molecular Biology, RECOMB 2020 - Padua, Italy
Duration: May 10 2020May 13 2020

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume12074 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference24th Annual Conference on Research in Computational Molecular Biology, RECOMB 2020


  • Batch effect removal
  • Data integration
  • Dimensionality reduction
  • Domain adversarial training
  • Single-cell RNA-seq

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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