scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species.
IF: 13.994
Cited by: 11


In single cell analyses, cell types are conventionally identified based on expressions of known marker genes, whose identifications are time-consuming and irreproducible. To solve this issue, many supervised approaches have been developed to identify cell types based on the rapid accumulation of public datasets. However, these approaches are sensitive to batch effects or biological variations since the data distributions are different in cross-platforms or species predictions. In this study, we developed scAdapt, a virtual adversarial domain adaptation network, to transfer cell labels between datasets with batch effects. scAdapt used both the labeled source and unlabeled target data to train an enhanced classifier and aligned the labeled source centroids and pseudo-labeled target centroids to generate a joint embedding. The scAdapt was demonstrated to outperform existing methods for classification in simulated, cross-platforms, cross-species, spatial transcriptomic and COVID-19 immune datasets. Further quantitative evaluations and visualizations for the aligned embeddings confirm the superiority in cell mixing and the ability to preserve discriminative cluster structure present in the original datasets.


Spatial Transcriptomics
batch correction
batch effects
single cell RNA-seq
single cell classification
spatial transcriptomic
virtual adversarial training

MeSH terms

Single-Cell Analysis
Species Specificity
Whole Exome Sequencing


Zhou, Xiang
Chai, Hua
Zeng, Yuansong
Zhao, Huiying
Yang, Yuedong

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