Abstract
Single-cell RNA sequencing (RNA-seq) has been demonstrated to be a proven method for quantifying gene-expression heterogeneity and providing insight into the transcriptome at the single-cell level. When combining multiple single-cell transcriptome datasets for analysis, it is common to first correct the batch effect. Most of the state-of-the-art processing methods are unsupervised, i.e., they do not utilize single-cell cluster labeling information, which could improve the performance of batch correction methods, especially in the case of multiple cell types. To better utilize known labels for complex dataset scenarios, we propose a novel deep learning model named IMAAE (i.e., integrating multiple single-cell datasets via an adversarial autoencoder) to correct the batch effects. After conducting experiments with various dataset scenarios, the results show that IMAAE outperforms existing methods for both qualitative measures and quantitative evaluation. In addition, IMAAE is able to retain both corrected dimension reduction data and corrected gene expression data. These features make it a potential new option for large-scale single-cell gene expression data analysis.