scRDAN: a robust domain adaptation network for cell type annotation across single-cell RNA sequencing data

Single-cell RNA sequencing technology facilitates the recognition of diverse cell types and subgroups, playing a crucial role in investigating cellular heterogeneity. Cell type annotation, a crucial process in single-cell RNA sequencing analysis, is often influenced by noise and batch effects. To address these challenges, we propose scRDAN, which is a robust domain adaptation network comprising three modules: the denoising domain adaptation module, the fine-grained discrimination module, and the robustness enhancement module. The denoising domain adaptation module mitigates noise interference through feature reconstruction in domains, while leveraging adversarial learning to align data distributions, improving annotation accuracy and robustness against batch effects. The fine-grained discrimination module maintains intra-class compactness and enhances inter-class separability, reducing feature overlap and improving cell type distinction. Finally, the robustness enhancement module introduces noise from various perspectives in both domains, enhancing robustness and generalization. We evaluate scRDAN on simulated, cross-platforms, and cross-species datasets, comparing it with advanced methods. Results demonstrate that scRDAN outperforms existing methods in handling batch effects and cell type annotation.