FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data.

ABSTRACT: Integrating single-cell and spatial omics data remains challenging due to strong batch effects across experiments and platforms. Existing methods focus on minimizing these effects but cannot disentangle technical variation from true biological signals. Here, we present FADVI, a variational autoencoder framework partitioning the latent space into batch-specific, label-related, and residual subspaces. By combining supervised classification, adversarial training, and cross-covariance penalty, FADVI enforces independent representations that preserve biological variation while correcting batch effects. Benchmarking across scRNA-seq, scATAC-seq, and high-resolution spatial transcriptomics datasets, FADVI consistently outperformed state-of-the-art integration methods. FADVI also enables feature a

SUBMITTER: Liu W 

PROVIDER: S-EPMC12637411 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature