scE ² TM improves single-cell embedding interpretability and reveals cellular perturbation signatures

Single-cell RNA sequencing technologies have revolutionized our understanding of cellular heterogeneity, yet computational methods often struggle to balance performance with biological interpretability. Embedded topic models have been widely used for interpretable single-cell embedding learning. However, these models suffer from the potential problem of interpretation collapse, where topics semantically collapse towards each other, resulting in redundant topics and incomplete capture of biological variation. Furthermore, the rise of single-cell foundation models creates opportunities to harness external biological knowledge for guiding model embeddings. Here, we present scE ² TM, an external knowledge-guided embedded topic model that provides a high-quality cell embedding and interpretation for scRNA-seq analysis. Through embedding clustering regularization method, each topic is constrained to be the center of a separately aggregated gene cluster, enabling it to capture unique biological information. Across 20 scRNA-seq datasets, scE ² TM achieves superior clustering performance compared with seven state-of-the-art methods. A comprehensive interpretability benchmark further shows that scE ² TM-learned topics exhibit higher diversity and stronger consistency with underlying biological pathways. Modeling interferon-stimulated PBMCs, scE ² TM simulates topic perturbations that drive control cells toward stimulated-like transcriptional states, faithfully mirroring experimental interferon responses. In melanoma, scE ² TM identifies malignant-specific topics and extrapolates them to unseen patient data, revealing gene programs associated with patient survival.