scCausalVI disentangles single-cell perturbation responses with causality-aware generative model

Abstract Single-cell RNA sequencing provides detailed insights into cellular heterogeneity and responses to external stimuli. However, distinguishing inherent cellular variation from extrinsic effects induced by external stimuli remains a major analytical challenge. Here, we present scCausalVI, a causality-aware generative model designed to disentangle these sources of variation. scCausalVI decouples intrinsic cellular states from treatment effects through a deep structural causal network that explicitly models the causal mechanisms governing cell-state-specific responses to external perturbations while accounting for technical variations. Our model integrates structural causal modeling with cross-condition in silico prediction to infer gene expression profiles under hypothetical scenarios. Comprehensive benchmarking demonstrates that scCausalVI outperforms existing methods in disentangling causal relationships, quantifying treatment effects, generalizing to unseen cell types, and separating biological signals from technical variation in multi-source data integration. Applied to COVID-19 datasets, scCausalVI effectively identifies treatment-responsive populations and delineates molecular signatures of cellular susceptibility. Code availability Software is available at https://github.com/ShaokunAn/scCausalVI .