Causal disentanglement for single-cell representations and controllable counterfactual generation

Conducting disentanglement learning on single-cell omics data offers a promising alternative to traditional black-box representation learning by separating the semantic concepts embedded in a biological process. We present CausCell, which incorporates the causal relationships among disentangled concepts within a diffusion model to perform disentanglement learning, with the aim of increasing the explainability, generalizability and controllability of single-cell data, including spatial and temporal omics data, relative to those of the existing black-box representation learning models. Two quantitative evaluation scenarios, i.e., disentanglement and reconstruction, are presented to conduct the first comprehensive single-cell disentanglement learning benchmark, which demonstrates that CausCell outperforms the state-of-the-art methods in both scenarios. Additionally, CausCell can implement controllable generation by intervening with the concepts of single-cell data when given a causal structure. It also has the potential to uncover biological insights by generating counterfactuals from small and noisy single-cell datasets.