Prediction of Single-Cell perturbation response based on Direction-Constrained diffusion Schrödinger Bridge

Objective

Predicting transcriptional responses to external perturbations at the single-cell level is essential for understanding gene regulatory networks, drug discovery, and personalized interventions. The exponential increase in perturbation conditions creates data sparsity, making it difficult to capture dynamic responses and necessitating computational modeling.

Methods

We present Direction-Constrained Diffusion Schrödinger Bridge (DC-DSB), a generative framework that learns probabilistic trajectories between unperturbed and post-perturbation distributions by minimizing path-space KL divergence. To enhance conditional control, DC-DSB integrates hierarchical representations derived from experimental variables and biological prior knowledge. We further introduce a direction-constrained conditioning strategy that injects condition signals along the biologically relevant perturbation trajectory, thereby improving modeling quality and training stability.

Results

DC-DSB improves expression prediction accuracy and generalization to unseen combinations over baselines. By modeling dynamic expression trajectories and co-expression structures under perturbation, DC-DSB enables the discovery of synergistic and antagonistic gene interactions and supports the progressive reconstruction of regulatory pathways.

Conclusion

DC-DSB provides a biologically consistent and generalizable framework for single-cell perturbation modeling. Its trajectory-based and condition-aware architecture overcomes the limitations of static mappings and facilitates downstream analyses in gene regulation and drug discovery.