MultiFlow: coupled flow matching for predicting single-cell multiomic perturbation responses in unseen cellular contexts

MultiFlow couples RNA and ATAC flow matching to predict paired single-cell multiomic perturbation responses, achieving strongest overall performance on unseen cellular contexts in multiome benchmarks.

• Why it matters: Most single-cell perturbation models predict transcription alone, leaving coordinated RNA–ATAC changes and context-dependent perturbation effects insufficiently modeled.
• What they did: MultiFlow uses bidirectional information exchange between RNA and ATAC generative flows to learn how their joint distribution depends on cellular context and perturbation identity.
• The result: It accurately reproduces paired RNA–ATAC states and population distributions, and outperforms modality-specific perturbation-prediction methods while preserving perturbation-induced cross-modal coordination.