Intervention-Aware Multiscale Representation Learning from Imaging Phenomics and Perturbation Transcriptomics

arXiv:2604.22832v1 Announce Type: cross Abstract: Microscopy-based phenotypic profiling is scalable for drug discovery but lacks the mechanistic depth of transcriptomics, which remains costly and scarce. Existing multimodal approaches either use images to support other modalities or naively align representations by sample identity, ignoring cell-type and dose variations in weakly paired data-limiting generalization to unseen interventions. In this paper, we introduce an intervention-aware distil