Conditional Neural Optimal Transport for Predicting Cellular Phenotypes from Molecular Structure
This study addresses the challenge of cellular phenotypic characterization arising from the vastness of chemical space by proposing a Molecule-Conditioned Neural Optimal Transport model. Conditioning on molecular structures, this approach integrates Monge-gap regularization with compressed representation space transport to learn mappings from negative controls to perturbed phenotypes, effectively overcoming static coupling failures in large-scale datasets. Experimental results demonstrate that the proposed framework significantly outperforms baseline methods on unseen active molecules by accurately recovering specific phenotypes and mitigating technical variation. Furthermore, it enables cross-batch phenotypic comparison and zero-shot generalization, validating its efficacy for virtual screening applications in drug discovery.