Paper Detail
Yoshitaka Inoue, Minoh Jeong, Alfred Hero, Rui Kuang, Augustin Luna
Scarce data and tumor heterogeneity limit patient-level cancer treatment-response prediction. Existing approaches predict response from pretreatment molecular profiles and drug representations, without explicitly modeling the molecular changes expected under treatment. We propose PerturbRx, a treatment-conditioned representation learning framework that learns intervention-induced latent transitions and uses them as patient-drug response features. PerturbRx trains a drug- and dose-conditioned transition predictor from context-matched but cell-unpaired control and treated single-cell populations, then freezes and transfers the predictor to pretreatment patient profiles without requiring post-treatment measurements. The transition is combined with patient and drug representations to predict response. Across TCGA and patient-derived xenograft benchmarks, PerturbRx achieves the strongest aggregate predictive performance among the evaluated methods. These results support perturbation-pretrained latent transitions as useful representations for patient-level drug-response prediction.
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@article{inoue2026perturbrx,
title = {PerturbRx: Learning Treatment-Conditioned Latent Transitions for Patient Drug Response Prediction},
author = {Yoshitaka Inoue and Minoh Jeong and Alfred Hero and Rui Kuang and Augustin Luna},
year = {2026},
abstract = {Scarce data and tumor heterogeneity limit patient-level cancer treatment-response prediction. Existing approaches predict response from pretreatment molecular profiles and drug representations, without explicitly modeling the molecular changes expected under treatment. We propose PerturbRx, a treatment-conditioned representation learning framework that learns intervention-induced latent transitions and uses them as patient-drug response features. PerturbRx trains a drug- and dose-conditioned tra},
url = {https://arxiv.org/abs/2608.21349},
keywords = {q-bio.QM, cs.LG},
eprint = {2608.21349},
archiveprefix = {arXiv},
}
{}