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PerturbRx: Learning Treatment-Conditioned Latent Transitions for Patient Drug Response Prediction

Research Bioinformatics AI

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TL;DR - PerturbRx predicts patient-level cancer drug response by learning treatment- and dose-conditioned latent molecular transitions from single-cell perturbation data. It improves aggregate performance on TCGA and patient-derived xenograft benchmarks without requiring patients’ post-treatment measurements.

  • Learns intervention-induced transitions from context-matched but unpaired control and treated single-cell populations.
  • Freezes and transfers the pretrained transition predictor to pretreatment patient molecular profiles.
  • Combines predicted transitions with patient and drug representations for response prediction.
  • Addresses data scarcity and tumor heterogeneity by explicitly modeling expected treatment-driven molecular changes.

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PerturbRx: Learning Treatment-Conditioned Latent Transitions for Patient Drug Response Prediction

arXiv q-bio.QM Yoshitaka Inoue, Minoh Jeong, Alfred Hero, Rui Kuang, Augustin Luna 2026-08-21 arXiv:2608.21349
Public signals Semantic Scholar citations 0 · Semantic Scholar influential citations 0
Providers: Hugging Face · N/A OpenAlex · N/A Publisher · N/A Semantic Scholar · Citations 0 · Influential citations 0 X · N/A Fetched 2026-09-17 14:29:33.709967 UTC

TL;DR - PerturbRx predicts patient-level cancer drug response by learning treatment- and dose-conditioned latent molecular transitions from single-cell perturbation data. It improves aggregate performance on TCGA and patient-derived xenograft benchmarks without requiring patients’ post-treatment measurements.

  • Learns intervention-induced transitions from context-matched but unpaired control and treated single-cell populations.
  • Freezes and transfers the pretrained transition predictor to pretreatment patient molecular profiles.
  • Combines predicted transitions with patient and drug representations for response prediction.
  • Addresses data scarcity and tumor heterogeneity by explicitly modeling expected treatment-driven molecular changes.
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