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bioRxiv · 10.64898/2025.12.09.693213

Drug Response Prediction Provides a Biologically Relevant Benchmark for Perturbation Response Models

Brouwer, N.·Damyanov, M.·Argelo, J.·Vis, D. J.·Reinders, M.·Wessels, L.
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Abstract

Perturbation response models (PRMs) predict transcriptional responses to interventions such as gene knockout or drug treatments. While simple baseline models match PRMs in reconstructing post-treatment profiles, we show that drug response predictors trained on PRM-generated profiles significantly outperform those trained on baseline or pre-treatment profiles. Unlike simple baseline models, PRMs preserve variation in response-relevant genes, making them a highly valuable tool for predicting drug response.

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Brouwer, N., Damyanov, M., Argelo, J., Vis, D. J., Reinders, M., Wessels, L.. 2025-12-11. Drug Response Prediction Provides a Biologically Relevant Benchmark for Perturbation Response Models. https://doi.org/10.64898/2025.12.09.693213

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