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Training distribution determines the ceiling of drug-blind cancer sensitivity prediction

arXiv 2605.20885 ↗First posted 20 May 2026cs.LG q-bio.QMcited by 0

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Abstract (arXiv)

Precision oncology requires predicting which drugs will suppress a specific tumor from its molecular profile, but drug-blind sensitivity prediction has plateaued despite increasingly complex drug representations. Here we show that this stagnation reflects a metric artifact rather than a representational bottleneck. The standard benchmark, global Pearson r, is dominated by between-drug potency differences that a trivial drug-mean predictor captures without any cell-specific learning. Per-drug Pearson r, which isolates within-drug cell ranking, reveals that no drug encoding improves over cell-only features across four independent datasets. A controlled experiment channeling mechanism-of-action identity as either a drug feature or a training-distribution constraint identifies the cause. Supplying MoA as a feature yields negligible benefit, whereas using it to stratify training raises per-drug r substantially for targeted kinase inhibitors, because pan-cancer co-training suppresses pathway-specific sensitivity signals. Mechanism-stratified training and response matching from pilot observations provide two deployable strategies that together recover the principal sources of predictive gain in drug-blind sensitivity prediction.

Key facts. No citing papers in the map yet (data through 14 Oct 2026). Builds on 2 of its 23 references that are in the map. First posted on arXiv 20 May 2026.

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References · 2

  1. 2017Attention Is All You Needcited by 60,361
  2. 2020ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Predictioncited by 337

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