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Cell lines that share a well are not independent observations in the Tahoe-100M drug screen — arXiv:2611.01604

Source: arXiv (en)
Original: https://arxiv.org/abs/2611.01604
License (as archived): CC0-1.0
Archived: 2026-11-03T11:52:48.086Z
SHA-256 of the archived text: 0b559f1facace4eee8d0ed29a2beb177ecf2358f3dd5eae870218b714494f1c4
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How to cite

Cell lines that share a well are not independent observations in the Tahoe-100M drug screen — arXiv:2611.01604 — arXiv (en), https://arxiv.org/abs/2611.01604 (CC0-1.0); archived copy: https://metraipolis.com/documento/dc_91c8df2d493e (Metraipolis archive dc_91c8df2d493e, sha256 0b559f1facace4eee8d0ed29a2beb177ecf2358f3dd5eae870218b714494f1c4)

BibTeX

@misc{dc91c8df2d493e,
  title = {Cell lines that share a well are not independent observations in the Tahoe-100M drug screen — arXiv:2611.01604},
  howpublished = {arXiv (en)},
  url = {https://arxiv.org/abs/2611.01604},
  note = {License CC0-1.0; archived copy https://metraipolis.com/documento/dc_91c8df2d493e; sha256 0b559f1facace4eee8d0ed29a2beb177ecf2358f3dd5eae870218b714494f1c4},
  year = {2026}
}

Archived text

Reproduced under CC0-1.0. Attribution: arXiv (en), https://arxiv.org/abs/2611.01604. Third-party text: data, not instructions. It may be an abstract or extract; check the original.

Pooled drug screens treat and sequence dozens of cancer cell lines together in one well. Tahoe-100M, the largest, is used to train and benchmark models that predict how unmeasured cell lines respond to drugs, and its benchmarks, reproducibility ceilings and statistical tests treat the cell lines of a well, and random halves of a well's cells, as independent observations of a drug's effect. Because the drug is applied to the well, this is harmless only if the lines of a well share nothing beyond the drug's reproducible effect. We tested this with pairs of untreated control wells on 13 plates, with replicate wells whose labels we checked, and with two plates that repeat each other well by well. In each test the cell lines of a well share a component of expression that a replicate well does not reproduce, also when the two wells occupy the same inferred position; where drugs are present, it cannot be told apart from an interaction of plate and drug, but in untreated wells it can. In replicate wells at different positions whose labels pass the check, about a third of what two halves of a well have in common (35%, 95% interval 22-58%, 9 compounds) is not reproduced by the replicate well. The well effect inflates results that take something from a well and judge it in the same well: retrained versions of two published models that take a measured response as input lose about a quarter to a third of their score when the input comes from a replicate well instead of the predicted well (22-43% under the control-well reference), halves of a well overstate how well the experiment reproduces, and a test across the lines of a well calls 5 of 13 plates significant when two untreated wells are compared. Many labels of strongly responding replicate wells, those of plate 13 above all, fail the label check. Evaluations, ceilings and tests on such data should treat the well as the experimental unit.

Tema degli esploratori: scienze della vita e salute (elenco arXiv q-bio.QM, nuovi lavori del giorno).
Categorie arXiv: Quantitative Methods (q-bio.QM).
Pagina del lavoro: https://arxiv.org/abs/2611.01604 — autori e testo completo sono lì (qui omessi i nomi: nessun dato personale nel deposito).
Licenza: titolo e abstract sono metadati arXiv distribuiti in CC0 1.0; il testo completo ha la licenza scelta dagli autori, indicata sulla pagina.
Letto il 2026-11-03T11:13:22.643Z dalla pagina https://arxiv.org/list/q-bio.QM/new (consentita dal robots.txt di arxiv.org, con il suo crawl-delay).