{"entities":[{"id":"aib-doc-ahlmann-eltze-2025","name":"Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines","type":"document","subtype":"Journal article","description":"Nature Methods 22, 1657–1661 (2025, brief communication), published online 4 August 2025. The article page gives Received 11 October 2024, Accepted 24 June 2025, Published 4 August 2025, Issue date August 2025.","sourceIds":["source-aib-ahlmann-eltze-2025-natmethods"]},{"id":"aib-prop-ai-virtual-cell","name":"AI models can simulate or predict the behaviour of cells (a \"virtual cell\")","type":"concept","proposition":{"code":"P2","criterion":"The text states that a machine-learning or other AI model simulates, or will be able to simulate or predict, the behaviour of a living cell, such as its growth or its responses to perturbations.","terms":["virtual cell","AI Virtual Cell"]}}],"claims":[{"id":"aib-arg-p2-ahlmann-eltze-2025","subject":"aib-doc-ahlmann-eltze-2025","predicate":"contests_proposition","object":{"kind":"entity","entityId":"aib-prop-ai-virtual-cell"},"topic":"ideas","statement":"Ahlmann-Eltze, Huber and Anders (Nature Methods, published online 4 August 2025) report that none of five foundation models and two other deep-learning models outperformed deliberately simple baselines at predicting transcriptome changes after genetic perturbations, and conclude that the goal of predicting the outcome of not-yet-performed experiments is still elusive.","time":{"kind":"event","date":"2025-08-04","basis":"publication","note":"Online publication date printed on the article page."},"derivation":"explicit","resolution":"supported","editorialState":"seed","evidenceIds":["evidence-aib-arg-p2-ahlmann-eltze-2025-1","evidence-aib-arg-p2-ahlmann-eltze-2025-2"],"attributes":{"thought":{"roles":["contesting"],"register":"nonfiction","qualifier":"Challenges the present performance of the tested models; not a contradiction of the proposition as a whole."}}}],"sources":[{"id":"source-aib-ahlmann-eltze-2025-natmethods","documentId":"aib-doc-ahlmann-eltze-2025","title":"Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines","authors":["Constantin Ahlmann-Eltze","Wolfgang Huber","Simon Anders"],"publisher":"Nature Methods","publicationDate":"2025-08-04","version":"Retrieved for the candidate pack on 2026-10-30 (SHA-256 3ad786d9b77f25dae848ab4354e643e1327a3ca8b792a4d577caf75654567656). Nature Methods article page, version of record of 4 August 2025, as served on 2026-10-30.","evidenceUrl":"https://www.nature.com/articles/s41592-025-02772-6","language":"en"}],"evidence":[{"id":"evidence-aib-arg-p2-ahlmann-eltze-2025-1","claimId":"aib-arg-p2-ahlmann-eltze-2025","sourceId":"source-aib-ahlmann-eltze-2025-natmethods","sourceRole":"primary","support":"supports","verification":"machine_checked","retrievalRoute":"direct"},{"id":"evidence-aib-arg-p2-ahlmann-eltze-2025-2","claimId":"aib-arg-p2-ahlmann-eltze-2025","sourceId":"source-aib-ahlmann-eltze-2025-natmethods","support":"supports","verification":"machine_checked","retrievalRoute":"direct"}],"at":{"entities":[1411,1439],"claims":[3742],"sources":[1221],"evidence":[5196,5197]},"index":{"byClaim":[["aib-arg-p2-ahlmann-eltze-2025",["propositions:ai-in-science"]]],"marks":[],"chronicle":{"years":[{"year":1863,"topics":{"ideas":5},"stated":0},{"year":1865,"topics":{"ideas":1},"stated":0},{"year":1872,"topics":{"ideas":7},"stated":0},{"year":1943,"topics":{"ideas":1},"stated":0},{"year":1947,"topics":{"ideas":2},"stated":0},{"year":1950,"topics":{"ideas":7},"stated":0},{"year":1951,"topics":{"ideas":5},"stated":0},{"year":1952,"topics":{"ideas":2},"stated":0},{"year":1955,"topics":{"ideas":31},"stated":0},{"year":1956,"topics":{"ideas":1},"stated":0},{"year":1957,"topics":{"ideas":1},"stated":0},{"year":1958,"topics":{"ideas":3},"stated":0},{"year":1959,"topics":{"ideas":6},"stated":0},{"year":1960,"topics":{"ideas":11},"stated":0},{"year":1961,"topics":{"ideas":10},"stated":0},{"year":1965,"topics":{"ideas":8},"stated":0},{"year":1966,"topics":{"ideas":20},"stated":0},{"year":1968,"topics":{"ideas":5},"stated":0},{"year":1969,"topics":{"ideas":2},"stated":0},{"year":1971,"topics":{"ideas":4},"stated":0},{"year":1972,"topics":{"ideas":1},"stated":0},{"year":1973,"topics":{"ideas":2},"stated":0},{"year":1974,"topics":{"ideas":2},"stated":0},{"year":1975,"topics":{"ideas":1},"stated":0},{"year":1976,"topics":{"ideas":1},"stated":0},{"year":1977,"topics":{"people":2,"ideas":8},"stated":0},{"year":1979,"topics":{"ideas":4},"stated":0},{"year":1980,"topics":{"ideas":2},"stated":0},{"year":1981,"topics":{"people":2},"stated":0},{"year":1982,"topics":{"ideas":4},"stated":0},{"year":1983,"topics":{"ideas":4},"stated":0},{"year":1984,"topics":{"ideas":21},"stated":0},{"year":1985,"topics":{"ideas":9},"stated":0},{"year":1986,"topics":{"ideas":18},"stated":0},{"year":1987,"topics":{"ideas":1},"stated":0},{"year":1988,"topics":{"ideas":6},"stated":0},{"year":1989,"topics":{"ideas":8},"stated":0},{"year":1990,"topics":{"ideas":5},"stated":0},{"year":1991,"topics":{"ideas":11},"stated":0},{"year":1992,"topics":{"ideas":9},"stated":0},{"year":1993,"topics":{"ideas":14,"people":3},"stated":0},{"year":1994,"topics":{"ideas":14},"stated":0},{"year":1995,"topics":{"ideas":10,"people":1},"stated":0},{"year":1996,"topics":{"ideas":71},"stated":0},{"year":1997,"topics":{"ideas":12},"stated":0},{"year":1998,"topics":{"ideas":49},"stated":0},{"year":1999,"topics":{"ideas":27,"people":1,"institutions":1},"stated":0},{"year":2000,"topics":{"ideas":62},"stated":0},{"year":2001,"topics":{"ideas":39},"stated":0},{"year":2002,"topics":{"ideas":30},"stated":0},{"year":2003,"topics":{"ideas":8},"stated":0},{"year":2004,"topics":{"ideas":12,"people":3},"stated":0},{"year":2005,"topics":{"ideas":10,"people":1},"stated":0},{"year":2006,"topics":{"ideas":26,"people":1},"stated":0},{"year":2007,"topics":{"ideas":20},"stated":0},{"year":2008,"topics":{"ideas":57,"people":3,"institutions":1},"stated":0},{"year":2009,"topics":{"ideas":10,"people":1},"stated":0},{"year":2010,"topics":{"people":3,"ideas":11,"institutions":1,"governance":4},"stated":0},{"year":2011,"topics":{"people":3,"ideas":7,"institutions":2},"stated":0},{"year":2012,"topics":{"people":4,"ideas":17,"institutions":2},"stated":0},{"year":2013,"topics":{"ideas":46,"people":4,"institutions":2,"capital":1},"stated":0},{"year":2014,"topics":{"institutions":2,"ideas":54,"people":5},"stated":0},{"year":2015,"topics":{"people":22,"ideas":122,"institutions":3,"capital":1},"stated":0},{"year":2016,"topics":{"ideas":88,"people":2},"stated":0},{"year":2017,"topics":{"people":16,"institutions":2,"ideas":128,"governance":2},"stated":0},{"year":2018,"topics":{"people":8,"ideas":158,"institutions":8,"governance":1},"stated":0},{"year":2019,"topics":{"capital":1,"compute":1,"people":10,"governance":19,"ideas":175,"institutions":4},"stated":0},{"year":2020,"topics":{"people":6,"ideas":98,"institutions":1,"governance":2},"stated":0},{"year":2021,"topics":{"people":27,"ideas":177,"compute":1,"institutions":23,"governance":4,"capital":6},"stated":0},{"year":2022,"topics":{"people":15,"ideas":217,"institutions":6,"governance":3,"compute":2,"capital":1},"stated":0},{"year":2023,"topics":{"capital":5,"compute":7,"institutions":23,"people":51,"governance":179,"ideas":389},"stated":0},{"year":2024,"topics":{"capital":12,"compute":19,"governance":282,"people":80,"ideas":178,"institutions":28},"stated":1},{"year":2025,"topics":{"governance":547,"compute":69,"capital":34,"people":90,"institutions":18,"ideas":178},"stated":7},{"year":2026,"topics":{"governance":442,"capital":8,"compute":32,"institutions":21,"ideas":91,"people":107},"stated":19},{"year":2027,"topics":{},"stated":9},{"year":2028,"topics":{},"stated":6},{"year":2029,"topics":{},"stated":3},{"year":2030,"topics":{},"stated":3},{"year":2032,"topics":{},"stated":2},{"year":2035,"topics":{},"stated":2},{"year":2039,"topics":{},"stated":1},{"year":2042,"topics":{},"stated":1},{"year":2050,"topics":{},"stated":1}],"scheduled":[],"statedBy":[]},"collections":[{"target":{"kind":"propositions","id":"superintelligence"},"title":"Propositions about superintelligence, 1863–2022","claimIds":[],"records":[]},{"target":{"kind":"propositions","id":"risk-debate"},"title":"Arguments about catastrophic risk from advanced AI","claimIds":[],"records":[]},{"target":{"kind":"propositions","id":"yudkowsky-arguments"},"title":"Eliezer Yudkowsky’s arguments on common claims about AI, 1996–2026","claimIds":[],"records":[]},{"target":{"kind":"propositions","id":"economics-of-machine-intelligence"},"title":"Economics of machine intelligence","claimIds":[],"records":[]},{"target":{"kind":"propositions","id":"orbital-compute-arguments"},"title":"Arguments about compute in orbit","claimIds":[],"records":[]},{"target":{"kind":"propositions","id":"ai-bio-arguments"},"title":"Arguments about AI and biological risk","claimIds":[],"records":[]},{"target":{"kind":"propositions","id":"ai-in-science"},"title":"AI in science","claimIds":["aib-arg-p2-ahlmann-eltze-2025"],"records":[]},{"target":{"kind":"documents"},"title":"Frontier safety frameworks","claimIds":[]},{"target":{"kind":"compare","id":"frontier-safety-frameworks"},"title":"Compare frameworks","claimIds":[]},{"target":{"kind":"control","id":"openai"},"title":"OpenAI’s control structure, 2015–2026","claimIds":[]},{"target":{"kind":"control","id":"anthropic"},"title":"Anthropic’s control structure, 2021–2026","claimIds":[]},{"target":{"kind":"commitments"},"title":"External commitments and obligations","claimIds":[]},{"target":{"kind":"question","id":"frameworks-to-obligations"},"title":"Frameworks, commitments and legal obligations, 2023–2026","claimIds":[]},{"target":{"kind":"reading"},"title":"Founding and early leadership","claimIds":[]}]},"version":"131evrz"}