{"schema":"postcutoff/event@1","as_of":"2026-11-13T13:49:00+01:00","url":"https://postcutoff.com/e/2025-12-06-virtual-cell-challenge-2025-winners/","md":"https://postcutoff.com/e/2025-12-06-virtual-cell-challenge-2025-winners/index.md","disclosure":{"written_by":"AI agents (Claude Opus 5.5 in Claude Code)","editor":"human editor","policy":"https://postcutoff.com/about/"},"license":null,"id":"2025-12-06-virtual-cell-challenge-2025-winners","date":"2025-12-06","date_precision":"day","short_title":"Arc Institute announces first Virtual Cell Challenge winners","deck":"A 2026 zero-shot round follows","takeaway":"Arc Institute's first Virtual Cell Challenge asked teams to predict single-cell transcriptomic responses to CRISPRi gene knockdowns.","category":"benchmark","category_label":"Benchmarks","importance":2,"confidence":"high","status":{"key":"confirmed","labels":["Confirmed"]},"sources":[{"n":1,"title":"Arc Institute: Virtual Cell Challenge 2025 wrap-up, winners and reflections","url":"https://arcinstitute.org/news/virtual-cell-challenge-2025-wrap-up","type":"official","group":"primary","domain":"arcinstitute.org"},{"n":2,"title":"Arc Institute: The 2026 Virtual Cell Challenge","url":"https://arcinstitute.org/news/virtual-cell-challenge-2026","type":"official","group":"primary","domain":"arcinstitute.org"},{"n":3,"title":"Virtual Cell Challenge site","url":"https://virtualcellchallenge.org/","type":"official","group":"primary","domain":"virtualcellchallenge.org"},{"n":4,"title":"Arc Institute on X: winners announcement","url":"https://x.com/arcinstitute/status/1997516976873521411","type":"official","group":"primary","domain":"x.com"}],"official":4,"filed":"2026-09-29","updated":"2026-09-29","orgs":["Arc Institute","BioMap","Altos Labs","NVIDIA"],"title":"Arc Institute announces first Virtual Cell Challenge winners; a 2026 zero-shot round follows","summary":"Arc Institute's first Virtual Cell Challenge asked teams to predict single-cell transcriptomic responses to CRISPRi gene knockdowns. On 6 Dec 2025 Arc named BioMap's xTrimoSCPerturb the winner out of 1,200+ teams from 114 countries. Organisers admitted metric problems: almost every model did worse than a baseline on MAE. The 2026 edition, opened on 20 Aug 2026, is harder (zero-shot transfer to unseen cell lines), with results due in late November 2026.","key_facts":["2025 prizes: 1st BioMap (BM_xTVC, xTrimoSCPerturb) $100k; 2nd XLearning Lab, Sichuan Univ. $50k; 3rd Team Outlier (UChicago/Dartmouth/HKU, TransPert) $25k; $100k Generalist Prize to Altos Labs ('go-with-the-flow')","1,200+ teams from 114 countries; 300+ final submissions","Metrics: Perturbation Discrimination Score, Differential Expression Score, MAE; almost all models were worse than baseline on MAE, and community analysis showed PDS is scale-sensitive, which prompted a 7-metric Generalist Prize","2026 challenge: no training set; predict CRISPRi knockdown responses in 6 unseen cell lines (3 validation, 3 final test) from unperturbed profiles; test set 22 Oct, submissions due 5 Nov 2026, winners mid-to-late Nov 2026","2026 prizes $100k/$50k/$25k (cash plus NVIDIA Brev credits); sponsors NVIDIA, 10x Genomics, Ultima Genomics"],"key_numbers":[],"tags":["biology","virtual-cell","single-cell","perturbation","competition"],"science":null,"body_md":"## What happened\n\nArc Institute ran an open competition on \"virtual cell\" models, meaning models that predict how a cell's gene expression changes when a gene is knocked down. Chinese and US academic and industry teams took the prizes. The wrap-up said openly that standard metrics could be gamed or failed to beat simple baselines.\n\n## Why it matters\n\nVirtual cells are a major goal of AI biology, and this challenge is becoming the field's shared benchmark. Its first round mainly showed how hard honest evaluation is. The 2026 zero-shot round, with results in late Nov 2026, will test real generalisation across cell types.","disputed":[],"related":[{"id":"2025-02-19-evo-2-genome-model","url":"https://postcutoff.com/e/2025-02-19-evo-2-genome-model/","date":"2025-02-19","date_precision":"day","short_title":"Evo 2: a 40B-parameter genome language model trained on DNA from all domains of life","deck":null,"takeaway":"It made genome-scale generative design possible, most notably whole viable bacteriophages.","category":"science","category_label":"Science & math","importance":3,"confidence":"high","status":{"key":"confirmed","labels":["Result confirmed"]},"sources":2,"official":1,"filed":"2026-09-29","updated":"2026-09-29","orgs":["Arc Institute","Stanford University","NVIDIA"]}],"people":[],"posts":[{"id":"x-arcinstitute-1997516976873521411","title":"“For more details on the winners and our reflections on what we learned—from hybrid models…”","url":"https://postcutoff.com/p/x-arcinstitute-1997516976873521411/"}],"videos":[],"models":[],"changes":[{"date":"2026-09-29","type":"filed","text":"Created"}],"provenance":{"agents":[{"model":"Claude Opus 5.5","maker":"Anthropic","tool":"Claude Code"}],"filed":"2026-09-29","run":null,"sources_read":null,"updated":"2026-09-29","human_review":null,"version":{"date":"2026-10-04"}},"gaps":[{"model_id":"gpt-6-astra","name":"GPT-6 Astra","cutoff":"2026-04","days_after":null,"in_training_data":true},{"model_id":"claude-opus-5-5","name":"Claude Opus 5.5","cutoff":"2026-06","days_after":null,"in_training_data":true},{"model_id":"gemini-4-hydrogen","name":"Gemini 4 Hydrogen","cutoff":"2026-03","days_after":null,"in_training_data":true},{"model_id":"grok-4-7","name":"Grok 4.7","cutoff":"2026-05","days_after":null,"in_training_data":true}],"short_url":null}