Arc Institute announces first Virtual Cell Challenge winners; a 2026 zero-shot round follows
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
What happened
Arc 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.
Why it matters
Virtual 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.
Changelog
- 2026-09-29: created
Related posts (1)
- Arc Institute Arc Institute @arcinstitute · x · 2025-12-07
Cited as a source by: 2025-12-06-virtual-cell-challenge-2025-winners
Related events
Sources (4)
- officialArc Institute: Virtual Cell Challenge 2025 wrap-up, winners and reflections
- officialArc Institute: The 2026 Virtual Cell Challenge
- officialVirtual Cell Challenge site
- officialArc Institute on X: winners announcement
id: 2025-12-06-virtual-cell-challenge-2025-winners · updated 2026-09-29 · open in the interactive timeline