Virtual Cell Challenge 2026: Benchmarking zero-shot generalization across cellular contexts.
Arc Virtual Cell Initiative Team, Goodarzi H. · Cell · 2026-08-26
Virtual Cell Challenge 2026 paper: benchmarking zero-shot generalization across contexts.
Tag: Benchmark & validation
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An Empirical Comparison of Virtual Cell Models: Perturbation Prediction, Representation, and the Baseline Gap
Denvis O. · Research Square · 2026-07-22
Empirical comparison of virtual cell models: the baseline gap persists.
Signal, Bounds, and Baselines: Principles for Evaluating Virtual Cell Perturbation Models
Vollenweider M, Bühlmann P. · bioRxiv · 2026-04-22
Signal, Bounds, and Baselines: principles for evaluating virtual cell perturbation models.
scPRINT-2: Towards the next-generation of cell foundation models and benchmarks
Kalfon J, Peyré G, Cantini L. · bioRxiv · 2025-12-15
scPRINT-2: next-gen cell foundation models and benchmarks.
AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential.
Ma C, Zhang H, Rao Y, Jiang X, Liu B, Sun Z, Song Z, Gao Y, Cui Y, Liu X, Li Z. · NPJ digital medicine · 2025-12-11
Review of AI virtual cell models in preclinical research: technical pathways and validation.
Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation.
Viñas Torné R, Wiatrak M, Piran Z, Fan S, Jiang L, Teichmann SA, Nitzan M, Brbić M. · Nature biotechnology · 2025-08-25
Systema: evaluating perturbation prediction beyond systematic variation.
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines.
Ahlmann-Eltze C, Huber W, Anders S. · Nature methods · 2025-08-04
Ahlmann-Eltze, Huber, Anders: deep models don't beat simple linear baselines for perturbation prediction.
Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction
Hasanaj E, Cole E, Mohammadi S, Addagudi S, Zhang X, Song L, Xing EP. · bioRxiv · 2025-06-28
Multimodal benchmarking of FM representations for perturbation response.
Virtual Cell Challenge: Toward a Turing test for the virtual cell.
Roohani YH et al. · Cell · 2025-06-01
Arc Institute perspective launching the Virtual Cell Challenge as a 'Turing test' for virtual cells.
Benchmarking foundation cell models for post-perturbation RNA-seq prediction.
Csendes G, Sanz G, Szalay KZ, Szalai B. · BMC genomics · 2025-04-23
Csendes et al.: foundation cell models vs simple baselines for post-perturbation prediction.
Zero-shot evaluation reveals limitations of single-cell foundation models.
Kedzierska KZ, Crawford L, Amini AP, Lu AX. · Genome biology · 2025-04-18
Kedzierska et al.: zero-shot limitations of scGPT/Geneformer.
PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction
Wenteler A, Occhetta M, Branson N, Curean V, Huebner M, Dee W, Connell W, Chung SP, Hawkins-Hooker A, Ektefaie Y, Valdez Córdova CM, Gallagher-Syed A. · bioRxiv · 2024-10-03
PertEval-scFM: benchmarking scFMs for perturbation effect prediction.