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GEARS is a graph model predicting the effect of gene knockouts; the perturbation benchmarks around it showed how hard the problem is.
GEARS is a graph neural network from Stanford that predicts the transcriptional effect of gene perturbations by reasoning over gene-gene relationship graphs, which lets it extrapolate to perturbations, including combinations, it has never seen. The Nature Biotechnology 2023 paper introduced the approach and set an early standard for the task. Its lasting influence is on evaluation: benchmark studies in 2024 and 2025 found that many single-cell foundation models barely beat simple baselines such as predicting the mean response, which exposed weak baselines across the field and sharpened standards through efforts like the Virtual Cell Challenge. Combinatorial perturbation prediction remains its distinctive strength. For a newcomer: GEARS predicts what happens when you knock out a gene, and the contests built around it showed how hard that prediction really is.
GEARS is a graph neural network over gene relationships.
Query for this technology: (TITLE:"GEARS and perturbation prediction benchmarks" OR ABSTRACT:"GEARS and perturbation prediction benchmarks") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about GEARS and perturbation prediction benchmarks, not a curated reading list.
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell, Stanford Health Care / Stanford Cancer Institute and the tag virtual-cell.
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell, CRISPR functional genomics and the tag virtual-cell.
Shares Stanford Health Care / Stanford Cancer Institute and the tag virtual-cell.
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tag virtual-cell.
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tag virtual-cell.
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tag virtual-cell.
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tag virtual-cell.
Shares Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell and the tag virtual-cell.