GEARS and perturbation prediction benchmarks
GEARS is a graph model predicting the effect of gene knockouts; the perturbation benchmarks around it showed how hard the problem is.
GEARS (Nature Biotechnology 2023) used gene-gene graphs to predict unseen perturbations; 2024-25 benchmark studies found many foundation models barely beat simple baselines, sharpening evaluation standards (e.g. Virtual Cell Challenge).
How it works
GEARS is a graph neural network over gene relationships.
- Combinatorial perturbations
- Weak baselines exposed field-wide
Latest papers
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