Foundation Models Improve Perturbation Response Prediction
Elijah Cole, Geert-Jan Huizing, Sohan Addagudi, Nicholas Ho, Euxhen Hasanaj, Merel Kuijs, Toby Johnstone, Maria Carilli, Alec Davi, Caleb N. Ellington, Christoph Feinauer, Pan Li, Romain Menegaux, Shahin Mohammadi, Yanjun Shao, , Eric P. Xing
This study evaluates foundation models for predicting cellular responses to perturbations, finding that some pretrained embeddings improve predictions while others do not.
bioRxiv · Feb 19, 2026 · PreprintBioinformatics