Retrieval; Fitness prediction; End-to-end

Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction

Ruben Weitzman, Peter Mørch Groth, Lood van Niekerk, Aoi Otani, Yarin Gal, Debora Marks, Pascal Notin

ICML, 2025. an end-to-end differentiable framework that learns to retrieve relevant protein homologs while simultaneously training for downstream tasks, achieving state-of-the-art fitness prediction performance while being orders of magnitude faster than traditional MSA-based approaches.