arxivcs.LG2026-06-25
PairSAE: Mechanistic Interpretability from Pair Representations in Protein Co-Folding
Giosue Migliorini, Aristofanis Rontogiannis, Grigori Guitchounts, Nicholas Franklin, Axel Elaldi, Olivia Viessmann
Foundation models for structural biology have achieved remarkable performance in predicting biomolecular structure and show promise for the design of proteins and small molecules. Yet understanding which internal features drive their outputs remains challenging. Standard sparse a…