PairSAE: Mechanistic Interpretability from Pair Representations in Protein Co-Folding

arXiv:2606.27440v1 Announce Type: new Abstract: 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 autoencoders (SAEs), effective on transformer-style sequence embeddings, do not transfer cleanly to pairformer-like architectures: naively operating on pairwise representati...