PairSAE: Mechanistic Interpretability from Pair Representations in Protein Co-Folding
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 representations yields a quadratic blow-up of features and obscures concepts distributed jointly across sequence and pair representations. We introduce PairSAE, which summarizes pairwise tensors via an N-mode SVD into token-wise interaction roles, then uses...
| Authors | Giosue Migliorini, Aristofanis Rontogiannis, Grigori Guitchounts et al. |
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| Primary category | cs.LG |
| Published | 25 June 2026 |
| Last updated at source | 25 June 2026 |
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