4 papers
PairSAE: Mechanistic Interpretability from Pair Representations in Protein Co-Folding
Giosue Migliorini, Aristofanis Rontogiannis, Grigori Guitchounts +3
Foundation models for structural biology have achieved remarkable performance in predicting biomolecular structure and show promise for the design of proteins and small molecules.…
Relaxed Sequence Sampling for Diverse Protein Design
Joohwan Ko, Aristofanis Rontogiannis, Yih-En Andrew Ban +2
Protein design using structure prediction models such as AlphaFold2 has shown remarkable success, but existing approaches like relaxed sequence optimization (RSO) rely on single-pa…
Flash Invariant Point Attention
Andrew Liu, Axel Elaldi, Nicholas T Franklin +4
Invariant Point Attention (IPA) is a key algorithm for geometry-aware modeling in structural biology, central to many protein and RNA models. However, its quadratic complexity limi…
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba
Andrew Liu, Axel Elaldi, Nathan Russell +1
Efficient encoding and representation of large 3D molecular structures with high fidelity is critical for biomolecular design applications. Despite this, many representation learni…