Author

Ayan Goel

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#machine learning May 2026

Structure-Aware Masking for Protein Representation Learning

Bucket Masking is introduced, a structure-aware masking strategy that selects groups of residues based on their proximity in three-dimensional space, preferentially masking structurally coupled regions during training, and enables up to a 14% improvement over standard random masking in downstream protein fitness predic...

Thomas Walton, Ayan Goel, Amirali Aghazadeh · arXiv.org · 1 citation

#machine learning Preprint Sep 2026

Learning Task-Specific Antibody Representations via Function-Aware Masking

This work introduces function-aware masking, a family of pretraining algorithms that align mask placement with specific functional priors (e.g., from IMGT annotations or structure predictions) to shape the learned representation space, and demonstrates that informed mask placement provides a parameter-free mechanism fo...

Ayan Goel, Thomas Walton, Amirali Aghazadeh · 0 citations