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cs.LG2026
Learning Task-Specific Antibody Representations via Function-Aware Masking
Ayan Goel, Thomas A. Walton, Amirali Aghazadeh
Antibody-specific language models pretrained via masked language modeling (MLM) learn representations that are critical for downstream sequence design and property prediction tasks…
cs.LG2026
Structure-Aware Masking for Protein Representation Learning
Thomas Walton, Ayan Goel, Amirali Aghazadeh
Masked language modeling (MLM) is the standard objective for training protein language models, typically implemented by randomly masking individual residues at a fixed rate (e.g.,…
cs.LG2025
SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding
Thomas Walton, Darin Tsui, Aryan Musharaf +1
Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference i…