3 papers
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.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…
cs.CL2025
Link Prediction for Event Logs in the Process Industry
Anastasia Zhukova, Thomas Walton, Christian E. Lobmüller +1
In the era of graph-based retrieval-augmented generation (RAG), link prediction is a significant preprocessing step for improving the quality of fragmented or incomplete domain-spe…