2 papers
q-bio.QM2026
Greater than the Sum of Its Parts: Building Substructure into Protein Encoding Models
Robert Calef, Arthur Liang, Manolis Kellis +1
Protein representation learning has advanced rapidly with the scale-up of sequence and structure supervision, but most models still encode proteins either as per-residue token sequ…
cs.LG2024
Towards Probabilistically-Sound Beam Search with Masked Language Models
Creston Brooks, Robert Calef, Charlie Cowen-Breen +1
Beam search with masked language models (MLMs) is challenging in part because joint probability distributions over sequences are not readily available, unlike for autoregressive mo…