Variational auto-encoding of protein sequences. - Sam Sinai; Eric D. Kelsic; George M. Church; Martin A. Nowak (CoRR, 2017)

AdaLead: A simple and robust adaptive greedy search algorithm for sequence design. - Sam Sinai; Richard Wang; Alexander Whatley; Stewart Slocum; Elina Locane; Eric D. Kelsic (CoRR, 2020)

A primer on model-guided exploration of fitness landscapes for biological sequence design. - Sam Sinai; Eric D. Kelsic (CoRR, 2020)

Forecasting labels under distribution-shift for machine-guided sequence design. - Lauren Berk Wheelock; Stephen Malina; Jeffrey Gerold; Sam Sinai (MLCB, 2022)

Beyond the training set: an intuitive method for detecting distribution shift in model-based optimization. - Farhan Damani; David H. Brookes; Theodore Sternlieb; Cameron Webster; Stephen Malina; Rishi Jajoo; Kathy Lin; Sam Sinai (CoRR, 2023)

Contrastive losses as generalized models of global epistasis. - David H. Brookes; Jakub Otwinowski; Sam Sinai (NeurIPS, 2024)

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery. - Peter St. John; Dejun Lin; Polina Binder; Malcolm Greaves; Vega Shah; John St. John; Adrian Lange; Patrick D. Hsu; Rajesh Illango; Arvind Ramanathan; Anima Anandkumar; David H. Brookes; et al. (CoRR, 2024)