A Literature-Based Knowledge Graph Embedding Method for Identifying Drug RepurposingOpportunities in Rare Diseases. - Daniel N. Sosa; Alexander Derry; Margaret G. Guo; Eric Wei; Connor Brinton; Russ B. Altman (PSB, 2020)

ATOM3D: Tasks On Molecules in Three Dimensions. - Raphael J. L. Townshend; Martin Vögele; Patricia Suriana; Alexander Derry; Alexander S. Powers; Yianni Laloudakis; Sidhika Balachandar; Brandon M. Anderson; Stephan Eismann; Risi Kondor; Russ B. Altman; Ron O. Dror (CoRR, 2020)

ATOM3D: Tasks on Molecules in Three Dimensions. - Raphael J. L. Townshend; Martin Vögele; Patricia Suriana; Alexander Derry; Alexander S. Powers; Yianni Laloudakis; Sidhika Balachandar; Bowen Jing; Brandon M. Anderson; Stephan Eismann; Risi Kondor; Russ B. Altman; et al. (NeurIPS Datasets and Benchmarks, 2021)

Data for "Training data composition affects performance of protein structure analysis algorithms" by A. Derry, K. A. Carpenter, & R. B. Altman. - Alexander Derry; Kristy A. Carpenter; Russ B. Altman (Zenodo, 2021)

Data for COLLAPSE: A representation learning framework for identification and characterization of protein structural sites. - Alexander Derry; Russ B. Altman (Zenodo, 2022)

Data for PARSE (Derry & Altman 2023). - Alexander Derry; Russ B. Altman (Zenodo, 2023)

Prospector Heads: Generalized Feature Attribution for Large Models & Data. - Gautam Machiraju; Alexander Derry; Arjun D. Desai; Neel Guha; Amir-Hossein Karimi; James Zou 001; Russ B. Altman; Christopher Ré; Parag Mallick (ICML, 2024)