Designing proteins with language models

Jeffrey A. Ruffolo and Ali Madani

[Paper] Nature Biotechnology 2024

ProGen2: Exploring the boundaries of protein language models

*Erik Nijkamp, *Jeffrey A. Ruffolo, Eli N. Weinstein, Nikhil Naik, Ali Madani

[Paper] [Code] Cell Systems 2023

Large language models generate functional protein sequences across diverse families

Ali Madani, Ben Krause, Eric R. Greene, Subu Subramanian, Benjamin P. Mohr, James M. Holton, Jose Luis Olmos Jr., Caiming Xiong, Zachary Z. Sun, Richard Socher, James S. Fraser, Nikhil Naik

[Blog] [Paper] [News & Views] [Science] Nature Biotechnology 2023

Deep Extrapolation for Attribute-Enhanced Generation

*Alvin Chan, *Ali Madani, Ben Krause, Nikhil Naik

[Blog] [Paper] [Code] NeurIPS 2021

FLIP: Benchmark tasks in fitness landscape inference for proteins

Christian Dallago, Jody Mou, Kadina E Johnston, Bruce Wittmann, Nick Bhattacharya, Samuel Goldman, Ali Madani, Kevin K Yang

[Paper] [Data] NeurIPS 2021

BERTology Meets Biology: Interpreting Attention in Protein Language Models

Jesse Vig, Ali Madani, Lav R. Varshney, Caiming Xiong, Richard Socher, Nazneen Rajani

[Paper] [Code] [Yannic Kilcher] [The Batch] ICLR 2021

ProGen: Language Modeling for Protein Generation

Ali Madani, Bryan McCann, Nikhil Naik, Nitish Shirish Keskar, Namrata Anand, Raphael R. Eguchi, Po-Ssu Huang, Richard Socher

[Paper] [Blog] [VentureBeat] [Import AI] NeurIPS MLSB Workshop 2020

Deep Learning-enabled Breast Cancer Hormonal Receptor Status Determination from Base-level H&E Stains

Nikhil Naik, Ali Madani, Andre Esteva, Nitish Keskar, Michael Press, Dan Ruderman, David Agus, Richard Socher

[Paper] [VentureBeat] Nature Communications 2020

Fast and accurate view classification of echocardiograms using deep learning

Ali Madani, Ramy Arnaout, Mohammad R.K. Mofrad, Rima Arnaout

[Paper] [CNET] [IEEE Spectrum] Nature: Digital Medicine 2018