BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery Article Swipe

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Peter C. St. John , Dejun Lin , P. Binder , Malcolm W. Greaves , Varun Shah , John St. John , Adrian Lange , Patrick D. Hsu , Rajesh Illango , Arvind Ramanathan , Anima Anandkumar , David H. Brookes , Akosua Busia , Anjali Mahajan , Stephen Malina , Neha Prasad , Sam Sinai , Lindsay Edwards , Thomas Gaudelet , Cristian Regep , Martin Steinegger , Burkhard Rost , Alexander Brace , Kyle Hippe , Luca Naef , Katsuo Kamata , George Armstrong , Kevin Boyd , Zhonglin Cao , H. Chou , Simon Chu , Allan dos Santos Costa , Sajad Darabi , Eric T. Dawson , Kieran Didi , Cong Fu , Mario Geiger , Michelle Gill , Darren J. Hsu , Gaurav Kaushik , Maria Korshunova , Steven Kothen-Hill , Yilin Lee , Meng Liu , Micha Livne , Zachary McClure , Jonathan Mitchell , Alireza Moradzadeh , Ohad Mosafi , Youssef S. G. Nashed , Saee Paliwal , Yuxing Peng , Sara Rabhi , Farhad Ramezanghorbani , Danny Reidenbach , Camir Ricketts , Brian Roland , Kushal Shah , Tyler C. Shimko , Hassan Sirelkhatim , Savitha Srinivasan , Abraham C. Stern , Dorota Toczydlowska , Srimukh Prasad Veccham , Niccolò Alberto Elia Venanzi , A. A. Vorontsov , J. Patrick Wilber , Isabel V. L. Wilkinson , Weng‐Keen Wong , Eva Xue , C. Ye , Xin Yu , Yang Zhang , Guoqing Zhou , Becca Zandstein , Christian Dallago , Bruno Trentini , Emine Küçükbenli , Saee Paliwal , Timur M. Rvachov , Eddie Calleja , Johnny Israeli , Harry Clifford , Risto Haukioja , Nicholas Haemel , Kyle Tretina , Neha Tadimeti , Anthony Costa ·

YOU? · · 2024 · Open Access · · DOI: https://doi.org/10.48550/arxiv.2411.10548

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language models (pLM) training on hundreds of graphical processing units (GPUs). We introduce the BioNeMo Framework to facilitate the training of computational biology and chemistry AI models across hundreds of GPUs. Its modular design allows the integration of individual components, such as data loaders, into existing workflows and is open to community contributions. We detail technical features of the BioNeMo Framework through use cases such as pLM pre-training and fine-tuning. On 256 NVIDIA A100s, BioNeMo Framework trains a three billion parameter BERT-based pLM on over one trillion tokens in 4.2 days. The BioNeMo Framework is open-source and free for everyone to use.

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Drug discovery Modular design Computer science Drug Drug development Data science Medicine Pharmacology Programming language Bioinformatics Biology

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Type: preprint
Language: en
Landing Page: http://arxiv.org/abs/2411.10548
PDF: https://arxiv.org/pdf/2411.10548
OA Status: green
Cited By: 9
Related Works: 10
OpenAlex ID: https://openalex.org/W4404569920

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DOI: https://doi.org/10.48550/arxiv.2411.10548

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Title: BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery

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Type: preprint

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Language: en

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Publication year: 2024

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Publication date: 2024-11-15

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Authors: Peter C. St. John, Dejun Lin, P. Binder, Malcolm W. Greaves, Varun Shah, John St. John, Adrian Lange, Patrick D. Hsu, Rajesh Illango, Arvind Ramanathan, Anima Anandkumar, David H. Brookes, Akosua Busia, Anjali Mahajan, Stephen Malina, Neha Prasad, Sam Sinai, Lindsay Edwards, Thomas Gaudelet, Cristian Regep, Martin Steinegger, Burkhard Rost, Alexander Brace, Kyle Hippe, Luca Naef, Katsuo Kamata, George Armstrong, Kevin Boyd, Zhonglin Cao, H. Chou, Simon Chu, Allan dos Santos Costa, Sajad Darabi, Eric T. Dawson, Kieran Didi, Cong Fu, Mario Geiger, Michelle Gill, Darren J. Hsu, Gaurav Kaushik, Maria Korshunova, Steven Kothen-Hill, Yilin Lee, Meng Liu, Micha Livne, Zachary McClure, Jonathan Mitchell, Alireza Moradzadeh, Ohad Mosafi, Youssef S. G. Nashed, Saee Paliwal, Yuxing Peng, Sara Rabhi, Farhad Ramezanghorbani, Danny Reidenbach, Camir Ricketts, Brian Roland, Kushal Shah, Tyler C. Shimko, Hassan Sirelkhatim, Savitha Srinivasan, Abraham C. Stern, Dorota Toczydlowska, Srimukh Prasad Veccham, Niccolò Alberto Elia Venanzi, A. A. Vorontsov, J. Patrick Wilber, Isabel V. L. Wilkinson, Weng‐Keen Wong, Eva Xue, C. Ye, Xin Yu, Yang Zhang, Guoqing Zhou, Becca Zandstein, Christian Dallago, Bruno Trentini, Emine Küçükbenli, Saee Paliwal, Timur M. Rvachov, Eddie Calleja, Johnny Israeli, Harry Clifford, Risto Haukioja, Nicholas Haemel, Kyle Tretina, Neha Tadimeti, Anthony Costa

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Landing page: https://arxiv.org/abs/2411.10548

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Concepts: Drug discovery, Modular design, Computer science, Drug, Drug development, Data science, Medicine, Pharmacology, Programming language, Bioinformatics, Biology

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Cited by: 9

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