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GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics

Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael Irvin, J. Gregory Pauloski, Logan Ward, Valerie Hayot, Murali Emani, Sam Foreman, Zhen Xie, Diangen Lin, Maulik Shukla, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Ian Foster, James J. Davis, Michael E. Papka, Thomas Brettin, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, Arvind Ramanathan
doi: https://doi.org/10.1101/2022.10.10.511571
Maxim Zvyagin
1Argonne National Laboratory
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Alexander Brace
1Argonne National Laboratory
2University of Chicago
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Kyle Hippe
1Argonne National Laboratory
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Yuntian Deng
3NVIDIA Inc.
4Harvard University
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Bin Zhang
5Cerebras Inc.
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Cindy Orozco Bohorquez
5Cerebras Inc.
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Austin Clyde
1Argonne National Laboratory
2University of Chicago
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Bharat Kale
6Northern Illinois University
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Danilo Perez-Rivera
1Argonne National Laboratory
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Heng Ma
1Argonne National Laboratory
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Carla M. Mann
1Argonne National Laboratory
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Michael Irvin
1Argonne National Laboratory
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J. Gregory Pauloski
2University of Chicago
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Logan Ward
1Argonne National Laboratory
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Valerie Hayot
2University of Chicago
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Murali Emani
1Argonne National Laboratory
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Sam Foreman
1Argonne National Laboratory
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Zhen Xie
1Argonne National Laboratory
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Diangen Lin
2University of Chicago
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Maulik Shukla
1Argonne National Laboratory
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Weili Nie
3NVIDIA Inc.
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Josh Romero
3NVIDIA Inc.
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Christian Dallago
3NVIDIA Inc.
7Technical University of Munich
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Arash Vahdat
3NVIDIA Inc.
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Chaowei Xiao
3NVIDIA Inc.
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Thomas Gibbs
3NVIDIA Inc.
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Ian Foster
1Argonne National Laboratory
2University of Chicago
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James J. Davis
1Argonne National Laboratory
2University of Chicago
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Michael E. Papka
1Argonne National Laboratory
8University of Illinois Chicago
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Thomas Brettin
1Argonne National Laboratory
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Rick Stevens
1Argonne National Laboratory
2University of Chicago
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Anima Anandkumar
3NVIDIA Inc.
9California Institute of Technology
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Venkatram Vishwanath
1Argonne National Laboratory
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Arvind Ramanathan
1Argonne National Laboratory
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  • For correspondence: ramanathana@anl.gov
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ABSTRACT

Our work seeks to transform how new and emergent variants of pandemic causing viruses, specially SARS-CoV-2, are identified and classified. By adapting large language models (LLMs) for genomic data, we build genome-scale language models (GenSLMs) which can learn the evolutionary landscape of SARS-CoV-2 genomes. By pretraining on over 110 million prokaryotic gene sequences, and then finetuning a SARS-CoV-2 specific model on 1.5 million genomes, we show that GenSLM can accurately and rapidly identify variants of concern. Thus, to our knowledge, GenSLM represents one of the first whole genome scale foundation models which can generalize to other prediction tasks. We demonstrate the scaling of GenSLMs on both GPU-based supercomputers and AI-hardware accelerators, achieving over 1.54 zettaflops in training runs. We present initial scientific insights gleaned from examining GenSLMs in tracking the evolutionary dynamics of SARS-CoV-2, noting that its full potential on large biological data is yet to be realized.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵† Joint first authors,

  • ↵* Contact authors: venkat{at}anl.gov, anima{at}caltech.edu, ramanathana{at}anl.gov

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 11, 2022.
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GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael Irvin, J. Gregory Pauloski, Logan Ward, Valerie Hayot, Murali Emani, Sam Foreman, Zhen Xie, Diangen Lin, Maulik Shukla, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Ian Foster, James J. Davis, Michael E. Papka, Thomas Brettin, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, Arvind Ramanathan
bioRxiv 2022.10.10.511571; doi: https://doi.org/10.1101/2022.10.10.511571
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GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael Irvin, J. Gregory Pauloski, Logan Ward, Valerie Hayot, Murali Emani, Sam Foreman, Zhen Xie, Diangen Lin, Maulik Shukla, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Ian Foster, James J. Davis, Michael E. Papka, Thomas Brettin, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, Arvind Ramanathan
bioRxiv 2022.10.10.511571; doi: https://doi.org/10.1101/2022.10.10.511571

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