Nathan C. Frey

34 papers A* 4Journal 24Unranked 6
YearRankTypeTitle / Venue / Authors
2025 A* conf
Concept Bottleneck Language Models For Protein Design.
ICLR
Aya Abdelsalam Ismail, Tuomas P. Oikarinen, Amy Wang, Julius Adebayo, Samuel Don Stanton, Héctor Corrada Bravo, Kyunghyun Cho, Nathan C. Frey
2025 A* conf
Generalists vs. Specialists: Evaluating LLMs on Highly-Constrained Biophysical Sequence Optimization Tasks.
ICML
Angelica Chen, Samuel Don Stanton, Frances Ding, Robert G. Alberstein, Andrew Martin Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey
2025 J jnl
Strain Problems Got You in a Twist? Try StrainRelief: A Quantum-Accurate Tool for Ligand Strain Calculations.
J. Chem. Inf. Model.
Ewan R. S. Wallace, Nathan C. Frey, Joshua A. Rackers
2025 J jnl
Strain Problems got you in a Twist? Try StrainRelief: A Quantum-Accurate Tool for Ligand Strain Calculations.
CoRR
Ewan R. S. Wallace, Nathan C. Frey, Joshua A. Rackers
2025 J jnl
Tokenized and continuous embedding compressions of protein sequence and structure.
Patterns
Amy X. Lu, Wilson Yan, Kevin K. Yang, Vladimir Gligorijevic, Kyunghyun Cho, Pieter Abbeel, Richard Bonneau, Nathan C. Frey
2024 J jnl
Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design.
CoRR
Natasa Tagasovska, Ji Won Park, Matthieu Kirchmeyer, Nathan C. Frey, Andrew Martin Watkins, Aya Abdelsalam Ismail, Arian Rokkum Jamasb, Edith Lee, Tyler Bryson, Stephen Ra, Kyunghyun Cho
2024 J jnl
Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms.
CoRR
Samuel Stanton, Robert G. Alberstein, Nathan C. Frey, Andrew M. Watkins, Kyunghyun Cho
2024 J jnl
Concept Bottleneck Language Models For protein design.
CoRR
Aya Abdelsalam Ismail, Tuomas P. Oikarinen, Amy Wang, Julius Adebayo, Samuel Stanton, Taylor Joren, Joseph Kleinhenz, Allen Goodman, Héctor Corrada Bravo, Kyunghyun Cho, Nathan C. Frey
2024 J jnl
LLMs are Highly-Constrained Biophysical Sequence Optimizers.
CoRR
Angelica Chen, Samuel Don Stanton, Robert G. Alberstein, Andrew M. Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey
2024 A* conf
Protein Discovery with Discrete Walk-Jump Sampling.
ICLR
Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hötzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
2023 J jnl
A Green(er) World for A.I.
CoRR
Dan Zhao, Nathan C. Frey, Joseph McDonald, Matthew Hubbell, David Bestor, Michael Jones, Andrew Prout, Vijay Gadepally, Siddharth Samsi
2023 J jnl
Neural scaling of deep chemical models.
Nat. Mac. Intell.
Nathan C. Frey, Ryan Soklaski, Simon Axelrod, Siddharth Samsi, Rafael Gómez-Bombarelli, Connor W. Coley, Vijay Gadepally
2023 A* conf
Protein Design with Guided Discrete Diffusion.
NeurIPS
Nate Gruver, Samuel Stanton, Nathan C. Frey, Tim G. J. Rudner, Isidro Hötzel, Julien Lafrance-Vanasse, Arvind Rajpal, Kyunghyun Cho, Andrew Gordon Wilson
2023 J jnl
Protein Design with Guided Discrete Diffusion.
CoRR
Nate Gruver, Samuel Stanton, Nathan C. Frey, Tim G. J. Rudner, Isidro Hötzel, Julien Lafrance-Vanasse, Arvind Rajpal, Kyunghyun Cho, Andrew Gordon Wilson
2023 J jnl
Protein Discovery with Discrete Walk-Jump Sampling.
CoRR
Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hötzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
2023 J jnl
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers.
CoRR
Michael Maser, Ji Won Park, Joshua Yao-Yu Lin, Jae Hyeon Lee, Nathan C. Frey, Andrew M. Watkins
2022 — conf
A Green(er) World for A.I.
IPDPS Workshops
Dan Zhao, Nathan C. Frey, Joseph McDonald, Matthew Hubbell, David Bestor, Michael Jones, Andrew Prout, Vijay Gadepally, Siddharth Samsi
2022 J jnl
A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences.
CoRR
Natasa Tagasovska, Nathan C. Frey, Andreas Loukas, Isidro Hötzel, Julien Lafrance-Vanasse, Ryan Lewis Kelly, Yan Wu, Arvind Rajpal, Richard Bonneau, Kyunghyun Cho, Stephen Ra, Vladimir Gligorijevic
2022 — conf
Benchmarking Resource Usage for Efficient Distributed Deep Learning.
HPEC
Nathan C. Frey, Baolin Li, Joseph McDonald, Dan Zhao, Michael Jones, David Bestor, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
2022 J jnl
Benchmarking Resource Usage for Efficient Distributed Deep Learning.
CoRR
Nathan C. Frey, Baolin Li, Joseph McDonald, Dan Zhao, Michael Jones, David Bestor, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
2022 — conf
Energy-aware neural architecture selection and hyperparameter optimization.
IPDPS Workshops
Nathan C. Frey, Dan Zhao, Simon Axelrod, Michael Jones, David Bestor, Vijay Gadepally, Rafael Gómez-Bombarelli, Siddharth Samsi
2022 J jnl
FastFlows: Flow-Based Models for Molecular Graph Generation.
CoRR
Nathan C. Frey, Vijay Gadepally, Bharath Ramsundar
2022 J jnl
Graph Contrastive Learning for Materials.
CoRR
Teddy Koker, Keegan Quigley, Will Spaeth, Nathan C. Frey, Lin Li
2022 — conf
Great Power, Great Responsibility: Recommendations for Reducing Energy for Training Language Models.
NAACL-HLT (Findings)
Joseph McDonald, Baolin Li, Nathan C. Frey, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
2022 J jnl
Great Power, Great Responsibility: Recommendations for Reducing Energy for Training Language Models.
CoRR
Joseph McDonald, Baolin Li, Nathan C. Frey, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
2022 — conf
Loss Curve Approximations for Fast Neural Architecture Ranking & Training Elasticity Estimation.
IPDPS Workshops
Dan Zhao, Nathan C. Frey, Vijay Gadepally, Siddharth Samsi
2022 J jnl
Roughness of Molecular Property Landscapes and Its Impact on Modellability.
J. Chem. Inf. Model.
Matteo Aldeghi, David E. Graff, Nathan C. Frey, Joseph A. Morrone, Edward O. Pyzer-Knapp, Kirk E. Jordan, Connor W. Coley
2022 J jnl
SELFIES and the future of molecular string representations.
CoRR
Mario Krenn, Qianxiang Ai, Senja Barthel, Nessa Carson, Angelo Frei, Nathan C. Frey, Pascal Friederich, Théophile Gaudin, Alberto Alexander Gayle, Kevin Maik Jablonka, Rafael F. Lameiro, Dominik Lemm, Alston Lo, Seyed Mohamad Moosavi, José Manuel Nápoles-Duarte, AkshatKumar Nigam, Robert Pollice, Kohulan Rajan, Ulrich Schatzschneider, Philippe Schwaller, Marta Skreta, Berend Smit, Felix Strieth-Kalthoff, Chong Sun, Gary Tom, Guido Falk von Rudorff, Andrew Wang, Andrew D. White, Adamo Young, Rose Yu, Alán Aspuru-Guzik
2022 J jnl
SELFIES and the future of molecular string representations.
Patterns
Mario Krenn, Qianxiang Ai, Senja Barthel, Nessa Carson, Angelo Frei, Nathan C. Frey, Pascal Friederich, Théophile Gaudin, Alberto Alexander Gayle, Kevin Maik Jablonka, Rafael F. Lameiro, Dominik Lemm, Alston Lo, Seyed Mohamad Moosavi, José Manuel Nápoles-Duarte, AkshatKumar Nigam, Robert Pollice, Kohulan Rajan, Ulrich Schatzschneider, Philippe Schwaller, Marta Skreta, Berend Smit, Felix Strieth-Kalthoff, Chong Sun, Gary Tom, Guido Falk von Rudorff, Andrew Wang, Andrew D. White, Adamo Young, Rose Yu, Alán Aspuru-Guzik
2022 — conf
The MIT Supercloud Workload Classification Challenge.
IPDPS Workshops
Benny J. Tang, Qiqi Chen, Matthew L. Weiss, Nathan C. Frey, Joseph McDonald, David Bestor, Charles Yee, William Arcand, William Bergeron, Chansup Byun, Daniel Edelman, Michael Houle, Matthew Hubbell, Michael Jones, Jeremy Kepner, Anna Klein, Adam Michaleas, Peter Michaleas, Lauren Milechin, Julia S. Mullen, Andrew Prout, Albert Reuther, Antonio Rosa, Andrew Bowne, Lindsey McEvoy, Baolin Li, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
2022 J jnl
The MIT Supercloud Workload Classification Challenge.
CoRR
Benny J. Tang, Qiqi Chen, Matthew L. Weiss, Nathan C. Frey, Joseph McDonald, David Bestor, Charles Yee, William Arcand, Chansup Byun, Daniel Edelman, Matthew Hubbell, Michael Jones, Jeremy Kepner, Anna Klein, Adam Michaleas, Peter Michaleas, Lauren Milechin, Julia S. Mullen, Andrew Prout, Albert Reuther, Antonio Rosa, Andrew Bowne, Lindsey McEvoy, Baolin Li, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
2021 J jnl
Bringing Atomistic Deep Learning to Prime Time.
CoRR
Nathan C. Frey, Siddharth Samsi, Bharath Ramsundar, Connor W. Coley, Vijay Gadepally
2021 J jnl
Scalable Geometric Deep Learning on Molecular Graphs.
CoRR
Nathan C. Frey, Siddharth Samsi, Joseph McDonald, Lin Li, Connor W. Coley, Vijay Gadepally
2021 J jnl
The Pseudo Projection Operator: Applications of Deep Learning to Projection Based Filtering in Non-Trivial Frequency Regimes.
CoRR
Matthew L. Weiss, Nathan C. Frey, Siddharth Samsi, Randy C. Paffenroth, Vijay Gadepally