Nathan C. Frey

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 27

Top Topics

Protein Sequences

Projection Operator

Top Venues

IPDPS Workshops

NAACL-HLT (Findings)

Publications

Samuel Stanton, Robert Alberstein, Nathan C. Frey, Andrew M. Watkins, Kyunghyun Cho
Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms. CoRR (2024)
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
Protein Discovery with Discrete Walk-Jump Sampling. ICLR (2024)
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
Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design. CoRR (2024)
Nate Gruver, Samuel Stanton, Nathan C. Frey, Tim G. J. Rudner, Isidro Hötzel, Julien Lafrance-Vanasse, Arvind Rajpal, Kyunghyun Cho, Andrew Gordon Wilson
Protein Design with Guided Discrete Diffusion. NeurIPS (2023)
Nate Gruver, Samuel Stanton, Nathan C. Frey, Tim G. J. Rudner, Isidro Hötzel, Julien Lafrance-Vanasse, Arvind Rajpal, Kyunghyun Cho, Andrew Gordon Wilson
Protein Design with Guided Discrete Diffusion. CoRR (2023)
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
Protein Discovery with Discrete Walk-Jump Sampling. CoRR (2023)
Dan Zhao, Nathan C. Frey, Joseph McDonald, Matthew Hubbell, David Bestor, Michael Jones, Andrew Prout, Vijay Gadepally, Siddharth Samsi
A Green(er) World for A.I. CoRR (2023)
Michael Maser, Ji Won Park, Joshua Yao-Yu Lin, Jae Hyeon Lee, Nathan C. Frey, Andrew M. Watkins
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers. CoRR (2023)
Nathan C. Frey, Ryan Soklaski, Simon Axelrod, Siddharth Samsi, Rafael Gómez-Bombarelli, Connor W. Coley, Vijay Gadepally
Neural scaling of deep chemical models. Nat. Mac. Intell. 5 (11) (2023)
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
SELFIES and the future of molecular string representations. CoRR (2022)
Nathan C. Frey, Vijay Gadepally, Bharath Ramsundar
FastFlows: Flow-Based Models for Molecular Graph Generation. CoRR (2022)
Joseph McDonald, Baolin Li, Nathan C. Frey, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
Great Power, Great Responsibility: Recommendations for Reducing Energy for Training Language Models. NAACL-HLT (Findings) (2022)
Nathan C. Frey, Baolin Li, Joseph McDonald, Dan Zhao, Michael Jones, David Bestor, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
Benchmarking Resource Usage for Efficient Distributed Deep Learning. CoRR (2022)
Dan Zhao, Nathan C. Frey, Vijay Gadepally, Siddharth Samsi
Loss Curve Approximations for Fast Neural Architecture Ranking & Training Elasticity Estimation. IPDPS Workshops (2022)
Dan Zhao, Nathan C. Frey, Joseph McDonald, Matthew Hubbell, David Bestor, Michael Jones, Andrew Prout, Vijay Gadepally, Siddharth Samsi
A Green(er) World for A.I. IPDPS Workshops (2022)
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
The MIT Supercloud Workload Classification Challenge. CoRR (2022)
Nathan C. Frey, Dan Zhao, Simon Axelrod, Michael Jones, David Bestor, Vijay Gadepally, Rafael Gómez-Bombarelli, Siddharth Samsi
Energy-aware neural architecture selection and hyperparameter optimization. IPDPS Workshops (2022)
Nathan C. Frey, Baolin Li, Joseph McDonald, Dan Zhao, Michael Jones, David Bestor, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
Benchmarking Resource Usage for Efficient Distributed Deep Learning. HPEC (2022)
Teddy Koker, Keegan Quigley, Will Spaeth, Nathan C. Frey, Lin Li
Graph Contrastive Learning for Materials. CoRR (2022)
Joseph McDonald, Baolin Li, Nathan C. Frey, Devesh Tiwari, Vijay Gadepally, Siddharth Samsi
Great Power, Great Responsibility: Recommendations for Reducing Energy for Training Language Models. CoRR (2022)
Matteo Aldeghi, David E. Graff, Nathan C. Frey, Joseph A. Morrone, Edward O. Pyzer-Knapp, Kirk E. Jordan, Connor W. Coley
Roughness of Molecular Property Landscapes and Its Impact on Modellability. J. Chem. Inf. Model. 62 (19) (2022)
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
SELFIES and the future of molecular string representations. Patterns 3 (10) (2022)
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
The MIT Supercloud Workload Classification Challenge. IPDPS Workshops (2022)
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
A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences. CoRR (2022)
Nathan C. Frey, Siddharth Samsi, Bharath Ramsundar, Connor W. Coley, Vijay Gadepally
Bringing Atomistic Deep Learning to Prime Time. CoRR (2021)
Matthew L. Weiss, Nathan C. Frey, Siddharth Samsi, Randy C. Paffenroth, Vijay Gadepally
The Pseudo Projection Operator: Applications of Deep Learning to Projection Based Filtering in Non-Trivial Frequency Regimes. CoRR (2021)
Nathan C. Frey, Siddharth Samsi, Joseph McDonald, Lin Li, Connor W. Coley, Vijay Gadepally
Scalable Geometric Deep Learning on Molecular Graphs. CoRR (2021)