Frey, Nathan C.

19 publications

ICLRW 2025 A Guided Design Framework for the Optimization of Therapeutic-like Antibodies Amy Wang, Zhe Sang, Samuel Don Stanton, Jennifer L. Hofmann, Saeed Izadi, Eliott Park, Jan Ludwiczak, Matthieu Kirchmeyer, Darcy Davidson, Andrew Maier, Tom Pritsky, Nathan C. Frey, Andrew Martin Watkins, Franziska Seeger

ICLRW 2025 All-Atom Protein Generation with Latent Diffusion Amy X. Lu, Wilson Yan, Sarah A Robinson, Simon Kelow, Kevin K Yang, Vladimir Gligorijevic, Kyunghyun Cho, Richard Bonneau, Pieter Abbeel, Nathan C. Frey

ICLR 2025 Concept Bottleneck Language Models for Protein Design Aya Abdelsalam Ismail, Tuomas Oikarinen, Amy Wang, Julius Adebayo, Samuel Don Stanton, Hector Corrada Bravo, Kyunghyun Cho, Nathan C. Frey

ICML 2025 Generalists vs. Specialists: Evaluating LLMs on Highly-Constrained Biophysical Sequence Optimization Tasks Angelica Chen, Samuel Don Stanton, Frances Ding, Robert G Alberstein, Andrew Martin Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey

ICLRW 2025 Guided Generation of B-Cell Receptors with Conditional Walk-Jump Sampling Taylor Joren, Sarah A Robinson, Homa MohammadiPeyhani, Sai Pooja Mahajan, Edith Lee, Stephen Lillington, Qixin Bei, Saeed Saremi, Jae Hyeon Lee, Richard Bonneau, Isidro Hotzel, Vladimir Gligorijevic, Simon Kelow, Nathan C. Frey

ICLRW 2025 Orchestrating Tool Ecosystem of Drug Discovery with Intention-Aware LLM Agents Mingyu Derek Ma, Karina Zadorozhny, Jesse Swanson, Nathan C. Frey, Keunwoo Choi, Maksim Eremeev, Sabrina J Mielke, Wenmo Sun, Melody Liu, Jonathan Wickes, Vladimir Gligorijevic, Richard Bonneau, Henri Dwyer, Kyunghyun Cho, Stephen Ra

ICMLW 2024 Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms Samuel Don Stanton, Robert G Alberstein, Nathan C. Frey, Andrew Martin Watkins, Kyunghyun Cho

ICMLW 2024 Compressing the Latent Space of Single-Sequence Protein Predictors for Multimodal Generation Amy X. Lu, Wilson Yan, Vladimir Gligorijevic, Pieter Abbeel, Kevin K Yang, Nathan C. Frey

ICMLW 2024 Cramming Protein Language Model Training in 24 GPU Hours Nathan C. Frey, Taylor Joren, Aya Abdelsalam Ismail, Allen Goodman, Richard Bonneau, Kyunghyun Cho, Vladimir Gligorijevic

NeurIPSW 2024 LLMs Are Highly-Constrained Biophysical Sequence Optimizers Angelica Chen, Samuel Don Stanton, Robert G Alberstein, Andrew Martin Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey

ICLR 2024 Protein Discovery with Discrete Walk-Jump Sampling Nathan C. Frey, Dan Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hotzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi

NeurIPSW 2023 Identifying Regularization Schemes That Make Feature Attributions Faithful Julius Adebayo, Samuel Don Stanton, Simon Kelow, Michael Maser, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Stephen Ra, Nathan C. Frey

ICLRW 2023 Learning Protein Family Manifolds with Smoothed Energy-Based Models Nathan C. Frey, Dan Berenberg, Joseph Kleinhenz, Isidro Hotzel, Julien Lafrance-Vanasse, Ryan Lewis Kelly, Yan Wu, Arvind Rajpal, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi

ICMLW 2023 Protein Design with Guided Discrete Diffusion Nate Gruver, Samuel Don Stanton, Nathan C. Frey, Tim G. J. Rudner, Isidro Hotzel, Julien Lafrance-Vanasse, Arvind Rajpal, Kyunghyun Cho, Andrew Gordon Wilson

ICLRW 2023 SupSiam: Non-Contrastive Auxiliary Loss for Learning from Molecular Conformers Michael Maser, Ji Won Park, Joshua Yao-Yu Lin, Jae Hyeon Lee, Nathan C. Frey, Andrew Martin Watkins

NeurIPSW 2022 A Pareto-Optimal Compositional Energy-Based Model for Sampling and Optimization of Protein Sequences Natasa Tagasovska, Nathan C. Frey, Andreas Loukas, Isidro Hotzel, Julien Lafrance-Vanasse, Ryan Lewis Kelly, Yan Wu, Arvind Rajpal, Richard Bonneau, Kyunghyun Cho, Stephen Ra, Vladimir Gligorijevic

NeurIPSW 2022 Graph Contrastive Learning for Materials Teddy Koker, Keegan Quigley, Will Spaeth, Nathan C. Frey, Lin Li

NeurIPSW 2021 Bringing Atomistic Deep Learning to Prime Time Nathan C. Frey, Siddharth Samsi, Bharath Ramsundar, Connor W. Coley, Vijay Gadepally

NeurIPSW 2021 Scalable Geometric Deep Learning on Molecular Graphs Nathan C. Frey, Siddharth Samsi, Joseph McDonald, Lin Li, Connor W. Coley, Vijay Gadepally