Andrew M. Watkins

According to our database, Andrew M. Watkins authored at least 20 papers between 2013 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2026

Disentangling multispecific antibody function with graph neural networks.

Joshua Southern, Changpeng Lu, Santrupti Nerli, Samuel Don Stanton, Andrew M. Watkins, Franziska Seeger, Frédéric A. Dreyer

CoRR, January, 2026

2025

Unified all-atom molecule generation with neural fields.

Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett, Karolis Martinkus, Joseph Kleinhenz, Emily K. Makowski, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Saeed Saremi

CoRR, November, 2025

Do we need equivariant models for molecule generation?

Ewa M. Nowara, Joshua A. Rackers, Patricia Suriana, Pan Kessel, Max Shen, Andrew Martin Watkins, Michael Maser

CoRR, July, 2025

Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins.

Frédéric A. Dreyer, Jan Ludwiczak, Karolis Martinkus, Brennan Abanades, Robert G. Alberstein, Pan Kessel, Pranav Rao, Jae Hyeon Lee, Richard Bonneau, Andrew M. Watkins, Franziska Seeger

CoRR, July, 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

Proceedings of the Forty-second International Conference on Machine Learning, 2025

2024

LLMs are Highly-Constrained Biophysical Sequence Optimizers.

Angelica Chen, Samuel Don Stanton, Robert G. Alberstein, Andrew M. Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey

CoRR, 2024

Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design.

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

CoRR, 2024

NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries.

Ewa M. Nowara, Pedro O. Pinheiro, Sai Pooja Mahajan, Omar Mahmood, Andrew Martin Watkins, Saeed Saremi, Michael Maser

CoRR, 2024

Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms.

Samuel Stanton, Robert G. Alberstein, Nathan C. Frey, Andrew M. Watkins, Kyunghyun Cho

CoRR, 2024

2023

MoleCLUEs: Optimizing Molecular Conformers by Minimization of Differentiable Uncertainty.

Michael Maser, Natasa Tagasovska, Jae Hyeon Lee, Andrew M. Watkins

CoRR, 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 M. Watkins

CoRR, 2023

3D molecule generation by denoising voxel grids.

Pedro O. Pinheiro, Joshua A. Rackers, Joseph Kleinhenz, Michael Maser, Omar Mahmood, Andrew M. Watkins, Stephen Ra, Vishnu Sresht, Saeed Saremi

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

OpenProteinSet: Training data for structural biology at scale.

Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2022

Deep learning models for predicting RNA degradation via dual crowdsourcing.

Hannah K. Wayment-Steele, Wipapat Kladwang, Andrew M. Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J. Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, King Yuen Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, Rhiju Das

Nat. Mac. Intell., December, 2022

PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design.

Ji Won Park, Samuel Stanton, Saeed Saremi, Andrew M. Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho

CoRR, 2022

Multi-segment preserving sampling for deep manifold sampler.

Daniel Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho

CoRR, 2022

2021

Predictive models of RNA degradation through dual crowdsourcing.

Hannah K. Wayment-Steele, Wipapat Kladwang, Andrew M. Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J. Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, Anthony Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, Eterna Participants, Rhiju Das

CoRR, 2021

2020

Better together: Elements of successful scientific software development in a distributed collaborative community.

Julia Koehler Leman, Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W. Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William R. Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland L. Dunbrack Jr., Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau

PLoS Comput. Biol., 2020

2016

Accurate <i>de novo</i> design of hyperstable constrained peptides.

Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, Surya V. S. R. K. Pulavarti, Quentin Kaas, Alexander Eletsky, Po-Ssu Huang, William A. Johnsen, Per Greisen, Gabriel J. Rocklin, Yifan Song, Thomas W. Linsky, Andrew M. Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos A. Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, David Baker

Nat., 2016

2013

HippDB: a database of readily targeted helical protein-protein interactions.

Christina M. Bergey, Andrew M. Watkins, Paramjit S. Arora

Bioinform., 2013