Watkins, Andrew Martin

9 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

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

NeurIPS 2025 Unified All-Atom Molecule Generation with Neural Fields Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett, Karolis Martinkus, Joseph Kleinhenz, Emily K. Makowski, Andrew Martin Watkins, Vladimir Gligorijevic, Richard Bonneau, Saeed Saremi

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

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

ICMLW 2024 NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries Ewa Nowara, Pedro O. Pinheiro, Sai Pooja Mahajan, Omar Mahmood, Andrew Martin Watkins, Saeed Saremi, Michael Maser

NeurIPSW 2023 MoleCLUEs: Molecular Conformers Maximally In-Distribution for Predictive Models Michael Maser, Natasa Tagasovska, Jae Hyeon Lee, Andrew Martin Watkins

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 PropertyDAG: Multi-Objective Bayesian Optimization of Partially Ordered, Mixed-Variable Properties for Biological Sequence Design Ji Won Park, Samuel Don Stanton, Saeed Saremi, Andrew Martin Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho