Ailie Marx — accepted AI-conference papers

2026

Inference-time optimization for experiment-grounded protein ensemble generation

Sai Advaith Maddipatla, Anar Rzayev, Marco Pegoraro, Ailie Marx, Martin Pacesa, Paul Schanda +2

ICML 2026poster

Protein function relies on dynamic conformational ensembles, yet current generative models like AlphaFold3 (AF3) often fail to produce ensembles that match experimental data. Recent experiment-guided generators attempt to address this by steering the reverse diffusion process. However, these methods…

Cited by 0 Source ↗Scholar ↗

2025

Inverse problems with experiment-guided AlphaFold

Sai Advaith Maddipatla, Nadav Bojan, Meital Bojan, Sanketh Vedula, Paul Schanda, Ailie Marx +1

ICML 2025poster

Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational heterogeneity revealed by diverse experimental modalities.…

Cited by 23 Source ↗PDF ↗Scholar ↗