← Search

Jeffrey Ouyang-Zhang

4 accepted papers

2026

Triangle Multiplication is All You Need for Biomolecular Structure Representations

ICLR 2026poster

AlphaFold has transformed protein structure prediction, but emerging applications such as virtual ligand screening, proteome-wide folding, and de novo binder design demand predictions at a massive scale, where runtime and memory costs become prohibitive. A major bottleneck lies in the Pairformer bac…

Cited by 0SourcecodeScholar
2025

Ambient Proteins - Training Diffusion Models on Noisy Structures

NeurIPS 2025spotlight

We present Ambient Protein Diffusion, a framework for training protein diffusion models that generates structures with unprecedented diversity and quality. State-of-the-art generative models are trained on computationally derived structures from AlphaFold2 (AF), as experimentally determined structur…

Cited by 0SourceScholar
2025

Distilling Structural Representations into Protein Sequence Models

ICLR 2025poster

Protein language (or sequence) models, like the popular ESM2, are now widely used tools for extracting evolution-based protein representations and have achieved significant success on core downstream biological tasks. A major open problem is how to obtain representations that best capture both the s…

Cited by 1SourcePDFScholar
2023

Predicting a Protein's Stability under a Million Mutations

NeurIPS 2023poster

Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary pressure of all extant proteins makes identifying the scarce number of mutations that will improve thermodynamic stability challenging. Deep learning has recently emerged as a powerful tool for identifying…