Jeffrey Ouyang-Zhang

Jeffrey Ouyang-Zhang

Postdoc at MIT/Biohub

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I am a postdoctoral researcher at MIT and Biohub, advised by Sergey Ovchinnikov and Aly A Khan.

I recently finished my PhD at The University of Texas at Austin, advised by Philipp Krähenbühl and Adam Klivans. I was previously a research assistant at UC Berkeley, working with Professors Jitendra Malik and Amir Zamir. I graduated from UC Berkeley with a Bachelors of Science degree.

I am broadly interested in applying machine learning to biological applications.

Publications

Pearl

Pearl: A Foundation Model for Placing Every Atom in the Right Location

Genesis Research: Jeffrey Ouyang-Zhang, contributor

Paper
PairMixer

Triangle Multiplication is All You Need for Biomolecular Structure Representations

Jeffrey Ouyang-Zhang, Pranav Murugan, Daniel Jesus Diaz, Gianluca Scarpellini, Richard Strong Bowen, Nate Gruver, Adam Klivans, Philipp Kraehenbuehl, Aleksandra Faust, Maruan Al-Shedivat

ICLR 2026

Paper Code Weights Poster
Ambient Proteins

Ambient Proteins: Training Diffusion Models on Low Quality Structures

Giannis Daras*, Jeffrey Ouyang-Zhang*, Krithika Ravishankar, William Daspit, Costis Daskalakis, Qiang Liu, Adam Klivans, Daniel J. Diaz

NeurIPS 2025 (Spotlight)

Paper Code Weights Poster
ISM

Distilling Structural Representations into Protein Sequence Models

Jeffrey Ouyang-Zhang, Chengyue Gong, Yue Zhao, Philipp Krähenbühl, Adam R Klivans, Daniel J Diaz

ICLR 2025

Paper Code Weights Poster
Mutate Everything

Predicting a Protein's Stability under a Million Mutations

Jeffrey Ouyang-Zhang, Daniel J Diaz, Adam R Klivans, Philipp Krähenbühl

NeurIPS 2023

Paper Code Poster
Stability Oracle

Stability Oracle: A Structure-Based Graph-Transformer for Identifying Stabilizing Mutations

Daniel J Diaz, Chengyue Gong, Jeffrey Ouyang-Zhang, James M Loy, Jordan Wells, David Yang, Andrew D Ellington, Alex Dimakis, Adam R Klivans

Nature Communications 2024

Paper
NMS Strikes Back NMS Strikes Back

NMS Strikes Back

Jeffrey Ouyang-Zhang, Jang Hyun Cho, Xingyi Zhou, Philipp Krähenbühl

ArXiv 2022

Paper Code
Side-Tuning Side-Tuning

Side-Tuning: A Baseline for Network Adaptation via Additive Side Networks

Jeffrey O. Zhang, Alexander Sax, Amir Zamir, Leonidas Guibas, Jitendra Malik

ECCV 2020 (Spotlight)

Paper Website
Mid-Level Visual Priors Mid-Level Visual Priors

Learning to Navigate Using Mid-Level Visual Priors

Alexander Sax, Jeffrey O. Zhang, Bradley Emi, Amir Zamir, Silvio Savarese, Leonidas Guibas, Jitendra Malik

CoRL 2019 (Winner of CVPR 2019 Habitat Challenge)

Paper Website Workshop Poster
StarCraft II StarCraft II

Modular Architecture for StarCraft II with Deep Reinforcement Learning

Dennis Lee*, Haoran Tang*, Jeffrey O. Zhang, Huazhe Xu, Trevor Darrell, Pieter Abbeel

AIIDE 2018

Paper Website