Zuobai Zhang 「张作柏」

I am a third-year PhD student at Mila - Québec AI Institute supervised by Prof. Jian Tang. Before that, I received my B.S. in Computer Science from Fudan University advised by Prof. Zhongzhi Zhang. I was also a machine learning engineering intern at ByteDance Inc., where I worked on recommender systems under the supervision of Yitan Li.

Email: zuobai.zhang [at] mila.quebec

Github   /   Google Scholar   /   CV   /   Twitter


My research interests include machine learning for drug discovery, especially for protein science. I also have general internest in AI4Science and machine learning techniques, e.g., deep generative models, geometric deep learning and self-supervised learning.

(* denotes equal contribution)
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
Kang Jin*, Zuobai Zhang*, Ke Zhang, Francesca Viggiani, Claire Callahan, Jian Tang, Bruce J Aronow, Jian Shu
Pretrainable Geometric Graph Neural Network for Antibody Affinity Maturation
Huiyu Cai*, Zuobai Zhang*, Mingkai Wang*, Bozitao Zhong*, Yanling Wu, Tianlei Ying, Jian Tang
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing
Yangtian Zhang*, Zuobai Zhang*, Bozitao Zhong, Sanchit Misra, Jian Tang
NeurIPS 2023
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction
Zuobai Zhang*, Minghao Xu*, Aurelie Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang
NeurIPS 2023 (spotlight)
FusionRetro: Molecule Representation Fusion via In-context Reactions for Retrosynthetic Planning
Songtao Liu, Zhengkai Tu*, Minkai Xu*, Zuobai Zhang*, Peilin Zhao, Jian Tang, Rex Ying, Lu Lin, Dinghao Wu
ICML 2023
Enhancing Protein Language Models with Structure-based Encoder and Pre-training
Zuobai Zhang, Minghao Xu, Vijil Chenthamarakshan, Aurelie Lozano, Payel Das, Jian Tang
ICLR 2023 Machine Learning for Drug Discovery Workshop
Protein Representation Learning by Geometric Structure Pretraining
Zuobai Zhang, Minghao Xu, Arian Jamasb, Vijil Chenthamarakshan, Aurelie Lozano, Payel Das, Jian Tang
ICLR 2023
ICML 2022 Pre-Training Workshop
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding
Minghao Xu*, Zuobai Zhang*, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Chang Ma, Runcheng Liu, Jian Tang
NeurIPS 2022 Datasets and Benchmarks Track
Effects of Stubbornness on Opinion Dynamics
Wanyue Xu, Liwang Zhu, Jiale Guan, Zuobai Zhang, Zhongzhi Zhang
CIKM 2022
Neural-Symbolic Models for Logical Queries on Knowledge Graphs
Zhaocheng Zhu, Mikhail Galkin, Zuobai Zhang, Jian Tang
ICML 2022
A Roadmap for Big Model
I'm a co-first author of this paper.
Structured Multi-task Learning for Molecular Property Prediction
Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang
NeurIPS 2021 AI for Science Workshop
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery
Zhaocheng Zhu, Chence Shi, Zuobai Zhang, Shengchao Liu, Minghao Xu, Xinyu Yuan, Yangtian Zhang, Junkun Chen, Huiyu Cai, Jiarui Lu, Chang Ma, Runcheng Liu, Louis-Pascal Xhonneux, Meng Qu, Jian Tang
Biharmonic Distance-Based Performance Metric for Second-Order Noisy Consensus Networks
Yuhao Yi, Bingjia Yang, Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Stacy Patterson
IEEE Transactions on Information Theory
Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction
Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal Xhonneux, Jian Tang
NeurIPS 2021
Learning Interpretable Cellular and Gene Signature Embeddings from Single-Cell Transcriptomic Data
Yifan Zhao*, Huiyu Cai*, Zuobai Zhang, Jian Tang, Yue Li
Nature Communications
Minimizing Spectral Radius of Non-Backtracking Matrix by Edge Removal
Zuobai Zhang, Zhongzhi Zhang, Guanrong Chen
CIKM 2021
Coherence Scaling of Noisy Second-Order Scale-Free Consensus Network
Wanyue Xu, Bin Wu, Zuobai Zhang, Zhongzhi Zhang, Haibin Kan, Guanrong Chen
IEEE Transactions on Cybernetics
Opinion Dynamics Incorporating High-Order Interactions
Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Guanrong Chen
ICDM 2020 (short paper)
Power-Law Graphs Have Minimal Scaling of Kemeny Constant for Random Walks
Wanyue Xu, Yibin Sheng, Zuobai Zhang, Haibin Kan, Zhongzhi Zhang
WWW 2020
Fast Approximation of Coherence for Second-Order Noisy Consensus Networks
Zuobai Zhang, Wanyue Xu, Yuhao Yi, Zhongzhi Zhang
IEEE Transactions on Cybernetics
Nearly Linear Time Algorithm for Mean Hitting Times of Random Walks on a Graph
Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang
WSDM 2020
TorchProtein: A flexible machine learning library for protein science.

A machine learning library for protein science based on TorchDrug, providing representation learning models for both sequences and structures, and fundamental protein tasks like function prediction, structure prediction.

[Homepage] [Github] [Twitter]
TorchDrug: A powerful and flexible machine learning platform for drug discovery.

A machine learning platform designed for drug discovery, covering techniques from graph machine learning, deep generative models to reinforcement learning.

[Homepage] [Github] [Twitter]

Outstanding Undergraduates Graduates of Shanghai, Jun. 2021

Scholarships for Outstanding Academic Individuals at Fudan University, Dec. 2020

Shanghai Scholarship (Top 1%), Oct. 2020

SenseTime Scholarship (29 undergrads from China), Jan. 2020

Chinese National Scholarship (Top 1%), Oct. 2019

Wish Scholarship, May 2019

Chun Tsung Scholar Program, Apr. 2019

Chinese National Scholarship (Top 1%), Oct. 2018

Gold Medal, ACM-ICPC Asia Regional Contest EC-Final, Dec. 2017

Gold Medal, ACM-ICPC Asia Regional Contest Qingdao Site, Nov. 2017

Silver Medal, National Olympiad in Informatics, National Finals, Jul. 2016

Updated at Oct. 2023