Zuobai Zhang

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 36

Top Topics

Protein Structure

Top Venues

IEEE Trans. Cybern.

Publications

Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation. CoRR (2024)
Jiarui Lu, Bozitao Zhong, Zuobai Zhang, Jian Tang
Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling. ICLR (2024)
Jiarui Lu, Zuobai Zhang, Bozitao Zhong, Chence Shi, Jian Tang
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations. CoRR (2024)
Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
Structure-Informed Protein Language Model. CoRR (2024)
Arian R. Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell
Evaluating representation learning on the protein structure universe. CoRR (2024)
Arian Rokkum Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell
Evaluating Representation Learning on the Protein Structure Universe. ICLR (2024)
Chuanrui Wang, Bozitao Zhong, Zuobai Zhang, Narendra Chaudhary, Sanchit Misra, Jian Tang
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design. CoRR (2023)
Yangtian Zhang, Zuobai Zhang, Bozitao Zhong, Sanchit Misra, Jian Tang
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing. CoRR (2023)
Zuobai Zhang, Minghao Xu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
Enhancing Protein Language Models with Structure-based Encoder and Pre-training. CoRR (2023)
Songtao Liu, Zhengkai Tu, Minkai Xu, Zuobai Zhang, Lu Lin, Rex Ying, Jian Tang, Peilin Zhao, Dinghao Wu
FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning. ICML (2023)
Zuobai Zhang, Minghao Xu, Arian Rokkum Jamasb, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
Protein Representation Learning by Geometric Structure Pretraining. ICLR (2023)
Yangtian Zhang, Zuobai Zhang, Bozitao Zhong, Sanchit Misra, Jian Tang
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing. NeurIPS (2023)
Zuobai Zhang, Minghao Xu, Aurélie C. Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang
Physics-Inspired Protein Encoder Pre-Training via Siamese Sequence-Structure Diffusion Trajectory Prediction. CoRR (2023)
Zuobai Zhang, Minghao Xu, Aurélie C. Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction. NeurIPS (2023)
Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang
Structured Multi-task Learning for Molecular Property Prediction. CoRR (2022)
Zhaocheng Zhu, Mikhail Galkin, Zuobai Zhang, Jian Tang
Neural-Symbolic Models for Logical Queries on Knowledge Graphs. CoRR (2022)
Zuobai Zhang, Wanyue Xu, Yuhao Yi, Zhongzhi Zhang
Fast Approximation of Coherence for Second-Order Noisy Consensus Networks. IEEE Trans. Cybern. 52 (1) (2022)
Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang
Structured Multi-task Learning for Molecular Property Prediction. AISTATS (2022)
Wanyue Xu, Liwang Zhu, Jiale Guan, Zuobai Zhang, Zhongzhi Zhang
Effects of Stubbornness on Opinion Dynamics. CIKM (2022)
Yuhao Yi, Bingjia Yang, Zuobai Zhang, Zhongzhi Zhang, Stacy Patterson
Biharmonic Distance-Based Performance Metric for Second-Order Noisy Consensus Networks. IEEE Trans. Inf. Theory 68 (2) (2022)
Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Chang Ma, Runcheng Liu, Jian Tang
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding. NeurIPS (2022)
Wanyue Xu, Liwang Zhu, Jiale Guan, Zuobai Zhang, Zhongzhi Zhang
Effects of Stubbornness on Opinion Dynamics. CoRR (2022)
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 A. C. Xhonneux, Meng Qu, Jian Tang
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery. CoRR (2022)
Songtao Liu, Rex Ying, Zuobai Zhang, Peilin Zhao, Jian Tang, Lu Lin, Dinghao Wu
Metro: Memory-Enhanced Transformer for Retrosynthetic Planning via Reaction Tree. CoRR (2022)
Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Chang Ma, Runcheng Liu, Jian Tang
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding. CoRR (2022)
Zuobai Zhang, Minghao Xu, Arian R. Jamasb, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
Protein Representation Learning by Geometric Structure Pretraining. CoRR (2022)
Zhaocheng Zhu, Mikhail Galkin, Zuobai Zhang, Jian Tang
Neural-Symbolic Models for Logical Queries on Knowledge Graphs. ICML (2022)
Wanyue Xu, Bin Wu, Zuobai Zhang, Zhongzhi Zhang, Haibin Kan, Guanrong Chen
Coherence Scaling of Noisy Second-Order Scale-Free Consensus Networks. IEEE Trans. Cybern. 52 (7) (2022)
Wanyue Xu, Bin Wu, Zuobai Zhang, Zhongzhi Zhang, Haibin Kan, Guanrong Chen
Coherence Scaling of Noisy Second-Order Scale-Free Consensus Networks. CoRR (2021)
Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal A. C. Xhonneux, Jian Tang
Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction. CoRR (2021)
Zuobai Zhang, Zhongzhi Zhang, Guanrong Chen
Minimizing Spectral Radius of Non-Backtracking Matrix by Edge Removal. CIKM (2021)
Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal A. C. Xhonneux, Jian Tang
Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction. NeurIPS (2021)
Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Guanrong Chen
Opinion Dynamics Incorporating Higher-Order Interactions. CoRR (2021)
Wanyue Xu, Yibin Sheng, Zuobai Zhang, Haibin Kan, Zhongzhi Zhang
Power-Law Graphs Have Minimal Scaling of Kemeny Constant for Random Walks. WWW (2020)
Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang
Nearly Linear Time Algorithm for Mean Hitting Times of Random Walks on a Graph. WSDM (2020)
Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Guanrong Chen
Opinion Dynamics Incorporating Higher-Order Interactions. ICDM (2020)