Zuobai Zhang

According to our database, Zuobai Zhang authored at least 33 papers between 2020 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching.

Tomas Geffner, Kieran Didi, Zhonglin Cao, Danny Reidenbach, Zuobai Zhang, Christian Dallago, Emine Küçükbenli, Karsten Kreis, Arash Vahdat

CoRR, July, 2025

Means of Hitting Times for Random Walks on Graphs: Connections, Computation, and Optimization.

Haisong Xia, Wanyue Xu, Zuobai Zhang, Zhongzhi Zhang

ACM Trans. Knowl. Discov. Data, February, 2025

Proteina: Scaling Flow-based Protein Structure Generative Models.

Tomas Geffner, Kieran Didi, Zuobai Zhang, Danny Reidenbach, Zhonglin Cao, Jason Yim, Mario Geiger, Christian Dallago, Emine Küçükbenli, Arash Vahdat, Karsten Kreis

Proceedings of the Thirteenth International Conference on Learning Representations, 2025

2024

Opinion dynamics in social networks incorporating higher-order interactions.

Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Guanrong Chen

Data Min. Knowl. Discov., November, 2024

Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations.

Jiarui Lu, Zuobai Zhang, Bozitao Zhong, Chence Shi, Jian Tang

CoRR, 2024

ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation.

Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang

CoRR, 2024

Structure-Informed Protein Language Model.

Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang

CoRR, 2024

Multi-Scale Representation Learning for Protein Fitness Prediction.

Zuobai Zhang, Pascal Notin, Yining Huang, Aurélie C. Lozano, Vijil Chenthamarakshan, Debora S. Marks, Payel Das, Jian Tang

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024

Cell ontology guided transcriptome foundation model.

Xinyu Yuan, Zhihao Zhan, Zuobai Zhang, Manqi Zhou, Jianan Zhao, Boyu Han, Yue Li, Jian Tang

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024

Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling.

Jiarui Lu, Bozitao Zhong, Zuobai Zhang, Jian Tang

Proceedings of the Twelfth International Conference on Learning Representations, 2024

Evaluating Representation Learning on the Protein Structure Universe.

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

Proceedings of the Twelfth International Conference on Learning Representations, 2024

2023

PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design.

Chuanrui Wang, Bozitao Zhong, Zuobai Zhang, Narendra Chaudhary, Sanchit Misra, Jian Tang

CoRR, 2023

Enhancing Protein Language Models with Structure-based Encoder and Pre-training.

Zuobai Zhang, Minghao Xu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang

CoRR, 2023

Physics-Inspired Protein Encoder Pre-Training via Siamese Sequence-Structure Diffusion Trajectory Prediction.

Zuobai Zhang, Minghao Xu, Aurélie C. Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang

CoRR, 2023

DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing.

Yangtian Zhang, Zuobai Zhang, Bozitao Zhong, Sanchit Misra, Jian Tang

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction.

Zuobai Zhang, Minghao Xu, Aurélie C. Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning.

Songtao Liu, Zhengkai Tu, Minkai Xu, Zuobai Zhang, Lu Lin, Rex Ying, Jian Tang, Peilin Zhao, Dinghao Wu

Proceedings of the International Conference on Machine Learning, 2023

Protein Representation Learning by Geometric Structure Pretraining.

Zuobai Zhang, Minghao Xu, Arian Rokkum Jamasb, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang

Proceedings of the Eleventh International Conference on Learning Representations, 2023

2022

Biharmonic Distance-Based Performance Metric for Second-Order Noisy Consensus Networks.

Yuhao Yi, Bingjia Yang, Zuobai Zhang, Zhongzhi Zhang, Stacy Patterson

IEEE Trans. Inf. Theory, 2022

Fast Approximation of Coherence for Second-Order Noisy Consensus Networks.

Zuobai Zhang, Wanyue Xu, Yuhao Yi, Zhongzhi Zhang

IEEE Trans. Cybern., 2022

Coherence Scaling of Noisy Second-Order Scale-Free Consensus Networks.

Wanyue Xu, Bin Wu, Zuobai Zhang, Zhongzhi Zhang, Haibin Kan, Guanrong Chen

IEEE Trans. Cybern., 2022

Metro: Memory-Enhanced Transformer for Retrosynthetic Planning via Reaction Tree.

Songtao Liu, Rex Ying, Zuobai Zhang, Peilin Zhao, Jian Tang, Lu Lin, Dinghao Wu

CoRR, 2022

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, Jun-Kun Chen, Huiyu Cai, Jiarui Lu, Chang Ma, Runcheng Liu, Louis-Pascal A. C. Xhonneux, Meng Qu, Jian Tang

CoRR, 2022

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

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

Neural-Symbolic Models for Logical Queries on Knowledge Graphs.

Zhaocheng Zhu, Mikhail Galkin, Zuobai Zhang, Jian Tang

Proceedings of the International Conference on Machine Learning, 2022

Effects of Stubbornness on Opinion Dynamics.

Wanyue Xu, Liwang Zhu, Jiale Guan, Zuobai Zhang, Zhongzhi Zhang

Proceedings of the 31st ACM International Conference on Information & Knowledge Management, 2022

Structured Multi-task Learning for Molecular Property Prediction.

Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang

Proceedings of the International Conference on Artificial Intelligence and Statistics, 2022

2021

scETM: single-cell Embedded Topic Model.

Yi Zhao, Huiyu Cai, Zuobai Zhang, Jian Tang, Yue Li

Dataset, August, 2021

Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction.

Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal A. C. Xhonneux, Jian Tang

Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021

Minimizing Spectral Radius of Non-Backtracking Matrix by Edge Removal.

Zuobai Zhang, Zhongzhi Zhang, Guanrong Chen

Proceedings of the CIKM '21: The 30th ACM International Conference on Information and Knowledge Management, Virtual Event, Queensland, Australia, November 1, 2021

2020

Power-Law Graphs Have Minimal Scaling of Kemeny Constant for Random Walks.

Wanyue Xu, Yibin Sheng, Zuobai Zhang, Haibin Kan, Zhongzhi Zhang

Proceedings of the WWW '20: The Web Conference 2020, Taipei, Taiwan, April 20-24, 2020, 2020

Nearly Linear Time Algorithm for Mean Hitting Times of Random Walks on a Graph.

Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang

Proceedings of the WSDM '20: The Thirteenth ACM International Conference on Web Search and Data Mining, 2020

Opinion Dynamics Incorporating Higher-Order Interactions.

Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Guanrong Chen

Proceedings of the 20th IEEE International Conference on Data Mining, 2020