Opinion Dynamics Incorporating Higher-Order Interactions. - Zuobai Zhang; Wanyue Xu; Zhongzhi Zhang; Guanrong Chen (ICDM, 2020)

Nearly Linear Time Algorithm for Mean Hitting Times of Random Walks on a Graph. - Zuobai Zhang; Wanyue Xu; Zhongzhi Zhang (WSDM, 2020)

Power-Law Graphs Have Minimal Scaling of Kemeny Constant for Random Walks. - Wanyue Xu; Yibin Sheng; Zuobai Zhang; Haibin Kan; Zhongzhi Zhang (WWW, 2020)

Minimizing Spectral Radius of Non-Backtracking Matrix by Edge Removal. - Zuobai Zhang; Zhongzhi Zhang; Guanrong Chen (CIKM, 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 005 (NeurIPS, 2021)

scETM: single-cell Embedded Topic Model. - Yi Zhao; Huiyu Cai; Zuobai Zhang; Jian Tang 005; Yue Li (Zenodo, 2021)

Structured Multi-task Learning for Molecular Property Prediction. - Shengchao Liu; Meng Qu; Zuobai Zhang; Huiyu Cai; Jian Tang 005 (AISTATS, 2022)

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 001; Zuobai Zhang; Jian Tang 005 (ICML, 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 005 (NeurIPS, 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; et al. (CoRR, 2022)

Metro: Memory-Enhanced Transformer for Retrosynthetic Planning via Reaction Tree. - Songtao Liu; Rex Ying; Zuobai Zhang; Peilin Zhao; Jian Tang 005; Lu Lin 001; Dinghao Wu (CoRR, 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)

Fast Approximation of Coherence for Second-Order Noisy Consensus Networks. - Zuobai Zhang; Wanyue Xu; Yuhao Yi; Zhongzhi Zhang (IEEE Trans. Cybern., 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)

Protein Representation Learning by Geometric Structure Pretraining. - Zuobai Zhang; Minghao Xu; Arian Rokkum Jamasb; Vijil Chenthamarakshan; Aurélie C. Lozano; Payel Das; Jian Tang 005 (ICLR, 2023)

FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning. - Songtao Liu; Zhengkai Tu; Minkai Xu; Zuobai Zhang; Lu Lin 001; Rex Ying; Jian Tang 005; Peilin Zhao; Dinghao Wu (ICML, 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 005 (NeurIPS, 2023)

DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing. - Yangtian Zhang; Zuobai Zhang; Bozitao Zhong; Sanchit Misra; Jian Tang 005 (NeurIPS, 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 005 (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 005 (CoRR, 2023)

PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design. - Chuanrui Wang; Bozitao Zhong; Zuobai Zhang; Narendra Chaudhary; Sanchit Misra; Jian Tang 005 (CoRR, 2023)

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 005; Jianlin Cheng; Pietro Lio; Tom L. Blundell (ICLR, 2024)

Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling. - Jiarui Lu; Bozitao Zhong; Zuobai Zhang; Jian Tang 005 (ICLR, 2024)

Cell ontology guided transcriptome foundation model. - Xinyu Yuan; Zhihao Zhan; Zuobai Zhang; Manqi Zhou; Jianan Zhao 002; Boyu Han; Yue Li; Jian Tang 005 (NeurIPS, 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 005 (NeurIPS, 2024)

Structure-Informed Protein Language Model. - Zuobai Zhang; Jiarui Lu; Vijil Chenthamarakshan; Aurélie C. Lozano; Payel Das; Jian Tang 005 (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 005 (CoRR, 2024)

Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations. - Jiarui Lu; Zuobai Zhang; Bozitao Zhong; Chence Shi; Jian Tang 005 (CoRR, 2024)

Opinion dynamics in social networks incorporating higher-order interactions. - Zuobai Zhang; Wanyue Xu; Zhongzhi Zhang; Guanrong Chen (Data Min. Knowl. Discov., 2024)

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 (ICLR, 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, 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, 2025)