| 2026 | KDD | Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates. | Kaiyuan Gao, Yusong Wang, Haoxiang Guan, Zun Wang, Qizhi Pei, John E. Hopcroft, Kun He, Lijun Wu |
| 2025 | ICLR | 3D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modeling. | Qizhi Pei, Rui Yan, Kaiyuan Gao, Jinhua Zhu, Lijun Wu |
| 2025 | ICLR | Fast and Accurate Blind Flexible Docking. | Zizhuo Zhang, Lijun Wu, Kaiyuan Gao, Jiangchao Yao, Tao Qin, Bo Han |
| 2025 | KDD | FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation. | Kaiyuan Gao, Qizhi Pei, Gongbo Zhang, Jinhua Zhu, Kun He, Lijun Wu |
| 2025 | KDD | CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions. | Yangzhe Peng, Kaiyuan Gao, Liang He, Yuheng Cong, Haiguang Liu, Kun He, Lijun Wu |
| 2024 | ACL | BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning. | Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan |
| 2023 | EMNLP | BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations. | Qizhi Pei, Wei Zhang, Jinhua Zhu, Kehan Wu, Kaiyuan Gao, Lijun Wu, Yingce Xia, Rui Yan |
| 2023 | ICLR | NAGphormer: A Tokenized Graph Transformer for Node Classification in Large Graphs. | Jinsong Chen, Kaiyuan Gao, Gaichao Li, Kun He |
| 2023 | KDD | Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design. | Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Tianbo Peng, Yingce Xia, Liang He, Shufang Xie, Tao Qin, Haiguang Liu, Kun He, Tie-Yan Liu |
| 2016 | DDECS | Low power voltage sensing through capacitance to digital conversion. | Delong Shang, Yuqing Xu, Kaiyuan Gao, Fei Xia, Alex Yakovlev |