| 2026 | AAAI | Efficient Protein Optimization via Structure-aware Hamiltonian Dynamics. | Jiahao Wang, Shuangjia Zheng |
| 2025 | CVPR | Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery. | Jiahua Rao, Hanjing Lin, Leyu Chen, Jiancong Xie, Shuangjia Zheng, Yuedong Yang |
| 2025 | ICLR | Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization. | Zichen Wang, Yaokun Ji, Jianing Tian, Shuangjia Zheng |
| 2025 | KDD | Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Molecular Graph Learning. | Jiahua Rao, Hanjing Lin, Jiancong Xie, Zhen Wang, Shuangjia Zheng, Yuedong Yang |
| 2024 | KDD | Causal Subgraph Learning for Generalizable Inductive Relation Prediction. | Mei Li, Xiaoguang Liu, Hua Ji, Shuangjia Zheng |
| 2022 | IJCAI | Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. | Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang |
| 2021 | AAAI | Communicative Message Passing for Inductive Relation Reasoning. | Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu |
| 2021 | IJCAI | Learning Attributed Graph Representation with Communicative Message Passing Transformer. | Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang |
| 2020 | IJCAI | Communicative Representation Learning on Attributed Molecular Graphs. | Ying Song, Shuangjia Zheng, Zhangming Niu, Zhang-Hua Fu, Yutong Lu, Yuedong Yang |