| 2025 | AAAI | Generalized Implicit Neural Representations for Dynamic Molecular Surface Modeling. | Fang Wu, Bozhen Hu, Stan Z. Li |
| 2025 | ICLR | MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction. | Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Lirong Wu, Siyuan Li, Yufei Huang, Jun Xia, Bozhen Hu, Stan Z. Li |
| 2025 | ICLR | ReNovo: Retrieval-Based \emph{De Novo} Mass Spectrometry Peptide Sequencing. | Shaorong Chen, Jun Xia, Jingbo Zhou, Lecheng Zhang, Zhangyang Gao, Bozhen Hu, Cheng Tan, Wenjie Du, Stan Z. Li |
| 2024 | AAAI | Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody Designer. | Cheng Tan, Zhangyang Gao, Lirong Wu, Jun Xia, Jiangbin Zheng, Xihong Yang, Yue Liu, Bozhen Hu, Stan Z. Li |
| 2024 | AAAI | PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction. | Lirong Wu, Yufei Huang, Cheng Tan, Zhangyang Gao, Bozhen Hu, Haitao Lin, Zicheng Liu, Stan Z. Li |
| 2024 | ICASSP | Deep Manifold Transformation for Protein Representation Learning. | Bozhen Hu, Zelin Zang, Cheng Tan, Stan Z. Li |
| 2024 | ICLR | RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design. | Cheng Tan, Yijie Zhang, Zhangyang Gao, Bozhen Hu, Siyuan Li, Zicheng Liu, Stan Z. Li |
| 2024 | ICML | A Graph is Worth K Words: Euclideanizing Graph using Pure Transformer. | Zhangyang Gao, Daize Dong, Cheng Tan, Jun Xia, Bozhen Hu, Stan Z. Li |
| 2023 | ICASSP | Deep Manifold Graph Auto-Encoder For Attributed Graph Embedding. | Bozhen Hu, Zelin Zang, Jun Xia, Lirong Wu, Cheng Tan, Stan Z. Li |
| 2023 | ICASSP | Global-Context Aware Generative Protein Design. | Cheng Tan, Zhangyang Gao, Jun Xia, Bozhen Hu, Stan Z. Li |
| 2023 | ICASSP | Wordreg: Mitigating the Gap between Training and Inference with Worst-Case Drop Regularization. | Jun Xia, Ge Wang, Bozhen Hu, Cheng Tan, Jiangbin Zheng, Yongjie Xu, Stan Z. Li |
| 2023 | ICLR | Mole-BERT: Rethinking Pre-training Graph Neural Networks for Molecules. | Jun Xia, Chengshuai Zhao, Bozhen Hu, Zhangyang Gao, Cheng Tan, Yue Liu, Siyuan Li, Stan Z. Li |
| 2022 | WWW | SimGRACE: A Simple Framework for Graph Contrastive Learning without Data Augmentation. | Jun Xia, Lirong Wu, Jintao Chen, Bozhen Hu, Stan Z. Li |