| 2025 | AAAI | dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. | Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li |
| 2025 | AAAI | FoldToken: Learning Protein Language via Vector Quantization and Beyond. | Zhangyang Gao, Cheng Tan, Jue Wang, Yufei Huang, Lirong Wu, Stan Z. Li |
| 2025 | AAAI | Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization. | Lirong Wu, Haitao Lin, Yufei Huang, Zhangyang Gao, Cheng Tan, Yunfan Liu, Tailin Wu, Stan Z. Li |
| 2025 | CVPR | DaCapo: Score Distillation as Stacked Bridge for Fast and High-quality 3D Editing. | Yufei Huang, Bangyan Liao, Yuqi Hu, Haitao Lin, Lirong Wu, Siyuan Li, Cheng Tan, Zicheng Liu, Yunfan Liu, Zelin Zang, Chang Yu, Zhen Lei |
| 2025 | ICLR | EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow. | Yufei Huang, Yunshu Liu, Lirong Wu, Haitao Lin, Cheng Tan, Odin Zhang, Zhangyang Gao, Siyuan Li, Zicheng Liu, Yunfan Liu, Tailin Wu, 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 | CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. | Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Cheng Tan, Zicheng Liu, Zhifeng Gao, Stan Z. Li |
| 2025 | ICLR | A Simple yet Effective ΔΔG Predictor is An Unsupervised Antibody Optimizer and Explainer. | Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Guojiang Zhao, Zhifeng Gao, 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 | Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction. | Yufei Huang, Siyuan Li, Lirong Wu, Jin Su, Haitao Lin, Odin Zhang, Zihan Liu, Zhangyang Gao, Jiangbin Zheng, 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 | CIKM | Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation. | Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Stan Z. Li |
| 2024 | ICLR | Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks. | Tianyu Fan, Lirong Wu, Yufei Huang, Haitao Lin, Cheng Tan, Zhangyang Gao, Stan Z. Li |
| 2024 | ICLR | MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding. | Lirong Wu, Yijun Tian, Yufei Huang, Siyuan Li, Haitao Lin, Nitesh V. Chawla, Stan Z. Li |
| 2024 | ICML | Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge. | Yufei Huang, Odin Zhang, Lirong Wu, Cheng Tan, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan Z. Li |
| 2024 | ICML | Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective. | Cheng Tan, Zhangyang Gao, Hanqun Cao, Xingran Chen, Ge Wang, Lirong Wu, Jun Xia, Jiangbin Zheng, Stan Z. Li |
| 2024 | ICML | GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation. | Haitao Lin, Lirong Wu, Yufei Huang, Yunfan Liu, Odin Zhang, Yuanqing Zhou, Rui Sun, Stan Z. Li |
| 2024 | ICML | PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching. | Haitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang, Lirong Wu, Zicheng Liu, Yufei Huang, Stan Z. Li |
| 2024 | ICML | Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning. | Lirong Wu, Yijun Tian, Haitao Lin, Yufei Huang, Siyuan Li, Nitesh V. Chawla, Stan Z. Li |
| 2024 | IGARSS | A Fast BP Imaging Algorithm Based on Coordinate System Grouping. | Shichao Chen, Yabo Liu, Lirong Wu, Ling Wang, Ming Liu |
| 2023 | AAAI | Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting It into MLPs: An Effective GNN-to-MLP Distillation Framework. | Lirong Wu, Haitao Lin, Yufei Huang, Tianyu Fan, Stan Z. Li |
| 2023 | CVPR | Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning. | Cheng Tan, Zhangyang Gao, Lirong Wu, Yongjie Xu, Jun Xia, Siyuan Li, 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 | ICML | Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs. | Lirong Wu, Haitao Lin, Yufei Huang, Stan Z. Li |
| 2022 | AAAI | Conditional Local Convolution for Spatio-Temporal Meteorological Forecasting. | Haitao Lin, Zhangyang Gao, Yongjie Xu, Lirong Wu, Ling Li, Stan Z. Li |
| 2022 | CIKM | Are Gradients on Graph Structure Reliable in Gray-box Attacks? | Zihan Liu, Yun Luo, Lirong Wu, Siyuan Li, Zicheng Liu, Stan Z. Li |
| 2022 | CVPR | Hyperspherical Consistency Regularization. | Cheng Tan, Zhangyang Gao, Lirong Wu, Siyuan Li, Stan Z. Li |
| 2022 | CVPR | SimVP: Simpler yet Better Video Prediction. | Zhangyang Gao, Cheng Tan, Lirong Wu, Stan Z. Li |
| 2022 | ECCV | AutoMix: Unveiling the Power of Mixup for Stronger Classifiers. | Zicheng Liu, Siyuan Li, Di Wu, Zihan Liu, Zhiyuan Chen, Lirong Wu, Stan Z. Li |
| 2022 | ICASSP | OT Cleaner: Label Correction as Optimal Transport. | Jun Xia, Cheng Tan, Lirong Wu, Yongjie Xu, Stan Z. Li |
| 2022 | ICML | ProGCL: Rethinking Hard Negative Mining in Graph Contrastive Learning. | Jun Xia, Lirong Wu, Ge Wang, Jintao Chen, 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 |
| 2022 | WACV | Generalized Clustering and Multi-Manifold Learning with Geometric Structure Preservation. | Lirong Wu, Zicheng Liu, Jun Xia, Zelin Zang, Siyuan Li, Stan Z. Li |
| 2020 | WACV | A GAN-based Tunable Image Compression System. | Lirong Wu, Kejie Huang, Haibin Shen |
| 2006 | ISDA | Ramp Shape Optimum Design for Airplane Land-Based Ski-Jump Takeoff via NSGA II. | Xun-Kai Wei, Chong Duan, Ying Hong Li, Lirong Wu |