ML Anthology

Gao, Zhangyang

42 publications

NeurIPS 2025 AlphaFold Database Debiasing for Robust Inverse Folding Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Siyuan Li, Yufei Huang, Stan Z. Li
ICLR 2025 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
AAAI 2025 FoldToken: Learning Protein Language via Vector Quantization and Beyond Zhangyang Gao, Cheng Tan, Jue Wang, Yufei Huang, Lirong Wu, Stan Z. Li
CVPR 2025 From Words to Structured Visuals: A Benchmark and Framework for Text-to-Diagram Generation and Editing Jingxuan Wei, Cheng Tan, Qi Chen, Gaowei Wu, Siyuan Li, Zhangyang Gao, Linzhuang Sun, Bihui Yu, Ruifeng Guo
ICCV 2025 G2PDiffusion: Cross-Species Genotype-to-Phenotype Prediction via Evolutionary Diffusion Mengdi Liu, Zhangyang Gao, Hong Chang, Stan Z. Li, Shiguang Shan, Xilin Chen
ICLR 2025 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
NeurIPS 2025 ProtInvTree: Deliberate Protein Inverse Folding with Reward-Guided Tree Search Mengdi Liu, Xiaoxue Cheng, Zhangyang Gao, Hong Chang, Cheng Tan, Shiguang Shan, Xilin Chen
ICLR 2025 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
AAAI 2025 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
IJCAI 2025 SketchAgent: Generating Structured Diagrams from Hand-Drawn Sketches Cheng Tan, Qi Chen, Jingxuan Wei, Gaowei Wu, Zhangyang Gao, Siyuan Li, Bihui Yu, Ruifeng Guo, Stan Z. Li
AAAI 2025 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
ICML 2024 A Graph Is Worth $k$ Words: Euclideanizing Graph Using Pure Transformer Zhangyang Gao, Daize Dong, Cheng Tan, Jun Xia, Bozhen Hu, Stan Z. Li
NeurIPS 2024 AdaNovo: Towards Robust \emph{De Novo} Peptide Sequencing in Proteomics Against Data Biases Jun Xia, Shaorong Chen, Jingbo Zhou, Xiaojun Shan, Wenjie Du, Zhangyang Gao, Cheng Tan, Bozhen Hu, Jiangbin Zheng, Stan Z. Li
ECCV 2024 Boosting the Power of Small Multimodal Reasoning Models to Match Larger Models with Self-Consistency Training Cheng Tan, Jingxuan Wei, Zhangyang Gao, Linzhuang Sun, Siyuan Li, Ruifeng Guo, BiHui Yu, Stan Z. Li
AAAI 2024 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
ICML 2024 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
ICLR 2024 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
NeurIPS 2024 FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning Sizhe Liu, Jun Xia, Lecheng Zhang, Yuchen Liu, Yue Liu, Wenjie Du, Zhangyang Gao, Bozhen Hu, Cheng Tan, Hongxin Xiang, Stan Z. Li
CVPR 2024 General Point Model Pretraining with Autoencoding and Autoregressive Zhe Li, Zhangyang Gao, Cheng Tan, Bocheng Ren, Laurence T. Yang, Stan Z. Li
ECML-PKDD 2024 Interpretable and Generalizable Spatiotemporal Predictive Learning with Disentangled Consistency Jingxuan Wei, Cheng Tan, Zhangyang Gao, Linzhuang Sun, Bihui Yu, Ruifeng Guo, Stan Z. Li
ICLR 2024 KW-Design: Pushing the Limit of Protein Design via Knowledge Refinement Zhangyang Gao, Cheng Tan, Xingran Chen, Yijie Zhang, Jun Xia, Siyuan Li, Stan Z. Li
CVPR 2024 MLIP: Enhancing Medical Visual Representation with Divergence Encoder and Knowledge-Guided Contrastive Learning Zhe Li, Laurence T. Yang, Bocheng Ren, Xin Nie, Zhangyang Gao, Cheng Tan, Stan Z. Li
AAAI 2024 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
NeurIPS 2024 ProtGO: Function-Guided Protein Modeling for Unified Representation Learning Bozhen Hu, Cheng Tan, Yongjie Xu, Zhangyang Gao, Jun Xia, Lirong Wu, Stan Z. Li
AAAI 2024 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
ICLR 2024 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
ICML 2024 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
NeurIPS 2024 UniIF: Unified Molecule Inverse Folding Zhangyang Gao, Jue Wang, Cheng Tan, Lirong Wu, Yufei Huang, Siyuan Li, Zhirui Ye, Stan Z. Li
ECML-PKDD 2023 Co-Supervised Pre-Training of Pocket and Ligand Zhangyang Gao, Cheng Tan, Jun Xia, Stan Z. Li
ECML-PKDD 2023 Learning to Augment Graph Structure for Both Homophily and Heterophily Graphs Lirong Wu, Cheng Tan, Zihan Liu, Zhangyang Gao, Haitao Lin, Stan Z. Li
ICLR 2023 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
NeurIPS 2023 OpenSTL: A Comprehensive Benchmark of Spatio-Temporal Predictive Learning Cheng Tan, Siyuan Li, Zhangyang Gao, Wenfei Guan, Zedong Wang, Zicheng Liu, Lirong Wu, Stan Z. Li
ICLR 2023 PiFold: Toward Effective and Efficient Protein Inverse Folding Zhangyang Gao, Cheng Tan, Stan Z. Li
NeurIPS 2023 ProteinInvBench: Benchmarking Protein Inverse Folding on Diverse Tasks, Models, and Metrics Zhangyang Gao, Cheng Tan, Yijie Zhang, Xingran Chen, Lirong Wu, Stan Z. Li
ECML-PKDD 2023 Target-Aware Molecular Graph Generation Cheng Tan, Zhangyang Gao, Stan Z. Li
CVPR 2023 Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning Cheng Tan, Zhangyang Gao, Lirong Wu, Yongjie Xu, Jun Xia, Siyuan Li, Stan Z. Li
NeurIPS 2023 Understanding the Limitations of Deep Models for Molecular Property Prediction: Insights and Solutions Jun Xia, Lecheng Zhang, Xiao Zhu, Yue Liu, Zhangyang Gao, Bozhen Hu, Cheng Tan, Jiangbin Zheng, Siyuan Li, Stan Z. Li
AAAI 2022 Conditional Local Convolution for Spatio-Temporal Meteorological Forecasting Haitao Lin, Zhangyang Gao, Yongjie Xu, Lirong Wu, Ling Li, Stan Z. Li
ECML-PKDD 2022 GraphMixup: Improving Class-Imbalanced Node Classification by Reinforcement Mixup and Self-Supervised Context Prediction Lirong Wu, Jun Xia, Zhangyang Gao, Haitao Lin, Cheng Tan, Stan Z. Li
CVPR 2022 Hyperspherical Consistency Regularization Cheng Tan, Zhangyang Gao, Lirong Wu, Siyuan Li, Stan Z. Li
CVPR 2022 SimVP: Simpler yet Better Video Prediction Zhangyang Gao, Cheng Tan, Lirong Wu, Stan Z. Li
ICMLW 2022 Target-Aware Molecular Graph Generation Cheng Tan, Zhangyang Gao, Stan Z. Li