Zhangyang Gao - researchr alias

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Viewing Publication 1 - 51 from 51

2025

EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled FlowYufei Huang 0002, Yunshu Liu, Lirong Wu, Haitao Lin, Cheng Tan 0012, Odin Zhang, Zhangyang Gao, Siyuan Li 0002, Zicheng Liu 0006, Yunfan Liu 0002, Tailin Wu, Stan Z. Li. iclr 2025: [doi]

SimVPv2: Towards Simple Yet Powerful Spatiotemporal Predictive LearningCheng Tan 0012, Zhangyang Gao, Siyuan Li 0002, Stan Z. Li. tmm, 27:5170-5184, 2025. [doi]

dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding AntigenCheng Tan 0012, Yijie Zhang, Zhangyang Gao, Yufei Huang 0002, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan Z. Li. AAAI 2025: 782-790 [doi]

SketchAgent: Generating Structured Diagrams from Hand-Drawn SketchesCheng Tan 0012, Qi Chen, Jingxuan Wei, Gaowei Wu, Zhangyang Gao, Siyuan Li 0002, Bihui Yu, Ruifeng Guo, Stan Z. Li. IJCAI 2025: 1918-1926 [doi]

MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification PredictionCheng Tan 0012, Zhenxiao Cao, Zhangyang Gao, Lirong Wu, Siyuan Li 0002, Yufei Huang 0002, Jun Xia 0001, Bozhen Hu, Stan Z. Li. iclr 2025: [doi]

USTEP: Spatio-Temporal Predictive Learning Under a Unified ViewCheng Tan 0012, Jue Wang, Zhangyang Gao, Siyuan Li 0002, Stan Z. Li. pami, 47(8):7064-7080, August 2025. [doi]

ReNovo: Retrieval-Based \emph{De Novo} Mass Spectrometry Peptide SequencingShaorong Chen, Jun Xia 0001, Jingbo Zhou, Lecheng Zhang, Zhangyang Gao, Bozhen Hu, Cheng Tan 0012, Wenjie Du, Stan Z. Li. iclr 2025: [doi]

FoldToken: Learning Protein Language via Vector Quantization and BeyondZhangyang Gao, Cheng Tan 0012, Jue Wang 0004, Yufei Huang 0002, Lirong Wu, Stan Z. Li. AAAI 2025: 219-227 [doi]

An Extensive Survey With Empirical Studies on Deep Temporal Point ProcessHaitao Lin, Cheng Tan 0012, Lirong Wu, Zicheng Liu 0006, Zhangyang Gao, Stan Z. Li. tkde, 37(4):1599-1619, April 2025. [doi]

From Words to Structured Visuals: A Benchmark and Framework for Text-to-Diagram Generation and EditingJingxuan Wei, Cheng Tan 0012, Qi Chen, Gaowei Wu, Siyuan Li 0002, Zhangyang Gao, Linzhuang Sun, Bihui Yu, Ruifeng Guo. cvpr 2025: 13315-13325 [doi]

Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity OptimizationLirong Wu, Haitao Lin, Yufei Huang 0002, Zhangyang Gao, Cheng Tan 0012, Yunfan Liu 0012, Tailin Wu, Stan Z. Li. AAAI 2025: 895-904 [doi]

2024

AdaNovo: Towards Robust \emph{De Novo} Peptide Sequencing in Proteomics against Data BiasesJun Xia 0001, Shaorong Chen, Jingbo Zhou, Xiaojun Shan, Wenjie Du, Zhangyang Gao, Cheng Tan 0012, Bozhen Hu, Jiangbin Zheng, Stan Z. Li. nips 2024: [doi]

Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion BridgeYufei Huang 0002, Odin Zhang, Lirong Wu, Cheng Tan 0012, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan Z. Li. icml 2024: [doi]

Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody DesignerCheng Tan 0012, Zhangyang Gao, Lirong Wu, Jun Xia, Jiangbin Zheng, Xihong Yang, Yue Liu 0008, Bozhen Hu, Stan Z. Li. AAAI 2024: 15222-15230 [doi]

Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching PerspectiveCheng Tan 0012, Zhangyang Gao, Hanqun Cao, Xingran Chen, Ge Wang, Lirong Wu, Jun Xia, Jiangbin Zheng, Stan Z. Li. icml 2024: [doi]

R3Design: deep tertiary structure-based RNA sequence design and beyondCheng Tan 0012, Yijie Zhang, Zhangyang Gao, Hanqun Cao, Siyuan Li 0002, Siqi Ma, Mathieu Blanchette, Stan Z. Li. bib, 26(1), 2024. [doi]

Boosting the Power of Small Multimodal Reasoning Models to Match Larger Models with Self-consistency TrainingCheng Tan 0012, Jingxuan Wei, Zhangyang Gao, Linzhuang Sun, Siyuan Li, Ruifeng Guo, Bihui Yu, Stan Z. Li. eccv 2025: 305-322 [doi]

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA DesignCheng Tan 0012, Yijie Zhang, Zhangyang Gao, Bozhen Hu, Siyuan Li, Zicheng Liu 0006, Stan Z. Li. iclr 2024: [doi]

A Survey on Generative Diffusion ModelsHanqun Cao, Cheng Tan 0012, Zhangyang Gao, Yilun Xu, Guangyong Chen, Pheng-Ann Heng, Stan Z. Li. tkde, 36(7):2814-2830, July 2024. [doi]

Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training TasksTianyu Fan, Lirong Wu, Yufei Huang 0002, Haitao Lin, Cheng Tan 0012, Zhangyang Gao, Stan Z. Li. iclr 2024: [doi]

A Graph is Worth K Words: Euclideanizing Graph using Pure TransformerZhangyang Gao, Daize Dong, Cheng Tan 0012, Jun Xia, Bozhen Hu, Stan Z. Li. icml 2024: [doi]

UniIF: Unified Molecule Inverse FoldingZhangyang Gao, Jue Wang 0004, Cheng Tan 0012, Lirong Wu, Yufei Huang 0002, Siyuan Li 0002, Zhirui Ye, Stan Z. Li. nips 2024: [doi]

KW-Design: Pushing the Limit of Protein Design via Knowledge RefinementZhangyang Gao, Cheng Tan 0012, Xingran Chen, Yijie Zhang, Jun Xia, Siyuan Li, Stan Z. Li. iclr 2024: [doi]

ProtGO: Function-Guided Protein Modeling for Unified Representation LearningBozhen Hu, Cheng Tan 0012, Yongjie Xu, Zhangyang Gao, Jun Xia 0001, Lirong Wu, Stan Z. Li. nips 2024: [doi]

Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property PredictionYufei Huang, Siyuan Li, Lirong Wu, Jin Su, Haitao Lin, Odin Zhang, Zihan Liu, Zhangyang Gao, Jiangbin Zheng, Stan Z. Li. AAAI 2024: 12662-12670 [doi]

Text-To-AMP: Antimicrobial Peptide Design Guided by Natural TextYixuan Huang, Yang Xiao, Alexander Teng, Fei Ye, Yiyao Yu, Chenyi Lei, Ruihao Zhang, Zhangyang Gao, Cheng Tan 0012, Xiao Liu. bibm 2024: 6036-6043 [doi]

General Point Model Pretraining with Autoencoding and AutoregressiveZhe Li, Zhangyang Gao, Cheng Tan 0012, Bocheng Ren, Laurence T. Yang, Stan Z. Li. cvpr 2024: 20954-20964 [doi]

MLIP: Enhancing Medical Visual Representation with Divergence Encoder and Knowledge-guided Contrastive LearningZhe Li, Laurence T. Yang, Bocheng Ren, Xin Nie, Zhangyang Gao, Cheng Tan 0012, Stan Z. Li. cvpr 2024: 11704-11714 [doi]

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational LearningSizhe Liu, Jun Xia 0001, Lecheng Zhang, Yuchen Liu, Yue Liu 0008, Wenjie Du, Zhangyang Gao, Bozhen Hu, Cheng Tan 0012, Hongxin Xiang, Stan Z. Li. nips 2024: [doi]

Interpretable and Generalizable Spatiotemporal Predictive Learning with Disentangled ConsistencyJingxuan Wei, Cheng Tan 0012, Zhangyang Gao, Linzhuang Sun, Bihui Yu, Ruifeng Guo, Stan Z. Li. pkdd 2024: 3-20 [doi]

Enhancing human-like multimodal reasoning: a new challenging dataset and comprehensive frameworkJingxuan Wei, Cheng Tan 0012, Zhangyang Gao, Linzhuang Sun, Siyuan Li, Bihui Yu, Ruifeng Guo, Stan Z. Li. nca, 36(33):20849-20861, November 2024. [doi]

PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction PredictionLirong Wu, Yufei Huang, Cheng Tan 0012, Zhangyang Gao, Bozhen Hu, Haitao Lin, Zicheng Liu 0006, Stan Z. Li. AAAI 2024: 310-319 [doi]

A Teacher-Free Graph Knowledge Distillation Framework With Dual Self-DistillationLirong Wu, Haitao Lin, Zhangyang Gao, Guojiang Zhao, Stan Z. Li. tkde, 36(9):4375-4385, September 2024. [doi]

Beyond Homophily and Homogeneity Assumption: Relation-Based Frequency Adaptive Graph Neural NetworksLirong Wu, Haitao Lin, Bozhen Hu, Cheng Tan 0012, Zhangyang Gao, Zicheng Liu 0006, Stan Z. Li. tnn, 35(6):8497-8509, June 2024. [doi]

DiscoGNN: A Sample-Efficient Framework for Self-Supervised Graph Representation LearningJun Xia, Shaorong Chen, Yue Liu 0008, Zhangyang Gao, Jiangbin Zheng, Xihong Yang, Stan Z. Li. icde 2024: 2876-2888 [doi]

AQND: An asymmetric quorum-based neighbor discovery protocol for reducing delay in sensor based systemsZiqing Xia, Zhangyang Gao, Anfeng Liu, Neal N. Xiong. isci, 654:119820, January 2024. [doi]

2023

Target-Aware Molecular Graph GenerationCheng Tan 0012, Zhangyang Gao, Stan Z. Li. pkdd 2023: 410-427 [doi]

Global-Context Aware Generative Protein DesignCheng Tan 0012, Zhangyang Gao, Jun Xia, Bozhen Hu, Stan Z. Li. icassp 2023: 1-5 [doi]

Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive LearningCheng Tan 0012, Zhangyang Gao, Lirong Wu, Yongjie Xu, Jun Xia, Siyuan Li, Stan Z. Li. cvpr 2023: 18770-18782 [doi]

OpenSTL: A Comprehensive Benchmark of Spatio-Temporal Predictive LearningCheng Tan 0012, Siyuan Li, Zhangyang Gao, Wenfei Guan, Zedong Wang, Zicheng Liu 0006, Lirong Wu, Stan Z. Li. nips 2023: [doi]

PiFold: Toward effective and efficient protein inverse foldingZhangyang Gao, Cheng Tan 0012, Stan Z. Li. iclr 2023: [doi]

Co-supervised Pre-training of Pocket and LigandZhangyang Gao, Cheng Tan 0012, Jun Xia, Stan Z. Li. pkdd 2023: 405-421 [doi]

ProteinInvBench: Benchmarking Protein Inverse Folding on Diverse Tasks, Models, and MetricsZhangyang Gao, Cheng Tan 0012, Yijie Zhang, Xingran Chen, Lirong Wu, Stan Z. Li. nips 2023: [doi]

Learning to Augment Graph Structure for both Homophily and Heterophily GraphsLirong Wu, Cheng Tan 0012, Zihan Liu, Zhangyang Gao, Haitao Lin, Stan Z. Li. pkdd 2023: 3-18 [doi]

Self-Supervised Learning on Graphs: Contrastive, Generative, or PredictiveLirong Wu, Haitao Lin, Cheng Tan 0012, Zhangyang Gao, Stan Z. Li. tkde, 35(4):4216-4235, April 2023. [doi]

Understanding the Limitations of Deep Models for Molecular property prediction: Insights and SolutionsJun Xia, Lecheng Zhang, Xiao Zhu, Yue Liu 0008, Zhangyang Gao, Bozhen Hu, Cheng Tan 0012, Jiangbin Zheng, Siyuan Li, Stan Z. Li. nips 2023: [doi]

Mole-BERT: Rethinking Pre-training Graph Neural Networks for MoleculesJun Xia, Chengshuai Zhao, Bozhen Hu, Zhangyang Gao, Cheng Tan 0012, Yue Liu, Siyuan Li, Stan Z. Li. iclr 2023: [doi]

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