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• unicode name:黄余飞
• affiliation:Zhejiang University, Hangzhou, China
• affiliation:Westlake University, Hangzhou, China

• Yufei Huang
• Yufei Huang0001 —University of Pittsburgh, School of Medicine, PA, USA(and 2 more)
• Yufei Huang0003 — South China Normal University, College of Mathematical Science, Guangzhou, China
• Yufei Huang0004 — Southeast University, National Mobile Communications Research Laboratory, Nanjing, China
• Yufei Huang0005 — Tianjin University, College of Intelligence and Computing, China
• Yufei Huang0006 —Trinity College, Business School, Dublin, Ireland(and 3 more)
• Yufei Huang0007 — Guangzhou Civil Aviation College, Department of Mathematics Teaching, China
• Yufei Huang0008 — Tsinghua University, Department of Computer Science and Technology, BNRist, Beijing, China
• Yufei Huang0009 — Beijing Institute of Spacecraft System Engineering, China
• Yufei Huang0010 — Hebei Normal University, College of Mathematics and Information Science, Shijiazhuang, China

• Yufei Huang0011 — Fujian Agriculture and Forestry University, Fuzhou, China
• Yufei Huang0012 — Rutgers University, Department of Industrial and Systems Engineering, New Brunswick, NJ, USA
• Yufei Huang0013 — Hechi University, School of Artificial Intelligence and Manufacturing, Yizhou, China
• Yufei Huang0014 — Xiamen University of Technology, School of Opto-Electronic and Conmmunication Engineering, China
• Yufei Huang0015 — University of Electronic Science and Technology of China, National Key Laboratory of Wireless Communications, Chengdu, China
• Yufei Huang0016 — South China Agricultural University, College of Mathematics and Informatics, Guangzhou, China
• Yufei Huang0017 — Shanghai Jiao Tong University, School of Medicine, Ruijin Hospital, Radiology Department, China
• Yufei Huang0018 — China Medical University, School of Intelligent Medicine, Department of Biomedical Engineering, Liaoning, China
• Yufei Huang0019 — Fujian Medical University, School of Basic Medical Sciences, Fuzhou, China
• Yufei Huang0020 — Peking University, Center for Data Science, Beijing, China
• Yufei Huang0021 — Tencent, LLM Department, China
• Yufei Huang0022 — Beijing Film Academy, China

• Freeman Yufei Huang — Queen's University, Department of Computing and Information Science, Kingston, ON, Canada
• Yuefei Huang —Tsinghua University, State Key Laboratory of Hydroscience and Engineering, Beijing, China(and 1 more)

• 2025
• 
  [j3]
  Dou Nie,Huifeng Zhao,Odin Zhang,Gaoqi Weng,Hui Zhang,Jieyu Jin,Haitao Lin,Yufei Huang,Liwei Liu,Dan Li,Tingjun Hou,Yu Kang:
  Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation.J. Chem. Inf. Model.65(1):173-186 (2025)
• 
  [j2]
  Odin Zhang,Jieyu Jin,Zhenxing Wu,Jintu Zhang,Po Yuan,Yuntao Yu,Haitao Lin,Haiyang Zhong,Xujun Zhang,Chenqing Hua,Weibo Zhao,Zhengshuo Zhang,Kejun Ying,Yufei Huang,Huifeng Zhao,Yu Kang,Peichen Pan,Jike Wang,Dong Guo,Shuangjia Zheng,Chang-Yu Hsieh,Tingjun Hou:
  ECloudGen: leveraging electron clouds as a latent variable to scale up structure-based molecular design.Nat. Comput. Sci.5(11):1017-1028 (2025)
• 
  [c25]
  Zhangyang Gao,Cheng Tan,Jue Wang,Yufei Huang,Lirong Wu,Stan Z. Li:
  FoldToken: Learning Protein Language via Vector Quantization and Beyond.AAAI2025:219-227
• 
  [c24]
  Cheng Tan,Yijie Zhang,Zhangyang Gao,Yufei Huang,Haitao Lin,Lirong Wu,Fandi Wu,Mathieu Blanchette,Stan Z. Li:
  dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen.AAAI2025:782-790
• 
  [c23]
  Lirong Wu,Haitao Lin,Yufei Huang,Zhangyang Gao,Cheng Tan,Yunfan Liu,Tailin Wu,Stan Z. Li:
  Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization.AAAI2025:895-904
• 
  [c22]
  Yufei Huang,Bangyan Liao,Yuqi Hu,Haitao Lin,Lirong Wu,Siyuan Li,Cheng Tan,Zicheng Liu,Yunfan Liu,Zelin Zang,Chang Yu,Zhen Lei:
  DaCapo: Score Distillation as Stacked Bridge for Fast and High-quality 3D Editing.CVPR2025:16304-16313
• 
  [c21]
  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:
  EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow.ICLR2025
• 
  [c20]
  Cheng Tan,Zhenxiao Cao,Zhangyang Gao,Lirong Wu,Siyuan Li,Yufei Huang,Jun Xia,Bozhen Hu,Stan Z. Li:
  MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction.ICLR2025
• 
  [c19]
  Haitao Lin,Guojiang Zhao,Odin Zhang,Yufei Huang,Lirong Wu,Cheng Tan,Zicheng Liu,Zhifeng Gao,Stan Z. Li:
  CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph.ICLR2025
• 
  [c18]
  Lirong Wu,Yunfan Liu,Haitao Lin,Yufei Huang,Guojiang Zhao,Zhifeng Gao,Stan Z. Li:
  A Simple yet Effective ΔΔG Predictor is An Unsupervised Antibody Optimizer and Explainer.ICLR2025
• 
  [i37]
  Lirong Wu,Haitao Lin,Yufei Huang,Zhangyang Gao,Cheng Tan,Yunfan Liu,Tailin Wu,Stan Z. Li:
  Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization.CoRRabs/2501.00013 (2025)
• 
  [i36]
  Lirong Wu,Yunfan Liu,Haitao Lin,Yufei Huang,Guojiang Zhao,Zhifeng Gao,Stan Z. Li:
  A Simple yet Effective DDG Predictor is An Unsupervised Antibody Optimizer and Explainer.CoRRabs/2502.06913 (2025)
• 
  [i35]
  Cheng Tan,Yijie Zhang,Zhangyang Gao,Yufei Huang,Haitao Lin,Lirong Wu,Fandi Wu,Mathieu Blanchette,Stan Z. Li:
  dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen.CoRRabs/2503.01910 (2025)
• 
  [i34]
  Fengyuan Dai,Zifeng Zhuang,Yufei Huang,Siteng Huang,Bangyan Liao,Donglin Wang,Fajie Yuan:
  VARD: Efficient and Dense Fine-Tuning for Diffusion Models with Value-based RL.CoRRabs/2505.15791 (2025)
• 
  [i33]
  Haitao Lin,Odin Zhang,Jia Xu,Yunfan Liu,Zheng Chen,Lirong Wu,Yufei Huang,Zhifeng Gao,Stan Z. Li:
  Tokenizing Electron Cloud in Protein-Ligand Interaction Learning.CoRRabs/2505.19014 (2025)
• 
  [i32]
  Cheng Tan,Zhenxiao Cao,Zhangyang Gao,Siyuan Li,Yufei Huang,Stan Z. Li:
  AlphaFold Database Debiasing for Robust Inverse Folding.CoRRabs/2506.08365 (2025)
• 
  [i31]
  Changxi Chi,Jun Xia,Yufei Huang,Jingbo Zhou,Siyuan Li,Yunfan Liu,Chang Yu,Stan Z. Li:
  Unlasting: Unpaired Single-Cell Multi-Perturbation Estimation by Dual Conditional Diffusion Implicit Bridges.CoRRabs/2506.21107 (2025)
• 
  [i30]
  Changxi Chi,Yufei Huang,Jun Xia,Jiangbin Zheng,Yunfan Liu,Zelin Zang,Stan Z. Li:
  Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges.CoRRabs/2511.13124 (2025)
• 2024
• 
  [j1]
  Lirong Wu,Haitao Lin,Zihan Liu,Zicheng Liu,Yufei Huang,Stan Z. Li:
  Homophily-Enhanced Self-Supervision for Graph Structure Learning: Insights and Directions.IEEE Trans. Neural Networks Learn. Syst.35(9):12358-12372 (2024)
• 
  [c17]
  Lirong Wu,Yufei Huang,Cheng Tan,Zhangyang Gao,Bozhen Hu,Haitao Lin,Zicheng Liu,Stan Z. Li:
  PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction.AAAI2024:310-319
• 
  [c16]
  Yufei Huang,Siyuan Li,Lirong Wu,Jin Su,Haitao Lin,Odin Zhang,Zihan Liu,Zhangyang Gao,Jiangbin Zheng,Stan Z. Li:
  Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction.AAAI2024:12662-12670
• 
  [c15]
  Lirong Wu,Yunfan Liu,Haitao Lin,Yufei Huang,Stan Z. Li:
  Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation.CIKM2024:2554-2563
• 
  [c14]
  Tianyu Fan,Lirong Wu,Yufei Huang,Haitao Lin,Cheng Tan,Zhangyang Gao,Stan Z. Li:
  Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks.ICLR2024
• 
  [c13]
  Lirong Wu,Yijun Tian,Yufei Huang,Siyuan Li,Haitao Lin,Nitesh V. Chawla,Stan Z. Li:
  MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding.ICLR2024
• 
  [c12]
  Yufei Huang,Odin Zhang,Lirong Wu,Cheng Tan,Haitao Lin,Zhangyang Gao,Siyuan Li,Stan Z. Li:
  Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge.ICML2024:20474-20489
• 
  [c11]
  Siyuan Li,Zedong Wang,Zicheng Liu,Di Wu,Cheng Tan,Jiangbin Zheng,Yufei Huang,Stan Z. Li:
  VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling.ICML2024:28717-28733
• 
  [c10]
  Haitao Lin,Lirong Wu,Yufei Huang,Yunfan Liu,Odin Zhang,Yuanqing Zhou,Rui Sun,Stan Z. Li:
  GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation.ICML2024:30346-30361
• 
  [c9]
  Haitao Lin,Odin Zhang,Huifeng Zhao,Dejun Jiang,Lirong Wu,Zicheng Liu,Yufei Huang,Stan Z. Li:
  PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching.ICML2024:30510-30528
• 
  [c8]
  Lirong Wu,Yijun Tian,Haitao Lin,Yufei Huang,Siyuan Li,Nitesh V. Chawla,Stan Z. Li:
  Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning.ICML2024:53847-53859
• 
  [c7]
  Zhangyang Gao,Jue Wang,Cheng Tan,Lirong Wu,Yufei Huang,Siyuan Li,Zhirui Ye,Stan Z. Li:
  UniIF: Unified Molecule Inverse Folding.NeurIPS2024
• 
  [c6]
  Bozhen Hu,Cheng Tan,Jun Xia,Yue Liu,Lirong Wu,Jiangbin Zheng,Yongjie Xu,Yufei Huang,Stan Z. Li:
  Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure.NeurIPS2024
• 
  [i29]
  Lirong Wu,Yufei Huang,Cheng Tan,Zhangyang Gao,Bozhen Hu,Haitao Lin,Zicheng Liu,Stan Z. Li:
  PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction.CoRRabs/2402.08198 (2024)
• 
  [i28]
  Yufei Huang,Odin Zhang,Lirong Wu,Cheng Tan,Haitao Lin,Zhangyang Gao,Siyuan Li,Stan Z. Li:
  Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge.CoRRabs/2402.11459 (2024)
• 
  [i27]
  Lirong Wu,Yijun Tian,Yufei Huang,Siyuan Li,Haitao Lin,Nitesh V. Chawla,Stan Z. Li:
  MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding.CoRRabs/2402.14391 (2024)
• 
  [i26]
  Rui Sun,Lirong Wu,Haitao Lin,Yufei Huang,Stan Z. Li:
  Enhancing Protein Predictive Models via Proteins Data Augmentation: A Benchmark and New Directions.CoRRabs/2403.00875 (2024)
• 
  [i25]
  Tianyu Fan,Lirong Wu,Yufei Huang,Haitao Lin,Cheng Tan,Zhangyang Gao,Stan Z. Li:
  Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks.CoRRabs/2403.01400 (2024)
• 
  [i24]
  Zhangyang Gao,Cheng Tan,Jue Wang,Yufei Huang,Lirong Wu,Stan Z. Li:
  FoldToken: Learning Protein Language via Vector Quantization and Beyond.CoRRabs/2403.09673 (2024)
• 
  [i23]
  Odin Zhang,Yufei Huang,Shichen Cheng,Mengyao Yu,Xujun Zhang,Haitao Lin,Yundian Zeng,Mingyang Wang,Zhenxing Wu,Huifeng Zhao,Zaixi Zhang,Chenqing Hua,Yu Kang,Sunliang Cui,Peichen Pan,Chang-Yu Hsieh,Tingjun Hou:
  Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation.CoRRabs/2404.00014 (2024)
• 
  [i22]
  Odin Zhang,Haitao Lin,Hui Zhang,Huifeng Zhao,Yufei Huang,Yuansheng Huang,Dejun Jiang,Chang-Yu Hsieh,Peichen Pan,Tingjun Hou:
  Deep Lead Optimization: Leveraging Generative AI for Structural Modification.CoRRabs/2404.19230 (2024)
• 
  [i21]
  Haitao Lin,Odin Zhang,Huifeng Zhao,Dejun Jiang,Lirong Wu,Zicheng Liu,Yufei Huang,Stan Z. Li:
  PPFlow: Target-aware Peptide Design with Torsional Flow Matching.CoRRabs/2405.06642 (2024)
• 
  [i20]
  Lirong Wu,Yijun Tian,Haitao Lin,Yufei Huang,Siyuan Li,Nitesh V. Chawla,Stan Z. Li:
  Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning.CoRRabs/2405.10348 (2024)
• 
  [i19]
  Siyuan Li,Zedong Wang,Zicheng Liu,Di Wu,Cheng Tan,Jiangbin Zheng,Yufei Huang,Stan Z. Li:
  VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling.CoRRabs/2405.10812 (2024)
• 
  [i18]
  Zhangyang Gao,Jue Wang,Cheng Tan,Lirong Wu,Yufei Huang,Siyuan Li,Zhirui Ye,Stan Z. Li:
  UniIF: Unified Molecule Inverse Folding.CoRRabs/2405.18968 (2024)
• 
  [i17]
  Zicheng Liu,Jiahui Li,Siyuan Li,Zelin Zang,Cheng Tan,Yufei Huang,Yajing Bai,Stan Z. Li:
  GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models.CoRRabs/2406.01627 (2024)
• 
  [i16]
  Haitao Lin,Guojiang Zhao,Odin Zhang,Yufei Huang,Lirong Wu,Zicheng Liu,Siyuan Li,Cheng Tan,Zhifeng Gao,Stan Z. Li:
  CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph.CoRRabs/2406.10840 (2024)
• 
  [i15]
  Lirong Wu,Yunfan Liu,Haitao Lin,Yufei Huang,Stan Z. Li:
  Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation.CoRRabs/2407.14768 (2024)
• 
  [i14]
  Cheng Tan,Zhenxiao Cao,Zhangyang Gao,Lirong Wu,Siyuan Li,Yufei Huang,Jun Xia,Bozhen Hu,Stan Z. Li:
  MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction.CoRRabs/2411.01856 (2024)
• 2023
• 
  [c5]
  Lirong Wu,Haitao Lin,Yufei Huang,Tianyu Fan,Stan Z. Li:
  Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting It into MLPs: An Effective GNN-to-MLP Distillation Framework.AAAI2023:10351-10360
• 
  [c4]
  Lirong Wu,Haitao Lin,Yufei Huang,Stan Z. Li:
  Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs.ICML2023:37571-37581
• 
  [c3]
  Haitao Lin,Yufei Huang,Odin Zhang,Yunfan Liu,Lirong Wu,Siyuan Li,Zhiyuan Chen,Stan Z. Li:
  Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration.NeurIPS2023
• 
  [i13]
  Lirong Wu,Yufei Huang,Haitao Lin,Stan Z. Li:
  A Survey on Protein Representation Learning: Retrospect and Prospect.CoRRabs/2301.00813 (2023)
• 
  [i12]
  Yufei Huang,Lirong Wu,Haitao Lin,Jiangbin Zheng,Ge Wang,Stan Z. Li:
  Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy.CoRRabs/2302.10888 (2023)
• 
  [i11]
  Jiangbin Zheng,Ge Wang,Yufei Huang,Bozhen Hu,Siyuan Li,Cheng Tan,Xinwen Fan,Stan Z. Li:
  Lightweight Contrastive Protein Structure-Sequence Transformation.CoRRabs/2303.11783 (2023)
• 
  [i10]
  Lirong Wu,Haitao Lin,Yufei Huang,Tianyu Fan,Stan Z. Li:
  Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting it into MLPs: An Effective GNN-to-MLP Distillation Framework.CoRRabs/2305.10758 (2023)
• 
  [i9]
  Lirong Wu,Haitao Lin,Yufei Huang,Stan Z. Li:
  Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs.CoRRabs/2306.05628 (2023)
• 
  [i8]
  Haitao Lin,Yufei Huang,Haotian Zhang,Lirong Wu,Siyuan Li,Zhiyuan Chen,Stan Z. Li:
  Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration.CoRRabs/2306.13769 (2023)
• 
  [i7]
  Yufei Huang,Siyuan Li,Jin Su,Lirong Wu,Odin Zhang,Haitao Lin,Jingqi Qi,Zihan Liu,Zhangyang Gao,Yuyang Liu,Jiangbin Zheng,Stan Z. Li:
  Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction.CoRRabs/2310.11466 (2023)
• 
  [i6]
  Jiangbin Zheng,Siyuan Li,Yufei Huang,Zhangyang Gao,Cheng Tan,Bozhen Hu,Jun Xia,Ge Wang,Stan Z. Li:
  MMDesign: Multi-Modality Transfer Learning for Generative Protein Design.CoRRabs/2312.06297 (2023)
• 2022
• 
  [c2]
  Jiangbin Zheng,Yile Wang,Ge Wang,Jun Xia,Yufei Huang,Guojiang Zhao,Yue Zhang,Stan Z. Li:
  Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings.ACL (1)2022:8154-8163
• 
  [c1]
  Lirong Wu,Haitao Lin,Yufei Huang,Stan Z. Li:
  Knowledge Distillation Improves Graph Structure Augmentation for Graph Neural Networks.NeurIPS2022
• 
  [i5]
  Lirong Wu,Yufei Huang,Haitao Lin,Zicheng Liu,Tianyu Fan,Stan Z. Li:
  Automated Graph Self-supervised Learning via Multi-teacher Knowledge Distillation.CoRRabs/2210.02099 (2022)
• 
  [i4]
  Jiangbin Zheng,Yile Wang,Ge Wang,Jun Xia,Yufei Huang,Guojiang Zhao,Yue Zhang,Stan Z. Li:
  Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings.CoRRabs/2210.16848 (2022)
• 
  [i3]
  Haitao Lin,Yufei Huang,Meng Liu,Xuanjing Li,Shuiwang Ji,Stan Z. Li:
  DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding.CoRRabs/2211.11214 (2022)
• 
  [i2]
  Bozhen Hu,Jun Xia,Jiangbin Zheng,Cheng Tan,Yufei Huang,Yongjie Xu,Stan Z. Li:
  Protein Language Models and Structure Prediction: Connection and Progression.CoRRabs/2211.16742 (2022)
• 
  [i1]
  Haitao Lin,Lirong Wu,Yongjie Xu,Yufei Huang,Siyuan Li,Guojiang Zhao,Stan Z. Li:
  Non-equispaced Fourier Neural Solvers for PDEs.CoRRabs/2212.04689 (2022)

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