Yufei Huang 0002 - researchr alias

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Viewing Publication 1 - 19 from 19

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]

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]

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]

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]

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding GraphHaitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang 0002, Lirong Wu, Cheng Tan 0012, Zicheng Liu 0006, Zhifeng Gao, Stan Z. Li. iclr 2025: [doi]

Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular GenerationDou Nie, Huifeng Zhao, Odin Zhang, Gaoqi Weng, Hui Zhang, Jieyu Jin, Haitao Lin, Yufei Huang 0002, Liwei Liu, Dan Li 0013, Tingjun Hou, Yu Kang 0002. jcisd, 65(1):173-186, 2025. [doi]

A Simple yet Effective ΔΔG Predictor is An Unsupervised Antibody Optimizer and ExplainerLirong Wu, Yunfan Liu 0002, Haitao Lin, Yufei Huang 0002, Guojiang Zhao, Zhifeng Gao, Stan Z. Li. iclr 2025: [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

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]

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]

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]

Learning Complete Protein Representation by Dynamically Coupling of Sequence and StructureBozhen Hu, Cheng Tan 0012, Jun Xia 0001, Yue Liu 0008, Lirong Wu, Jiangbin Zheng, Yongjie Xu, Yufei Huang 0002, Stan Z. Li. nips 2024: [doi]

VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence ModelingSiyuan Li, Zedong Wang, Zicheng Liu 0006, Di Wu 0057, Cheng Tan 0012, Jiangbin Zheng, Yufei Huang 0002, Stan Z. Li. icml 2024: [doi]

PPFLOW: Target-Aware Peptide Design with Torsional Flow MatchingHaitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang 0002, Lirong Wu, Zicheng Liu 0006, Yufei Huang 0002, Stan Z. Li. icml 2024: [doi]

GeoAB: Towards Realistic Antibody Design and Reliable Affinity MaturationHaitao Lin, Lirong Wu, Yufei Huang 0002, Yunfan Liu 0002, Odin Zhang, Yuanqing Zhou, Rui Sun, Stan Z. Li. icml 2024: [doi]

Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge DistillationLirong Wu, Yunfan Liu 0002, Haitao Lin, Yufei Huang 0002, Stan Z. Li. CIKM 2024: 2554-2563 [doi]

Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt LearningLirong Wu, Yijun Tian 0001, Haitao Lin, Yufei Huang 0002, Siyuan Li, Nitesh V. Chawla, Stan Z. Li. icml 2024: [doi]

MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein EmbeddingLirong Wu, Yijun Tian 0001, Yufei Huang 0002, Siyuan Li, Haitao Lin, Nitesh V. Chawla, Stan Z. Li. iclr 2024: [doi]

Homophily-Enhanced Self-Supervision for Graph Structure Learning: Insights and DirectionsLirong Wu, Haitao Lin, Zihan Liu, Zicheng Liu 0006, Yufei Huang 0002, Stan Z. Li. tnn, 35(9):12358-12372, September 2024. [doi]

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