Huang, Yufei

31 publications

TMLR 2026 ACDiT: Interpolating Autoregressive Conditional Modeling and Diffusion Transformer Jinyi Hu, Shengding Hu, Yuxuan Song, Yufei Huang, Mingxuan Wang, Hao Zhou, Zhiyuan Liu, Wei-Ying Ma, Maosong Sun

ICML 2025 A Generic Family of Graphical Models: Diversity, Efficiency, and Heterogeneity Yufei Huang, Changhu Wang, Junjie Tang, Weichi Wu, Ruibin Xi

ICLR 2025 A Simple yet Effective $\Delta\Delta G$ Predictor Is an Unsupervised Antibody Optimizer and Explainer Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Guojiang Zhao, Zhifeng Gao, Stan Z. Li

ICLRW 2025 ACDiT: Interpolating Autoregressive Conditional Modeling and Diffusion Transformer Jinyi Hu, Shengding Hu, Yuxuan Song, Yufei Huang, Mingxuan Wang, Hao Zhou, Zhiyuan Liu, Wei-Ying Ma, Maosong Sun

NeurIPS 2025 AlphaFold Database Debiasing for Robust Inverse Folding Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Siyuan Li, Yufei Huang, Stan Z. Li

ICLR 2025 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

CVPR 2025 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

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

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

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

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

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

NeurIPSW 2024 GeneGench: Systematic Evaluation of Genomic Foundation Models and Beyond Zicheng Liu, Jiahui Li, Lei Xin, Siyuan Li, Chang Yu, Zelin Zang, Cheng Tan, Yufei Huang, Yajingbai, Jun Xia, Stan Z. Li

ICML 2024 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

NeurIPS 2024 Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure Bozhen Hu, Cheng Tan, Jun Xia, Yue Liu, Lirong Wu, Jiangbin Zheng, Yongjie Xu, Yufei Huang, Stan Z. Li

ICML 2024 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

ICLR 2024 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

ICML 2024 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

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

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

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

ICML 2024 VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling Siyuan Li, Zedong Wang, Zicheng Liu, Di Wu, Cheng Tan, Jiangbin Zheng, Yufei Huang, Stan Z. Li

AAAI 2023 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

NeurIPS 2023 Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration Haitao Lin, Yufei Huang, Odin Zhang, Yunfan Liu, Lirong Wu, Siyuan Li, Zhiyuan Chen, Stan Z. Li

NeurIPSW 2023 Leveraging Foundation Models to Improve Lightweight Clients in Federated Learning Xidong Wu, Wan-Yi Lin, Devin Willmott, Filipe Condessa, Yufei Huang, Zhenzhen Li, Madan Ganesh

ICLRW 2023 Non-Equispaced Fourier Neural Solvers for PDEs Haitao Lin, Lirong Wu, Yongjie Xu, Yufei Huang, Siyuan Li, Guojiang Zhao, Stan Z. Li

ICML 2023 Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs Lirong Wu, Haitao Lin, Yufei Huang, Stan Z. Li

NeurIPS 2022 Knowledge Distillation Improves Graph Structure Augmentation for Graph Neural Networks Lirong Wu, Haitao Lin, Yufei Huang, Stan Z. Li

AAAI 2021 Interpretable Self-Supervised Facial Micro-Expression Learning to Predict Cognitive State and Neurological Disorders Arun Das, Jeffrey Mock, Yufei Huang, Edward J. Golob, Peyman Najafirad