Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings. - Jiangbin Zheng 002; Yile Wang 001; Ge Wang; Jun Xia 001; Yufei Huang 002; Guojiang Zhao; Yue Zhang 004; Stan Z. Li (ACL (1), 2022)

Knowledge Distillation Improves Graph Structure Augmentation for Graph Neural Networks. - Lirong Wu; Haitao Lin; Yufei Huang 002; Stan Z. Li (NeurIPS, 2022)

Automated Graph Self-supervised Learning via Multi-teacher Knowledge Distillation. - Lirong Wu; Yufei Huang 002; Haitao Lin; Zicheng Liu 006; Tianyu Fan; Stan Z. Li (CoRR, 2022)

DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding. - Haitao Lin; Yufei Huang 002; Meng Liu 015; Xuanjing Li; Shuiwang Ji; Stan Z. Li (CoRR, 2022)

Protein Language Models and Structure Prediction: Connection and Progression. - Bozhen Hu; Jun Xia 001; Jiangbin Zheng 002; Cheng Tan 012; Yufei Huang 002; Yongjie Xu; Stan Z. Li (CoRR, 2022)

Non-equispaced Fourier Neural Solvers for PDEs. - Haitao Lin; Lirong Wu; Yongjie Xu; Yufei Huang 002; Siyuan Li 002; Guojiang Zhao; Stan Z. Li (CoRR, 2022)

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 002; Tianyu Fan; Stan Z. Li (AAAI, 2023)

Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs. - Lirong Wu; Haitao Lin; Yufei Huang 002; Stan Z. Li (ICML, 2023)

Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration. - Haitao Lin; Yufei Huang 002; Odin Zhang; Yunfan Liu 002; Lirong Wu; Siyuan Li 002; Zhiyuan Chen 008; Stan Z. Li (NeurIPS, 2023)

A Survey on Protein Representation Learning: Retrospect and Prospect. - Lirong Wu; Yufei Huang 002; Haitao Lin; Stan Z. Li (CoRR, 2023)

Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy. - Yufei Huang 002; Lirong Wu; Haitao Lin; Jiangbin Zheng 002; Ge Wang; Stan Z. Li (CoRR, 2023)

Lightweight Contrastive Protein Structure-Sequence Transformation. - Jiangbin Zheng 002; Ge Wang; Yufei Huang 002; Bozhen Hu; Siyuan Li 002; Cheng Tan 012; Xinwen Fan; Stan Z. Li (CoRR, 2023)

Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration. - Haitao Lin; Yufei Huang 002; Haotian Zhang; Lirong Wu; Siyuan Li 002; Zhiyuan Chen 008; Stan Z. Li (CoRR, 2023)

Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction. - Yufei Huang 002; Siyuan Li 002; Jin Su; Lirong Wu; Odin Zhang; Haitao Lin; Jingqi Qi; Zihan Liu; Zhangyang Gao; Yuyang Liu; Jiangbin Zheng 002; Stan Z. Li (CoRR, 2023)

MMDesign: Multi-Modality Transfer Learning for Generative Protein Design. - Jiangbin Zheng 002; Siyuan Li 002; Yufei Huang 002; Zhangyang Gao; Cheng Tan 012; Bozhen Hu; Jun Xia 001; Ge Wang; Stan Z. Li (CoRR, 2023)

Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction. - Yufei Huang 002; Siyuan Li 002; Lirong Wu; Jin Su; Haitao Lin; Odin Zhang; Zihan Liu; Zhangyang Gao; Jiangbin Zheng 002; 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 002; Cheng Tan 012; Zhangyang Gao; Bozhen Hu; Haitao Lin; Zicheng Liu 006; Stan Z. Li (AAAI, 2024)

Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation. - Lirong Wu; Yunfan Liu 002; Haitao Lin; Yufei Huang 002; Stan Z. Li (CIKM, 2024)

Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks. - Tianyu Fan; Lirong Wu; Yufei Huang 002; Haitao Lin; Cheng Tan 012; Zhangyang Gao; Stan Z. Li (ICLR, 2024)

MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding. - Lirong Wu; Yijun Tian 001; Yufei Huang 002; Siyuan Li 002; Haitao Lin; Nitesh V. Chawla; Stan Z. Li (ICLR, 2024)

Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge. - Yufei Huang 002; Odin Zhang; Lirong Wu; Cheng Tan 012; Haitao Lin; Zhangyang Gao; Siyuan Li 002; Stan Z. Li (ICML, 2024)

VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling. - Siyuan Li 002; Zedong Wang; Zicheng Liu 006; Di Wu 057; Cheng Tan 012; Jiangbin Zheng 002; Yufei Huang 002; Stan Z. Li (ICML, 2024)

GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation. - Haitao Lin; Lirong Wu; Yufei Huang 002; Yunfan Liu 002; Odin Zhang; Yuanqing Zhou; Rui Sun; Stan Z. Li (ICML, 2024)

PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching. - Haitao Lin; Odin Zhang; Huifeng Zhao; Dejun Jiang 002; Lirong Wu; Zicheng Liu 006; Yufei Huang 002; Stan Z. Li (ICML, 2024)

Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning. - Lirong Wu; Yijun Tian 001; Haitao Lin; Yufei Huang 002; Siyuan Li 002; Nitesh V. Chawla; Stan Z. Li (ICML, 2024)

UniIF: Unified Molecule Inverse Folding. - Zhangyang Gao; Jue Wang 004; Cheng Tan 012; Lirong Wu; Yufei Huang 002; Siyuan Li 002; Zhirui Ye; Stan Z. Li (NeurIPS, 2024)

Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure. - Bozhen Hu; Cheng Tan 012; Jun Xia 001; Yue Liu 008; Lirong Wu; Jiangbin Zheng 002; Yongjie Xu; Yufei Huang 002; Stan Z. Li (NeurIPS, 2024)

Enhancing Protein Predictive Models via Proteins Data Augmentation: A Benchmark and New Directions. - Rui Sun; Lirong Wu; Haitao Lin; Yufei Huang 002; Stan Z. Li (CoRR, 2024)

Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. - Odin Zhang; Yufei Huang 002; Shichen Cheng; Mengyao Yu; Xujun Zhang; Haitao Lin; Yundian Zeng; Mingyang Wang 004; Zhenxing Wu; Huifeng Zhao; Zaixi Zhang; Chenqing Hua; et al. (CoRR, 2024)

Deep Lead Optimization: Leveraging Generative AI for Structural Modification. - Odin Zhang; Haitao Lin; Hui Zhang; Huifeng Zhao; Yufei Huang 002; Yuansheng Huang; Dejun Jiang 002; Chang-Yu Hsieh; Peichen Pan; Tingjun Hou (CoRR, 2024)

Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning. - Lirong Wu; Yijun Tian 001; Haitao Lin; Yufei Huang 002; Siyuan Li 002; Nitesh V. Chawla; Stan Z. Li (CoRR, 2024)

GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models. - Zicheng Liu 006; Jiahui Li; Siyuan Li 002; Zelin Zang; Cheng Tan 012; Yufei Huang 002; Yajing Bai; Stan Z. Li (CoRR, 2024)

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. - Haitao Lin; Guojiang Zhao; Odin Zhang; Yufei Huang 002; Lirong Wu; Zicheng Liu 006; Siyuan Li 002; Cheng Tan 012; Zhifeng Gao; Stan Z. Li (CoRR, 2024)

Homophily-Enhanced Self-Supervision for Graph Structure Learning: Insights and Directions. - Lirong Wu; Haitao Lin; Zihan Liu; Zicheng Liu 006; Yufei Huang 002; Stan Z. Li (IEEE Trans. Neural Networks Learn. Syst., 2024)

dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen. - Cheng Tan 012; Yijie Zhang; Zhangyang Gao; Yufei Huang 002; Haitao Lin; Lirong Wu; Fandi Wu; Mathieu Blanchette; Stan Z. Li (AAAI, 2025)

FoldToken: Learning Protein Language via Vector Quantization and Beyond. - Zhangyang Gao; Cheng Tan 012; Jue Wang 004; Yufei Huang 002; Lirong Wu; Stan Z. Li (AAAI, 2025)

Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization. - Lirong Wu; Haitao Lin; Yufei Huang 002; Zhangyang Gao; Cheng Tan 012; Yunfan Liu 002; Tailin Wu; Stan Z. Li (AAAI, 2025)

DaCapo: Score Distillation as Stacked Bridge for Fast and High-quality 3D Editing. - Yufei Huang 002; Bangyan Liao; Yuqi Hu; Haitao Lin; Lirong Wu; Siyuan Li 002; Cheng Tan 012; Zicheng Liu 006; Yunfan Liu 002; Zelin Zang; Chang Yu 001; Zhen Lei 001 (CVPR, 2025)

EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow. - Yufei Huang 002; Yunshu Liu; Lirong Wu; Haitao Lin; Cheng Tan 012; Odin Zhang; Zhangyang Gao; Siyuan Li 002; Zicheng Liu 006; Yunfan Liu 002; Tailin Wu; Stan Z. Li (ICLR, 2025)

MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction. - Cheng Tan 012; Zhenxiao Cao; Zhangyang Gao; Lirong Wu; Siyuan Li 002; Yufei Huang 002; Jun Xia 001; Bozhen Hu; Stan Z. Li (ICLR, 2025)

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. - Haitao Lin; Guojiang Zhao; Odin Zhang; Yufei Huang 002; Lirong Wu; Cheng Tan 012; Zicheng Liu 006; Zhifeng Gao; Stan Z. Li (ICLR, 2025)

A Simple yet Effective ΔΔG Predictor is An Unsupervised Antibody Optimizer and Explainer. - Lirong Wu; Yunfan Liu 002; Haitao Lin; Yufei Huang 002; Guojiang Zhao; Zhifeng Gao; Stan Z. Li (ICLR, 2025)

Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation. - Dou Nie; Huifeng Zhao; Odin Zhang; Gaoqi Weng; Hui Zhang; Jieyu Jin; Haitao Lin; Yufei Huang 002; Liwei Liu; Dan Li 013; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2025)

A Simple yet Effective DDG Predictor is An Unsupervised Antibody Optimizer and Explainer. - Lirong Wu; Yunfan Liu 002; Haitao Lin; Yufei Huang 002; Guojiang Zhao; Zhifeng Gao; Stan Z. Li (CoRR, 2025)

VARD: Efficient and Dense Fine-Tuning for Diffusion Models with Value-based RL. - Fengyuan Dai; Zifeng Zhuang; Yufei Huang 002; Siteng Huang; Bangyan Liao; Donglin Wang; Fajie Yuan (CoRR, 2025)

Tokenizing Electron Cloud in Protein-Ligand Interaction Learning. - Haitao Lin; Odin Zhang; Jia Xu; Yunfan Liu 002; Zheng Chen 014; Lirong Wu; Yufei Huang 002; Zhifeng Gao; Stan Z. Li (CoRR, 2025)

AlphaFold Database Debiasing for Robust Inverse Folding. - Cheng Tan 012; Zhenxiao Cao; Zhangyang Gao; Siyuan Li 002; Yufei Huang 002; Stan Z. Li (CoRR, 2025)

Unlasting: Unpaired Single-Cell Multi-Perturbation Estimation by Dual Conditional Diffusion Implicit Bridges. - Changxi Chi; Jun Xia 001; Yufei Huang 002; Jingbo Zhou; Siyuan Li 002; Yunfan Liu 002; Chang Yu 001; Stan Z. Li (CoRR, 2025)