A Lightweight Spatial and Temporal Multi-Feature Fusion Network for Defect Detection. - Bozhen Hu; Bin Gao 003; Wai Lok Woo; Lingfeng Ruan; Jikun Jin; Yang Yang; Yongjie Yu (IEEE Trans. Image Process., 2021)

SimGRACE: A Simple Framework for Graph Contrastive Learning without Data Augmentation. - Jun Xia 001; Lirong Wu; Jintao Chen; Bozhen Hu; Stan Z. Li (WWW, 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)

Deep Manifold Graph Auto-Encoder For Attributed Graph Embedding. - Bozhen Hu; Zelin Zang; Jun Xia 001; Lirong Wu; Cheng Tan 012; Stan Z. Li (ICASSP, 2023)

Global-Context Aware Generative Protein Design. - Cheng Tan 012; Zhangyang Gao; Jun Xia 001; Bozhen Hu; Stan Z. Li (ICASSP, 2023)

Wordreg: Mitigating the Gap between Training and Inference with Worst-Case Drop Regularization. - Jun Xia 001; Ge Wang; Bozhen Hu; Cheng Tan 012; Jiangbin Zheng 002; Yongjie Xu; Stan Z. Li (ICASSP, 2023)

Mole-BERT: Rethinking Pre-training Graph Neural Networks for Molecules. - Jun Xia 001; Chengshuai Zhao; Bozhen Hu; Zhangyang Gao; Cheng Tan 012; Yue Liu 008; Siyuan Li 002; Stan Z. Li (ICLR, 2023)

Understanding the Limitations of Deep Models for Molecular property prediction: Insights and Solutions. - Jun Xia 001; Lecheng Zhang; Xiao Zhu; Yue Liu 008; Zhangyang Gao; Bozhen Hu; Cheng Tan 012; Jiangbin Zheng 002; Siyuan Li 002; Stan Z. Li (NeurIPS, 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)

Segment Anything in Defect Detection. - Bozhen Hu; Bin Gao 003; Cheng Tan 012; Tongle Wu; 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)

Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody Designer. - Cheng Tan 012; Zhangyang Gao; Lirong Wu; Jun Xia 001; Jiangbin Zheng 002; Xihong Yang; Yue Liu 008; Bozhen Hu; 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)

Deep Manifold Transformation for Protein Representation Learning. - Bozhen Hu; Zelin Zang; Cheng Tan 012; Stan Z. Li (ICASSP, 2024)

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design. - Cheng Tan 012; Yijie Zhang; Zhangyang Gao; Bozhen Hu; Siyuan Li 002; Zicheng Liu 006; Stan Z. Li (ICLR, 2024)

A Graph is Worth K Words: Euclideanizing Graph using Pure Transformer. - Zhangyang Gao; Daize Dong; Cheng Tan 012; Jun Xia 001; Bozhen Hu; Stan Z. Li (ICML, 2024)

AdaNovo: Towards Robust emph{De Novo} Peptide Sequencing in Proteomics against Data Biases. - Jun Xia 001; Shaorong Chen; Jingbo Zhou; Xiaojun Shan; Wenjie Du 003; Zhangyang Gao; Cheng Tan 012; Bozhen Hu; Jiangbin Zheng 002; 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)

ProtGO: Function-Guided Protein Modeling for Unified Representation Learning. - Bozhen Hu; Cheng Tan 012; Yongjie Xu; Zhangyang Gao; Jun Xia 001; Lirong Wu; Stan Z. Li (NeurIPS, 2024)

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning. - Sizhe Liu; Jun Xia 001; Lecheng Zhang; Yuchen Liu; Yue Liu 008; Wenjie Du 003; Zhangyang Gao; Bozhen Hu; Cheng Tan 012; Hongxin Xiang; Stan Z. Li (NeurIPS, 2024)

Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation. - Yongjie Xu; Zelin Zang; Bozhen Hu; Yue Yuan; Cheng Tan 012; Jun Xia 001; Stan Z. Li (Briefings Bioinform., 2024)

Beyond Homophily and Homogeneity Assumption: Relation-Based Frequency Adaptive Graph Neural Networks. - Lirong Wu; Haitao Lin; Bozhen Hu; Cheng Tan 012; Zhangyang Gao; Zicheng Liu 006; Stan Z. Li (IEEE Trans. Neural Networks Learn. Syst., 2024)

Generalized Implicit Neural Representations for Dynamic Molecular Surface Modeling. - Fang Wu 002; Bozhen Hu; Stan Z. Li (AAAI, 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)

ReNovo: Retrieval-Based emph{De Novo} Mass Spectrometry Peptide Sequencing. - Shaorong Chen; Jun Xia 001; Jingbo Zhou; Lecheng Zhang; Zhangyang Gao; Bozhen Hu; Cheng Tan 012; Wenjie Du 003; Stan Z. Li (ICLR, 2025)

Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature. - Sizhe Qiu; Bozhen Hu; Jing Zhao; Weiren Xu; Aidong Yang (Briefings Bioinform., 2025)

PFMBench: Protein Foundation Model Benchmark. - Zhangyang Gao; Hao Wang 074; Cheng Tan 012; Chenrui Xu; Mengdi Liu; Bozhen Hu; Linlin Chao; Xiaoming Zhang; Stan Z. Li (CoRR, 2025)

EnTao-GPM: DNA Foundation Model for Predicting the Germline Pathogenic Mutations. - Zekai Lin; Haoran Sun; Yucheng Guo; Yujie Yang; Yanwen Wang; Bozhen Hu; Chonghang Ye; Qirong Yang; Fan Zhong; Xiaoming Zhang; Lei Liu (CoRR, 2025)