PASH at TREC 2020 Deep Learning Track: Dense Matching for Nested Ranking. - Yixuan Qiao; Hao Chen; Liyu Cao; Liping Chen; Pengyong Li; Jun Wang 123; Peng Gao 015; Yuan Ni; Guotong Xie (TREC, 2020)

Learn molecular representations from large-scale unlabeled molecules for drug discovery. - Pengyong Li; Jun Wang 123; Yixuan Qiao; Hao Chen; Yihuan Yu; Xiaojun Yao; Peng Gao 015; Guotong Xie; Sen Song (CoRR, 2020)

Pairwise Half-graph Discrimination: A Simple Graph-level Self-supervised Strategy for Pre-training Graph Neural Networks. - Pengyong Li; Jun Wang 123; Ziliang Li; Yixuan Qiao; Xianggen Liu; Fei Ma; Peng Gao 015; Sen Song; Guotong Xie (IJCAI, 2021)

TrimNet: learning molecular representation from triplet messages for biomedicine. - Pengyong Li; Yuquan Li; Chang-Yu Hsieh; Shengyu Zhang 002; Xianggen Liu; Huanxiang Liu; Sen Song; Xiaojun Yao (Briefings Bioinform., 2021)

An effective self-supervised framework for learning expressive molecular global representations to drug discovery. - Pengyong Li; Jun Wang 123; Yixuan Qiao; Hao Chen; Yihuan Yu; Xiaojun Yao; Peng Gao 015; Guotong Xie; Sen Song (Briefings Bioinform., 2021)

Pairwise Half-graph Discrimination: A Simple Graph-level Self-supervised Strategy for Pre-training Graph Neural Networks. - Pengyong Li; Jun Wang 123; Ziliang Li; Yixuan Qiao; Xianggen Liu; Fei Ma; Peng Gao 015; Seng Song; Guotong Xie (CoRR, 2021)

Simulated annealing for optimization of graphs and sequences. - Xianggen Liu; Pengyong Li; Fandong Meng; Hao Zhou 012; Huasong Zhong; Jie Zhou 016; Lili Mou; Sen Song (Neurocomputing, 2021)

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity. - Xianggen Liu; Yunan Luo; Pengyong Li; Sen Song; Jian Peng 001 (PLoS Comput. Biol., 2021)

HCL: Improving Graph Representation with Hierarchical Contrastive Learning. - Jun Wang 123; Weixun Li; Changyu Hou; Xin Tang; Yixuan Qiao; Rui Fang; Pengyong Li; Peng Gao 015; Guotong Xie (ISWC, 2022)

CandidateDrug4Cancer: An Open Molecular Graph Learning Benchmark on Drug Discovery for Cancer. - Xianbin Ye; Ziliang Li; Fei Ma; Zongbi Yi; Pengyong Li; Jun Wang 123; Peng Gao 015; Yixuan Qiao; Guotong Xie (CoRR, 2022)

An adaptive graph learning method for automated molecular interactions and properties predictions. - Yuquan Li; Chang-Yu Hsieh; Ruiqiang Lu; Xiaoqing Gong; Xiaorui Wang; Pengyong Li; Shuo Liu; Yanan Tian; Dejun Jiang 002; Jiaxian Yan; Qifeng Bai; Huanxiang Liu; et al. (Nat. Mach. Intell., 2022)

Improving drug-target affinity prediction via feature fusion and knowledge distillation. - Ruiqiang Lu; Jun Wang 123; Pengyong Li; Yuquan Li; Shuoyan Tan; Yiting Pan; Huanxiang Liu; Peng Gao 015; Guotong Xie; Xiaojun Yao (Briefings Bioinform., 2023)

Deep generative model for drug design from protein target sequence. - Yangyang Chen 006; Zixu Wang; Lei Wang; Jianmin Wang 016; Pengyong Li; Dongsheng Cao 001; Xiangxiang Zeng; Xiucai Ye; Tetsuya Sakurai (J. Cheminformatics, 2023)

Improving drug response prediction via integrating gene relationships with deep learning. - Pengyong Li; Zhengxiang Jiang; Tianxiao Liu; Xinyu Liu; Hui Qiao; Xiaojun Yao (Briefings Bioinform., 2024)

Secure architecture for Industrial Edge of Things(IEoT): A hierarchical perspective. - Pengyong Li; Jiaqi Xia; Qian Wang 028; Yujie Zhang; Meng Wu 003 (Comput. Networks, 2024)

PT-ADP: A personalized privacy-preserving federated learning scheme based on transaction mechanism. - Jiaqi Xia; Pengyong Li; Yiming Mao 010; Meng Wu (Inf. Sci., 2024)

A deep learning approach for rational ligand generation with toxicity control via reactive building blocks. - Pengyong Li; Kaihao Zhang; Tianxiao Liu; Ruiqiang Lu; Yangyang Chen 006; Xiaojun Yao; Lin Gao; Xiangxiang Zeng (Nat. Comput. Sci., 2024)

MuLDOM: Forecasting Multivariate Anomalies on Edge Devices in IIoT Using Multibranch LSTM and Differential Overfitting Mitigation Model. - Pengyong Li; Meng Wu 003; YuJie Zhang; Jiaqi Xia; Qian Wang 028 (IEEE Internet Things J., 2024)

SFML: A personalized, efficient, and privacy-preserving collaborative traffic classification architecture based on split learning and mutual learning. - Jiaqi Xia; Meng Wu 003; Pengyong Li (Future Gener. Comput. Syst., 2025)