Shuangjia Zheng

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 46

Top Topics

Graph Representation

Amino Acid Residues

Top Venues

J. Chem. Inf. Model.

J. Cheminformatics

Publications

Jiahua Rao, Jiancong Xie, Hanjing Lin, Shuangjia Zheng, Zhen Wang, Yuedong Yang
Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks. CoRR (2024)
Chenqing Hua, Connor W. Coley, Guy Wolf, Doina Precup, Shuangjia Zheng
Effective Protein-Protein Interaction Exploration with PPIretrieval. CoRR (2024)
Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang
Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. J. Chem. Inf. Model. 64 (6) (2024)
Mei Li, Xiaoguang Liu, Hua Ji, Shuangjia Zheng
Causal Subgraph Learning for Generalizable Inductive Relation Prediction. KDD (2024)
Deqin Liu, Sheng Chen, Shuangjia Zheng, Sen Zhang, Yuedong Yang
SE(3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation. BIBM (2023)
Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang
Subgraph-Aware Few-Shot Inductive Link Prediction Via Meta-Learning. IEEE Trans. Knowl. Data Eng. 35 (6) (2023)
Jingbang Chen, Yian Wang, Xingwei Qu, Shuangjia Zheng, Yaodong Yang, Hao Dong, Jie Fu
Mixup-Augmented Meta-Learning for Sample-Efficient Fine-Tuning of Protein Simulators. CoRR (2023)
Sijie Mai, Ying Zeng, Shuangjia Zheng, Haifeng Hu
Hybrid Contrastive Learning of Tri-Modal Representation for Multimodal Sentiment Analysis. IEEE Trans. Affect. Comput. 14 (3) (2023)
Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang
Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. IJCAI (2022)
Wei Lu, Qifeng Wu, Jixian Zhang, Jiahua Rao, Chengtao Li, Shuangjia Zheng
TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction. NeurIPS (2022)
Shuangjia Zheng, Youhai Tan, Zhenyu Wang, Chengtao Li, Zhiqing Zhang, Xu Sang, Hongming Chen, Yuedong Yang
Accelerated rational PROTAC design via deep learning and molecular simulations. Nat. Mac. Intell. 4 (9) (2022)
Jiahua Rao, Shuangjia Zheng, Yutong Lu, Yuedong Yang
Quantitative evaluation of explainable graph neural networks for molecular property prediction. Patterns 3 (12) (2022)
Youhai Tan, Lingxue Dai, Weifeng Huang, Yinfeng Guo, Shuangjia Zheng, Jinping Lei, Hongming Chen, Yuedong Yang
DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. J. Chem. Inf. Model. 62 (23) (2022)
Qianmu Yuan, Sheng Chen, Jiahua Rao, Shuangjia Zheng, Huiying Zhao, Yuedong Yang
AlphaFold2-aware protein-DNA binding site prediction using graph transformer. Briefings Bioinform. 23 (2) (2022)
Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang
Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. CoRR (2022)
Penglei Wang, Shuangjia Zheng, Yize Jiang, Chengtao Li, Junhong Liu, Chang Wen, Atanas Patronov, Dahong Qian, Hongming Chen, Yuedong Yang
Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. J. Chem. Inf. Model. 62 (5) (2022)
Sijie Mai, Shuangjia Zheng, Ya Sun, Ying Zeng, Yuedong Yang, Haifeng Hu
Dynamic graph dropout for subgraph-based relation prediction. Knowl. Based Syst. 250 (2022)
Zhe Sun, Shuangjia Zheng, Huiying Zhao, Zhangming Niu, Yutong Lu, Yi Pan, Yuedong Yang
To Improve Prediction of Binding Residues With DNA, RNA, Carbohydrate, and Peptide Via Multi-Task Deep Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Jiahua Rao, Shuangjia Zheng, Yuedong Yang
Integrating supercomputing and artificial intelligence for life science. Patterns 3 (12) (2022)
Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang
Subgraph-aware Few-Shot Inductive Link Prediction via Meta-Learning. CoRR (2021)
Shuangjia Zheng, Jiahua Rao, Ying Song, Jixian Zhang, Xianglu Xiao, Evandro Fei Fang, Yuedong Yang, Zhangming Niu
PharmKG: a dedicated knowledge graph benchmark for bomedical data mining. Briefings Bioinform. 22 (4) (2021)
Jianwen Chen, Shuangjia Zheng, Huiying Zhao, Yuedong Yang
Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. J. Cheminformatics 13 (1) (2021)
Lizhao Hu, Yuyao Yang, Shuangjia Zheng, Jun Xu, Ting Ran, Hongming Chen
Kinase Inhibitor Scaffold Hopping with Deep Learning Approaches. J. Chem. Inf. Model. 61 (10) (2021)
Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu
Communicative Message Passing for Inductive Relation Reasoning. AAAI (2021)
Shuangjia Zheng, Ying Song, Zhang Pan, Chengtao Li, Le Song, Yuedong Yang
Molecular Attributes Transfer from Non-Parallel Data. CoRR (2021)
Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang
Learning Attributed Graph Representations with Communicative Message Passing Transformer. CoRR (2021)
Jianzhao Gao, Shuangjia Zheng, Mengting Yao, Peikun Wu
Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method. Bioinform. 38 (1) (2021)
Ying Song, Shuangjia Zheng, Liang Li, Xiang Zhang, Xiaodong Zhang, Ziwang Huang, Jianwen Chen, Ruixuan Wang, Huiying Zhao, Yutian Chong, Jun Shen, Yunfei Zha, Yuedong Yang
Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (6) (2021)
Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang
Deep scaffold hopping with multimodal transformer neural networks. J. Cheminformatics 13 (1) (2021)
Jiahao Wang, Shuangjia Zheng, Jianwen Chen, Yuedong Yang
Meta Learning for Low-Resource Molecular Optimization. J. Chem. Inf. Model. 61 (4) (2021)
Pan Zhang, Shuangjia Zheng, Jianwen Chen, Yaoqi Zhou, Yuedong Yang
DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. BIBM (2021)
Sijie Mai, Ying Zeng, Shuangjia Zheng, Haifeng Hu
Hybrid Contrastive Learning of Tri-Modal Representation for Multimodal Sentiment Analysis. CoRR (2021)
Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang, Ruibo Wu
BioNavi-NP: Biosynthesis Navigator for Natural Products. CoRR (2021)
Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang
Learning Attributed Graph Representation with Communicative Message Passing Transformer. IJCAI (2021)
Jiahua Rao, Shuangjia Zheng, Yuedong Yang
Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction. CoRR (2021)
Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu
Communicative Message Passing for Inductive Relation Reasoning. CoRR (2020)
Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang
Predicting drug-protein interaction using quasi-visual question answering system. Nat. Mach. Intell. 2 (2) (2020)
Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang
RetroXpert: Decompose Retrosynthesis Prediction like a Chemist. CoRR (2020)
Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang
Publisher Correction: Predicting drug-protein interaction using quasi-visual question answering system. Nat. Mach. Intell. 2 (9) (2020)
Ying Song, Shuangjia Zheng, Zhangming Niu, Zhang-Hua Fu, Yutong Lu, Yuedong Yang
Communicative Representation Learning on Attributed Molecular Graphs. IJCAI (2020)
Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang
Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. J. Chem. Inf. Model. 60 (1) (2020)
Shimin Su, Yuyao Yang, Hanlin Gan, Shuangjia Zheng, Fenglong Gu, Chao Zhao, Jun Xu
Predicting the Feasibility of Copper(I)-Catalyzed Alkyne-Azide Cycloaddition Reactions Using a Recurrent Neural Network with a Self-Attention Mechanism. J. Chem. Inf. Model. 60 (3) (2020)
Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang
RetroXpert: Decompose Retrosynthesis Prediction Like A Chemist. NeurIPS (2020)
Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang
Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks. CoRR (2019)
Shuangjia Zheng, Xin Yan, Yuedong Yang, Jun Xu
Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism. J. Chem. Inf. Model. 59 (2) (2019)
Shuangjia Zheng, Xin Yan, Qiong Gu, Yuedong Yang, Yunfei Du, Yutong Lu, Jun Xu
QBMG: quasi-biogenic molecule generator with deep recurrent neural network. J. Cheminformatics 11 (1) (2019)