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2020 – today
- 2024
[j24]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): 1945-1954 (2024)- [c9]Mei Li, Xiaoguang Liu, Hua Ji, Shuangjia Zheng:
Causal Subgraph Learning for Generalizable Inductive Relation Prediction. KDD 2024: 1610-1620 - [i15]Chenqing Hua, Connor W. Coley, Guy Wolf, Doina Precup, Shuangjia Zheng:
Effective Protein-Protein Interaction Exploration with PPIretrieval. CoRR abs/2402.03675 (2024) - [i14]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 abs/2402.04710 (2024) - [i13]Chenqing Hua, Bozitao Zhong, Sitao Luan, Liang Hong, Guy Wolf, Doina Precup, Shuangjia Zheng:
Reactzyme: A Benchmark for Enzyme-Reaction Prediction. CoRR abs/2408.13659 (2024) - [i12]Chenqing Hua, Yong Liu, Dinghuai Zhang, Odin Zhang, Sitao Luan, Kevin K. Yang, Guy Wolf, Doina Precup, Shuangjia Zheng:
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics. CoRR abs/2410.00327 (2024) - 2023
- [j23]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): 2276-2289 (2023) - [j22]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): 6512-6517 (2023) - [c8]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: 120-123 - [i11]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 abs/2308.15116 (2023) - 2022
- [j21]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) - [j20]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): 1308-1317 (2022) - [j19]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): 5907-5917 (2022) - [j18]Sijie Mai, Shuangjia Zheng, Ya Sun, Ying Zeng, Yuedong Yang, Haifeng Hu:
Dynamic graph dropout for subgraph-based relation prediction. Knowl. Based Syst. 250: 109172 (2022) - [j17]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): 739-748 (2022) - [j16]Jiahua Rao, Shuangjia Zheng, Yutong Lu, Yuedong Yang:
Quantitative evaluation of explainable graph neural networks for molecular property prediction. Patterns 3(12): 100628 (2022) - [j15]Jiahua Rao, Shuangjia Zheng, Yuedong Yang:
Integrating supercomputing and artificial intelligence for life science. Patterns 3(12): 100653 (2022) - [j14]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): 3735-3743 (2022) - [c7]Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang:
Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. IJCAI 2022: 3919-3925 - [c6]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 - [i10]Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang:
Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. CoRR abs/2205.05957 (2022) - 2021
- [j13]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) - [j12]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): 94-98 (2021) - [j11]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): 7 (2021) - [j10]Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang:
Deep scaffold hopping with multimodal transformer neural networks. J. Cheminformatics 13(1): 87 (2021) - [j9]Jiahao Wang, Shuangjia Zheng, Jianwen Chen, Yuedong Yang:
Meta Learning for Low-Resource Molecular Optimization. J. Chem. Inf. Model. 61(4): 1627-1636 (2021) - [j8]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): 4900-4912 (2021) - [j7]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): 2775-2780 (2021) - [c5]Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu:
Communicative Message Passing for Inductive Relation Reasoning. AAAI 2021: 4294-4302 - [c4]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: 118-124 - [c3]Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang:
Learning Attributed Graph Representation with Communicative Message Passing Transformer. IJCAI 2021: 2242-2248 - [i9]Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang, Ruibo Wu:
BioNavi-NP: Biosynthesis Navigator for Natural Products. CoRR abs/2105.13121 (2021) - [i8]Jiahua Rao, Shuangjia Zheng, Yuedong Yang:
Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction. CoRR abs/2107.04119 (2021) - [i7]Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang:
Learning Attributed Graph Representations with Communicative Message Passing Transformer. CoRR abs/2107.08773 (2021) - [i6]Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang:
Subgraph-aware Few-Shot Inductive Link Prediction via Meta-Learning. CoRR abs/2108.00954 (2021) - [i5]Sijie Mai, Ying Zeng, Shuangjia Zheng, Haifeng Hu:
Hybrid Contrastive Learning of Tri-Modal Representation for Multimodal Sentiment Analysis. CoRR abs/2109.01797 (2021) - [i4]Shuangjia Zheng, Ying Song, Zhang Pan, Chengtao Li, Le Song, Yuedong Yang:
Molecular Attributes Transfer from Non-Parallel Data. CoRR abs/2111.15146 (2021) - 2020
- [j6]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): 47-55 (2020) - [j5]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): 1165-1174 (2020) - [j4]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): 134-140 (2020) - [j3]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): 551 (2020) - [c2]Ying Song, Shuangjia Zheng, Zhangming Niu, Zhang-Hua Fu, Yutong Lu, Yuedong Yang:
Communicative Representation Learning on Attributed Molecular Graphs. IJCAI 2020: 2831-2838 - [c1]Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang:
RetroXpert: Decompose Retrosynthesis Prediction Like A Chemist. NeurIPS 2020 - [i3]Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang:
RetroXpert: Decompose Retrosynthesis Prediction like a Chemist. CoRR abs/2011.02893 (2020) - [i2]Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu:
Communicative Message Passing for Inductive Relation Reasoning. CoRR abs/2012.08911 (2020)
2010 – 2019
- 2019
- [j2]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): 5:1-5:12 (2019) - [j1]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): 914-923 (2019) - [i1]Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang:
Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks. CoRR abs/1907.01356 (2019)
Coauthor Index
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last updated on 2024-11-06 21:36 CET by the dblp team
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