Wen Zhang

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 48

Top Topics

Matrix Factorization

Graph Embedding

Computational Methods

Ensemble Learning

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Zhengyi Li, Menglu Li, Lida Zhu, Wen Zhang
Improving PTM Site Prediction by Coupling of Multi-Granularity Structure and Multi-Scale Sequence Representation. CoRR (2024)
Xinyue Li, Zhankun Xiong, Wen Zhang, Shichao Liu
Deep learning for drug-drug interaction prediction: A comprehensive review. Quant. Biol. 12 (1) (2024)
Menglu Li, Zhiwei Wang, Luotao Liu, Xuan Liu, Wen Zhang
Subgraph-Aware Graph Kernel Neural Network for Link Prediction in Biological Networks. IEEE J. Biomed. Health Informatics 28 (7) (2024)
Feng Huang, Wen Zhang
Coefficient Decomposition for Spectral Graph Convolution. CoRR (2024)
Ziyan Wang, Zhankun Xiong, Feng Huang, Xuan Liu, Wen Zhang
ZeroDDI: A Zero-Shot Drug-Drug Interaction Event Prediction Method with Semantic Enhanced Learning and Dual-Modal Uniform Alignment. CoRR (2024)
Kexin Zhang, Feng Huang, Luotao Liu, Zhankun Xiong, Hongyu Zhang, Yuan Quan, Wen Zhang
Heterogeneous Causal Metapath Graph Neural Network for Gene-Microbe-Disease Association Prediction. CoRR (2024)
Yuhang Xia, Yongkang Wang, Zhiwei Wang, Wen Zhang
A comprehensive review of molecular optimization in artificial intelligence-based drug discovery. Quant. Biol. 12 (1) (2024)
Yongkang Wang, Xuan Liu, Feng Huang, Zhankun Xiong, Wen Zhang
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation. AAAI (2024)
Shichao Liu, Yang Zhang, Yuxin Cui, Yang Qiu, Yifan Deng, Zhongfei Zhang, Wen Zhang
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (2) (2023)
Shen Han, Haitao Fu, Yuyang Wu, Ganglan Zhao, Zhenyu Song, Feng Huang, Zhongfei Zhang, Shichao Liu, Wen Zhang
HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction. Briefings Bioinform. 24 (5) (2023)
Xuan Liu, Wen Zhang
A subcomponent-guided deep learning method for interpretable cancer drug response prediction. PLoS Comput. Biol. 19 (8) (2023)
Haitao Fu, Cecheng Zhao, Xiaohui Niu, Wen Zhang
DRLM: A Robust Drug Representation Learning Method and its Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Yifan Deng, Yang Qiu, Xinran Xu, Shichao Liu, Zhongfei Zhang, Shanfeng Zhu, Wen Zhang
META-DDIE: predicting drug-drug interaction events with few-shot learning. Briefings Bioinform. 23 (1) (2022)
Zhaoyang Chu, Feng Huang, Haitao Fu, Yuan Quan, Xionghui Zhou, Shichao Liu, Wen Zhang
Hierarchical graph representation learning for the prediction of drug-target binding affinity. Inf. Sci. 613 (2022)
Ziyan Wang, Chengzhi Hong, Xuan Liu, Zhankun Xiong, Feng Liu, Wen Zhang
Predicting drug transcriptional response similarity using Signed Graph Convolutional Network. BIBM (2022)
Zhaoyang Chu, Shichao Liu, Wen Zhang
Hierarchical Graph Representation Learning for the Prediction of Drug-Target Binding Affinity. CoRR (2022)
Xuan Liu, Congzhi Song, Shichao Liu, Menglu Li, Xionghui Zhou, Wen Zhang
Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction. Bioinform. 38 (20) (2022)
Shuai Liu, Xinran Xu, Zhihao Yang, Xiaohan Zhao, Shichao Liu, Wen Zhang
EPIHC: Improving Enhancer-Promoter Interaction Prediction by Using Hybrid Features and Communicative Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Zhankun Xiong, Feng Huang, Ziyan Wang, Shichao Liu, Wen Zhang
A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (5) (2022)
Yang Qiu, Yang Zhang, Yifan Deng, Shichao Liu, Wen Zhang
A Comprehensive Review of Computational Methods For Drug-Drug Interaction Detection. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (4) (2022)
Yuzhuo Dai, Shilong Zhang, Yue Tang, Wolfgang Mayer, Jixiang Li, Hongyu Li, Zhonghao Zhang, Haiqin Li, Ying Wang, Wen Zhang, Qin Jiang, Hong-Yu Zhang, Bing Li, Zaiwen Feng
GMFQP: An Ontology-mediated Gut Microbiota Federated Query Platform. BIBM (2022)
Guangzhan Zhang, Menglu Li, Huan Deng, Xinran Xu, Xuan Liu, Wen Zhang
SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations. Briefings Bioinform. 23 (1) (2022)
Xiangan Chen, Shuai Liu, Wen Zhang
Predicting Coding Potential of RNA Sequences by Solving Local Data Imbalance. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (2) (2022)
Wen Zhang, Zhishuai Li, Wenzheng Guo, Weitai Yang, Feng Huang
A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (2) (2021)
Feng Huang, Xiang Yue, Zhankun Xiong, Zhouxin Yu, Shichao Liu, Wen Zhang
Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations. Briefings Bioinform. 22 (3) (2021)
Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun
Graph embedding on biomedical networks: methods, applications and evaluations. Bioinform. 36 (4) (2020)
Yuchong Gong, Yanqing Niu, Wen Zhang, Xiaohong Li
A network embedding-based multiple information integration method for the MiRNA-disease association prediction. BMC Bioinform. 20 (1) (2019)
Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun
Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations. CoRR (2019)
Shuang Zhou, Xiang Yue, Xinran Xu, Shichao Liu, Wen Zhang, Yanqing Niu
LncRNA-miRNA interaction prediction from the heterogeneous network through graph embedding ensemble learning. BIBM (2019)
Wen Zhang, Kanghong Jing, Feng Huang, Yanlin Chen, Bolin Li, Jinghao Li, Jing Gong
SFLLN: A sparse feature learning ensemble method with linear neighborhood regularization for predicting drug-drug interactions. Inf. Sci. 497 (2019)
Feng Huang, Zhankun Xiong, Guan Zhang, Zhouxin Yu, Xinran Xu, Wen Zhang
Predicting microRNA-disease associations from knowledge graph using tensor decomposition with relational constraints. CoRR (2019)
Wen Zhang, Yanlin Chen, Dingfang Li, Xiang Yue
Manifold regularized matrix factorization for drug-drug interaction prediction. J. Biomed. Informatics 88 (2018)
Wen Zhang, Guifeng Tang, Siman Wang, Yanlin Chen, Shuang Zhou, Xiaohong Li
Sequence-derived linear neighborhood propagation method for predicting lncRNA-miRNA interactions. BIBM (2018)
Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang, Feng Liu
Predicting drug-disease associations by using similarity constrained matrix factorization. BMC Bioinform. 19 (1) (2018)
Wen Zhang, Qianlong Qu, Yunqiu Zhang, Wei Wang
The linear neighborhood propagation method for predicting long non-coding RNA-protein interactions. Neurocomputing 273 (2018)
Wen Zhang, Xinrui Liu, Yanlin Chen, Wenjian Wu, Wei Wang, Xiaohong Li
Feature-derived graph regularized matrix factorization for predicting drug side effects. Neurocomputing 287 (2018)
Wen Zhang, Weitai Yang, Xiaoting Lu, Feng Huang, Fei Luo
The Bi-Direction Similarity Integration Method for Predicting Microbe-Disease Associations. IEEE Access 6 (2018)
Guifeng Tang, Jingwen Shi, Wenjian Wu, Xiang Yue, Wen Zhang
Sequence-based bacterial small RNAs prediction using ensemble learning strategies. BMC Bioinform. (20) (2018)
Wen Zhang, Feng Huang, Xiang Yue, Xiaoting Lu, Weitai Yang, Zhishuai Li, Feng Liu
Prediction of Drug-Disease Associations and Their Effects by Signed Network-Based Nonnegative Matrix Factorization. BIBM (2018)
Wen Zhang, Xiaoting Lu, Weitai Yang, Feng Huang, Binlu Wang, Alan Wang, Qi Zhao
HNGRNMF: Heterogeneous Network-based Graph Regularized Nonnegative Matrix Factorization for predicting events of microbe-disease associations. BIBM (2018)
Wen Zhang, Xiang Yue, Guifeng Tang, Wenjian Wu, Feng Huang, Xining Zhang
SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions. PLoS Comput. Biol. 14 (12) (2018)
Wen Zhang, Yanlin Chen, Feng Liu, Fei Luo, Gang Tian, Xiaohong Li
Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data. BMC Bioinform. 18 (1) (2017)
Wen Zhang, Xiang Yue, Yanlin Chen, Weiran Lin, Bolin Li, Feng Liu, Xiaohong Li
Predicting drug-disease associations based on the known association bipartite network. BIBM (2017)
Wen Zhang, Xiang Yue, Feng Liu, Yanlin Chen, Shikui Tu, Xining Zhang
A unified frame of predicting side effects of drugs by using linear neighborhood similarity. BMC Syst. Biol. 11 (6) (2017)
Wen Zhang, Jingwen Shi, Guifeng Tang, Wenjian Wu, Xiang Yue, Dingfang Li
Predicting small RNAs in bacteria via sequence learning ensemble method. BIBM (2017)
Dingfang Li, Longqiang Luo, Wen Zhang, Feng Liu, Fei Luo
A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs. BMC Bioinform. 17 (2016)
Wen Zhang, Hua Zou, Longqiang Luo, Qianchao Liu, Weijian Wu, Wenyi Xiao
Predicting potential side effects of drugs by recommender methods and ensemble learning. Neurocomputing 173 (2016)
Wen Zhang, Yanlin Chen, Shikui Tu, Feng Liu, Qianlong Qu
Drug side effect prediction through linear neighborhoods and multiple data source integration. BIBM (2016)
Wen Zhang, Feng Liu, Longqiang Luo, Jingxia Zhang
Predicting drug side effects by multi-label learning and ensemble learning. BMC Bioinform. 16 (2015)
Dingfang Li, Wen Zhang
Gene Selection Using Rough Set Theory. RSKT (2006)