Wen Zhang

According to our database, Wen Zhang authored at least 86 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Subgraph-Aware Graph Kernel Neural Network for Link Prediction in Biological Networks.

Menglu Li, Zhiwei Wang, Luotao Liu, Xuan Liu, Wen Zhang

IEEE J. Biomed. Health Informatics, July, 2024

DeepCRBP: improved predicting function of circRNA-RBP binding sites with deep feature learning.

Zishan Xu, Linlin Song, Shichao Liu, Wen Zhang

Frontiers Comput. Sci., April, 2024

A comprehensive review of molecular optimization in artificial intelligence-based drug discovery.

Yuhang Xia, Yongkang Wang, Zhiwei Wang, Wen Zhang

Quant. Biol., 2024

Deep learning for drug-drug interaction prediction: A comprehensive review.

Xinyue Li, Zhankun Xiong, Wen Zhang, Shichao Liu

Quant. Biol., 2024

ZeroDDI: A Zero-Shot Drug-Drug Interaction Event Prediction Method with Semantic Enhanced Learning and Dual-Modal Uniform Alignment.

Ziyan Wang, Zhankun Xiong, Feng Huang, Xuan Liu, Wen Zhang

CoRR, 2024

Heterogeneous Causal Metapath Graph Neural Network for Gene-Microbe-Disease Association Prediction.

Kexin Zhang, Feng Huang, Luotao Liu, Zhankun Xiong, Hongyu Zhang, Yuan Quan, Wen Zhang

CoRR, 2024

Coefficient Decomposition for Spectral Graph Convolution.

Feng Huang, Wen Zhang

CoRR, 2024

Improving PTM Site Prediction by Coupling of Multi-Granularity Structure and Multi-Scale Sequence Representation.

Zhengyi Li, Menglu Li, Lida Zhu, Wen Zhang

CoRR, 2024

A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation.

Yongkang Wang, Xuan Liu, Feng Huang, Zhankun Xiong, Wen Zhang

Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024

2023

HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction.

Shen Han, Haitao Fu, Yuyang Wu, Ganglan Zhao, Zhenyu Song, Feng Huang, Zhongfei Zhang, Shichao Liu, Wen Zhang

Briefings Bioinform., September, 2023

Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks.

Shichao Liu, Yang Zhang, Yuxin Cui, Yang Qiu, Yifan Deng, Zhongfei Zhang, Wen Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

DRLM: A Robust Drug Representation Learning Method and its Applications.

Haitao Fu, Cecheng Zhao, Xiaohui Niu, Wen Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

A subcomponent-guided deep learning method for interpretable cancer drug response prediction.

Xuan Liu, Wen Zhang

PLoS Comput. Biol., 2023

Multi-view Contrastive Learning Hypergraph Neural Network for Drug-Microbe-Disease Association Prediction.

Luotao Liu, Feng Huang, Xuan Liu, Zhankun Xiong, Menglu Li, Congzhi Song, Wen Zhang

Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence, 2023

Causal Intervention for Measuring Confidence in Drug-Target Interaction Prediction.

Wenting Ye, Chen Li, Yang Xie, Wen Zhang, Hong-Yu Zhang, Bowen Wang, Debo Cheng, Zaiwen Feng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

Multi-Relational Contrastive Learning Graph Neural Network for Drug-Drug Interaction Event Prediction.

Zhankun Xiong, Shichao Liu, Feng Huang, Ziyan Wang, Xuan Liu, Zhongfei Zhang, Wen Zhang

Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023

2022

Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction.

Xuan Liu, Congzhi Song, Shichao Liu, Menglu Li, Xionghui Zhou, Wen Zhang

Bioinform., October, 2022

A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs.

Zhankun Xiong, Feng Huang, Ziyan Wang, Shichao Liu, Wen Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

A Comprehensive Review of Computational Methods For Drug-Drug Interaction Detection.

Yang Qiu, Yang Zhang, Yifan Deng, Shichao Liu, Wen Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

EPIHC: Improving Enhancer-Promoter Interaction Prediction by Using Hybrid Features and Communicative Learning.

Shuai Liu, Xinran Xu, Zhihao Yang, Xiaohan Zhao, Shichao Liu, Wen Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Predicting Coding Potential of RNA Sequences by Solving Local Data Imbalance.

Xiangan Chen, Shuai Liu, Wen Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Hierarchical graph representation learning for the prediction of drug-target binding affinity.

Zhaoyang Chu, Feng Huang, Haitao Fu, Yuan Quan, Xionghui Zhou, Shichao Liu, Wen Zhang

Inf. Sci., 2022

Hierarchical Graph Representation Learning for the Prediction of Drug-Target Binding Affinity.

Zhaoyang Chu, Shichao Liu, Wen Zhang

CoRR, 2022

MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks.

Haitao Fu, Feng Huang, Xuan Liu, Yang Qiu, Wen Zhang

Bioinform., 2022

SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations.

Guangzhan Zhang, Menglu Li, Huan Deng, Xinran Xu, Xuan Liu, Wen Zhang

Briefings Bioinform., 2022

A heterogeneous network-based method with attentive meta-path extraction for predicting drug-target interactions.

Hongzhun Wang, Feng Huang, Zhankun Xiong, Wen Zhang

Briefings Bioinform., 2022

GraphCDR: a graph neural network method with contrastive learning for cancer drug response prediction.

Xuan Liu, Congzhi Song, Feng Huang, Haitao Fu, Wenjie Xiao, Wen Zhang

Briefings Bioinform., 2022

PHIAF: prediction of phage-host interactions with GAN-based data augmentation and sequence-based feature fusion.

Menglu Li, Wen Zhang

Briefings Bioinform., 2022

META-DDIE: predicting drug-drug interaction events with few-shot learning.

Yifan Deng, Yang Qiu, Xinran Xu, Shichao Liu, Zhongfei Zhang, Shanfeng Zhu, Wen Zhang

Briefings Bioinform., 2022

Predicting drug transcriptional response similarity using Signed Graph Convolutional Network.

Ziyan Wang, Chengzhi Hong, Xuan Liu, Zhankun Xiong, Feng Liu, Wen Zhang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

GMFQP: An Ontology-mediated Gut Microbiota Federated Query Platform.

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

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021

A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations.

Wen Zhang, Zhishuai Li, Wenzheng Guo, Weitai Yang, Feng Huang

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

A spatiotemporal estimation method for hourly rainfall based on F-SVD in the recommender system.

Hua Chen, Sheng Sheng, Chong-Yu Xu, Zhiyu Li, Wen Zhang, Shaowen Wang, Shenglian Guo

Environ. Model. Softw., 2021

HampDTI: a heterogeneous graph automatic meta-path learning method for drug-target interaction prediction.

Hongzhun Wang, Feng Huang, Wen Zhang

CoRR, 2021

Predicting drug-disease associations through layer attention graph convolutional network.

Zhouxin Yu, Feng Huang, Xiaohan Zhao, Wenjie Xiao, Wen Zhang

Briefings Bioinform., 2021

ADEIP: an integrated platform of age-dependent expression and immune profiles across human tissues.

Xuan Liu, Wenbo Chen, Yu Fang, Siqi Yang, Liuping Chang, Xingyu Chen, Haidong Ye, Xinyu Tang, Shan Zhong, Wen Zhang, Zhiqiang Dong, Leng Han, Chunjiang He

Briefings Bioinform., 2021

Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations.

Feng Huang, Xiang Yue, Zhankun Xiong, Zhouxin Yu, Shichao Liu, Wen Zhang

Briefings Bioinform., 2021

CSGNN: Contrastive Self-Supervised Graph Neural Network for Molecular Interaction Prediction.

Chengshuai Zhao, Shuai Liu, Feng Huang, Shichao Liu, Wen Zhang

Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, 2021

A Graph-based Approach for Integrating Biological Heterogeneous Data Based on Connecting Ontology.

Shilong Zhang, Yue Tang, Jing Yan, Linye Li, Tong Li, Jixiang Li, Peilin Xie, Yuanshuai Gu, Jiakang Xu, Zaiwen Feng, Wen Zhang, Jingbo Xia, Wolfgang Mayer, Hong-Yu Zhang, Guang-Cun He, Keqing He

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

Predicting Drug-miRNA Resistance with Layer Attention Graph Convolution Network and Multi Channel Feature Extraction.

Haorui Wang, Shahanavaj Khan, Shichao Liu, Fang Zheng, Wen Zhang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020

ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types.

Jiang Li, Yawen Xue, Muhammad Talal Amin, Yanbo Yang, Jiajun Yang, Wen Zhang, Wenqian Yang, Xiaohui Niu, Hong-Yu Zhang, Jing Gong

Nucleic Acids Res., 2020

Graph embedding and ensemble learning for predicting gene-disease associations.

Haorui Wang, Xiaochan Wang, Zhouxin Yu, Wen Zhang

Int. J. Data Min. Bioinform., 2020

Graph embedding on biomedical networks: methods, applications and evaluations.

Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun

Bioinform., 2020

A multimodal deep learning framework for predicting drug-drug interaction events.

Yifan Deng, Xinran Xu, Yang Qiu, Jingbo Xia, Wen Zhang, Shichao Liu

Bioinform., 2020

ItLnc-BXE: A Bagging-XGBoost-Ensemble Method With Comprehensive Sequence Features for Identification of Plant lncRNAs.

Guangyan Zhang, Ziru Liu, Jichen Dai, Zilan Yu, Shuai Liu, Wen Zhang

IEEE Access, 2020

2019

SFLLN: A sparse feature learning ensemble method with linear neighborhood regularization for predicting drug-drug interactions.

Wen Zhang, Kanghong Jing, Feng Huang, Yanlin Chen, Bolin Li, Jinghao Li, Jing Gong

Inf. Sci., 2019

Predicting microRNA-disease associations from knowledge graph using tensor decomposition with relational constraints.

Feng Huang, Zhankun Xiong, Guan Zhang, Zhouxin Yu, Xinran Xu, Wen Zhang

CoRR, 2019

PtLnc-BXE: Prediction of plant lncRNAs using a Bagging-XGBoost-ensemble method with multiple features.

Guangyan Zhang, Ziru Liu, Jichen Dai, Zilan Yu, Shuai Liu, Wen Zhang

CoRR, 2019

A network embedding-based multiple information integration method for the MiRNA-disease association prediction.

Yuchong Gong, Yanqing Niu, Wen Zhang, Xiaohong Li

BMC Bioinform., 2019

Predicting CircRNA-Disease Associations Through Linear Neighborhood Label Propagation Method.

Wen Zhang, Chenglin Yu, Xiaochan Wang, Feng Liu

IEEE Access, 2019

Efficient Network Representations Learning: An Edge-Centric Perspective.

Shichao Liu, Shuangfei Zhai, Lida Zhu, Fuxi Zhu, Zhongfei (Mark) Zhang, Wen Zhang

Proceedings of the Knowledge Science, Engineering and Management, 2019

LncRNA-miRNA interaction prediction from the heterogeneous network through graph embedding ensemble learning.

Shuang Zhou, Xiang Yue, Xinran Xu, Shichao Liu, Wen Zhang, Yanqing Niu

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

LncPred-IEL: A Long Non-coding RNA Prediction Method using Iterative Ensemble Learning.

Yanzhen Xu, Xiaohan Zhao, Shuai Liu, Shichao Liu, Yanqing Niu, Wen Zhang, Leyi Wei

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

Predicting gene-disease associations from the heterogeneous network using graph embedding.

Xiaochan Wang, Yuchong Gong, Jing Yi, Wen Zhang

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

Detection of Cell Types from Single-cell RNA-seq Data using Similarity via Kernel Preserving Learning Embedding.

Zeming Liu, Feng Liu, Chengzhi Hong, Meng Gao, Yi-Ping Phoebe Chen, Shichao Liu, Wen Zhang

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

Structural Network Embedding using Multi-modal Deep Auto-encoders for Predicting Drug-drug Interactions.

Shichao Liu, Ziyang Huang, Yang Qiu, Yi-Ping Phoebe Chen, Wen Zhang

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions.

Wen Zhang, Xiang Yue, Guifeng Tang, Wenjian Wu, Feng Huang, Xining Zhang

PLoS Comput. Biol., 2018

Manifold regularized matrix factorization for drug-drug interaction prediction.

Wen Zhang, Yanlin Chen, Dingfang Li, Xiang Yue

J. Biomed. Informatics, 2018

The linear neighborhood propagation method for predicting long non-coding RNA-protein interactions.

Wen Zhang, Qianlong Qu, Yunqiu Zhang, Wei Wang

Neurocomputing, 2018

Feature-derived graph regularized matrix factorization for predicting drug side effects.

Wen Zhang, Xinrui Liu, Yanlin Chen, Wenjian Wu, Wei Wang, Xiaohong Li

Neurocomputing, 2018

Predicting drug-disease associations by using similarity constrained matrix factorization.

Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang, Feng Liu

BMC Bioinform., 2018

Sequence-based bacterial small RNAs prediction using ensemble learning strategies.

Guifeng Tang, Jingwen Shi, Wenjian Wu, Xiang Yue, Wen Zhang

BMC Bioinform., 2018

The Bi-Direction Similarity Integration Method for Predicting Microbe-Disease Associations.

Wen Zhang, Weitai Yang, Xiaoting Lu, Feng Huang, Fei Luo

IEEE Access, 2018

Sequence-derived linear neighborhood propagation method for predicting lncRNA-miRNA interactions.

Wen Zhang, Guifeng Tang, Siman Wang, Yanlin Chen, Shuang Zhou, Xiaohong Li

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Prediction of Drug-Disease Associations and Their Effects by Signed Network-Based Nonnegative Matrix Factorization.

Wen Zhang, Feng Huang, Xiang Yue, Xiaoting Lu, Weitai Yang, Zhishuai Li, Feng Liu

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

HNGRNMF: Heterogeneous Network-based Graph Regularized Nonnegative Matrix Factorization for predicting events of microbe-disease associations.

Wen Zhang, Xiaoting Lu, Weitai Yang, Feng Huang, Binlu Wang, Alan Wang, Qi Zhao

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017

A unified frame of predicting side effects of drugs by using linear neighborhood similarity.

Wen Zhang, Xiang Yue, Feng Liu, Yanlin Chen, Shikui Tu, Xining Zhang

BMC Syst. Biol., 2017

Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods.

Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng

BMC Bioinform., 2017

Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data.

Wen Zhang, Yanlin Chen, Feng Liu, Fei Luo, Gang Tian, Xiaohong Li

BMC Bioinform., 2017

Predicting drug-disease associations based on the known association bipartite network.

Wen Zhang, Xiang Yue, Yanlin Chen, Weiran Lin, Bolin Li, Feng Liu, Xiaohong Li

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

Predicting small RNAs in bacteria via sequence learning ensemble method.

Wen Zhang, Jingwen Shi, Guifeng Tang, Wenjian Wu, Xiang Yue, Dingfang Li

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016

Predicting potential side effects of drugs by recommender methods and ensemble learning.

Wen Zhang, Hua Zou, Longqiang Luo, Qianchao Liu, Weijian Wu, Wenyi Xiao

Neurocomputing, 2016

A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs.

Dingfang Li, Longqiang Luo, Wen Zhang, Feng Liu, Fei Luo

BMC Bioinform., 2016

Multi-Domain Manifold Learning for Drug-Target Interaction Prediction.

Ruichu Cai, Zhenjie Zhang, Srinivasan Parthasarathy, Anthony K. H. Tung, Zhifeng Hao, Wen Zhang

Proceedings of the 2016 SIAM International Conference on Data Mining, 2016

The prediction of human splicing branchpoints by multi-label learning.

Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Drug side effect prediction through linear neighborhoods and multiple data source integration.

Wen Zhang, Yanlin Chen, Shikui Tu, Feng Liu, Qianlong Qu

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

Predicting drug side effects by multi-label learning and ensemble learning.

Wen Zhang, Feng Liu, Longqiang Luo, Jingxia Zhang

BMC Bioinform., 2015

2013

Predicting immunogenic T-cell epitopes by combining various sequence-derived features.

Wen Zhang, Juan Liu, Yi Xiong, Meng Ke, Ke Zhang

Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2012

Predicting linear B-cell epitopes by using sequence-derived structural and physicochemical features.

Wen Zhang, Juan Liu, Meng Zhao, Qingjiao Li

Int. J. Data Min. Bioinform., 2012

2011

Prediction of conformational B-cell epitopes from 3D structures by random forest with a distance-based feature.

Wen Zhang, Yi Xiong, Meng Zhao, Hua Zou, Xinghuo Ye, Juan Liu

BMC Bioinform., 2011

Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties.

Yi Xiong, Wen Zhang, Tao Zeng, Juan Liu

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2010

Quantitative prediction of MHC-II binding affinity using particle swarm optimization.

Wen Zhang, Juan Liu, Yanqing Niu

Artif. Intell. Medicine, 2010

2009

Quantitative prediction of MHC-II peptide binding affinity using relevance vector machine.

Wen Zhang, Juan Liu, Yanqing Niu

Appl. Intell., 2009

2008

A Bayesian regression approach to the prediction of MHC-II binding affinity.

Wen Zhang, Juan Liu, Yanqing Niu, Lian Wang, Xihao Hu

Comput. Methods Programs Biomed., 2008

Quantitative Prediction of MHC-II Peptide Binding Affinity Using Global Description of Peptide Sequences.

Wen Zhang, Juan Liu, Yanqing Niu, Lian Wang, Zhi Zhang

Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics, 2008

2006

Gene Selection Using Rough Set Theory.

Dingfang Li, Wen Zhang

Proceedings of the Rough Sets and Knowledge Technology, First International Conference, 2006