Wen Zhang

99 papers A* 7A 2Journal 66Unranked 24
YearRankTypeTitle / Venue / Authors
2025 J jnl
3A Multi-Classification Division-Aggregation Framework for Fake News Detection.
IEEE Trans. Big Data
Wen Zhang, Haitao Fu, Huan Wang, Zhiguo Gong, Pan Zhou, Di Wang
2025 — conf
Enhancing Drug-Drug Interaction Prediction via Drug-Centric Hierarchical Augmentation.
BIBM
Ziwen Cui, Muhammad Asif Ali, Huan Wang, Ruigang Liu, Wen Zhang, Di Wang
2025 J jnl
GNNDRP: Graph Neural Network With Multi-Task Learning for Drug Response Prediction.
IEEE Trans. Comput. Biol. Bioinform.
Congzhi Song, Xuan Liu, Zhankun Xiong, Luotao Liu, Wen Zhang
2025 A conf
Geometric Heterogeneous Graph Neural Network for Protein-Ligand Binding Affinity Prediction.
CIKM
Feng Huang, Yuhang Xia, Ziyan Wang, Liuqing Yang, Wen Zhang
2025 J jnl
Guest Editorial: The Cutting-Edge Artificial Intelligence Techniques and Their Applications in Drug Discovery.
IEEE J. Biomed. Health Informatics
Wen Zhang, Qi Zhao, Yuru wang
2025 — conf
PKAG-DDI: Pairwise Knowledge-Augmented Language Model for Drug-Drug Interaction Event Text Generation.
ACL (1)
Ziyan Wang, Zhankun Xiong, Feng Huang, Wen Zhang
2024 A* conf
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation.
AAAI
Yongkang Wang, Xuan Liu, Feng Huang, Zhankun Xiong, Wen Zhang
2024 J jnl
A Network Enhancement Method to Identify Spurious Drug-Drug Interactions.
IEEE ACM Trans. Comput. Biol. Bioinform.
Huan Wang, Ziwen Cui, Yinguang Yang, Baijing Wang, Lida Zhu, Wen Zhang
2024 J jnl
A comprehensive review of molecular optimization in artificial intelligence-based drug discovery.
Quant. Biol.
Yuhang Xia, Yongkang Wang, Zhiwei Wang, Wen Zhang
2024 J jnl
A multi-stream network for retrosynthesis prediction.
Frontiers Comput. Sci.
Qiang Zhang, Juan Liu, Wen Zhang, Feng Yang, Zhihui Yang, Xiaolei Zhang
2024 J jnl
Coefficient Decomposition for Spectral Graph Convolution.
CoRR
Feng Huang, Wen Zhang
2024 J jnl
Deep learning for drug-drug interaction prediction: A comprehensive review.
Quant. Biol.
Xinyue Li, Zhankun Xiong, Wen Zhang, Shichao Liu
2024 J jnl
DeepCRBP: improved predicting function of circRNA-RBP binding sites with deep feature learning.
Frontiers Comput. Sci.
Zishan Xu, Linlin Song, Shichao Liu, Wen Zhang
2024 A* conf
Heterogeneous Causal Metapath Graph Neural Network for Gene-Microbe-Disease Association Prediction.
IJCAI
Kexin Zhang, Feng Huang, Luotao Liu, Zhankun Xiong, Hongyu Zhang, Yuan Quan, Wen Zhang
2024 J jnl
Heterogeneous Causal Metapath Graph Neural Network for Gene-Microbe-Disease Association Prediction.
CoRR
Kexin Zhang, Feng Huang, Luotao Liu, Zhankun Xiong, Hongyu Zhang, Yuan Quan, Wen Zhang
2024 J jnl
Improving PTM Site Prediction by Coupling of Multi-Granularity Structure and Multi-Scale Sequence Representation.
CoRR
Zhengyi Li, Menglu Li, Lida Zhu, Wen Zhang
2024 A* conf
Improving Paratope and Epitope Prediction by Multi-Modal Contrastive Learning and Interaction Informativeness Estimation.
IJCAI
Zhiwei Wang, Yongkang Wang, Wen Zhang
2024 J jnl
Subgraph-Aware Graph Kernel Neural Network for Link Prediction in Biological Networks.
IEEE J. Biomed. Health Informatics
Menglu Li, Zhiwei Wang, Luotao Liu, Xuan Liu, Wen Zhang
2024 J jnl
ZeroDDI: A Zero-Shot Drug-Drug Interaction Event Prediction Method with Semantic Enhanced Learning and Dual-Modal Uniform Alignment.
CoRR
Ziyan Wang, Zhankun Xiong, Feng Huang, Xuan Liu, Wen Zhang
2024 A* conf
ZeroDDI: A Zero-Shot Drug-Drug Interaction Event Prediction Method with Semantic Enhanced Learning and Dual-modal Uniform Alignment.
IJCAI
Ziyan Wang, Zhankun Xiong, Feng Huang, Xuan Liu, Wen Zhang
2023 J jnl
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation.
CoRR
Yongkang Wang, Xuan Liu, Feng Huang, Zhankun Xiong, Wen Zhang
2023 J jnl
A subcomponent-guided deep learning method for interpretable cancer drug response prediction.
PLoS Comput. Biol.
Xuan Liu, Wen Zhang
2023 — conf
Causal Intervention for Measuring Confidence in Drug-Target Interaction Prediction.
BIBM
Wenting Ye, Chen Li, Yang Xie, Wen Zhang, Hong-Yu Zhang, Bowen Wang, Debo Cheng, Zaiwen Feng
2023 J jnl
DRLM: A Robust Drug Representation Learning Method and its Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Haitao Fu, Cecheng Zhao, Xiaohui Niu, Wen Zhang
2023 J jnl
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shichao Liu, Yang Zhang, Yuxin Cui, Yang Qiu, Yifan Deng, Zhongfei Zhang, Wen Zhang
2023 J jnl
HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction.
Briefings Bioinform.
Shen Han, Haitao Fu, Yuyang Wu, Ganglan Zhao, Zhenyu Song, Feng Huang, Zhongfei Zhang, Shichao Liu, Wen Zhang
2023 A* conf
Multi-Relational Contrastive Learning Graph Neural Network for Drug-Drug Interaction Event Prediction.
AAAI
Zhankun Xiong, Shichao Liu, Feng Huang, Ziyan Wang, Xuan Liu, Zhongfei Zhang, Wen Zhang
2023 A* conf
Multi-view Contrastive Learning Hypergraph Neural Network for Drug-Microbe-Disease Association Prediction.
IJCAI
Luotao Liu, Feng Huang, Xuan Liu, Zhankun Xiong, Menglu Li, Congzhi Song, Wen Zhang
2022 J jnl
A Comprehensive Review of Computational Methods For Drug-Drug Interaction Detection.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yang Qiu, Yang Zhang, Yifan Deng, Shichao Liu, Wen Zhang
2022 J jnl
A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zhankun Xiong, Feng Huang, Ziyan Wang, Shichao Liu, Wen Zhang
2022 J jnl
A heterogeneous network-based method with attentive meta-path extraction for predicting drug-target interactions.
Briefings Bioinform.
Hongzhun Wang, Feng Huang, Zhankun Xiong, Wen Zhang
2022 J jnl
EPIHC: Improving Enhancer-Promoter Interaction Prediction by Using Hybrid Features and Communicative Learning.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuai Liu, Xinran Xu, Zhihao Yang, Xiaohan Zhao, Shichao Liu, Wen Zhang
2022 — conf
GMFQP: An Ontology-mediated Gut Microbiota Federated Query Platform.
BIBM
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
2022 J jnl
GraphCDR: a graph neural network method with contrastive learning for cancer drug response prediction.
Briefings Bioinform.
Xuan Liu, Congzhi Song, Feng Huang, Haitao Fu, Wenjie Xiao, Wen Zhang
2022 J jnl
Hierarchical Graph Representation Learning for the Prediction of Drug-Target Binding Affinity.
CoRR
Zhaoyang Chu, Shichao Liu, Wen Zhang
2022 J jnl
Hierarchical graph representation learning for the prediction of drug-target binding affinity.
Inf. Sci.
Zhaoyang Chu, Feng Huang, Haitao Fu, Yuan Quan, Xionghui Zhou, Shichao Liu, Wen Zhang
2022 J jnl
META-DDIE: predicting drug-drug interaction events with few-shot learning.
Briefings Bioinform.
Yifan Deng, Yang Qiu, Xinran Xu, Shichao Liu, Zhongfei Zhang, Shanfeng Zhu, Wen Zhang
2022 J jnl
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks.
Bioinform.
Haitao Fu, Feng Huang, Xuan Liu, Yang Qiu, Wen Zhang
2022 J jnl
Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction.
Bioinform.
Xuan Liu, Congzhi Song, Shichao Liu, Menglu Li, Xionghui Zhou, Wen Zhang
2022 J jnl
PHIAF: prediction of phage-host interactions with GAN-based data augmentation and sequence-based feature fusion.
Briefings Bioinform.
Menglu Li, Wen Zhang
2022 J jnl
Predicting Coding Potential of RNA Sequences by Solving Local Data Imbalance.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiangan Chen, Shuai Liu, Wen Zhang
2022 — conf
Predicting drug transcriptional response similarity using Signed Graph Convolutional Network.
BIBM
Ziyan Wang, Chengzhi Hong, Xuan Liu, Zhankun Xiong, Feng Liu, Wen Zhang
2022 J jnl
SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations.
Briefings Bioinform.
Guangzhan Zhang, Menglu Li, Huan Deng, Xinran Xu, Xuan Liu, Wen Zhang
2021 J jnl
A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations.
IEEE ACM Trans. Comput. Biol. Bioinform.
Wen Zhang, Zhishuai Li, Wenzheng Guo, Weitai Yang, Feng Huang
2021 — conf
A Graph-based Approach for Integrating Biological Heterogeneous Data Based on Connecting Ontology.
BIBM
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
2021 J jnl
A spatiotemporal estimation method for hourly rainfall based on F-SVD in the recommender system.
Environ. Model. Softw.
Hua Chen, Sheng Sheng, Chong-Yu Xu, Zhiyu Li, Wen Zhang, Shaowen Wang, Shenglian Guo
2021 J jnl
ADEIP: an integrated platform of age-dependent expression and immune profiles across human tissues.
Briefings Bioinform.
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
2021 A* conf
CSGNN: Contrastive Self-Supervised Graph Neural Network for Molecular Interaction Prediction.
IJCAI
Chengshuai Zhao, Shuai Liu, Feng Huang, Shichao Liu, Wen Zhang
2021 J jnl
HampDTI: a heterogeneous graph automatic meta-path learning method for drug-target interaction prediction.
CoRR
Hongzhun Wang, Feng Huang, Wen Zhang
2021 — conf
Predicting Drug-miRNA Resistance with Layer Attention Graph Convolution Network and Multi Channel Feature Extraction.
BIBM
Haorui Wang, Shahanavaj Khan, Shichao Liu, Fang Zheng, Wen Zhang
2021 J jnl
Predicting drug-disease associations through layer attention graph convolutional network.
Briefings Bioinform.
Zhouxin Yu, Feng Huang, Xiaohan Zhao, Wenjie Xiao, Wen Zhang
2021 J jnl
Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations.
Briefings Bioinform.
Feng Huang, Xiang Yue, Zhankun Xiong, Zhouxin Yu, Shichao Liu, Wen Zhang
2020 J jnl
A multimodal deep learning framework for predicting drug-drug interaction events.
Bioinform.
Yifan Deng, Xinran Xu, Yang Qiu, Jingbo Xia, Wen Zhang, Shichao Liu
2020 J jnl
Graph embedding and ensemble learning for predicting gene-disease associations.
Int. J. Data Min. Bioinform.
Haorui Wang, Xiaochan Wang, Zhouxin Yu, Wen Zhang
2020 J jnl
Graph embedding on biomedical networks: methods, applications and evaluations.
Bioinform.
Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun
2020 J jnl
ItLnc-BXE: A Bagging-XGBoost-Ensemble Method With Comprehensive Sequence Features for Identification of Plant lncRNAs.
IEEE Access
Guangyan Zhang, Ziru Liu, Jichen Dai, Zilan Yu, Shuai Liu, Wen Zhang
2020 J jnl
ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types.
Nucleic Acids Res.
Jiang Li, Yawen Xue, Muhammad Talal Amin, Yanbo Yang, Jiajun Yang, Wen Zhang, Wenqian Yang, Xiaohui Niu, Hong-Yu Zhang, Jing Gong
2019 J jnl
A network embedding-based multiple information integration method for the MiRNA-disease association prediction.
BMC Bioinform.
Yuchong Gong, Yanqing Niu, Wen Zhang, Xiaohong Li
2019 — conf
Detection of Cell Types from Single-cell RNA-seq Data using Similarity via Kernel Preserving Learning Embedding.
BIBM
Zeming Liu, Feng Liu, Chengzhi Hong, Meng Gao, Yi-Ping Phoebe Chen, Shichao Liu, Wen Zhang
2019 — conf
Efficient Network Representations Learning: An Edge-Centric Perspective.
KSEM (2)
Shichao Liu, Shuangfei Zhai, Lida Zhu, Fuxi Zhu, Zhongfei (Mark) Zhang, Wen Zhang
2019 J jnl
Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations.
CoRR
Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun
2019 — conf
LncPred-IEL: A Long Non-coding RNA Prediction Method using Iterative Ensemble Learning.
BIBM
Yanzhen Xu, Xiaohan Zhao, Shuai Liu, Shichao Liu, Yanqing Niu, Wen Zhang, Leyi Wei
2019 — conf
LncRNA-miRNA interaction prediction from the heterogeneous network through graph embedding ensemble learning.
BIBM
Shuang Zhou, Xiang Yue, Xinran Xu, Shichao Liu, Wen Zhang, Yanqing Niu
2019 J jnl
Predicting CircRNA-Disease Associations Through Linear Neighborhood Label Propagation Method.
IEEE Access
Wen Zhang, Chenglin Yu, Xiaochan Wang, Feng Liu
2019 — conf
Predicting gene-disease associations from the heterogeneous network using graph embedding.
BIBM
Xiaochan Wang, Yuchong Gong, Jing Yi, Wen Zhang
2019 J jnl
Predicting microRNA-disease associations from knowledge graph using tensor decomposition with relational constraints.
CoRR
Feng Huang, Zhankun Xiong, Guan Zhang, Zhouxin Yu, Xinran Xu, Wen Zhang
2019 J jnl
PtLnc-BXE: Prediction of plant lncRNAs using a Bagging-XGBoost-ensemble method with multiple features.
CoRR
Guangyan Zhang, Ziru Liu, Jichen Dai, Zilan Yu, Shuai Liu, Wen Zhang
2019 J jnl
SFLLN: A sparse feature learning ensemble method with linear neighborhood regularization for predicting drug-drug interactions.
Inf. Sci.
Wen Zhang, Kanghong Jing, Feng Huang, Yanlin Chen, Bolin Li, Jinghao Li, Jing Gong
2019 — conf
Structural Network Embedding using Multi-modal Deep Auto-encoders for Predicting Drug-drug Interactions.
BIBM
Shichao Liu, Ziyang Huang, Yang Qiu, Yi-Ping Phoebe Chen, Wen Zhang
2018 J jnl
Feature-derived graph regularized matrix factorization for predicting drug side effects.
Neurocomputing
Wen Zhang, Xinrui Liu, Yanlin Chen, Wenjian Wu, Wei Wang, Xiaohong Li
2018 — conf
HNGRNMF: Heterogeneous Network-based Graph Regularized Nonnegative Matrix Factorization for predicting events of microbe-disease associations.
BIBM
Wen Zhang, Xiaoting Lu, Weitai Yang, Feng Huang, Binlu Wang, Alan Wang, Qi Zhao
2018 J jnl
Manifold regularized matrix factorization for drug-drug interaction prediction.
J. Biomed. Informatics
Wen Zhang, Yanlin Chen, Dingfang Li, Xiang Yue
2018 J jnl
Predicting drug-disease associations by using similarity constrained matrix factorization.
BMC Bioinform.
Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang, Feng Liu
2018 — conf
Prediction of Drug-Disease Associations and Their Effects by Signed Network-Based Nonnegative Matrix Factorization.
BIBM
Wen Zhang, Feng Huang, Xiang Yue, Xiaoting Lu, Weitai Yang, Zhishuai Li, Feng Liu
2018 J jnl
SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions.
PLoS Comput. Biol.
Wen Zhang, Xiang Yue, Guifeng Tang, Wenjian Wu, Feng Huang, Xining Zhang
2018 J jnl
Sequence-based bacterial small RNAs prediction using ensemble learning strategies.
BMC Bioinform.
Guifeng Tang, Jingwen Shi, Wenjian Wu, Xiang Yue, Wen Zhang
2018 — conf
Sequence-derived linear neighborhood propagation method for predicting lncRNA-miRNA interactions.
BIBM
Wen Zhang, Guifeng Tang, Siman Wang, Yanlin Chen, Shuang Zhou, Xiaohong Li
2018 J jnl
The Bi-Direction Similarity Integration Method for Predicting Microbe-Disease Associations.
IEEE Access
Wen Zhang, Weitai Yang, Xiaoting Lu, Feng Huang, Fei Luo
2018 J jnl
The linear neighborhood propagation method for predicting long non-coding RNA-protein interactions.
Neurocomputing
Wen Zhang, Qianlong Qu, Yunqiu Zhang, Wei Wang
2017 J jnl
A unified frame of predicting side effects of drugs by using linear neighborhood similarity.
BMC Syst. Biol.
Wen Zhang, Xiang Yue, Feng Liu, Yanlin Chen, Shikui Tu, Xining Zhang
2017 — conf
Predicting drug-disease associations based on the known association bipartite network.
BIBM
Wen Zhang, Xiang Yue, Yanlin Chen, Weiran Lin, Bolin Li, Feng Liu, Xiaohong Li
2017 J jnl
Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods.
BMC Bioinform.
Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng
2017 J jnl
Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data.
BMC Bioinform.
Wen Zhang, Yanlin Chen, Feng Liu, Fei Luo, Gang Tian, Xiaohong Li
2017 — conf
Predicting small RNAs in bacteria via sequence learning ensemble method.
BIBM
Wen Zhang, Jingwen Shi, Guifeng Tang, Wenjian Wu, Xiang Yue, Dingfang Li
2016 J jnl
A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs.
BMC Bioinform.
Dingfang Li, Longqiang Luo, Wen Zhang, Feng Liu, Fei Luo
2016 — conf
Drug side effect prediction through linear neighborhoods and multiple data source integration.
BIBM
Wen Zhang, Yanlin Chen, Shikui Tu, Feng Liu, Qianlong Qu
2016 A conf
Multi-Domain Manifold Learning for Drug-Target Interaction Prediction.
SDM
Ruichu Cai, Zhenjie Zhang, Srinivasan Parthasarathy, Anthony K. H. Tung, Zhifeng Hao, Wen Zhang
2016 J jnl
Predicting potential side effects of drugs by recommender methods and ensemble learning.
Neurocomputing
Wen Zhang, Hua Zou, Longqiang Luo, Qianchao Liu, Weijian Wu, Wenyi Xiao
2016 — conf
The prediction of human splicing branchpoints by multi-label learning.
BIBM
Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng
2015 J jnl
Predicting drug side effects by multi-label learning and ensemble learning.
BMC Bioinform.
Wen Zhang, Feng Liu, Longqiang Luo, Jingxia Zhang
2013 — conf
Predicting immunogenic T-cell epitopes by combining various sequence-derived features.
BIBM
Wen Zhang, Juan Liu, Yi Xiong, Meng Ke, Ke Zhang
2012 J jnl
Predicting linear B-cell epitopes by using sequence-derived structural and physicochemical features.
Int. J. Data Min. Bioinform.
Wen Zhang, Juan Liu, Meng Zhao, Qingjiao Li
2011 — conf
Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties.
BIBM
Yi Xiong, Wen Zhang, Tao Zeng, Juan Liu
2011 J jnl
Prediction of conformational B-cell epitopes from 3D structures by random forest with a distance-based feature.
BMC Bioinform.
Wen Zhang, Yi Xiong, Meng Zhao, Hua Zou, Xinghuo Ye, Juan Liu
2010 J jnl
Quantitative prediction of MHC-II binding affinity using particle swarm optimization.
Artif. Intell. Medicine
Wen Zhang, Juan Liu, Yanqing Niu
2009 J jnl
Quantitative prediction of MHC-II peptide binding affinity using relevance vector machine.
Appl. Intell.
Wen Zhang, Juan Liu, Yanqing Niu
2008 J jnl
A Bayesian regression approach to the prediction of MHC-II binding affinity.
Comput. Methods Programs Biomed.
Wen Zhang, Juan Liu, Yanqing Niu, Lian Wang, Xihao Hu
2008 — conf
Quantitative Prediction of MHC-II Peptide Binding Affinity Using Global Description of Peptide Sequences.
BMEI (1)
Wen Zhang, Juan Liu, Yanqing Niu, Lian Wang, Zhi Zhang
2006 — conf
Gene Selection Using Rough Set Theory.
RSKT
Dingfang Li, Wen Zhang