% csauthors.net - beta - BibTeX bibliography of Hong-Bin Shen
@inproceedings{conf/aimsa/ShenYW04,
title = {Outlier Detecting in Fuzzy Switching Regression Models.},
year = {2004},
booktitle = {AIMSA},
author = {{Hong-Bin Shen} and {Jie Yang 002} and {Shitong Wang 001}},
publisher = {Springer},
booktitle = {Artificial Intelligence: Methodology, Systems, and Applications, 11th International Conference, AIMSA 2004, Varna, Bulgaria, September 2-4, 2004, Proceedings}
}
@inproceedings{conf/rsctc/ShenWY04,
title = {Fuzzy Taxonomic, Quantitative Database and Mining Generalized Association Rules.},
year = {2004},
booktitle = {Rough Sets and Current Trends in Computing},
author = {{Hong-Bin Shen} and {Shitong Wang 001} and {Jie Yang 002}},
publisher = {Springer},
booktitle = {Rough Sets and Current Trends in Computing, 4th International Conference, RSCTC 2004, Uppsala, Sweden, June 1-5, 2004, Proceedings}
}
@article{journals/soco/WangCSZ04,
title = {Note on the relationship between probabilistic and fuzzy clustering.},
year = {2004},
journal = {Soft Comput.},
author = {{Shitong Wang 001} and {Korris Fu-Lai Chung} and {Hong-Bin Shen} and {Ruiqiang Zhu}}
}
@article{journals/asc/WangCHD05,
title = {Cascaded centralized TSK fuzzy system: universal approximator and high interpretation.},
year = {2005},
journal = {Appl. Soft Comput.},
author = {{Shitong Wang 001} and {Fu-Lai Chung} and {Hong-Bin Shen} and {Dewen Hu}}
}
@article{journals/ida/ShenYCDW05,
title = {Performing clustering analysis on collaborative models.},
year = {2005},
journal = {Intell. Data Anal.},
author = {{Hong-Bin Shen} and {Jie Yang 002} and {Ningjiang Chen} and {Yifei Dong} and {Shitong Wang 001}}
}
@article{journals/ida/WangCS05,
title = {Fuzzy taxonomy, quantitative database and mining generalized association rules.},
year = {2005},
journal = {Intell. Data Anal.},
author = {{Shitong Wang 001} and {Korris Fu-Lai Chung} and {Hong-Bin Shen}}
}
@inproceedings{conf/csr/LiuYSW06,
title = {A New Scaling Kernel-Based Fuzzy System with Low Computational Complexity.},
year = {2006},
booktitle = {CSR},
author = {{Xiaojun Liu} and {Jie Yang 002} and {Hong-Bin Shen} and {Xiangyang Wang}},
publisher = {Springer},
booktitle = {Computer Science - Theory and Applications, First International Symposium on Computer Science in Russia, CSR 2006, St. Petersburg, Russia, June 8-12, 2006, Proceedings}
}
@article{journals/bioinformatics/ShenC06,
title = {Ensemble classifier for protein fold pattern recognition.},
year = {2006},
journal = {Bioinform.},
author = {{Hong-Bin Shen} and {Kuo-Chen Chou}}
}
@article{journals/soco/ShenYWL06,
title = {Attribute weighted mercer kernel based fuzzy clustering algorithm for general non-spherical datasets.},
year = {2006},
journal = {Soft Comput.},
author = {{Hong-Bin Shen} and {Jie Yang 002} and {Shitong Wang 001} and {Xiaojun Liu}}
}
@article{journals/bioinformatics/SongTSMBWAW10,
title = {Cascleave: towards more accurate prediction of caspase substrate cleavage sites.},
year = {2010},
journal = {Bioinform.},
author = {{Jiangning Song} and {Hao Tan} and {Hong-Bin Shen} and {Khalid Mahmood 001} and {Sarah E. Boyd} and {Geoffrey I. Webb} and {Tatsuya Akutsu} and {James C. Whisstock}}
}
@article{journals/jcc/ZhuYSCS10,
title = {Improving the accuracy of predicting disulfide connectivity by feature selection.},
year = {2010},
journal = {J. Comput. Chem.},
author = {{Lin Zhu} and {Jie Yang 002} and {Jiangning Song} and {Kuo-Chen Chou} and {Hong-Bin Shen}}
}
@article{journals/candc/JiaoHS11,
title = {Large-scale mining co-expressed genes in Arabidopsis anther: From pair to group.},
year = {2011},
journal = {Comput. Biol. Chem.},
author = {{Qing-Ju Jiao} and {Yan Huang} and {Hong-Bin Shen}}
}
@article{journals/ijon/YinLS11,
title = {Gaussian kernel optimization: Complex problem and a simple solution.},
year = {2011},
journal = {Neurocomputing},
author = {{Jiang-Bo Yin} and {Tao Li} and {Hong-Bin Shen}}
}
@article{journals/jbcb/SongTBSMWAWP11,
title = {Bioinformatic Approaches for Predicting substrates of Proteases.},
year = {2011},
journal = {J. Bioinform. Comput. Biol.},
author = {{Jiangning Song} and {Hao Tan} and {Sarah E. Boyd} and {Hong-Bin Shen} and {Khalid Mahmood 001} and {Geoffrey I. Webb} and {Tatsuya Akutsu} and {James C. Whisstock} and {Robert N. Pike}}
}
@inproceedings{conf/iscide/YangXS12,
title = {Automated Classification of Protein Subcellular Location Patterns on Images of Human Reproductive Tissues.},
year = {2012},
booktitle = {IScIDE},
author = {{Fan Yang} and {Ying-Ying Xu} and {Hong-Bin Shen}},
publisher = {Springer},
booktitle = {Intelligent Science and Intelligent Data Engineering - Third Sino-foreign-interchange Workshop, IScIDE 2012, Nanjing, China, October 15-17, 2012. Revised Selected Papers}
}
@article{journals/bmcbi/ZhangYLFHS12,
title = {Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features.},
year = {2012},
journal = {BMC Bioinform.},
author = {{Ya-Nan Zhang} and {Dong-Jun Yu} and {Shu-Sen Li} and {Yong-Xian Fan} and {Yan Huang} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/XuYZS13,
title = {An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues.},
year = {2013},
journal = {Bioinform.},
author = {{Ying-Ying Xu} and {Fan Yang} and {Yang Zhang 040} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/YangJZS13,
title = {High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling.},
year = {2013},
journal = {Bioinform.},
author = {{Jing Yang} and {Richard Jang} and {Yang Zhang 040} and {Hong-Bin Shen}}
}
@article{journals/cmmm/ShenSTLH13,
title = {Translational Bioinformatics and Computational Systems Medicine.},
year = {2013},
journal = {Comput. Math. Methods Medicine},
author = {{Bairong Shen} and {Hong-Bin Shen} and {Tianhai Tian} and {Qiang Lü} and {Guang Hu}}
}
@article{journals/ijon/LeiYS13,
title = {GFO: A data driven approach for optimizing the Gaussian function based similarity metric in computational biology.},
year = {2013},
journal = {Neurocomputing},
author = {{Jian-Bo Lei} and {Jiang-Bo Yin} and {Hong-Bin Shen}}
}
@article{journals/ijon/YuHTSYY13,
title = {Improving protein-ATP binding residues prediction by boosting SVMs with random under-sampling.},
year = {2013},
journal = {Neurocomputing},
author = {{Dong-Jun Yu} and {Jun Hu 011} and {Zhenmin Tang} and {Hong-Bin Shen} and {Jian Yang 003} and {Jing-Yu Yang 001}}
}
@article{journals/jcc/YuHHSQTY13,
title = {TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble.},
year = {2013},
journal = {J. Comput. Chem.},
author = {{Dong-Jun Yu} and {Jun Hu 011} and {Yan Huang} and {Hong-Bin Shen} and {Yong Qi} and {Zhenmin Tang} and {Jing-Yu Yang 001}}
}
@article{journals/tcbb/YuHYSTY13,
title = {Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering.},
year = {2013},
journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},
author = {{Dong-Jun Yu} and {Jun Hu 011} and {Jing Yang} and {Hong-Bin Shen} and {Jinhui Tang 001} and {Jing-Yu Yang 001}}
}
@inproceedings{conf/ccpr/JingS14,
title = {A Novel Two-Stage Multi-objective Ant Colony Optimization Approach for Epistasis Learning.},
year = {2014},
booktitle = {CCPR (2)},
author = {{Peng-Jie Jing} and {Hong-Bin Shen}},
publisher = {Springer},
booktitle = {Pattern Recognition - 6th Chinese Conference, CCPR 2014, Changsha, China, November 17-19, 2014. Proceedings, Part II}
}
@inproceedings{conf/ccpr/SunS14,
title = {A Global Eigenvalue-Driven Balanced Deconvolution Approach for Network Direct-Coupling Analysis.},
year = {2014},
booktitle = {CCPR (2)},
author = {{Hai-Ping Sun} and {Hong-Bin Shen}},
publisher = {Springer},
booktitle = {Pattern Recognition - 6th Chinese Conference, CCPR 2014, Changsha, China, November 17-19, 2014. Proceedings, Part II}
}
@inproceedings{conf/ccpr/XiaoS14,
title = {Sequence-Based Prediction of Protein-Protein Binding Residues in Alpha-Helical Membrane Proteins.},
year = {2014},
booktitle = {CCPR (2)},
author = {{Feng Xiao} and {Hong-Bin Shen}},
publisher = {Springer},
booktitle = {Pattern Recognition - 6th Chinese Conference, CCPR 2014, Changsha, China, November 17-19, 2014. Proceedings, Part II}
}
@article{journals/bmcbi/YuHYYYS14,
title = {Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble.},
year = {2014},
journal = {BMC Bioinform.},
author = {{Dong-Jun Yu} and {Jun Hu 011} and {Hui Yan} and {Xibei Yang} and {Jing-Yu Yang 001} and {Hong-Bin Shen}}
}
@article{journals/ijon/FanS14,
title = {Predicting pupylation sites in prokaryotic proteins using pseudo-amino acid composition and extreme learning machine.},
year = {2014},
journal = {Neurocomputing},
author = {{Yong-Xian Fan} and {Hong-Bin Shen}}
}
@article{journals/ijon/YangXWS14,
title = {Image-based classification of protein subcellular location patterns in human reproductive tissue by ensemble learning global and local features.},
year = {2014},
journal = {Neurocomputing},
author = {{Fan Yang} and {Ying-Ying Xu} and {Shitong Wang 001} and {Hong-Bin Shen}}
}
@article{journals/tfs/CheungDS14,
title = {OptiFel: A Convergent Heterogeneous Particle Swarm Optimization Algorithm for Takagi-Sugeno Fuzzy Modeling.},
year = {2014},
journal = {IEEE Trans. Fuzzy Syst.},
author = {{Ngaam J. Cheung} and {Xueming Ding} and {Hong-Bin Shen}}
}
@article{journals/apin/CheungDS15,
title = {A supervised particle swarm algorithm for real-parameter optimization.},
year = {2015},
journal = {Appl. Intell.},
author = {{Ngaam J. Cheung} and {Xueming Ding} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/JingS15,
title = {MACOED: a multi-objective ant colony optimization algorithm for SNP epistasis detection in genome-wide association studies.},
year = {2015},
journal = {Bioinform.},
author = {{Peng-Jie Jing} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/XuYZS15,
title = {Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning.},
year = {2015},
journal = {Bioinform.},
author = {{Ying-Ying Xu} and {Fan Yang} and {Yang Zhang 040} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/YangHJZS15,
title = {Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins.},
year = {2015},
journal = {Bioinform.},
author = {{Jing Yang} and {Bao-Ji He} and {Richard Jang} and {Yang Zhang 040} and {Hong-Bin Shen}}
}
@article{journals/eor/CheungXDS15,
title = {Modeling nonlinear dynamic biological systems with human-readable fuzzy rules optimized by convergent heterogeneous particle swarm.},
year = {2015},
journal = {Eur. J. Oper. Res.},
author = {{Ngaam J. Cheung} and {Zhenkai Xu} and {Xueming Ding} and {Hong-Bin Shen}}
}
@article{journals/jcisd/XiaoS15,
title = {Prediction Enhancement of Residue Real-Value Relative Accessible Surface Area in Transmembrane Helical Proteins by Solving the Output Preference Problem of Machine Learning-Based Predictors.},
year = {2015},
journal = {J. Chem. Inf. Model.},
author = {{Feng Xiao} and {Hong-Bin Shen}}
}
@article{journals/tcbb/YuLHYYS15,
title = {Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression.},
year = {2015},
journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},
author = {{Dong-Jun Yu} and {Yang Li 107} and {Jun Hu 011} and {Xibei Yang} and {Jing-Yu Yang 001} and {Hong-Bin Shen}}
}
@inproceedings{conf/bmei/ZhangS16,
title = {Improve signal peptide prediction by using functional domain information.},
year = {2016},
booktitle = {CISP-BMEI},
author = {{Yi-Ze Zhang} and {Hong-Bin Shen}},
publisher = {IEEE},
booktitle = {9th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics, CISP-BMEI 2016, Datong, China, October 15-17, 2016}
}
@inproceedings{conf/ccpr/ZhouYS16,
title = {A New Subcellular Localization Predictor for Human Proteins Considering the Correlation of Annotation Features and Protein Multi-localization.},
year = {2016},
booktitle = {CCPR (2)},
author = {{Hang Zhou} and {Yang Yang 030} and {Hong-Bin Shen}},
booktitle = {Pattern Recognition - 7th Chinese Conference, CCPR 2016, Chengdu, China, November 5-7, 2016, Proceedings, Part II}
}
@article{journals/bioinformatics/XuYS16,
title = {Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction.},
year = {2016},
journal = {Bioinform.},
author = {{Ying-Ying Xu} and {Fan Yang} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/YangJZS16,
title = {R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter.},
year = {2016},
journal = {Bioinform.},
author = {{Jing Yang} and {Qi-Yu Jin} and {Biao Zhang} and {Hong-Bin Shen}}
}
@article{journals/candc/HuLYSY16,
title = {GPCR-drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure.},
year = {2016},
journal = {Comput. Biol. Chem.},
author = {{Jun Hu 011} and {Yang Li 107} and {Jing-Yu Yang 001} and {Hong-Bin Shen} and {Dong-Jun Yu}}
}
@article{journals/ijon/HuLYYSY16,
title = {KNN-based dynamic query-driven sample rescaling strategy for class imbalance learning.},
year = {2016},
journal = {Neurocomputing},
author = {{Jun Hu 011} and {Yang Li 107} and {Wuxia Yan} and {Jing-Yu Yang 001} and {Hong-Bin Shen} and {Dong-Jun Yu}}
}
@article{journals/ijon/WeiHYSY16,
title = {Protein-protein interaction sites prediction by ensembling SVM and sample-weighted random forests.},
year = {2016},
journal = {Neurocomputing},
author = {{Zhisen Wei} and {Ke Han} and {Jing-Yu Yang 001} and {Hong-Bin Shen} and {Dong-Jun Yu}}
}
@article{journals/jcc/CheungDS16,
title = {Protein folds recognized by an intelligent predictor based-on evolutionary and structural information.},
year = {2016},
journal = {J. Comput. Chem.},
author = {{Ngaam J. Cheung} and {Xueming Ding} and {Hong-Bin Shen}}
}
@article{journals/jota/CheungDS16,
title = {A Non-homogeneous Firefly Algorithm and Its Convergence Analysis.},
year = {2016},
journal = {J. Optim. Theory Appl.},
author = {{Ngaam J. Cheung} and {Xueming Ding} and {Hong-Bin Shen}}
}
@article{journals/tcbb/YinXS16,
title = {Enhancing the Prediction of Transmembrane β-Barrel Segments with Chain Learning and Feature Sparse Representation.},
year = {2016},
journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},
author = {{Xi Yin 004} and {Ying-Ying Xu} and {Hong-Bin Shen}}
}
@inproceedings{conf/acpr/HuX0S17,
title = {Deep Learning-Based Classification of Protein Subcellular Localization from Immunohistochemistry Images.},
year = {2017},
booktitle = {ACPR},
author = {{Jin-Xian Hu} and {Ying-Ying Xu} and {Yang Yang 030} and {Hong-Bin Shen}},
publisher = {IEEE Computer Society},
booktitle = {4th IAPR Asian Conference on Pattern Recognition, ACPR 2017, Nanjing, China, November 26-29, 2017}
}
@inproceedings{conf/acpr/Zhang0S17,
title = {Detection of Curvilinear Centerline by Using Hough Voting.},
year = {2017},
booktitle = {ACPR},
author = {{Hanjin Zhang} and {Yang Yang 030} and {Hong-Bin Shen}},
publisher = {IEEE Computer Society},
booktitle = {4th IAPR Asian Conference on Pattern Recognition, ACPR 2017, Nanjing, China, November 26-29, 2017}
}
@inproceedings{conf/bmei/GengS17,
title = {A protein structure refinement method using bi-objective particle swarm optimization algorithm.},
year = {2017},
booktitle = {CISP-BMEI},
author = {{Ling Geng} and {Hong-Bin Shen}},
publisher = {IEEE},
booktitle = {10th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics, CISP-BMEI 2017, Shanghai, China, October 14-16, 2017}
}
@inproceedings{conf/bmei/YangS17,
title = {Resolution determination method of a cryo-EM density map based on multi-scale spectral signal to noise analysis.},
year = {2017},
booktitle = {CISP-BMEI},
author = {{Yu-Jiao Yang} and {Hong-Bin Shen}},
publisher = {IEEE},
booktitle = {10th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics, CISP-BMEI 2017, Shanghai, China, October 14-16, 2017}
}
@article{journals/bioinformatics/HeMWSZ17,
title = {NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers.},
year = {2017},
journal = {Bioinform.},
author = {{Baoji He} and {S. M. Mortuza} and {Yanting Wang} and {Hong-Bin Shen} and {Yang Zhang 040}}
}
@article{journals/bioinformatics/ZhouYS17,
title = {Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features.},
year = {2017},
journal = {Bioinform.},
author = {{Hang Zhou} and {Yang Yang 030} and {Hong-Bin Shen}}
}
@article{journals/bmcbi/PanS17,
title = {RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.},
year = {2017},
journal = {BMC Bioinform.},
author = {{Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/fcsc/ShaoDSZ17,
title = {Deep model-based feature extraction for predicting protein subcellular localizations from bio-images.},
year = {2017},
journal = {Frontiers Comput. Sci.},
author = {{Wei Shao 005} and {Yi Ding} and {Hong-Bin Shen} and {Daoqiang Zhang}}
}
@article{journals/jcisd/ZhangS17,
title = {Signal-3L 2.0: A Hierarchical Mixture Model for Enhancing Protein Signal Peptide Prediction by Incorporating Residue-Domain Cross-Level Features.},
year = {2017},
journal = {J. Chem. Inf. Model.},
author = {{Yi-Ze Zhang} and {Hong-Bin Shen}}
}
@article{journals/tcbb/HuLZYSY17,
title = {Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs.},
year = {2017},
journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},
author = {{Jun Hu 011} and {Yang Li 107} and {Ming Zhang} and {Xibei Yang} and {Hong-Bin Shen} and {Dong-Jun Yu}}
}
@article{journals/tcyb/CheungDS17,
title = {A Nonhomogeneous Cuckoo Search Algorithm Based on Quantum Mechanism for Real Parameter Optimization.},
year = {2017},
journal = {IEEE Trans. Cybern.},
author = {{Ngaam J. Cheung} and {Xueming Ding} and {Hong-Bin Shen}}
}
@inproceedings{conf/bibm/Ji0S18,
title = {IterVM: An Iterative Model for Single-Particle Cryo-EM Image Clustering Based on Variational Autoencoder and Multi-Reference Alignment.},
year = {2018},
booktitle = {BIBM},
author = {{Guowei Ji} and {Yang Yang 030} and {Hong-Bin Shen}},
publisher = {IEEE Computer Society},
booktitle = {IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, December 3-6, 2018}
}
@inproceedings{conf/bibm/Li0S18,
title = {HMIML: Hierarchical Multi-Instance Multi-Label Learning of Drosophila Embryogenesis Images Using Convolutional Neural Networks.},
year = {2018},
booktitle = {BIBM},
author = {{Tiange Li} and {Yang Yang 030} and {Hong-Bin Shen}},
publisher = {IEEE Computer Society},
booktitle = {IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, December 3-6, 2018}
}
@inproceedings{conf/icdm/XiaoC0ZS18,
title = {Prediction of MicroRNA Subcellular Localization by Using a Sequence-to-Sequence Model.},
year = {2018},
booktitle = {ICDM},
author = {{Yiqun Xiao} and {Jiaxun Cai} and {Yang Yang 030} and {Hai Zhao 001} and {Hong-Bin Shen}},
publisher = {IEEE Computer Society},
booktitle = {IEEE International Conference on Data Mining, ICDM 2018, Singapore, November 17-20, 2018}
}
@article{journals/access/ZhangYS18,
title = {Line Junction Detection Without Prior-Delineation of Curvilinear Structure in Biomedical Images.},
year = {2018},
journal = {IEEE Access},
author = {{Hanjin Zhang} and {Yang Yang 030} and {Hong-Bin Shen}}
}
@article{journals/access/ZhangYS18a,
title = {Detection of Curvilinear Structure in Images by a Multi-Centered Hough Forest Method.},
year = {2018},
journal = {IEEE Access},
author = {{Hanjin Zhang} and {Yang Yang 030} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/CaoPYHS18,
title = {The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier.},
year = {2018},
journal = {Bioinform.},
author = {{Zhen Cao} and {Xiaoyong Pan} and {Yang Yang 030} and {Yan Huang} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/PanS18,
title = {Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks.},
year = {2018},
journal = {Bioinform.},
author = {{Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/YangFQXS18,
title = {MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association.},
year = {2018},
journal = {Bioinform.},
author = {{Yang Yang 030} and {Xiaofeng Fu} and {Wenhao Qu} and {Yiqun Xiao} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/YangS18,
title = {MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain.},
year = {2018},
journal = {Bioinform.},
author = {{Jing Yang} and {Hong-Bin Shen}}
}
@article{journals/fcsc/XuYS18,
title = {Bioimage-based protein subcellular location prediction: a comprehensive review.},
year = {2018},
journal = {Frontiers Comput. Sci.},
author = {{Ying-Ying Xu} and {Li-Xiu Yao} and {Hong-Bin Shen}}
}
@article{journals/ijon/PanS18,
title = {Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network.},
year = {2018},
journal = {Neurocomputing},
author = {{Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/ijon/ZhiMS18,
title = {High density cell tracking with accurate centroid detections and active area-based tracklet clustering.},
year = {2018},
journal = {Neurocomputing},
author = {{Xu-Hao Zhi} and {Shu Meng} and {Hong-Bin Shen}}
}
@article{journals/jcisd/YangWZS18,
title = {Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis.},
year = {2018},
journal = {J. Chem. Inf. Model.},
author = {{Yu-Jiao Yang} and {Shuai Wang} and {Biao Zhang} and {Hong-Bin Shen}}
}
@article{journals/pr/ZhiS18,
title = {Saliency driven region-edge-based top down level set evolution reveals the asynchronous focus in image segmentation.},
year = {2018},
journal = {Pattern Recognit.},
author = {{Xu-Hao Zhi} and {Hong-Bin Shen}}
}
@article{journals/tcbb/ShaoLXSZ18,
title = {An Organelle Correlation-Guided Feature Selection Approach for Classifying Multi-Label Subcellular Bio-Images.},
year = {2018},
journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},
author = {{Wei Shao 005} and {Mingxia Liu 001} and {Ying-Ying Xu} and {Hong-Bin Shen} and {Daoqiang Zhang}}
}
@article{journals/bioinformatics/YangZFS19,
title = {AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model.},
year = {2019},
journal = {Bioinform.},
author = {{Yang Yang 030} and {Mingyu Zhou} and {Qingwei Fang} and {Hong-Bin Shen}}
}
@article{journals/chinaf/PanFJS19,
title = {Identifying RNA-binding proteins using multi-label deep learning.},
year = {2019},
journal = {Sci. China Inf. Sci.},
author = {{Xiaoyong Pan} and {Yong-Xian Fan} and {Jue Jia} and {Hong-Bin Shen}}
}
@article{journals/jcisd/YinZYHS19,
title = {Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric.},
year = {2019},
journal = {J. Chem. Inf. Model.},
author = {{Shuo Yin} and {Biao Zhang} and {Yang Yang 030} and {Yan Huang} and {Hong-Bin Shen}}
}
@article{journals/ploscb/YangFS19,
title = {Predicting gene regulatory interactions based on spatial gene expression data and deep learning.},
year = {2019},
journal = {PLoS Comput. Biol.},
author = {{Yang Yang 030} and {Qingwei Fang} and {Hong-Bin Shen}}
}
@inproceedings{conf/bibm/HuCZ0S20,
title = {NiuEM: A Nested-iterative Unsupervised Learning Model for Single-particle Cryo-EM Image Processing.},
year = {2020},
booktitle = {BIBM},
author = {{Rui Hu} and {Jia-Ming Cai} and {Wangjie Zheng} and {Yang Yang 030} and {Hong-Bin Shen}},
publisher = {IEEE},
booktitle = {IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020, Virtual Event, South Korea, December 16-19, 2020}
}
@article{journals/bioinformatics/Long0S20,
title = {ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images.},
year = {2020},
journal = {Bioinform.},
author = {{Wei Long} and {Yang Yang 030} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/WangGZYHZS20,
title = {Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.},
year = {2020},
journal = {Bioinform.},
author = {{Di Wang} and {Ling Geng} and {Yu-Jun Zhao} and {Yang Yang 030} and {Yan Huang} and {Yang Zhang} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/XiaPS20,
title = {Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data.},
year = {2020},
journal = {Bioinform.},
author = {{Chun-Qiu Xia} and {Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/XuSM20,
title = {Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images.},
year = {2020},
journal = {Bioinform.},
author = {{Ying-Ying Xu} and {Hong-Bin Shen} and {Robert F. Murphy}}
}
@article{journals/jcisd/XieCCYS20,
title = {SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment.},
year = {2020},
journal = {J. Chem. Inf. Model.},
author = {{Rui Xie} and {Yu-Xuan Chen} and {Jia-Ming Cai} and {Yang Yang 030} and {Hong-Bin Shen}}
}
@article{journals/jcisd/ZhangPS20,
title = {Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring.},
year = {2020},
journal = {J. Chem. Inf. Model.},
author = {{Wei-Xun Zhang} and {Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/pr/PanS20,
title = {Scoring disease-microRNA associations by integrating disease hierarchy into graph convolutional networks.},
year = {2020},
journal = {Pattern Recognit.},
author = {{Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/bib/WuPYS21,
title = {Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network.},
year = {2021},
journal = {Briefings Bioinform.},
author = {{Hehe Wu} and {Xiaoyong Pan} and {Yang Yang 030} and {Hong-Bin Shen}}
}
@article{journals/bib/YangDPSCWWW21,
title = {RNA-binding protein recognition based on multi-view deep feature and multi-label learning.},
year = {2021},
journal = {Briefings Bioinform.},
author = {{Haitao Yang} and {Zhaohong Deng} and {Xiaoyong Pan} and {Hong-Bin Shen} and {Kup-Sze Choi} and {Lei Wang} and {Shitong Wang 001} and {Jing Wu}}
}
@article{journals/bioinformatics/LinPS21,
title = {lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning.},
year = {2021},
journal = {Bioinform.},
author = {{Yang Lin} and {Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/PanZWSCMN21,
title = {ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity.},
year = {2021},
journal = {Bioinform.},
author = {{Xiaoyong Pan} and {Jasper Zuallaert} and {Xi Wang} and {Hong-Bin Shen} and {Elda Posada Campos} and {Denys O. Marushchak} and {Wesley De Neve}}
}
@article{journals/corr/abs-2111-08457,
title = {A Novel TSK Fuzzy System Incorporating Multi-view Collaborative Transfer Learning for Personalized Epileptic EEG Detection.},
year = {2021},
journal = {CoRR},
author = {{Andong Li} and {Zhaohong Deng} and {Qiongdan Lou} and {Kup-Sze Choi} and {Hong-Bin Shen} and {Shitong Wang 001}}
}
@article{journals/jcisd/ChenXYHFS21,
title = {Fast Cryo-EM Image Alignment Algorithm Using Power Spectrum Features.},
year = {2021},
journal = {J. Chem. Inf. Model.},
author = {{Yu-Xuan Chen} and {Rui Xie} and {Yang Yang 030} and {Lin He} and {Dagan Feng 001} and {Hong-Bin Shen}}
}
@article{journals/tcbb/LongLYS21,
title = {FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks.},
year = {2021},
journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},
author = {{Wei Long} and {Tiange Li} and {Yang Yang 030} and {Hong-Bin Shen}}
}
@article{journals/bib/LiDYPWSCWWW22,
title = {circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier.},
year = {2022},
journal = {Briefings Bioinform.},
author = {{Hui Li} and {Zhaohong Deng} and {Haitao Yang} and {Xiaoyong Pan} and {Zhisheng Wei} and {Hong-Bin Shen} and {Kup-Sze Choi} and {Lei Wang} and {Shitong Wang 001} and {Jing Wu}}
}
@article{journals/bib/TuLSY22,
title = {SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images.},
year = {2022},
journal = {Briefings Bioinform.},
author = {{Yanlun Tu} and {Houchao Lei} and {Hong-Bin Shen} and {Yang Yang 030}}
}
@article{journals/bib/WangXSX22,
title = {Learning protein subcellular localization multi-view patterns from heterogeneous data of imaging, sequence and networks.},
year = {2022},
journal = {Briefings Bioinform.},
author = {{Ge Wang} and {Min-Qi Xue} and {Hong-Bin Shen} and {Ying-Ying Xu}}
}
@article{journals/bib/WuDPSCWWY22,
title = {MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction.},
year = {2022},
journal = {Briefings Bioinform.},
author = {{Qunzhuo Wu} and {Zhaohong Deng} and {Xiaoyong Pan} and {Hong-Bin Shen} and {Kup-Sze Choi} and {Shitong Wang 001} and {Jing Wu} and {Dong-Jun Yu}}
}
@article{journals/bib/ZhangLZSZ22,
title = {Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.},
year = {2022},
journal = {Briefings Bioinform.},
author = {{Biao Zhang} and {Dong Liu} and {Yang Zhang 040} and {Hong-Bin Shen} and {Gui-Jun Zhang}}
}
@article{journals/bioinformatics/FengXS22,
title = {CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks.},
year = {2022},
journal = {Bioinform.},
author = {{Shi-Hao Feng} and {Chun-Qiu Xia} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/ZhengLYS22,
title = {Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning.},
year = {2022},
journal = {Bioinform.},
author = {{Lujing Zheng} and {Zhenhuan Liu} and {Yang Yang 030} and {Hong-Bin Shen}}
}
@article{journals/cars/ZhuSSDX22,
title = {Improving segmentation and classification of renal tumors in small sample 3D CT images using transfer learning with convolutional neural networks.},
year = {2022},
journal = {Int. J. Comput. Assist. Radiol. Surg.},
author = {{Xi-Liang Zhu} and {Hong-Bin Shen} and {Haitao Sun} and {Li-Xia Duan} and {Ying-Ying Xu}}
}
@article{journals/corr/abs-2205-11798,
title = {Symbolic Expression Transformer: A Computer Vision Approach for Symbolic Regression.},
year = {2022},
journal = {CoRR},
author = {{Jiachen Li} and {Ye Yuan} and {Hong-Bin Shen}}
}
@article{journals/corr/abs-2205-11829,
title = {Unsupervised Difference Learning for Noisy Rigid Image Alignment.},
year = {2022},
journal = {CoRR},
author = {{Yu-Xuan Chen} and {Dagan Feng 001} and {Hong-Bin Shen}}
}
@article{journals/ploscb/XiaFXPS22,
title = {Fast protein structure comparison through effective representation learning with contrastive graph neural networks.},
year = {2022},
journal = {PLoS Comput. Biol.},
author = {{Chun-Qiu Xia} and {Shi-Hao Feng} and {Ying Xia} and {Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/symmetry/FangPS22,
title = {Recent Deep Learning Methodology Development for RNA-RNA Interaction Prediction.},
year = {2022},
journal = {Symmetry},
author = {{Yi Fang} and {Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/tcbb/FengXZS22,
title = {Ab-Initio Membrane Protein Amphipathic Helix Structure Prediction Using Deep Neural Networks.},
year = {2022},
journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},
author = {{Shi-Hao Feng} and {Chun-Qiu Xia} and {Pei-Dong Zhang} and {Hong-Bin Shen}}
}
@article{journals/tcyb/ZhangDWCZLSYW22,
title = {Transductive Multiview Modeling With Interpretable Rules, Matrix Factorization, and Cooperative Learning.},
year = {2022},
journal = {IEEE Trans. Cybern.},
author = {{Wei Zhang} and {Zhaohong Deng} and {Jun Wang 024} and {Kup-Sze Choi} and {Te Zhang} and {Xiaoqing Luo} and {Hong-Bin Shen} and {Wenhao Ying} and {Shitong Wang 001}}
}
@article{journals/tetci/LouDCSWW22,
title = {Robust Multi-Label Relief Feature Selection Based on Fuzzy Margin Co-Optimization.},
year = {2022},
journal = {IEEE Trans. Emerg. Top. Comput. Intell.},
author = {{Qiongdan Lou} and {Zhaohong Deng} and {Kup-Sze Choi} and {Hong-Bin Shen} and {Jun Wang 024} and {Shitong Wang 001}}
}
@article{journals/bioinformatics/HuYXS22,
title = {GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images.},
year = {2022},
month = {October},
journal = {Bioinform.},
author = {{Jin-Xian Hu} and {Yang Yang 030} and {Ying-Ying Xu} and {Hong-Bin Shen}}
}
@inproceedings{conf/bibm/GuoLCSY23,
title = {Isoform Function Prediction Based on Heterogeneous Graph Attention Networks.},
year = {2023},
booktitle = {BIBM},
author = {{Kuo Guo} and {Yifan Li} and {Hao Chen} and {Hong-Bin Shen} and {Yang Yang}},
publisher = {IEEE},
booktitle = {IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023, Istanbul, Turkiye, December 5-8, 2023}
}
@article{journals/bib/XiaFXPS23,
title = {Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network.},
year = {2023},
month = {January},
journal = {Briefings Bioinform.},
author = {{Chun-Qiu Xia} and {Shi-Hao Feng} and {Ying Xia} and {Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/bib/ZhangXS23,
title = {High-accuracy protein model quality assessment using attention graph neural networks.},
year = {2023},
month = {March},
journal = {Briefings Bioinform.},
author = {{Pei-Dong Zhang} and {Chun-Qiu Xia} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/FangPS23,
title = {De novodrug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment.},
year = {2023},
month = {April},
journal = {Bioinform.},
author = {{Yi Fang} and {Xiaoyong Pan} and {Hong-Bin Shen}}
}
@article{journals/bioinformatics/WuDZPCZSY23,
title = {MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering.},
year = {2023},
month = {August},
journal = {Bioinform.},
author = {{Qunzhuo Wu} and {Zhaohong Deng} and {Wei Zhang} and {Xiaoyong Pan} and {Kup-Sze Choi} and {Yun Zuo} and {Hong-Bin Shen} and {Dong-Jun Yu}}
}
@article{journals/pr/PanXXS23,
title = {Few-shot classification with task-adaptive semantic feature learning.},
year = {2023},
month = {September},
journal = {Pattern Recognit.},
author = {{Meihong Pan} and {Hongyi Xin} and {Chun-Qiu Xia} and {Hong-Bin Shen}}
}