Hong-Bin Shen

ORCID

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 82

Top Venues

Publications

Chun-Qiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen
Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network. Briefings Bioinform. 24 (1) (2023)
Pei-Dong Zhang, Chun-Qiu Xia, Hong-Bin Shen
High-accuracy protein model quality assessment using attention graph neural networks. Briefings Bioinform. 24 (2) (2023)
Kuo Guo, Yifan Li, Hao Chen, Hong-Bin Shen, Yang Yang
Isoform Function Prediction Based on Heterogeneous Graph Attention Networks. BIBM (2023)
Mei-Hong Pan, Hong-Yi Xin, Chun-Qiu Xia, Hong-Bin Shen
Few-shot classification with task-adaptive semantic feature learning. Pattern Recognit. 141 (2023)
Hui Li, Zhaohong Deng, Haitao Yang, Xiaoyong Pan, Zhisheng Wei, Hong-Bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang, Jing Wu
circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier. Briefings Bioinform. 23 (1) (2022)
Ge Wang, Min-Qi Xue, Hong-Bin Shen, Ying-Ying Xu
Learning protein subcellular localization multi-view patterns from heterogeneous data of imaging, sequence and networks. Briefings Bioinform. 23 (2) (2022)
Yu-Xuan Chen, Dagan Feng, Hong-Bin Shen
Unsupervised Difference Learning for Noisy Rigid Image Alignment. CoRR (2022)
Qiongdan Lou, Zhaohong Deng, Kup-Sze Choi, Hong-Bin Shen, Jun Wang, Shitong Wang
Robust Multi-Label Relief Feature Selection Based on Fuzzy Margin Co-Optimization. IEEE Trans. Emerg. Top. Comput. Intell. 6 (2) (2022)
Jin-Xian Hu, Yang Yang, Ying-Ying Xu, Hong-Bin Shen
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images. Bioinform. 38 (21) (2022)
Yi Fang, Xiaoyong Pan, Hong-Bin Shen
Recent Deep Learning Methodology Development for RNA-RNA Interaction Prediction. Symmetry 14 (7) (2022)
Yanlun Tu, Houchao Lei, Hong-Bin Shen, Yang Yang
SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images. Briefings Bioinform. 23 (2) (2022)
Qunzhuo Wu, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Shitong Wang, Jing Wu, Dong-Jun Yu
MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction. Briefings Bioinform. 23 (5) (2022)
Xi-Liang Zhu, Hong-Bin Shen, Haitao Sun, Li-Xia Duan, Ying-Ying Xu
Improving segmentation and classification of renal tumors in small sample 3D CT images using transfer learning with convolutional neural networks. Int. J. Comput. Assist. Radiol. Surg. 17 (7) (2022)
Jiachen Li, Ye Yuan, Hong-Bin Shen
Symbolic Expression Transformer: A Computer Vision Approach for Symbolic Regression. CoRR (2022)
Biao Zhang, Dong Liu, Yang Zhang, Hong-Bin Shen, Gui-Jun Zhang
Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning. Briefings Bioinform. 23 (2) (2022)
Shi-Hao Feng, Chun-Qiu Xia, Hong-Bin Shen
CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks. Bioinform. 38 (3) (2022)
Shi-Hao Feng, Chun-Qiu Xia, Pei-Dong Zhang, Hong-Bin Shen
Ab-Initio Membrane Protein Amphipathic Helix Structure Prediction Using Deep Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (2) (2022)
Lujing Zheng, Zhenhuan Liu, Yang Yang, Hong-Bin Shen
Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning. Bioinform. 38 (3) (2022)
Wei Zhang, Zhaohong Deng, Jun Wang, Kup-Sze Choi, Te Zhang, Xiaoqing Luo, Hong-Bin Shen, Wenhao Ying, Shitong Wang
Transductive Multiview Modeling With Interpretable Rules, Matrix Factorization, and Cooperative Learning. IEEE Trans. Cybern. 52 (10) (2022)
Chun-Qiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen
Fast protein structure comparison through effective representation learning with contrastive graph neural networks. PLoS Comput. Biol. 18 (3) (2022)
Yu-Xuan Chen, Rui Xie, Yang Yang, Lin He, Dagan Feng, Hong-Bin Shen
Fast Cryo-EM Image Alignment Algorithm Using Power Spectrum Features. J. Chem. Inf. Model. 61 (9) (2021)
Xiaoyong Pan, Jasper Zuallaert, Xi Wang, Hong-Bin Shen, Elda Posada Campos, Denys O. Marushchak, Wesley De Neve
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity. Bioinform. 36 (21) (2021)
Yang Lin, Xiaoyong Pan, Hong-Bin Shen
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning. Bioinform. 37 (16) (2021)
Wei Long, Tiange Li, Yang Yang, Hong-Bin Shen
FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (1) (2021)
Haitao Yang, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang, Jing Wu
RNA-binding protein recognition based on multi-view deep feature and multi-label learning. Briefings Bioinform. 22 (3) (2021)
Andong Li, Zhaohong Deng, Qiongdan Lou, Kup-Sze Choi, Hong-Bin Shen, Shitong Wang
A Novel TSK Fuzzy System Incorporating Multi-view Collaborative Transfer Learning for Personalized Epileptic EEG Detection. CoRR (2021)
Hehe Wu, Xiaoyong Pan, Yang Yang, Hong-Bin Shen
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network. Briefings Bioinform. 22 (6) (2021)
Ying-Ying Xu, Hong-Bin Shen, Robert F. Murphy
Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images. Bioinform. 36 (6) (2020)
Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang, Yang Zhang, Hong-Bin Shen
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinform. 36 (2) (2020)
Chun-Qiu Xia, Xiaoyong Pan, Hong-Bin Shen
Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data. Bioinform. 36 (10) (2020)
Rui Hu, Jia-Ming Cai, Wangjie Zheng, Yang Yang, Hong-Bin Shen
NiuEM: A Nested-iterative Unsupervised Learning Model for Single-particle Cryo-EM Image Processing. BIBM (2020)
Rui Xie, Yu-Xuan Chen, Jia-Ming Cai, Yang Yang, Hong-Bin Shen
SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment. J. Chem. Inf. Model. 60 (5) (2020)
Xiaoyong Pan, Hong-Bin Shen
Scoring disease-microRNA associations by integrating disease hierarchy into graph convolutional networks. Pattern Recognit. 105 (2020)
Wei Long, Yang Yang, Hong-Bin Shen
ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images. Bioinform. 36 (7) (2020)
Wei-Xun Zhang, Xiaoyong Pan, Hong-Bin Shen
Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring. J. Chem. Inf. Model. 60 (7) (2020)
Xiaoyong Pan, Yong-Xian Fan, Jue Jia, Hong-Bin Shen
Identifying RNA-binding proteins using multi-label deep learning. Sci. China Inf. Sci. 62 (1) (2019)
Yang Yang, Qingwei Fang, Hong-Bin Shen
Predicting gene regulatory interactions based on spatial gene expression data and deep learning. PLoS Comput. Biol. 15 (9) (2019)
Shuo Yin, Biao Zhang, Yang Yang, Yan Huang, Hong-Bin Shen
Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric. J. Chem. Inf. Model. 59 (4) (2019)
Yang Yang, Mingyu Zhou, Qingwei Fang, Hong-Bin Shen
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model. Bioinform. 35 (16) (2019)
Hanjin Zhang, Yang Yang, Hong-Bin Shen
Line Junction Detection Without Prior-Delineation of Curvilinear Structure in Biomedical Images. IEEE Access 6 (2018)
Xu-Hao Zhi, Shu Meng, Hong-Bin Shen
High density cell tracking with accurate centroid detections and active area-based tracklet clustering. Neurocomputing 295 (2018)
Xiaoyong Pan, Hong-Bin Shen
Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network. Neurocomputing 305 (2018)
Yiqun Xiao, Jiaxun Cai, Yang Yang, Hai Zhao, Hong-Bin Shen
Prediction of MicroRNA Subcellular Localization by Using a Sequence-to-Sequence Model. ICDM (2018)
Tiange Li, Yang Yang, Hong-Bin Shen
HMIML: Hierarchical Multi-Instance Multi-Label Learning of Drosophila Embryogenesis Images Using Convolutional Neural Networks. BIBM (2018)
Hanjin Zhang, Yang Yang, Hong-Bin Shen
Detection of Curvilinear Structure in Images by a Multi-Centered Hough Forest Method. IEEE Access 6 (2018)
Xu-Hao Zhi, Hong-Bin Shen
Saliency driven region-edge-based top down level set evolution reveals the asynchronous focus in image segmentation. Pattern Recognit. 80 (2018)
Zhen Cao, Xiaoyong Pan, Yang Yang, Yan Huang, Hong-Bin Shen
The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinform. 34 (13) (2018)
Yang Yang, Xiaofeng Fu, Wenhao Qu, Yiqun Xiao, Hong-Bin Shen
MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association. Bioinform. 34 (20) (2018)
Jing Yang, Hong-Bin Shen
MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain. Bioinform. 34 (2) (2018)
Yu-Jiao Yang, Shuai Wang, Biao Zhang, Hong-Bin Shen
Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis. J. Chem. Inf. Model. 58 (6) (2018)
Xiaoyong Pan, Hong-Bin Shen
Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks. Bioinform. 34 (20) (2018)
Wei Shao, Mingxia Liu, Ying-Ying Xu, Hong-Bin Shen, Daoqiang Zhang
An Organelle Correlation-Guided Feature Selection Approach for Classifying Multi-Label Subcellular Bio-Images. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (3) (2018)
Guowei Ji, Yang Yang, Hong-Bin Shen
IterVM: An Iterative Model for Single-Particle Cryo-EM Image Clustering Based on Variational Autoencoder and Multi-Reference Alignment. BIBM (2018)
Ying-Ying Xu, Li-Xiu Yao, Hong-Bin Shen
Bioimage-based protein subcellular location prediction: a comprehensive review. Frontiers Comput. Sci. 12 (1) (2018)
Hang Zhou, Yang Yang, Hong-Bin Shen
Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features. Bioinform. 33 (6) (2017)
Ngaam J. Cheung, Xueming Ding, Hong-Bin Shen
A Nonhomogeneous Cuckoo Search Algorithm Based on Quantum Mechanism for Real Parameter Optimization. IEEE Trans. Cybern. 47 (2) (2017)
Ling Geng, Hong-Bin Shen
A protein structure refinement method using bi-objective particle swarm optimization algorithm. CISP-BMEI (2017)
Baoji He, S. M. Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang
NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers. Bioinform. 33 (15) (2017)
Jin-Xian Hu, Ying-Ying Xu, Yang Yang, Hong-Bin Shen
Deep Learning-Based Classification of Protein Subcellular Localization from Immunohistochemistry Images. ACPR (2017)
Hanjin Zhang, Yang Yang, Hong-Bin Shen
Detection of Curvilinear Centerline by Using Hough Voting. ACPR (2017)
Yu-Jiao Yang, Hong-Bin Shen
Resolution determination method of a cryo-EM density map based on multi-scale spectral signal to noise analysis. CISP-BMEI (2017)
Wei Shao, Yi Ding, Hong-Bin Shen, Daoqiang Zhang
Deep model-based feature extraction for predicting protein subcellular localizations from bio-images. Frontiers Comput. Sci. 11 (2) (2017)
Xiaoyong Pan, Hong-Bin Shen
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach. BMC Bioinform. 18 (1) (2017)
Yi-Ze Zhang, Hong-Bin Shen
Signal-3L 2.0: A Hierarchical Mixture Model for Enhancing Protein Signal Peptide Prediction by Incorporating Residue-Domain Cross-Level Features. J. Chem. Inf. Model. 57 (4) (2017)
Jun Hu, Yang Li, Ming Zhang, Xibei Yang, Hong-Bin Shen, Dong-Jun Yu
Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (6) (2017)
Jun Hu, Yang Li, Wuxia Yan, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
KNN-based dynamic query-driven sample rescaling strategy for class imbalance learning. Neurocomputing 191 (2016)
Hang Zhou, Yang Yang, Hong-Bin Shen
A New Subcellular Localization Predictor for Human Proteins Considering the Correlation of Annotation Features and Protein Multi-localization. CCPR (2) (2016)
Jing Yang, Qi-Yu Jin, Biao Zhang, Hong-Bin Shen
residue contact map prediction using dynamic fusion strategy and Gaussian noise filter. Bioinform. 32 (16) (2016)
Yi-Ze Zhang, Hong-Bin Shen
Improve signal peptide prediction by using functional domain information. CISP-BMEI (2016)
Zhisen Wei, Ke Han, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
Protein-protein interaction sites prediction by ensembling SVM and sample-weighted random forests. Neurocomputing 193 (2016)
Ngaam J. Cheung, Xueming Ding, Hong-Bin Shen
Protein folds recognized by an intelligent predictor based-on evolutionary and structural information. J. Comput. Chem. 37 (4) (2016)
Jun Hu, Yang Li, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
GPCR-drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure. Comput. Biol. Chem. 60 (2016)
Ying-Ying Xu, Fan Yang, Hong-Bin Shen
Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction. Bioinform. 32 (14) (2016)
Ngaam J. Cheung, Xueming Ding, Hong-Bin Shen
A Non-homogeneous Firefly Algorithm and Its Convergence Analysis. J. Optim. Theory Appl. 170 (2) (2016)
Xi Yin, Ying-Ying Xu, Hong-Bin Shen
Enhancing the Prediction of Transmembrane β-Barrel Segments with Chain Learning and Feature Sparse Representation. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (6) (2016)
Ying-Ying Xu, Fan Yang, Yang Zhang, Hong-Bin Shen
Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning. Bioinform. 31 (7) (2015)
Feng Xiao, Hong-Bin Shen
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. J. Chem. Inf. Model. 55 (11) (2015)
Jing Yang, Bao-Ji He, Richard Jang, Yang Zhang, Hong-Bin Shen
structure prediction of cysteine-rich proteins. Bioinform. 31 (23) (2015)
Ngaam J. Cheung, Zhenkai Xu, Xueming Ding, Hong-Bin Shen
Modeling nonlinear dynamic biological systems with human-readable fuzzy rules optimized by convergent heterogeneous particle swarm. Eur. J. Oper. Res. 247 (2) (2015)
Peng-Jie Jing, Hong-Bin Shen
MACOED: a multi-objective ant colony optimization algorithm for SNP epistasis detection in genome-wide association studies. Bioinform. 31 (5) (2015)
Dong-Jun Yu, Yang Li, Jun Hu, Xibei Yang, Jing-Yu Yang, Hong-Bin Shen
Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (3) (2015)
Ngaam J. Cheung, Xueming Ding, Hong-Bin Shen
A supervised particle swarm algorithm for real-parameter optimization. Appl. Intell. 43 (4) (2015)
Hai-Ping Sun, Hong-Bin Shen
A Global Eigenvalue-Driven Balanced Deconvolution Approach for Network Direct-Coupling Analysis. CCPR (2) (2014)
Yong-Xian Fan, Hong-Bin Shen
Predicting pupylation sites in prokaryotic proteins using pseudo-amino acid composition and extreme learning machine. Neurocomputing 128 (2014)
Fan Yang, Ying-Ying Xu, Shitong Wang, Hong-Bin Shen
Image-based classification of protein subcellular location patterns in human reproductive tissue by ensemble learning global and local features. Neurocomputing 131 (2014)
Feng Xiao, Hong-Bin Shen
Sequence-Based Prediction of Protein-Protein Binding Residues in Alpha-Helical Membrane Proteins. CCPR (2) (2014)
Ngaam J. Cheung, Xueming Ding, Hong-Bin Shen
OptiFel: A Convergent Heterogeneous Particle Swarm Optimization Algorithm for Takagi-Sugeno Fuzzy Modeling. IEEE Trans. Fuzzy Syst. 22 (4) (2014)
Peng-Jie Jing, Hong-Bin Shen
A Novel Two-Stage Multi-objective Ant Colony Optimization Approach for Epistasis Learning. CCPR (2) (2014)
Dong-Jun Yu, Jun Hu, Hui Yan, Xibei Yang, Jing-Yu Yang, Hong-Bin Shen
Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble. BMC Bioinform. 15 (2014)
Dong-Jun Yu, Jun Hu, Jing Yang, Hong-Bin Shen, Jinhui Tang, Jing-Yu Yang
Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (4) (2013)
Bairong Shen, Hong-Bin Shen, Tianhai Tian, Qiang Lü, Guang Hu
Translational Bioinformatics and Computational Systems Medicine. Comput. Math. Methods Medicine 2013 (2013)
Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhenmin Tang, Jing-Yu Yang
TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble. J. Comput. Chem. 34 (11) (2013)
Ying-Ying Xu, Fan Yang, Yang Zhang, Hong-Bin Shen
Locator) reveals protein mislocalizations in cancer tissues. Bioinform. 29 (16) (2013)
Dong-Jun Yu, Jun Hu, Zhenmin Tang, Hong-Bin Shen, Jian Yang, Jing-Yu Yang
Improving protein-ATP binding residues prediction by boosting SVMs with random under-sampling. Neurocomputing 104 (2013)
Jing Yang, Richard Jang, Yang Zhang, Hong-Bin Shen
High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. Bioinform. 29 (20) (2013)
Jian-Bo Lei, Jiang-Bo Yin, Hong-Bin Shen
GFO: A data driven approach for optimizing the Gaussian function based similarity metric in computational biology. Neurocomputing 99 (2013)
Fan Yang, Ying-Ying Xu, Hong-Bin Shen
Automated Classification of Protein Subcellular Location Patterns on Images of Human Reproductive Tissues. IScIDE (2012)
Ya-Nan Zhang, Dong-Jun Yu, Shu-Sen Li, Yong-Xian Fan, Yan Huang, Hong-Bin Shen
Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features. BMC Bioinform. 13 (2012)
Qing-Ju Jiao, Yan Huang, Hong-Bin Shen
Large-scale mining co-expressed genes in Arabidopsis anther: From pair to group. Comput. Biol. Chem. 35 (2) (2011)
Jiang-Bo Yin, Tao Li, Hong-Bin Shen
Gaussian kernel optimization: Complex problem and a simple solution. Neurocomputing 74 (18) (2011)

Hong-Bin Shen.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Hong-Bin Shen