Hong-Bin Shen

According to our database1, Hong-Bin Shen authored at least 114 papers between 2004 and 2023.

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Bibliography

2023
Few-shot classification with task-adaptive semantic feature learning.
Pattern Recognit., September, 2023

MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering.
Bioinform., August, 2023

<i>De novo</i>drug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment.
Bioinform., April, 2023

High-accuracy protein model quality assessment using attention graph neural networks.
Briefings Bioinform., March, 2023

Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network.
Briefings Bioinform., January, 2023

Isoform Function Prediction Based on Heterogeneous Graph Attention Networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images.
Bioinform., October, 2022

Robust Multi-Label Relief Feature Selection Based on Fuzzy Margin Co-Optimization.
IEEE Trans. Emerg. Top. Comput. Intell., 2022

Transductive Multiview Modeling With Interpretable Rules, Matrix Factorization, and Cooperative Learning.
IEEE Trans. Cybern., 2022

Ab-Initio Membrane Protein Amphipathic Helix Structure Prediction Using Deep Neural Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Recent Deep Learning Methodology Development for RNA-RNA Interaction Prediction.
Symmetry, 2022

Fast protein structure comparison through effective representation learning with contrastive graph neural networks.
PLoS Comput. Biol., 2022

Unsupervised Difference Learning for Noisy Rigid Image Alignment.
CoRR, 2022

Symbolic Expression Transformer: A Computer Vision Approach for Symbolic Regression.
CoRR, 2022

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., 2022

Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning.
Bioinform., 2022

CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks.
Bioinform., 2022

Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.
Briefings Bioinform., 2022

MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction.
Briefings Bioinform., 2022

Learning protein subcellular localization multi-view patterns from heterogeneous data of imaging, sequence and networks.
Briefings Bioinform., 2022

SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images.
Briefings Bioinform., 2022

circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier.
Briefings Bioinform., 2022

2021
FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Fast Cryo-EM Image Alignment Algorithm Using Power Spectrum Features.
J. Chem. Inf. Model., 2021

A Novel TSK Fuzzy System Incorporating Multi-view Collaborative Transfer Learning for Personalized Epileptic EEG Detection.
CoRR, 2021

ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity.
Bioinform., 2021

lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning.
Bioinform., 2021

RNA-binding protein recognition based on multi-view deep feature and multi-label learning.
Briefings Bioinform., 2021

Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network.
Briefings Bioinform., 2021

2020
Scoring disease-microRNA associations by integrating disease hierarchy into graph convolutional networks.
Pattern Recognit., 2020

Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring.
J. Chem. Inf. Model., 2020

SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment.
J. Chem. Inf. Model., 2020

Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images.
Bioinform., 2020

Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data.
Bioinform., 2020

Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.
Bioinform., 2020

ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images.
Bioinform., 2020

NiuEM: A Nested-iterative Unsupervised Learning Model for Single-particle Cryo-EM Image Processing.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019
Predicting gene regulatory interactions based on spatial gene expression data and deep learning.
PLoS Comput. Biol., 2019

Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric.
J. Chem. Inf. Model., 2019

Identifying RNA-binding proteins using multi-label deep learning.
Sci. China Inf. Sci., 2019

AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model.
Bioinform., 2019

2018
An Organelle Correlation-Guided Feature Selection Approach for Classifying Multi-Label Subcellular Bio-Images.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Saliency driven region-edge-based top down level set evolution reveals the asynchronous focus in image segmentation.
Pattern Recognit., 2018

Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis.
J. Chem. Inf. Model., 2018

High density cell tracking with accurate centroid detections and active area-based tracklet clustering.
Neurocomputing, 2018

Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network.
Neurocomputing, 2018

Bioimage-based protein subcellular location prediction: a comprehensive review.
Frontiers Comput. Sci., 2018

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., 2018

MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association.
Bioinform., 2018

Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks.
Bioinform., 2018

The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier.
Bioinform., 2018

Detection of Curvilinear Structure in Images by a Multi-Centered Hough Forest Method.
IEEE Access, 2018

Line Junction Detection Without Prior-Delineation of Curvilinear Structure in Biomedical Images.
IEEE Access, 2018

Prediction of MicroRNA Subcellular Localization by Using a Sequence-to-Sequence Model.
Proceedings of the IEEE International Conference on Data Mining, 2018

HMIML: Hierarchical Multi-Instance Multi-Label Learning of Drosophila Embryogenesis Images Using Convolutional Neural Networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

IterVM: An Iterative Model for Single-Particle Cryo-EM Image Clustering Based on Variational Autoencoder and Multi-Reference Alignment.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017
A Nonhomogeneous Cuckoo Search Algorithm Based on Quantum Mechanism for Real Parameter Optimization.
IEEE Trans. Cybern., 2017

Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017

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., 2017

Deep model-based feature extraction for predicting protein subcellular localizations from bio-images.
Frontiers Comput. Sci., 2017

RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.
BMC Bioinform., 2017

Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features.
Bioinform., 2017

NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers.
Bioinform., 2017

Resolution determination method of a cryo-EM density map based on multi-scale spectral signal to noise analysis.
Proceedings of the 10th International Congress on Image and Signal Processing, 2017

A protein structure refinement method using bi-objective particle swarm optimization algorithm.
Proceedings of the 10th International Congress on Image and Signal Processing, 2017

Detection of Curvilinear Centerline by Using Hough Voting.
Proceedings of the 4th IAPR Asian Conference on Pattern Recognition, 2017

Deep Learning-Based Classification of Protein Subcellular Localization from Immunohistochemistry Images.
Proceedings of the 4th IAPR Asian Conference on Pattern Recognition, 2017

2016
Enhancing the Prediction of Transmembrane β-Barrel Segments with Chain Learning and Feature Sparse Representation.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

A Non-homogeneous Firefly Algorithm and Its Convergence Analysis.
J. Optim. Theory Appl., 2016

Protein folds recognized by an intelligent predictor based-on evolutionary and structural information.
J. Comput. Chem., 2016

Protein-protein interaction sites prediction by ensembling SVM and sample-weighted random forests.
Neurocomputing, 2016

KNN-based dynamic query-driven sample rescaling strategy for class imbalance learning.
Neurocomputing, 2016

GPCR-drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure.
Comput. Biol. Chem., 2016

R<sub>2</sub>C: improving <i>ab initio</i> residue contact map prediction using dynamic fusion strategy and Gaussian noise filter.
Bioinform., 2016

Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction.
Bioinform., 2016

A New Subcellular Localization Predictor for Human Proteins Considering the Correlation of Annotation Features and Protein Multi-localization.
Proceedings of the Pattern Recognition - 7th Chinese Conference, 2016

Improve signal peptide prediction by using functional domain information.
Proceedings of the 9th International Congress on Image and Signal Processing, 2016

2015
Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

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., 2015

Modeling nonlinear dynamic biological systems with human-readable fuzzy rules optimized by convergent heterogeneous particle swarm.
Eur. J. Oper. Res., 2015

Accurate disulfide-bonding network predictions improve <i>ab initio</i> structure prediction of cysteine-rich proteins.
Bioinform., 2015

Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning.
Bioinform., 2015

MACOED: a multi-objective ant colony optimization algorithm for SNP epistasis detection in genome-wide association studies.
Bioinform., 2015

A supervised particle swarm algorithm for real-parameter optimization.
Appl. Intell., 2015

2014
OptiFel: A Convergent Heterogeneous Particle Swarm Optimization Algorithm for Takagi-Sugeno Fuzzy Modeling.
IEEE Trans. Fuzzy Syst., 2014

Image-based classification of protein subcellular location patterns in human reproductive tissue by ensemble learning global and local features.
Neurocomputing, 2014

Predicting pupylation sites in prokaryotic proteins using pseudo-amino acid composition and extreme learning machine.
Neurocomputing, 2014

Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble.
BMC Bioinform., 2014

Sequence-Based Prediction of Protein-Protein Binding Residues in Alpha-Helical Membrane Proteins.
Proceedings of the Pattern Recognition - 6th Chinese Conference, 2014

A Global Eigenvalue-Driven Balanced Deconvolution Approach for Network Direct-Coupling Analysis.
Proceedings of the Pattern Recognition - 6th Chinese Conference, 2014

A Novel Two-Stage Multi-objective Ant Colony Optimization Approach for Epistasis Learning.
Proceedings of the Pattern Recognition - 6th Chinese Conference, 2014

2013
Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013

TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble.
J. Comput. Chem., 2013

Improving protein-ATP binding residues prediction by boosting SVMs with random under-sampling.
Neurocomputing, 2013

GFO: A data driven approach for optimizing the Gaussian function based similarity metric in computational biology.
Neurocomputing, 2013

Translational Bioinformatics and Computational Systems Medicine.
Comput. Math. Methods Medicine, 2013

High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling.
Bioinform., 2013

An image-based multi-label human protein subcellular localization predictor (<i>i</i>Locator) reveals protein mislocalizations in cancer tissues.
Bioinform., 2013

2012
Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features.
BMC Bioinform., 2012

Automated Classification of Protein Subcellular Location Patterns on Images of Human Reproductive Tissues.
Proceedings of the Intelligent Science and Intelligent Data Engineering, 2012

2011
Bioinformatic Approaches for Predicting substrates of Proteases.
J. Bioinform. Comput. Biol., 2011

Gaussian kernel optimization: Complex problem and a simple solution.
Neurocomputing, 2011

Large-scale mining co-expressed genes in Arabidopsis anther: From pair to group.
Comput. Biol. Chem., 2011

2010
Improving the accuracy of predicting disulfide connectivity by feature selection.
J. Comput. Chem., 2010

Cascleave: towards more accurate prediction of caspase substrate cleavage sites.
Bioinform., 2010

2006
Attribute weighted mercer kernel based fuzzy clustering algorithm for general non-spherical datasets.
Soft Comput., 2006

Ensemble classifier for protein fold pattern recognition.
Bioinform., 2006

A New Scaling Kernel-Based Fuzzy System with Low Computational Complexity.
Proceedings of the Computer Science, 2006

2005
Fuzzy taxonomy, quantitative database and mining generalized association rules.
Intell. Data Anal., 2005

Performing clustering analysis on collaborative models.
Intell. Data Anal., 2005

Cascaded centralized TSK fuzzy system: universal approximator and high interpretation.
Appl. Soft Comput., 2005

2004
Note on the relationship between probabilistic and fuzzy clustering.
Soft Comput., 2004

Fuzzy Taxonomic, Quantitative Database and Mining Generalized Association Rules.
Proceedings of the Rough Sets and Current Trends in Computing, 2004

Outlier Detecting in Fuzzy Switching Regression Models.
Proceedings of the Artificial Intelligence: Methodology, 2004


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