Dongjun Yu

According to our database1, Dongjun Yu authored at least 90 papers between 2003 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2024
Robust GEPSVM classifier: An efficient iterative optimization framework.
Inf. Sci., February, 2024

ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction.
Briefings Bioinform., January, 2024

GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference.
Briefings Bioinform., January, 2024

TM-search: An Efficient and Effective Tool for Protein Structure Database Search.
J. Chem. Inf. Model., 2024

2023
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.
Bioinform., December, 2023

MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction.
J. Chem. Inf. Model., November, 2023

Integrating unsupervised language model with multi-view multiple sequence alignments for high-accuracy inter-chain contact prediction.
Comput. Biol. Medicine, November, 2023

Robust generalized canonical correlation analysis.
Appl. Intell., September, 2023

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

TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level.
Briefings Bioinform., May, 2023

Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm.
J. Chem. Inf. Model., February, 2023

PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method.
Bioinform., January, 2023

VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants.
Briefings Bioinform., January, 2023

Prediction of Multiple Types of RNA Modifications via Biological Language Model.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

CPInformer for Efficient and Robust Compound-Protein Interaction Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation.
J. Chem. Inf. Model., 2023

Glee: A granularity filter for feature selection.
Eng. Appl. Artif. Intell., 2023

2022
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.
PLoS Comput. Biol., December, 2022

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.
Genom. Proteom. Bioinform., October, 2022

Robust Least Squares Twin Support Vector Regression With Adaptive FOA and PSO for Short-Term Traffic Flow Prediction.
IEEE Trans. Intell. Transp. Syst., 2022

Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Robust distance metric optimization driven GEPSVM classifier for pattern classification.
Pattern Recognit., 2022

Learning a robust classifier for short-term traffic state prediction.
Knowl. Based Syst., 2022

Learning Protein Embedding to Improve Protein Fold Recognition Using Deep Metric Learning.
J. Chem. Inf. Model., 2022

Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA.
J. Chem. Inf. Model., 2022

PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations.
J. Chem. Inf. Model., 2022

Robust ensemble method for short-term traffic flow prediction.
Future Gener. Comput. Syst., 2022

PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data.
Bioinform., 2022

ATPdock: a template-based method for ATP-specific protein-ligand docking.
Bioinform., 2022

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

MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network.
Briefings Bioinform., 2022

Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.
Briefings Bioinform., 2022

2021
SP-GAN: Self-Growing and Pruning Generative Adversarial Networks.
IEEE Trans. Neural Networks Learn. Syst., 2021

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks.
PLoS Comput. Biol., 2021

TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features.
J. Chem. Inf. Model., 2021

Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features.
Briefings Bioinform., 2021

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides.
Briefings Bioinform., 2021

PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection.
Briefings Bioinform., 2021

SAResNet: self-attention residual network for predicting DNA-protein binding.
Briefings Bioinform., 2021

Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation.
Briefings Bioinform., 2021

Improving protein fold recognition using triplet network and ensemble deep learning.
Briefings Bioinform., 2021

Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites.
Briefings Bioinform., 2021

2020
ASCENT: Active Supervision for Semi-Supervised Learning.
IEEE Trans. Knowl. Data Eng., 2020

TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network.
J. Chem. Inf. Model., 2020

TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree.
J. Comput. Aided Mol. Des., 2020

2019
Fast SRC using quadratic optimisation in downsized coefficient solution subspace.
Signal Process., 2019

Neighborhood attribute reduction: a multi-criterion approach.
Int. J. Mach. Learn. Cybern., 2019

Efficient and robust TWSVM classification via a minimum L1-norm distance metric criterion.
Mach. Learn., 2019

DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines.
J. Chem. Inf. Model., 2019

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.
Bioinform., 2019

DeepTF: Accurate Prediction of Transcription Factor Binding Sites by Combining Multi-scale Convolution and Long Short-Term Memory Neural Network.
Proceedings of the Intelligence Science and Big Data Engineering. Big Data and Machine Learning, 2019

2018
A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Least squares twin bounded support vector machines based on L1-norm distance metric for classification.
Pattern Recognit., 2018

L1-Norm GEPSVM Classifier Based on an Effective Iterative Algorithm for Classification.
Neural Process. Lett., 2018

ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons.
J. Chem. Inf. Model., 2018

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.
Bioinform., 2018

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

一种基于邻域协同表达的分类方法 (Neighborhood Collaborative Representation Based Classification Method).
计算机科学, 2017

Efficient and Robust TWSVM Classifier Based on L1-Norm Distance Metric for Pattern Classification.
Proceedings of the 4th IAPR Asian Conference on Pattern Recognition, 2017

Enhancing Protein-ATP and Protein-ADP Binding Sites Prediction Using Supervised Instance-Transfer Learning.
Proceedings of the 4th IAPR Asian Conference on Pattern Recognition, 2017

2016
Multi-label learning with label-specific feature reduction.
Knowl. Based Syst., 2016

Cost-sensitive rough set approach.
Inf. Sci., 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

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

α-Dominance relation and rough sets in interval-valued information systems.
Inf. Sci., 2015

Predicting Protein-Protein Interactions with Weighted PSSM Histogram and Random Forests.
Proceedings of the Intelligence Science and Big Data Engineering. Big Data and Machine Learning Techniques, 2015

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

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

Supervised Kernel Self-Organizing Map.
Proceedings of the Intelligent Science and Intelligent Data Engineering, 2012

2009
Difference Relation-Based Rough Set and Negative Rules in Incomplete Information System.
Int. J. Uncertain. Fuzziness Knowl. Based Syst., 2009

Dominance-based rough set approach to incomplete interval-valued information system.
Data Knowl. Eng., 2009

Combination of interval-valued fuzzy set and soft set.
Comput. Math. Appl., 2009

Learning a Self-organizing Map Model on a Riemannian Manifold.
Proceedings of the Mathematics of Surfaces XIII, 2009

A Riemannian Self-Organizing Map.
Proceedings of the Image Analysis and Processing, 2009

Geodesic Discriminant Analysis on Curved Riemannian Manifold.
Proceedings of the Sixth International Conference on Fuzzy Systems and Knowledge Discovery, 2009

2008
Dominance-based rough set approach and knowledge reductions in incomplete ordered information system.
Inf. Sci., 2008

2007
Generalization of Soft Set Theory: From Crisp to Fuzzy Case.
Proceedings of the Fuzzy Information and Engineering, 2007

2006
A Complete and Rapid Feature Extraction Method for Face Recognition.
Proceedings of the 18th International Conference on Pattern Recognition (ICPR 2006), 2006

Kernel-SOM Based Visualization of Financial Time Series Forecasting.
Proceedings of the First International Conference on Innovative Computing, Information and Control (ICICIC 2006), 30 August, 2006

Quantitative Measurement for Fuzzy System to Input and Rule Perturbations.
Proceedings of the Computational Intelligence, 2006

Feature extraction by structured stepwise nonparametric maximum margin criterion.
Proceedings of the 2006 IEEE International Conference on Granular Computing, 2006

2004
An efficient renovation on kernel Fisher discriminant analysis and face recognition experiments.
Pattern Recognit., 2004

2003
Integrating rough set theory and fuzzy neural network to discover fuzzy rules.
Intell. Data Anal., 2003


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