胡伦

2026

scKDGM: KAN-guided Dynamic Graph Masked Learning for Single-Cell RNA-seq Clustering

arXiv.org

DOI

2026

Reinforced Structural Reasoning for Receptive Field Optimization in GNN toward Interpretable Graph Clustering

Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2

DOI

2026

LLM-H2G: biomedical semantic-enhanced hypergraph contrastive learning for herb–disease association prediction

BMC Bioinformatics

DOI

2026

A Novel Graph Transformer Framework for Predicting Drug-Disease Associations With Structural Awareness

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2026

Graph Representation Learning in Complex Networks: Recent Advances and Open Challenges

Journal of Artificial Intelligence for Automation

DOI

2026

CQNetwork: Consensuality quantification network for interpretable identification of RNA N6-methyladenosine modification sites

Pattern Recognition

DOI

2026

DRHIN: An Integrated and Interactive Web Server for Drug Repositioning

Journal of Chemical Information and Modeling

DOI

2026

Patient-Visit-Spanned Hypergraph Learning for EHR-based Diagnosis Prediction

Proceedings of the Thirty-Fifth International Joint Conference on Artificial Intelligence

DOI

2026

StructAMP: A Residual Multi-Modal Framework for Leakage-Controlled Antimicrobial Peptide Prediction.

IEEE transactions on computational biology and bioinformatics

DOI

2026

Neighborhood Consensus-guided Reinforcement Learning for Scalable Deep Graph Clustering

IEEE transactions on multimedia

DOI

2026

Evaluating Large‐Language Models in Bioinformatics Applications

Advanced Computing

DOI

2026

Bayesian Multi-Modal Lstm with Dynamic Uncertainty Modeling for Net Fluid Removal Prediction

IEEE International Conference on Acoustics, Speech, and Signal Processing

DOI

2026

TIME: A Taylor-Inspired Mixed-Effects Model for IDH Prediction.

IEEE transactions on bio-medical engineering

DOI

2026

From Self-supervised Pre-training to Confounder-Aware Refinement: A New Approach for miRNA-Drug Association Prediction

International Conference on Intelligent Computing

DOI

2026

Spatial-spectral fusion enables drug repositioning by capturing indirect and long-range associations in biological networks

Bioinform.

DOI

2026

FD-MSGL: Drug Repositioning via Frequency-Domain Multi-Source Synergistic Graph Learning.

IEEE journal of biomedical and health informatics

DOI

2026

Dual-granularity feature learning reveals static and dynamic mechanisms of ncRNA-drug interactions.

IEEE journal of biomedical and health informatics

DOI

2025

Editorial: Special Issue on Graph Representation Learning in Drug Repositioning

Journal of Computational Biophysics and Chemistry

DOI

2025

DeepHIV: A Sequence-Based Deep Learning Model for Predicting HIV-1 Protease Cleavage Sites

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2025

GA-RLImpute: A Genetic Algorithm with Reinforcement Learning for Imputation of Medical Tabular Data

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2025

Improving Cancer Gene Identification via Mixture-of-Experts-Based Graph Representation Learning

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2025

MHGN: A Model for Drug Discovery Based on Molecular Hierarchical Graph Network

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2025

Regulation-aware graph learning for drug repositioning over heterogeneous biological network

Information Sciences

DOI

2025

Graph-Based Prediction of miRNA-Drug Associations With Multisource Information and Metapath Enhancement Matrices

IEEE journal of biomedical and health informatics

DOI

2025

A bijective inference network for interpretable identification of RNA N6-methyladenosine modification sites

Pattern Recognition

DOI

2025

Interpretable identification of cancer genes across biological networks via transformer-powered graph representation learning

Nature Biomedical Engineering

DOI

2025

Adversarial Domain Adaptation for Accurately Predicting the Associations between Herbal Compounds and Target Proteins

IEEE International Conference on Systems, Man and Cybernetics

DOI

2025

Capturing short-range and long-range dependencies of nucleotides for identifying RNA N6-methyladenosine modification sites

Comput. Biol. Medicine

DOI

2025

FMvPCI: A Multiview Fusion Neural Network for Identifying Protein Complex via Fuzzy Clustering

IEEE Transactions on Systems, Man & Cybernetics. Systems

DOI

2025

Link-Based Attributed Graph Clustering via Approximate Generative Bayesian Learning

IEEE Transactions on Systems, Man & Cybernetics. Systems

DOI

2025

Integrating Fuzzy Clustering and Graph Convolution Network to Accurately Identify Clusters From Attributed Graph

IEEE Transactions on Network Science and Engineering

DOI

2025

Identifying novel therapeutic targets of natural compounds in traditional Chinese medicine herbs with hypergraph representation learning

Briefings Bioinform.

DOI

2025

LLM-DDI: Leveraging Large Language Models for Drug-Drug Interaction Prediction on Biomedical Knowledge Graph

IEEE journal of biomedical and health informatics

DOI

2025

AMP-FreqNet:A Frequency-Domain Enhanced Model for Antimicrobial Peptide Prediction with Efficient Attention Mechanism

DOI

2025

Interpretability-guided RNA N6-methyladenosine modification site prediction with invertible neural networks

Communications Biology

DOI

2025

Consensus representation of multiple cell–cell graphs from gene signaling pathways for cell type annotation

BMC Biology

DOI

2025

EMM-DTI: ENHANCED MAMBA-BASED MODEL FOR DRUG-TARGET INTERACTION PREDICTION

Proceedings of the 9th International Conference on Electronic Information Technology and Computer Engineering

DOI

2025

Dual-Channel MiRNA Drug Resistance Prediction Model Based on Multimodal Feature Alignment

International Conference on Intelligent Computing

DOI

2025

Multi-View Contrastive Learning for Drug-Drug Interaction Event Prediction

IEEE journal of biomedical and health informatics

DOI

2025

Leveraging 3D Molecular Spatial Visual Information and Multi‐Perspective Representations for Drug Discovery

Advancement of science

DOI

2024

Fusing Higher and Lower-Order Biological Information for Drug Repositioning via Graph Representation Learning

IEEE Transactions on Emerging Topics in Computing

DOI

2024

Dual-Channel Learning Framework for Drug-Drug Interaction Prediction via Relation-Aware Heterogeneous Graph Transformer

AAAI Conference on Artificial Intelligence

DOI

2024

Knowledge-guided Protein Complex Identification with Fuzzy-based Graph Representation Learning

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2024

DNMDA: Deep Non-negative Matrix Factorization with Multi-level Integration for MiRNA-Drug Interaction Prediction

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2024

A Multi-view Nested Contrastive Learning Framework for Predicting Drug-Drug Interaction Events

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2024

Predicting the Associations between Herbal Compounds and Target Proteins via Hypergraph Convolutional Network

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2024

Dual-channel hypergraph convolutional network for predicting herb–disease associations

Briefings Bioinform.

DOI

2024

A heterogeneous information network learning model with neighborhood-level structural representation for predicting lncRNA-miRNA interactions

Computational and Structural Biotechnology Journal

DOI

2024

Toward Multilabel Classification for Multiple Disease Prediction Using Gut Microbiota Profiles

IEEE Transactions on Neural Networks and Learning Systems

DOI

2024

Knowledge Graph Neural Network With Spatial-Aware Capsule for Drug-Drug Interaction Prediction

IEEE journal of biomedical and health informatics

DOI

2024

Fuzzy-Based Deep Attributed Graph Clustering

IEEE transactions on fuzzy systems

DOI

2024

scPriorGraph: constructing biosemantic cell–cell graphs with prior gene set selection for cell type identification from scRNA-seq data

Genome Biology

DOI

2024

IDHPre: Intradialytic Hypotension Prediction Model Based on Fully Observed Features

International Conference on Intelligent Computing

DOI

2024

Learning Sequential and Structural Dependencies Between Nucleotides for RNA N6-Methyladenosine Site Identification

IEEE/CAA Journal of Automatica Sinica

DOI

2024

Motif-Aware miRNA-Disease Association Prediction via Hierarchical Attention Network

IEEE journal of biomedical and health informatics

DOI

2024

Discovering Consensus Regions for Interpretable Identification of RNA N6-Methyladenosine Modification Sites via Graph Contrastive Clustering

IEEE journal of biomedical and health informatics

DOI

2024

Editorial: Computing and artificial intelligence in digital therapeutics

Frontiers in Medicine

DOI

2024

GGANet: A Model for the Prediction of MiRNA-Drug Resistance Based on Contrastive Learning and Global Attention

International Conference on Intelligent Computing

DOI

2023

基于图注意力网络的环状RNA与疾病关联关系预测

《计算机技术与发展》

2023

Predicting Protein-Protein Interactions Using Sequence and Network Information via Variational Graph Autoencoder

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2023

Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks

BMC Bioinformatics

DOI

2023

Learning RNA sequence patterns to interpretably identify m6A modification sites

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2023

A Novel Graph Representation Learning Model for Drug Repositioning Using Graph Transition Probability Matrix Over Heterogenous Information Networks

International Conference on Intelligent Computing

DOI

2023

Artificial intelligence accelerates multi-modal biomedical process: A Survey

Neurocomputing

DOI

2023

A Deep Learning Approach Incorporating Data Missing Mechanism in Predicting Acute Kidney Injury in ICU

International Conference on Intelligent Computing

DOI

2023

FCAN-MOPSO: An Improved Fuzzy-Based Graph Clustering Algorithm for Complex Networks With Multiobjective Particle Swarm Optimization

IEEE transactions on fuzzy systems

DOI

2023

Multi-level Subgraph Representation Learning for Drug-Disease Association Prediction Over Heterogeneous Biological Information Network

International Conference on Intelligent Computing

DOI

2023

Drug-disease association prediction using semantic graph and function similarity representation learning over heterogeneous information networks.

Methods

DOI

2023

GA-ENs: A novel drug-target interactions prediction method by incorporating prior Knowledge Graph into dual Wasserstein Generative Adversarial Network with gradient penalty

Applied Soft Computing

DOI

2023

A Graph Deep Learning-Based Framework for Drug-Disease Association Identification with Chemical Structure Similarities

Journal of Computational Biophysics and Chemistry

DOI

2023

DeepCMI: a graph-based model for accurate prediction of circRNA-miRNA interactions with multiple information.

Briefings in Functional Genomics

DOI

2023

An Improved Graph Isomorphism Network for Accurate Prediction of Drug–Drug Interactions

Mathematics

DOI

2023

Drug Repositioning Method Based on Pre-trained Large Model and Network Embedding Representation

2023 IEEE International Conference on Data Mining Workshops (ICDMW)

DOI

2023

Knowledge graph embedding for profiling the interaction between transcription factors and their target genes

PLoS Comput. Biol.

DOI

2023

iGRLDTI: an improved graph representation learning method for predicting drug–target interactions over heterogeneous biological information network

Bioinform.

DOI

2022

Detection of Link Communities in Attributed Graphs via an Approximate Bayesian Generative Model

2022 5th International Conference on Artificial Intelligence and Big Data (ICAIBD)

DOI

2022

PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2022

RLFDDA: a meta-path based graph representation learning model for drug–disease association prediction

BMC Bioinformatics

DOI

2022

Attention-based Knowledge Graph Representation Learning for Predicting Drug-drug Interactions

Briefings Bioinform.

DOI

2022

Effectively predicting HIV-1 protease cleavage sites by using an ensemble learning approach

BMC Bioinformatics

DOI

2022

Multi-view heterogeneous molecular network representation learning for protein–protein interaction prediction

BMC Bioinformatics

DOI

2022

A Novel Fuzzy-Based MOPSO Algorithm for Identifying Clusters From Complex Networks

IEEE International Conference on Tools with Artificial Intelligence

DOI

2022

A geometric deep learning framework for drug repositioning over heterogeneous information networks

bioRxiv

DOI

2022

Incorporating higher order network structures to improve miRNA-disease association prediction based on functional modularity

Briefings Bioinform.

DOI

2022

Generalized Nesterov's Acceleration-Incorporated, Non-Negative and Adaptive Latent Factor Analysis

IEEE Transactions on Services Computing

DOI

2022

Predicting Drug-Disease Associations via Meta-path Representation Learning based on Heterogeneous Information Net works

International Conference on Intelligent Computing

DOI

2022

iGRLCDA: identifying circRNA-disease association based on graph representation learning

Briefings Bioinform.

DOI

2022

GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions

Briefings Bioinform.

DOI

2022

Predicting Drug-Target Interactions Over Heterogeneous Information Network

IEEE journal of biomedical and health informatics

DOI

2022

MRLDTI: A Meta-path-Based Representation Learning Model for Drug-Target Interaction Prediction

International Conference on Intelligent Computing

DOI

2022

An Algorithm of Inductively Identifying Clusters From Attributed Graphs

IEEE Transactions on Big Data

DOI

2022

A Fast Fuzzy Clustering Algorithm for Complex Networks via a Generalized Momentum Method

IEEE transactions on fuzzy systems

DOI

2022

PPAEDTI: Personalized Propagation Auto-Encoder Model for Predicting Drug-Target Interactions

IEEE journal of biomedical and health informatics

DOI

2022

A Distributed Framework for Large-scale Protein-protein Interaction Data Analysis and Prediction Using MapReduce

IEEE/CAA Journal of Automatica Sinica

DOI

2021

Identifying Protein Complexes From Protein-Protein Interaction Networks Based on Fuzzy Clustering and GO Semantic Information

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2021

A Novel Method to Predict Drug-Target Interactions Based on Large-Scale Graph Representation Learning

Cancers

DOI

2021

A survey on computational models for predicting protein-protein interactions

Briefings Bioinform.

DOI

2021

A deep learning algorithm for predicting protein-protein interactions with nonnegative latent factorization

2021 International Conference on Cyber-Physical Social Intelligence (ICCSI)

DOI

2021

Predicting Large-scale Protein-protein Interactions by Extracting Coevolutionary Patterns with MapReduce Paradigm

IEEE International Conference on Systems, Man and Cybernetics

DOI

2021

An Effective Link-Based Clustering Algorithm for Detecting Overlapping Protein Complexes in Protein-Protein Interaction Networks

IEEE Transactions on Network Science and Engineering

DOI

2021

HINGRL: predicting drug-disease associations with graph representation learning on heterogeneous information networks

Briefings Bioinform.

DOI

2021

SANE: A sequence combined attentive network embedding model for COVID-19 drug repositioning

Applied Soft Computing

DOI

2021

Predicting HIV-1 Protease Cleavage Sites With Positive-Unlabeled Learning

Frontiers in Genetics

DOI

2021

A deep learning method for repurposing antiviral drugs against new viruses via multi-view nonnegative matrix factorization and its application to SARS-CoV-2

Briefings Bioinform.

DOI

2021

An Ensemble Learning Algorithm for Predicting HIV-1 Protease Cleavage Sites

International Conference on Intelligent Computing

DOI

2021

Exploiting higher-order patterns for community detection in attributed graphs

Integr. Comput. Aided Eng.

DOI

2021

A Multi-graph Deep Learning Model for Predicting Drug-Disease Associations

International Conference on Intelligent Computing

DOI

2021

Learning from low-rank multimodal representations for predicting disease-drug associations

BMC Medical Informatics and Decision Making

DOI

2021

Incorporating Generalized Momentum Method to Accelerate Clustering Analysis of Complex Networks

2021 IEEE 17th International Conference on Automation Science and Engineering (CASE)

DOI

2021

A Novel Network-Based Algorithm for Predicting Protein-Protein Interactions Using Gene Ontology

Frontiers in Microbiology

DOI

2021

An Efficient Computational Model for Large-Scale Prediction of Protein–Protein Interactions Based on Accurate and Scalable Graph Embedding

Frontiers in Genetics

DOI

2020

Incorporating the Coevolving Information of Substrates in Predicting HIV-1 Protease Cleavage Sites

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2020

A Variational Bayesian Framework for Cluster Analysis in a Complex Network

IEEE Transactions on Knowledge and Data Engineering

DOI

2020

A Novel Stochastic Block Model for Network-Based Prediction of Protein-Protein Interactions

International Conference on Intelligent Computing

DOI

2020

The identification of variable-length coevolutionary patterns for predicting HIV-1 protease cleavage sites

IEEE International Conference on Systems, Man and Cybernetics

DOI

2020

A Highly Efficient Biomolecular Network Representation Model for Predicting Drug-Disease Associations

International Conference on Intelligent Computing

DOI

2020

HiSCF: leveraging higher-order structures for clustering analysis in biological networks

Bioinform.

DOI

2019

Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2019

Learning from Deep Representations of Multiple Networks for Predicting Drug-Target Interactions

International Conference on Intelligent Computing

DOI

2019

A Gated Recurrent Unit Model for Drug Repositioning by Combining Comprehensive Similarity Measures and Gaussian Interaction Profile Kernel

International Conference on Intelligent Computing

DOI

2019

Predicting Hospital Readmission of Diabetics using Deep Forest

IEEE International Conference on Healthcare Informatics

DOI

2019

A fast algorithm to identify coevolutionary patterns from protein sequences based on tree-based data structure

IEEE International Conference on Systems, Man and Cybernetics

DOI

2018

A gene–phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach

Bioinform.

DOI

2018

Learning Latent Factors for Community Identification and Summarization

IEEE Access

DOI

2017

Extracting Coevolutionary Features from Protein Sequences for Predicting Protein-Protein Interactions

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2017

Discovering second-order sub-structure associations in drug molecules for side-effect prediction

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2017

Identifying overlapping protein complexes in yeast protein interaction network via fuzzy clustering

IEEE International Conference on Fuzzy Systems

DOI

2017

Efficiently predicting large-scale protein-protein interactions using MapReduce

Comput. Biol. Chem.

DOI

2016

Fuzzy Clustering in a Complex Network Based on Content Relevance and Link Structures

IEEE transactions on fuzzy systems

DOI

2015

A density-based clustering approach for identifying overlapping protein complexes with functional preferences

BMC Bioinformatics

DOI

2015

Discovering Variable-Length Patterns in Protein Sequences for Protein-Protein Interaction Prediction

IEEE Transactions on Nanobioscience

DOI

2015

Discovering patterns in complex networks with applications to link analysis and clustering

2023

NutriFD: Proving the medicinal value of food nutrition based on food-disease association and treatment networks

arXiv preprint