郭菲

2026

HQMol: Hierarchical Fusion and Query-Guided Alignment for Molecular Graph-Language Modeling

Journal of Chemical Information and Modeling

DOI

2026

MAPLE: interpretable deep learning identifies selective antimicrobial peptides using joint evolutionary–physicochemical analysis

Briefings Bioinform.

DOI

2026

UDEC-MO: an uncertainty-guided deep embedded clustering framework for bulk and single-cell multi-omics data

Briefings in Bioinformatics

DOI

2026

PHScaffolding: a hypergraph clustering and dual-weight integration strategy for scaffolding with Pore-C reads

Briefings in Bioinformatics

DOI

2026

scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation

Briefings in Bioinformatics

DOI

2026

Hypergraph-Enhanced Multimodal Dynamics for Multi-Omics Classification via Intra- and Inter-Sample Fusion

Big Data Mining and Analytics

DOI

2026

Make Foundation Models Trustworthy Again: Causal Fine-Adaptation for Medical Image Segmentation

Proceedings of the AAAI Conference on Artificial Intelligence

DOI

2026

Discovery of dietary polyphenols targeting the autoinducer-2 quorum sensing system of pathogenic bacteria

Gut Microbes

DOI

2026

Motif-Aware Graph Attention Networks for Hemolytic Peptide Prediction

Lecture notes in computer science

DOI

2026

Enhancing Sample Discrimination: Drug-Drug Interaction Prediction Based on Bidirectional Event Semantics Guidance

Lecture notes in computer science

DOI

2026

A sequence knowledge-guided deep learning method for single-cell multi-omics translation

Genome biology

DOI

2026

MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction

PLoS Computational Biology

DOI

2026

HyperDeepTAD: a topologically associated domains detection method based on multiway chromatin interaction data and deep learning

BMC Genomics

DOI

2026

Graph-Embedded Deep Generative Clustering for Single-Cell Multi-Omics Data Integration

IEEE Transactions on Pattern Analysis and Machine Intelligence

DOI

2026

Refprogen: a reference-guided molecular generation model with protein-ligand joint representation for property-aware drug design

Expert Systems with Applications

DOI

2026

BioLemons: Latent Conditional Diffusion Model with VAE Embedding for Enhancing Spatial Transcriptomics

Lecture notes in computer science

DOI

2025

DMSD-CDFSAR: Distillation from Mixed-Source Domain for Cross-Domain Few-shot Action Recognition

Expert Systems With Applications，Vol. 270

DOI

2025

Foundation models in bioinformatics

National Science Review

DOI

2025

diPaRIS: Dynamic and Interpretable Protein‐RNA Interactions Prediction With U‐Shaped Network and Novel Structure Encoding

Advancement of science

DOI

2025

Revealing hidden regulatory dependencies: multi-perspective graph learning for single-cell gene regulatory network inference

Briefings in Bioinformatics

DOI

2025

LGATFormer: A Dual-Path Model Combining Line Graph Attention and Transformer for Gene Regulatory Network Inference

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2025

MultiPepDec: Decoupled Prompt Learning for Multi-Activity Therapeutic Peptides

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2025

MF-DocDDI: Drug Entity Multi-Feature Fusion for Document-Level Drug-Drug Interaction Relation Extraction

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2025

scMID: A Deep Multi-Omics Integration Framework for Comprehensive Single-Cell Data Analysis

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2025

Cancer survival prediction based on soft-label guided contrastive learning and global feature fusion

Bioinformatics

DOI

2025

HyperPhS: a pharmacophore-guided multimodal representation framework for metabolic stability prediction through contrastive hypergraph learning

Bioinformatics

DOI

2025

Prediction of ncRNA-Disease Association Based on Correntropy Induced Loss Matrix Factorization Model

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2025

Methyl-GP: accurate generic DNA methylation prediction based on a language model and representation learning

Nucleic Acids Research

DOI

2025

2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model

Bioinformatics

DOI

2025

Diff-SE: A Diffusion-Augmented Contrastive Learning Framework for Super-Enhancer Prediction

Journal of Chemical Information and Modeling

DOI

2025

Leveraging protein language models for cross-variant CRISPR/Cas9 sgRNA activity prediction

Bioinformatics

DOI

2025

RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language model

Bioinformatics

DOI

2025

deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model

Briefings in Bioinformatics

DOI

2025

MolInterAct: Multiscale Cross-Modal Interaction for Robust Molecular Representation Learning

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2025

Block sparse Bayes-based fuzzy system for RNA N6-methyladenosine sites prediction

PLoS Computational Biology

DOI

2025

Image-Enhanced Hybrid Encoding with Reinforced Contrastive Learning for Spatial Domain Identification in Spatial Transcriptomics

International Joint Conference on Artificial Intelligence

DOI

2025

SiamSegNet: A multimodal Segmentation Method Based on Cross-modal Generation for Medical Image Segmentation

Lecture notes in computer science

DOI

2025

SAMBA-Net: Enhancing Sarcomere Organization Evaluation with AI-Powered Multi-Modal Learning

Communications in computer and information science

DOI

2025

Exploring the repository of de novo-designed bifunctional antimicrobial peptides through deep learning

eLife

DOI

2025

Unlocking Dark Vision Potential for Medical Image Segmentation

International Joint Conference on Artificial Intelligence

DOI

2025

CGLoop: a neural network framework for chromatin loop prediction

BMC Genomics

DOI

2025

EnsembleSE: identification of super-enhancers based on ensemble learning

Briefings in Functional Genomics

DOI

2025

DynaPhArM: Adaptive and Physics-Constrained Modeling for Target-Drug Complexes with Drug-Specific Adaptations

neural information processing systems

DOI

2024

TranSiam: Aggregating multi-modal visual features with locality for medical image segmentation

Expert Systems With Applications，Vol. 237

DOI

2024

RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation

Bioinformatics

DOI

2024

DMAMP: A Deep-Learning Model for Detecting Antimicrobial Peptides and Their Multi-Activities

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2024

RGCNPPIS: A Residual Graph Convolutional Network for Protein-Protein Interaction Site Prediction

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2024

Comparative Analysis of Deep Generative Model for Industrial Enzyme Design

Current Bioinformatics

DOI

2024

Boundary-Aware Dual Biaffine Model for Sequential Sentence Classification in Biomedical Documents

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2024

PPRTGI: A Personalized PageRank Graph Neural Network for TF-Target Gene Interaction Detection

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2024

A-RFP: An Adaptive Residue Flexibility Prediction Method Improving Protein-ligand Docking Based on Homologous Proteins

Current Bioinformatics

DOI

2024

ComLMEss: Combining multiple protein language models enables accurate essential protein prediction

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2024

Multi-Task Driven Multi-Level Dynamical Fusion for Single-Cell Multi-Omics Cell Type Annotation

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2024

DP-BERT: a pre-trained deep language model for depression prediction using microarray data

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2024

NBCR-ac4C: A Deep Learning Framework Based on Multivariate BERT for Human mRNA N4-Acetylcytidine Sites Prediction

Journal of Chemical Information and Modeling

DOI

2024

Author response: Exploring the repository of de novo designed bifunctional antimicrobial peptides through deep learning

DOI

2024

Incorporating Water Molecules into Highly Accurate Binding Affinity Prediction for Proteins and Ligands

International Journal of Molecular Sciences

DOI

2024

MuSE: A deep learning model based on multi-feature fusion for super-enhancer prediction

Computational Biology and Chemistry

DOI

2024

CellCircLoc: Deep Neural Network for Predicting and Explaining Cell Line-Specific CircRNA Subcellular Localization

IEEE Journal of Biomedical and Health Informatics

DOI

2024

EPIMR: Prediction of Enhancer-Promoter Interactions by Multi-Scale ResNet on Image Representation

Big Data Mining and Analytics

DOI

2024

scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization

PLoS Computational Biology

DOI

2024

Structured Sparse Regularization-Based Deep Fuzzy Networks for RNA N6-Methyladenosine Sites Prediction

IEEE Transactions on Fuzzy Systems

DOI

2024

Fuzzy Neural Tangent Kernel Model for Identifying DNA N4-Methylcytosine Sites

IEEE Transactions on Fuzzy Systems

DOI

2024

Aggregate-aware model with bidirectional edge generation for medical image segmentation

Applied Soft Computing

DOI

2024

MTMol-GPT: De novo multi-target molecular generation with transformer-based generative adversarial imitation learning

PLoS Computational Biology

DOI

2024

Rapid screening of multi-point mutations for enzyme thermostability modification by utilizing computational tools

Future Generation Computer Systems

DOI

2024

Reviewer #3 (Public Review): Exploring the repository of de novo designed bifunctional antimicrobial peptides through deep learning

DOI

2024

Reviewer #1 (Public Review): Exploring the repository of de novo designed bifunctional antimicrobial peptides through deep learning

DOI

2024

Reviewer #2 (Public Review): Exploring the repository of de novo designed bifunctional antimicrobial peptides through deep learning

DOI

2024

Prediction of Protein–Protein Interactions Based on Integrating Deep Learning and Feature Fusion

International Journal of Molecular Sciences

DOI

2024

Drug–Drug Interaction Relation Extraction Based on Deep Learning: A Review

ACM Computing Surveys

DOI

2024

Design and structure of overlapping regions in PCA via deep learning

Synthetic and Systems Biotechnology

DOI

2023

A multi-scale multi-model deep neural network via ensemble strategy on high-throughput microscopy image for protein subcellular localization

Expert Systems With Applications，Vol. 212

DOI

2023

Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative Disease Diagnosis

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2023

MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway Inference

Briefings in Bioinformatics

DOI

2023

Improved structure-related prediction for insufficient homologous proteins using MSA enhancement and pre-trained language model

Briefings in Bioinformatics

DOI

2023

Low Rank Matrix Factorization Algorithm Based on Multi-Graph Regularization for Detecting Drug-Disease Association

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2023

IK-DDI: a novel framework based on instance position embedding and key external text for DDI extraction

Briefings in Bioinformatics

DOI

2023

ComDock: A novel approach for protein-protein docking with an efficient fusing strategy

Computers in Biology and Medicine

DOI

2023

PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions

Journal of Cheminformatics

DOI

2023

Identification of Drug–Side-Effect Association via Multiview Semisupervised Sparse Model

IEEE Transactions on Artificial Intelligence

DOI

2023

Multi-correntropy fusion based fuzzy system for predicting DNA N4-methylcytosine sites

Information Fusion

DOI

2023

Weighted Fuzzy System for Identifying DNA N4-Methylcytosine Sites With Kernel Entropy Component Analysis

IEEE Transactions on Artificial Intelligence

DOI

2023

A deep multiple kernel learning-based higher-order fuzzy inference system for identifying DNA N4-methylcytosine sites

Information Sciences

DOI

2023

Identification of DNA-binding protein based multiple kernel model

Mathematical Biosciences & Engineering

DOI

2023

Machine learning-aided scoring of synthesis difficulties for designer chromosomes

Science China Life Sciences

DOI

2022

BP-DDI: Drug-drug interaction prediction based on biological information and pharmacological text

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2022

Multi-scale Neighborhood Attention Transformer on U-Net for Medical Image Segmentation

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2022

Integrating Prior Knowledge with Graph Encoder for Gene Regulatory Inference from Single-cell RNA-Seq Data

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2022

Identification of drug-side effect association via restricted Boltzmann machines with penalized term

Briefings in Bioinformatics

DOI

2022

Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion

Briefings in Bioinformatics

DOI

2022

Multi-View Kernel Sparse Representation for Identification of Membrane Protein Types

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2022

Machine learning aided construction of the quorum sensing communication network for human gut microbiota

Nature Communications

DOI

2022

Two-Stage Deep Neural Network via Ensemble Learning for Melanoma Classification

Frontiers in Bioengineering and Biotechnology

DOI

2022

Inferring gene regulatory network via fusing gene expression image and RNA-seq data

Bioinformatics

DOI

2022

GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation

Briefings in Bioinformatics

DOI

2022

DeepBLI: A Transferable Multichannel Model for Detecting β-Lactamase-Inhibitor Interaction

Journal of Chemical Information and Modeling

DOI

2022

HDIContact: a novel predictor of residue–residue contacts on hetero-dimer interfaces via sequential information and transfer learning strategy

Briefings in Bioinformatics

DOI

2022

Sparse regularized joint projection model for identifying associations of non-coding RNAs and human diseases

Knowledge-Based Systems

DOI

2022

Shared subspace-based radial basis function neural network for identifying ncRNAs subcellular localization

Neural Networks

DOI

2022

Quorum sensing-based interactions among drugs, microbes, and diseases

Science China Life Sciences

DOI

2022

Identification of DNA N4-methylcytosine Sites via Multiview Kernel Sparse Representation Model

IEEE Transactions on Artificial Intelligence

DOI

2022

Identification of DNA N4-methylcytosine sites via fuzzy model on self representation

Applied Soft Computing

DOI

2022

A multi-layer multi-kernel neural network for determining associations between non-coding RNAs and diseases

Neurocomputing

DOI

2022

C-Loss Based Higher Order Fuzzy Inference Systems for Identifying DNA N4-Methylcytosine Sites

IEEE Transactions on Fuzzy Systems

DOI

2022

Res2Unet: A multi-scale channel attention network for retinal vessel segmentation

Neural Computing and Applications

DOI

2022

Comprehensive Analysis of Co-Mutations Identifies Cooperating Mechanisms of Tumorigenesis

Cancers

DOI

2021

Identification of drug–target interactions via multiple kernel-based triple collaborative matrix factorization

Briefings in Bioinformatics

DOI

2021

A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data

Briefings in Bioinformatics

DOI

2021

Laplacian Regularized Sparse Representation Based Classifier for Identifying DNA N4-Methylcytosine Sites via L2,1/2-Matrix Norm

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2021

Multi-AMP: detecting the antimicrobial peptides and their activities using the multi-task learning

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2021

Document-level DDI relation extraction with document-entity embedding

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2021

MIASNet: A medical image segmentation method predicting future based on past and current cases

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2021

GEU-Net: Rethinking the information transmission in the skip connection of U-Net architecture

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2021

Two-stage-vote ensemble framework based on integration of mutation data and gene interaction network for uncovering driver genes

Briefings in Bioinformatics

DOI

2021

Identify ncRNA Subcellular Localization via Graph Regularized k-Local Hyperplane Distance Nearest Neighbor Model on Multi-Kernel Learning

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2021

A Multichannel Deep Neural Network for Retina Vessel Segmentation via a Fusion Mechanism

Frontiers in Bioengineering and Biotechnology

DOI

2021

DeepFusionDTA: Drug-Target Binding Affinity Prediction With Information Fusion and Hybrid Deep-Learning Ensemble Model

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2021

A sequence-based multiple kernel model for identifying DNA-binding proteins

BMC Bioinformatics

DOI

2021

Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution

Briefings in Bioinformatics

DOI

2021

Inferring human microbe–drug associations via multiple kernel fusion on graph neural network

Knowledge-Based Systems

DOI

2021

Multi-Task Deep Supervision on Attention R2U-Net for Brain Tumor Segmentation

Frontiers in Oncology

DOI

2021

Identification of protein-nucleotide binding residues via graph regularized k-local hyperplane distance nearest neighbor model

Applied Intelligence

DOI

2021

Drug–disease associations prediction via Multiple Kernel-based Dual Graph Regularized Least Squares

Applied Soft Computing

DOI

2021

Identifying potential association on gene-disease network via dual hypergraph regularized least squares

BMC Genomics

DOI

2021

A systematic view of computational methods for identifying driver genes based on somatic mutation data

Briefings in Functional Genomics

DOI

2021

Identification of drug-target interactions via multi-view graph regularized link propagation model

Neurocomputing

DOI

2026

Accurate delineation of cellular niches via integrated spatial transcriptomics and histological imaging with SYMOL

Genome Research

DOI

2024

A generalizable framework for unlocking missing reactions in genome-scale metabolic networks using deep learning

arXiv preprint

2024

A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data

Genome Research

DOI

2023

Deep learning-driven automatic reconstruction of genome-scale metabolic networks

Research Square

DOI

2022

EAA-Net: Rethinking the Autoencoder Architecture with Intra-class Features for Medical Image Segmentation

arXiv preprint

2025

Catching mRNA’s Hiddens Marks: A Dual-Path Network by Contrastive Learning for N4-acetylcytidine Prediction

Frontiers in artificial intelligence and applications

DOI

2025

Beyond Slice-by-Slice: 3D Lesion Segmentation via Cross-Frame Prediction

Frontiers in artificial intelligence and applications

DOI