Interdisciplinary Sciences-Computational Life Sciences

Article	Citations
Generative Adversarial Networks Based on Fine-Grained Image Recognition for the Progression Prediction of Progressive Mild Cognitive Impairment	67
DP-ID: Interleaving and Denoising to Improve the Quality of DNA Storage Image	51
Unraveling Brain Synchronisation Dynamics by Explainable Neural Networks using EEG Signals: Application to Dyslexia Diagnosis	42
HRD-Informed Digital Histology Model for Predicting Platinum Chemo-Response and Prognosis in High-Grade Serous Ovarian Cancer	41
m6ADP-GCNPUAS: m6A-Disease Prediction via Graph Convolutional Network and Positive-Unlabeled Learning with Self-Adaptive Sampling	34
Parameter Estimation in Cellular Radiation Effects Using PSO-SQP and GA-SQP Hybrid Methods	34
AttResAMD: An Attention-Driven Deep Learning Framework for Expert-Level Automated Classification of Age-Related Macular Degeneration from Fundus Photography	32
An Integrated TCN-CrossMHA Model for Predicting circRNA-RBP Binding Sites	28
Deep Clustering-Based Metabolic Stratification of Non-Small Cell Lung Cancer Patients Through Integration of Somatic Mutation Profile and Network Propagation Algorithm	27
DCPPS: Prediction of Kinase-Specific Phosphorylation Sites Using Dynamic Embedding and Cross-Representation Interaction	26
Automated Brain Tumor Classification and Grading Using Multi-scale Graph Neural Network with Spatio-Temporal Transformer Attention Through MRI Scans	25
Cervical Cancer Classification From Pap Smear Images Using Deep Convolutional Neural Network Models	23
PDDGCN: A Parasitic Disease–Drug Association Predictor Based on Multi-view Fusion Graph Convolutional Network	21
Unveiling Putative Functions of Burkholderia pseudomallei K96243 Hypothetical Proteins Via High-Throughput Characterization of Structural Similarities	21
ResDeepSurv: A Survival Model for Deep Neural Networks Based on Residual Blocks and Self-attention Mechanism	21
GSF-DTA: An Innovative Graph-Sequence Fusion Framework for Drug-Target Affinity Prediction	20
Differential Diagnosis of DCIS and Fibroadenoma Based on Ultrasound Images: a Difference-Based Self-Supervised Approach	18
IRDRM: Exploring Biological Traits and Clinical Significance in Breast Cancer Through Gene Pairs and Somatic Mutation Profiles	18
CA-UNet Segmentation Makes a Good Ischemic Stroke Risk Prediction	17
A Domain Adaptive Interpretable Substructure-Aware Graph Attention Network for Drug–Drug Interaction Prediction	17
AIP-TranLAC: A Transformer-Based Method Integrating LSTM and Attention Mechanism for Predicting Anti-inflammatory Peptides	16
BiGM-lncLoc: Bi-level Multi-Graph Meta-Learning for Predicting Cell-Specific Long Noncoding RNAs Subcellular Localization	15
dbMisLoc: A Manually Curated Database of Conditional Protein Mis-localization Events	15
Developing a Novel Methodology by Integrating Deep Learning and HMM for Segmentation of Retinal Blood Vessels in Fundus Images	14
Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis	14

Interpretable Multimodal Molecular Language Model for Drug-Target Interaction Prediction	14
AMFCL: Predicting miRNA-Disease Associations Through Adaptive Multi-source Modality Fusion and Contrastive Learning	13
VHGAE: Drug-Target Interaction Prediction Model Based on Heterogeneous Graph Variational Autoencoder	13
Machine Learning Accelerates De Novo Design of Antimicrobial Peptides	13
Diagnosis of Pancreatic Cancer Using miRNA30e Biosensor	13
Cell Fate Dynamics Reconstruction Identifies TPT1 and PTPRZ1 Feedback Loops as Master Regulators of Differentiation in Pediatric Glioblastoma-Immune Cell Networks	13
EfficientNet-resDDSC: A Hybrid Deep Learning Model Integrating Residual Blocks and Dilated Convolutions for Inferring Gene Causality in Single-Cell Data	12
Adaptive Multi-Kernel Graph Neural Network for Drug-Drug Interaction Prediction	12
ViruSeg: Harnessing the Power of Large Language-Image Model for Enhanced Virus Image Segmentation	12
Development of an Expert-Level Right Ventricular Abnormality Detection Algorithm Based on Deep Learning	11
ESM-PsyPred: Leveraging Protein Language Models for Accurate Prediction of Psychrophilic Proteins	11
Exploring Deep Learning Models for Small Histopathology Datasets: Segmentation and Classification of Glomerular Crescent Lesions with Ablation, Interpretability, and Calibration Analyses	11
Drug Sensitivity Prediction Based on Multi-stage Multi-modal Drug Representation Learning	10
A Multi-view Molecular Pre-training with Generative Contrastive Learning	10
DCDA: CircRNA–Disease Association Prediction with Feed-Forward Neural Network and Deep Autoencoder	10
CR-deal: Explainable Neural Network for circRNA-RBP Binding Site Recognition and Interpretation	10
MKLNID: Identifying Melanoma-related Pathogenic Genes Through Multiple Kernel Learning and Network Impulsive Dynamics	10
MFFBi-Unet: Merging Dynamic Sparse Attention and Multi-scale Feature Fusion for Medical Image Segmentation	10
OptimDase: An Algorithm for Predicting DNA Binding Sites with Combined Feature Encoding	10
Review of Progress in Diagnostic Studies of Autism Spectrum Disorder Using Neuroimaging	9
Protein Multiple Conformation Prediction Using Multi-Objective Evolution Algorithm	9
Transformative Deep Neural Network Approaches in Kidney Ultrasound Segmentation: Empirical Validation with an Annotated Dataset	8
Construction and Application of Traditional Chinese Medicine Knowledge Graph Based on Large Language Model	8
Semantic Consistency Network with Edge Learner and Connectivity Enhancer for Cervical Tumor Segmentation from Histopathology Images	8
Interpretable Cancer Survival Prediction by Fusing Semantic Labelling of Cell Types and Whole Slide Images	8
Plant lncRNA-miRNA Interaction Prediction Based on Counterfactual Heterogeneous Graph Attention Network	8
scVAEBGM: Clustering Analysis of Single-Cell ATAC-seq Data Using a Deep Generative Model	8
Multi-Modal Fusion with Supervised Contrastive Learning Model for Early Alzheimer’s Disease Diagnosis and Multi-Modal Biomarker Identification	8
Correction to: Machine Learning Accelerates De Novo Design of Antimicrobial Peptides	8
Exploring Novel Fentanyl Analogues Using a Graph-Based Transformer Model	8
scEM: A New Ensemble Framework for Predicting Cell Type Composition Based on scRNA-Seq Data	8
Improving the Prediction of Potential Kinase Inhibitors with Feature Learning on Multisource Knowledge	8
DOTAD: A Database of Therapeutic Antibody Developability	7
Identifying Protein Phosphorylation Site-Disease Associations Based on Multi-Similarity Fusion and Negative Sample Selection by Convolutional Neural Network	7
BEST: Basic Embedding Search Tool Enhancing Discovery of Novel Enzyme	7
easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data	7
Classification of Glomerular Pathology Images in Children Using Convolutional Neural Networks with Improved SE-ResNet Module	7
A Framework Integrating Spiking Cortical Circuit Modeling and Simulation-Based Inference to Probe Biomarkers of Cortical Dysfunction in Alzheimer’s Disease	7
Predicting miRNA-Drug Interactions Based on Multi-source Feature Fusion of Heterogeneous Network	7
DiTSim: A Diffusion-Transformers Based Single-Cell ATAC-seq Data Simulator	7
CHL-DTI: A Novel High–Low Order Information Convergence Framework for Effective Drug–Target Interaction Prediction	7
IHDFN-DTI: Interpretable Hybrid Deep Feature Fusion Network for Drug–Target Interaction Prediction	7
stGNN: Spatially Informed Cell-Type Deconvolution Based on Deep Graph Learning and Statistical Modeling	6
IMF-DDI: Information Mapping and Fusion Framework for Drug-drug Interaction Prediction	6
PmliHFM: Predicting Plant miRNA-lncRNA Interactions with Hybrid Feature Mining Network	6
STFusion: A Spatial-Temporal Dual-Pathway Network with Multi-scale Attention Fusion for Early Diagnosis of Parkinson’s Disease	6
NPI-HGNN: A Heterogeneous Graph Neural Network-Based Approach for Predicting ncRNA-Protein Interactions	6
A Novel Deep Learning Model for Medical Image Segmentation with Convolutional Neural Network and Transformer	6
iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming	6
Multi-kernel Learning Fusion Algorithm Based on RNN and GRU for ASD Diagnosis and Pathogenic Brain Region Extraction	6

Diffusion Model-Based Multi-Channel EEG Representation and Forecasting for Early Epileptic Seizure Warning	6
Combining Global-Constrained Concept Factorization and a Regularized Gaussian Graphical Model for Clustering Single-Cell RNA-seq Data	6
BMRI-NET: A Deep Stacked Ensemble Model for Multi-class Brain Tumor Classification from MRI Images	6
CRBP-HFEF: Prediction of RBP-Binding Sites on circRNAs Based on Hierarchical Feature Expansion and Fusion	6
MTGGF: A Metabolism Type-Aware Graph Generative Model for Molecular Metabolite Prediction	6
EPI-Mind: Identifying Enhancer–Promoter Interactions Based on Transformer Mechanism	5
Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers	5
Efficient Storage and Analysis of Genomic Data: A k-mer Frequency Mapping and Image Representation Method	5
AMPFLDAP: Adaptive Message Passing and Feature Fusion on Heterogeneous Network for LncRNA-Disease Associations Prediction	5
CD47Binder: Identify CD47 Binding Peptides by Combining Next-Generation Phage Display Data and Multiple Peptide Descriptors	5
Predicting Drug Synergy and Discovering New Drug Combinations Based on a Graph Autoencoder and Convolutional Neural Network	5
A Semi-supervised Reinforcement Learning Framework Incorporating the Multi-scale IncepMambaNet Network for Glaucoma Progression Prediction	5
Top 10 Research Advances in Artificial Intelligence and Biomedical Science (2025)	5
Reinforced Collaborative-Competitive Representation for Biomedical Image Recognition	5
SANNO: A Graph-Transformer Enhanced Optimal Transport Tool for Spatial Transcriptomic Annotation	5
Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation	4
Complex Prediction in Large PPI Networks Using Expansion and Stripe of Core Cliques	4
Focal-DenseNet: A Risk Assessment Framework for Alzheimer’s Disease in Heterogeneous MRI Data	4
RNA Folding Based on 5 Beads Model and Multiscale Simulation	4
Viral Rebound After Antiviral Treatment: A Mathematical Modeling Study of the Role of Antiviral Mechanism of Action	4
ABEEM/MM Magnesium Force Field for Proteins and Aqueous Solutions	4
DynamicDTA: Drug-Target Binding Affinity Prediction Using Dynamic Descriptors and Graph Representation	4
A Multi-perspective Model for Protein–Ligand-Binding Affinity Prediction	4
Classification of Brain Tumors in MRI Images with Brain-CNXSAMNet: Integrating Hybrid ConvNeXt and Spatial Attention Module Networks	4
MOGANet: A Multi-omics Graph Attention Network for Cancer Diagnosis and Biomarker Identification	4
scRDiT: Generating Single-cell RNA-seq Data by Diffusion Transformers and Accelerating Sampling	4
EMMVEP: An Ensemble Method for Protein Missense Variant Effect Prediction Based on Multi-Source Feature Fusion	4
DASNet: A Convolutional Neural Network with SE Attention Mechanism for ccRCC Tumor Grading	4
EASNet: Edge-aware Segmentation Network for Skin Lesion Segmentation with Boundary-aware and Frequency Attention Mechanisms	4
A Self-attention Graph Convolutional Network for Precision Multi-tumor Early Diagnostics with DNA Methylation Data	4
GATRSyn: Advancing Anticancer Drug Synergy Prediction Through Graph Attention Networks and Transformer-based Feature Re-embedding	4
Predicting Protein–Ligand Binding Affinity Using Fusion Model of Spatial-Temporal Graph Neural Network and 3D Structure-Based Complex Graph	4
DeepPI: Alignment-Free Analysis of Flexible Length Proteins Based on Deep Learning and Image Generator	4
Multi-Network Co-expression Analysis Enhances Biological Insights from Single-Cell Gene Expression	4
Bilinear Perceptual Fusion Algorithm Based on Brain Functional and Structural Data for ASD Diagnosis and Regions of Interest Identification	4
Application of Semi-supervised Fuzzy Clustering Based on Knowledge Weighting and Cluster Center Learning to Mammary Molybdenum Target Image Segmentation	3
Empowering Graph Neural Network-Based Computational Drug Repositioning with Large Language Model-Inferred Knowledge Representation	3
A Novel Drug–Disease Association Prediction Method Based on Deep Non-Negative Matrix Factorization with Local Graph Feature	3
A Multi-modal Drug Target Affinity Prediction Based on Graph Features and Pre-trained Sequence Embeddings	3
BoT-Net: a lightweight bag of tricks-based neural network for efficient LncRNA–miRNA interaction prediction	3
DNA Methylation Recognition Using Hybrid Deep Learning with Dual Nucleotide Visualization Fusion Feature Encoding	3
Adap-BDCM: Adaptive Bilinear Dynamic Cascade Model for Classification Tasks on CNV Datasets	3
CSEL-BGC: A Bioinformatics Framework Integrating Machine Learning for Defining the Biosynthetic Evolutionary Landscape of Uncharacterized Antibacterial Natural Products	3
PDBms—An online tool for PDB file splitting and interactive molecular visualization	3
TrambaHLApan: A Transformer and Mamba-based Neoantigen Prediction Method Considering both Antigen Presentation and Immunogenicity	3
A Novel Detection Method for High-Order SNP Epistatic Interactions Based on Explicit-Encoding-Based Multitasking Harmony Search	3
MF-MNER: Multi-models Fusion for MNER in Chinese Clinical Electronic Medical Records	3
Accurately Predicting Cell Type Abundance from Spatial Histology Image Through HPCell	3
Improving language model of human genome for DNA–protein binding prediction based on task-specific pre-training	3
Self-Supervised Graph Representation Learning for Single-Cell Classification	3
WDGBANDTI: A Deep Graph Convolutional Network-Based Bilinear Attention Network for Drug-Target Interaction Prediction with Domain Adaptation	3
A Scalable and Robust Ensemble Deep Learning Method for Predicting Drug-Target Interactions	3
Multi-scale Multimodal Representation for Enhanced Survival Prediction in Computational Pathology	3
MLWNNR: LncRNA-Disease Association Prediction with Multi-Kernel Learning-Driven Weighted Nuclear Norm Regularization	3
LRT-CLUSTER: A New Clustering Algorithm Based on Likelihood Ratio Test to Identify Driving Genes	3
A Novel Dual-Level Momentum Distillation Method with Extreme Thresholding for Imputing Single-Cell RNA Sequencing Data	3
LPI-SKMSC: Predicting LncRNA–Protein Interactions with Segmented k-mer Frequencies and Multi-space Clustering	3
Drug Repositioning Based on Deep Sparse Autoencoder and Drug–Disease Similarity	3
SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics	3
UDEDB: A Comprehensive Database for Dynamic Molecular Expression Changes in Uterine Endometrium	3
BMPMDA: Prediction of MiRNA-Disease Associations Using a Space Projection Model Based on Block Matrix	3
sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs	3
A Graph Neural Network Framework with Equivariance and Heterogeneity for Drug Repositioning	3
TP-DDI: A Two-Pathway Deep Neural Network for Drug–Drug Interaction Prediction	3
Deep Learning-Based Modeling of Drug–Target Interaction Prediction Incorporating Binding Site Information of Proteins	3
CMedRAGBot: A Chinese Medical Chatbot Based on Graph RAG and Large Language Models	3
Identify Modules Associated with Immunotherapy Response from Mouse Tumor Profiles for Stratifying Cancer Patients	3
StoneNet: An Efficient Lightweight Model Based on Depthwise Separable Convolutions for Kidney Stone Detection from CT Images	2
A Multi-Task Deep Learning Approach for Simultaneous Sleep Staging and Apnea Detection for Elderly People	2
Sensing Compound Substructures Combined with Molecular Fingerprinting to Predict Drug-Target Interactions	2
Towards Reliable Healthcare Imaging: A Multifaceted Approach in Class Imbalance Handling for Medical Image Segmentation	2
GEnDDn: An lncRNA–Disease Association Identification Framework Based on Dual-Net Neural Architecture and Deep Neural Network	2
Joint Low Rank Representation with Symmetric Orthogonal Decomposition for Clustering of scRNA-seq Data	2
Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification	2
DSMR: Dual-Stream Networks with Refinement Module for Unsupervised Multi-modal Image Registration	2
A Novel Deep-Learning-Based CADx Architecture for Classification of Thyroid Nodules Using Ultrasound Images	2
misORFPred: A Novel Method to Mine Translatable sORFs in Plant Pri-miRNAs Using Enhanced Scalable k-mer and Dynamic Ensemble Voting Strategy	2
KGLAR: Deconvoluting Spatial Transcriptomics Data with Single-cell Transcriptomes through Knowledge-guided NMF and Least Angle Regression	2
AMPred-MFG: Investigating the Mutagenicity of Compounds Using Motif-Based Graph Combined with Molecular Fingerprints and Graph Attention Mechanism	2
MLDTA an Ensemble-Driven Multimodal Model with Dynamic Fusion for Drug–Target Affinity Prediction	2

HAFMMDA: HIN2vec-Based Attentional Factorization Machines for Predicting Microbe-Drug Associations	2
MetaV: A Pioneer in feature Augmented Meta-Learning Based Vision Transformer for Medical Image Classification	2
ScAGCN: Graph Convolutional Network with Adaptive Aggregation Mechanism for scRNA-seq Data Dimensionality Reduction	2
Predicting CircRNA-Disease Associations Based on Heterogeneous Graph Neural Network and Knowledge Graph Attribute Mining Attention	2
A Deep Neural Network for Predicting Synergistic Drug Combinations on Cancer	2
Computer-Aided Diagnosis of Complications After Liver Transplantation Based on Transfer Learning	2
GraphsformerCPI: Graph Transformer for Compound–Protein Interaction Prediction	2
ResNeXt-Based Rescoring Model for Proteoform Characterization in Top-Down Mass Spectra	2
ABTrans: A Transformer-based Model for Predicting Interaction between Anti-Aβ Antibodies and Peptides	2
Enhancing the Feature Representation of Protein Sequence Descriptors in Protein-Protein Interaction Prediction	2
ResNet-Powered Multi-Class Identification of Sequence Patterns for Genome Replication Timing Analysis	2
Reconstructing Waddington Landscape from Cell Migration and Proliferation	2
BES-Designer: A Web Tool to Design Guide RNAs for Base Editing to Simplify Library	2
PhaGCN_Cluster: A Scalable and Robust Framework for Automated Classification and Discovery of Viral Dark Matter from Metagenomes	2
Subgraph Neural Networks Enhanced by Global Similarity for Drug Repositioning	2
Synchronous Mutual Learning Network and Asynchronous Multi-Scale Embedding Network for miRNA-Disease Association Prediction	2
A Combined Manual Annotation and Deep-Learning Natural Language Processing Study on Accurate Entity Extraction in Hereditary Disease Related Biomedical Literature	2