Interdisciplinary Sciences-Computational Life Sciences

Article	Citations
Parameter Estimation in Cellular Radiation Effects Using PSO-SQP and GA-SQP Hybrid Methods	69
m6ADP-GCNPUAS: m6A-Disease Prediction via Graph Convolutional Network and Positive-Unlabeled Learning with Self-Adaptive Sampling	66
DP-ID: Interleaving and Denoising to Improve the Quality of DNA Storage Image	56
Unraveling Brain Synchronisation Dynamics by Explainable Neural Networks using EEG Signals: Application to Dyslexia Diagnosis	48
AttResAMD: An Attention-Driven Deep Learning Framework for Expert-Level Automated Classification of Age-Related Macular Degeneration from Fundus Photography	47
Computational Study of Methionine Methylation Process Catalyzed by SETD3	42
An Integrated TCN-CrossMHA Model for Predicting circRNA-RBP Binding Sites	37
Deep Clustering-Based Metabolic Stratification of Non-Small Cell Lung Cancer Patients Through Integration of Somatic Mutation Profile and Network Propagation Algorithm	35
DCPPS: Prediction of Kinase-Specific Phosphorylation Sites Using Dynamic Embedding and Cross-Representation Interaction	30
CA-UNet Segmentation Makes a Good Ischemic Stroke Risk Prediction	27
Cervical Cancer Classification From Pap Smear Images Using Deep Convolutional Neural Network Models	25
PDDGCN: A Parasitic Disease–Drug Association Predictor Based on Multi-view Fusion Graph Convolutional Network	24
Automated Brain Tumor Classification and Grading Using Multi-scale Graph Neural Network with Spatio-Temporal Transformer Attention Through MRI Scans	22
ResDeepSurv: A Survival Model for Deep Neural Networks Based on Residual Blocks and Self-attention Mechanism	21
Differential Diagnosis of DCIS and Fibroadenoma Based on Ultrasound Images: a Difference-Based Self-Supervised Approach	21
GSF-DTA: An Innovative Graph-Sequence Fusion Framework for Drug-Target Affinity Prediction	21
Unveiling Putative Functions of Burkholderia pseudomallei K96243 Hypothetical Proteins Via High-Throughput Characterization of Structural Similarities	20
AMFCL: Predicting miRNA-Disease Associations Through Adaptive Multi-source Modality Fusion and Contrastive Learning	20
Adaptive Multi-Kernel Graph Neural Network for Drug-Drug Interaction Prediction	19
Development of Electrochemical Biosensor for miR204-Based Cancer Diagnosis	18
BiGM-lncLoc: Bi-level Multi-Graph Meta-Learning for Predicting Cell-Specific Long Noncoding RNAs Subcellular Localization	17
ViruSeg: Harnessing the Power of Large Language-Image Model for Enhanced Virus Image Segmentation	17
Diagnosis of Pancreatic Cancer Using miRNA30e Biosensor	17
VHGAE: Drug-Target Interaction Prediction Model Based on Heterogeneous Graph Variational Autoencoder	17
Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis	14

Cell Fate Dynamics Reconstruction Identifies TPT1 and PTPRZ1 Feedback Loops as Master Regulators of Differentiation in Pediatric Glioblastoma-Immune Cell Networks	14
Developing a Novel Methodology by Integrating Deep Learning and HMM for Segmentation of Retinal Blood Vessels in Fundus Images	14
Machine Learning Accelerates De Novo Design of Antimicrobial Peptides	14
dbMisLoc: A Manually Curated Database of Conditional Protein Mis-localization Events	13
A Domain Adaptive Interpretable Substructure-Aware Graph Attention Network for Drug–Drug Interaction Prediction	13
AIP-TranLAC: A Transformer-Based Method Integrating LSTM and Attention Mechanism for Predicting Anti-inflammatory Peptides	13
EfficientNet-resDDSC: A Hybrid Deep Learning Model Integrating Residual Blocks and Dilated Convolutions for Inferring Gene Causality in Single-Cell Data	12
MKLNID: Identifying Melanoma-related Pathogenic Genes Through Multiple Kernel Learning and Network Impulsive Dynamics	11
MFFBi-Unet: Merging Dynamic Sparse Attention and Multi-scale Feature Fusion for Medical Image Segmentation	11
Development of an Expert-Level Right Ventricular Abnormality Detection Algorithm Based on Deep Learning	11
OptimDase: An Algorithm for Predicting DNA Binding Sites with Combined Feature Encoding	11
CR-deal: Explainable Neural Network for circRNA-RBP Binding Site Recognition and Interpretation	11
Single-Cell Transcriptome Analysis Reveals the Role of Pancreatic Secretome in COVID-19 Associated Multi-organ Dysfunctions	11
Drug Sensitivity Prediction Based on Multi-stage Multi-modal Drug Representation Learning	11
A Multi-view Molecular Pre-training with Generative Contrastive Learning	11
Transformative Deep Neural Network Approaches in Kidney Ultrasound Segmentation: Empirical Validation with an Annotated Dataset	10
scEM: A New Ensemble Framework for Predicting Cell Type Composition Based on scRNA-Seq Data	10
scVAEBGM: Clustering Analysis of Single-Cell ATAC-seq Data Using a Deep Generative Model	10
Protein Multiple Conformation Prediction Using Multi-Objective Evolution Algorithm	9
Correction to: Machine Learning Accelerates De Novo Design of Antimicrobial Peptides	9
DCDA: CircRNA–Disease Association Prediction with Feed-Forward Neural Network and Deep Autoencoder	9
Exploring Novel Fentanyl Analogues Using a Graph-Based Transformer Model	9
Review of Progress in Diagnostic Studies of Autism Spectrum Disorder Using Neuroimaging	9
Plant lncRNA-miRNA Interaction Prediction Based on Counterfactual Heterogeneous Graph Attention Network	9
Construction and Application of Traditional Chinese Medicine Knowledge Graph Based on Large Language Model	9
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
Improving the Prediction of Potential Kinase Inhibitors with Feature Learning on Multisource Knowledge	8
easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data	8
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
Identifying Protein Phosphorylation Site-Disease Associations Based on Multi-Similarity Fusion and Negative Sample Selection by Convolutional Neural Network	7
IDDLncLoc: Subcellular Localization of LncRNAs Based on a Framework for Imbalanced Data Distributions	7
iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming	7
MVGCNMDA: Multi-view Graph Augmentation Convolutional Network for Uncovering Disease-Related Microbes	7
BEST: Basic Embedding Search Tool Enhancing Discovery of Novel Enzyme	7
DOTAD: A Database of Therapeutic Antibody Developability	7
IMF-DDI: Information Mapping and Fusion Framework for Drug-drug Interaction Prediction	7
PmliHFM: Predicting Plant miRNA-lncRNA Interactions with Hybrid Feature Mining Network	7
IHDFN-DTI: Interpretable Hybrid Deep Feature Fusion Network for Drug–Target Interaction Prediction	7
CHL-DTI: A Novel High–Low Order Information Convergence Framework for Effective Drug–Target Interaction Prediction	7
Classification of Glomerular Pathology Images in Children Using Convolutional Neural Networks with Improved SE-ResNet Module	7
CRBP-HFEF: Prediction of RBP-Binding Sites on circRNAs Based on Hierarchical Feature Expansion and Fusion	7
BMRI-NET: A Deep Stacked Ensemble Model for Multi-class Brain Tumor Classification from MRI Images	7
RicENN: Prediction of Rice Enhancers with Neural Network Based on DNA Sequences	6
Dual Attention Mechanisms and Feature Fusion Networks Based Method for Predicting LncRNA-Disease Associations	6
Combining Global-Constrained Concept Factorization and a Regularized Gaussian Graphical Model for Clustering Single-Cell RNA-seq Data	6
SANNO: A Graph-Transformer Enhanced Optimal Transport Tool for Spatial Transcriptomic Annotation	6
Multi-kernel Learning Fusion Algorithm Based on RNN and GRU for ASD Diagnosis and Pathogenic Brain Region Extraction	6
MTGGF: A Metabolism Type-Aware Graph Generative Model for Molecular Metabolite Prediction	6

Diffusion Model-Based Multi-Channel EEG Representation and Forecasting for Early Epileptic Seizure Warning	6
Efficient Storage and Analysis of Genomic Data: A k-mer Frequency Mapping and Image Representation Method	6
stGNN: Spatially Informed Cell-Type Deconvolution Based on Deep Graph Learning and Statistical Modeling	6
A Novel Deep Learning Model for Medical Image Segmentation with Convolutional Neural Network and Transformer	6
NPI-HGNN: A Heterogeneous Graph Neural Network-Based Approach for Predicting ncRNA-Protein Interactions	6
Predicting Drug Synergy and Discovering New Drug Combinations Based on a Graph Autoencoder and Convolutional Neural Network	6
Complex Prediction in Large PPI Networks Using Expansion and Stripe of Core Cliques	5
A Self-attention Graph Convolutional Network for Precision Multi-tumor Early Diagnostics with DNA Methylation Data	5
Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers	5
AMPFLDAP: Adaptive Message Passing and Feature Fusion on Heterogeneous Network for LncRNA-Disease Associations Prediction	5
Predicting Protein–Ligand Binding Affinity Using Fusion Model of Spatial-Temporal Graph Neural Network and 3D Structure-Based Complex Graph	5
scRDiT: Generating Single-cell RNA-seq Data by Diffusion Transformers and Accelerating Sampling	5
Classification of Brain Tumors in MRI Images with Brain-CNXSAMNet: Integrating Hybrid ConvNeXt and Spatial Attention Module Networks	5
EPI-Mind: Identifying Enhancer–Promoter Interactions Based on Transformer Mechanism	5
CD47Binder: Identify CD47 Binding Peptides by Combining Next-Generation Phage Display Data and Multiple Peptide Descriptors	5
Visualizing a Field of Research for the Coronavirus Replication in Humans with Knowledge Mapping: Evidence from Web of Science	5
Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation	5
A Semi-supervised Reinforcement Learning Framework Incorporating the Multi-scale IncepMambaNet Network for Glaucoma Progression Prediction	5
Reinforced Collaborative-Competitive Representation for Biomedical Image Recognition	5
Top 10 Research Advances in Artificial Intelligence and Biomedical Science (2025)	5
EASNet: Edge-aware Segmentation Network for Skin Lesion Segmentation with Boundary-aware and Frequency Attention Mechanisms	4
A Multi-perspective Model for Protein–Ligand-Binding Affinity Prediction	4
Viral Rebound After Antiviral Treatment: A Mathematical Modeling Study of the Role of Antiviral Mechanism of Action	4
DASNet: A Convolutional Neural Network with SE Attention Mechanism for ccRCC Tumor Grading	4
Machine Learning Applications in Drug Repurposing	4
Bilinear Perceptual Fusion Algorithm Based on Brain Functional and Structural Data for ASD Diagnosis and Regions of Interest Identification	4
DynamicDTA: Drug-Target Binding Affinity Prediction Using Dynamic Descriptors and Graph Representation	4
RNA Folding Based on 5 Beads Model and Multiscale Simulation	4
DNA Methylation Recognition Using Hybrid Deep Learning with Dual Nucleotide Visualization Fusion Feature Encoding	4
Multi-feature Fusion Method Based on Linear Neighborhood Propagation Predict Plant LncRNA–Protein Interactions	4
PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest	4
DeepPI: Alignment-Free Analysis of Flexible Length Proteins Based on Deep Learning and Image Generator	4
BoT-Net: a lightweight bag of tricks-based neural network for efficient LncRNA–miRNA interaction prediction	4
WDGBANDTI: A Deep Graph Convolutional Network-Based Bilinear Attention Network for Drug-Target Interaction Prediction with Domain Adaptation	4
A Novel Dual-Level Momentum Distillation Method with Extreme Thresholding for Imputing Single-Cell RNA Sequencing Data	3
Empowering Graph Neural Network-Based Computational Drug Repositioning with Large Language Model-Inferred Knowledge Representation	3
Improving language model of human genome for DNA–protein binding prediction based on task-specific pre-training	3
SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics	3
sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs	3
tensorGSEA: Detecting Differential Pathways in Type 2 Diabetes via Tensor-Based Data Reconstruction	3
Self-Supervised Graph Representation Learning for Single-Cell Classification	3
TrambaHLApan: A Transformer and Mamba-based Neoantigen Prediction Method Considering both Antigen Presentation and Immunogenicity	3
FSCAM: CAM-Based Feature Selection for Clustering scRNA-seq	3
PDBms—An online tool for PDB file splitting and interactive molecular visualization	3
Drug Repositioning Based on Deep Sparse Autoencoder and Drug–Disease Similarity	3
A Multi-modal Drug Target Affinity Prediction Based on Graph Features and Pre-trained Sequence Embeddings	3
BMPMDA: Prediction of MiRNA-Disease Associations Using a Space Projection Model Based on Block Matrix	3
CSEL-BGC: A Bioinformatics Framework Integrating Machine Learning for Defining the Biosynthetic Evolutionary Landscape of Uncharacterized Antibacterial Natural Products	3
Correction to: Brain Tumor Detection and Classification Using Cycle Generative Adversarial Networks	3
MLWNNR: LncRNA-Disease Association Prediction with Multi-Kernel Learning-Driven Weighted Nuclear Norm Regularization	3
Deep Learning-Based Modeling of Drug–Target Interaction Prediction Incorporating Binding Site Information of Proteins	3
LPI-SKMSC: Predicting LncRNA–Protein Interactions with Segmented k-mer Frequencies and Multi-space Clustering	3
Application of Semi-supervised Fuzzy Clustering Based on Knowledge Weighting and Cluster Center Learning to Mammary Molybdenum Target Image Segmentation	3
Accurately Predicting Cell Type Abundance from Spatial Histology Image Through HPCell	3
TP-DDI: A Two-Pathway Deep Neural Network for Drug–Drug Interaction Prediction	3
A Novel Drug–Disease Association Prediction Method Based on Deep Non-Negative Matrix Factorization with Local Graph Feature	3
Adap-BDCM: Adaptive Bilinear Dynamic Cascade Model for Classification Tasks on CNV Datasets	3
A Scalable and Robust Ensemble Deep Learning Method for Predicting Drug-Target Interactions	3
MF-MNER: Multi-models Fusion for MNER in Chinese Clinical Electronic Medical Records	3
LRT-CLUSTER: A New Clustering Algorithm Based on Likelihood Ratio Test to Identify Driving Genes	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
ABTrans: A Transformer-based Model for Predicting Interaction between Anti-Aβ Antibodies and Peptides	2
Subgraph Neural Networks Enhanced by Global Similarity for Drug Repositioning	2
U-shaped Retinal Vessel Segmentation Based on Adaptive Aggregation of Feature Information	2
Predicting CircRNA-Disease Associations Based on Heterogeneous Graph Neural Network and Knowledge Graph Attribute Mining Attention	2
BES-Designer: A Web Tool to Design Guide RNAs for Base Editing to Simplify Library	2
ScAGCN: Graph Convolutional Network with Adaptive Aggregation Mechanism for scRNA-seq Data Dimensionality Reduction	2
Multiple Protein Subcellular Locations Prediction Based on Deep Convolutional Neural Networks with Self-Attention Mechanism	2
Enhancing the Feature Representation of Protein Sequence Descriptors in Protein-Protein Interaction Prediction	2
Clinical and Laboratory Approach to Diagnose COVID-19 Using Machine Learning	2
misORFPred: A Novel Method to Mine Translatable sORFs in Plant Pri-miRNAs Using Enhanced Scalable k-mer and Dynamic Ensemble Voting Strategy	2
AMPred-MFG: Investigating the Mutagenicity of Compounds Using Motif-Based Graph Combined with Molecular Fingerprints and Graph Attention Mechanism	2
Computer-Aided Diagnosis of Complications After Liver Transplantation Based on Transfer Learning	2
ResNeXt-Based Rescoring Model for Proteoform Characterization in Top-Down Mass Spectra	2
Identifying Visual Attention Features Accurately Discerning Between Autism and Typically Developing: a Deep Learning Framework	2
ResNet-Powered Multi-Class Identification of Sequence Patterns for Genome Replication Timing Analysis	2
Towards Reliable Healthcare Imaging: A Multifaceted Approach in Class Imbalance Handling for Medical Image Segmentation	2
Joint Low Rank Representation with Symmetric Orthogonal Decomposition for Clustering of scRNA-seq Data	2
A Novel Detection Method for High-Order SNP Epistatic Interactions Based on Explicit-Encoding-Based Multitasking Harmony Search	2

MetaV: A Pioneer in feature Augmented Meta-Learning Based Vision Transformer for Medical Image Classification	2
Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification	2
Synchronous Mutual Learning Network and Asynchronous Multi-Scale Embedding Network for miRNA-Disease Association Prediction	2
GraphsformerCPI: Graph Transformer for Compound–Protein Interaction Prediction	2
A Combined Manual Annotation and Deep-Learning Natural Language Processing Study on Accurate Entity Extraction in Hereditary Disease Related Biomedical Literature	2
A Multi-Task Deep Learning Approach for Simultaneous Sleep Staging and Apnea Detection for Elderly People	2
HAFMMDA: HIN2vec-Based Attentional Factorization Machines for Predicting Microbe-Drug Associations	2
Sensing Compound Substructures Combined with Molecular Fingerprinting to Predict Drug-Target Interactions	2
GEnDDn: An lncRNA–Disease Association Identification Framework Based on Dual-Net Neural Architecture and Deep Neural Network	2
Reconstructing Waddington Landscape from Cell Migration and Proliferation	2
CMedRAGBot: A Chinese Medical Chatbot Based on Graph RAG and Large Language Models	2
A Deep Neural Network for Predicting Synergistic Drug Combinations on Cancer	2
DSMR: Dual-Stream Networks with Refinement Module for Unsupervised Multi-modal Image Registration	2