Biodata Mining

Article	Citations
Investigating potential drug targets for IgA nephropathy and membranous nephropathy through multi-queue plasma protein analysis: a Mendelian randomization study based on SMR and co-localization analys	532
Transcriptome-based network analysis related to regulatory T cells infiltration identified RCN1 as a potential biomarker for prognosis in clear cell renal cell carcinoma	509
Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning	228
Exploring the common genetic basis of metabolic syndrome-related diseases and chronic kidney disease: insights from extensive genome-wide cross-trait analyses	104
CancerHubs Data Explorer: a web application for investigating mutation-enriched protein interaction hubs in human cancers	92
MOCAT: multi-omics integration with auxiliary classifiers enhanced autoencoder	85
Quantum Angle–distance kernel for ECG classification and anomaly detection: a quantum-inspired framework for biomedical signal analysis	77
A fairness-aware machine learning framework for maternal health in Ghana: integrating explainability, bias mitigation, and causal inference for ethical AI deployment	53
A simple guide to the use of Student’s t-test, Mann-Whitney U test, Chi-squared test, and Kruskal-Wallis test in biostatistics	51
Deep joint learning diagnosis of Alzheimer’s disease based on multimodal feature fusion	50
Processing imbalanced medical data at the data level with assisted-reproduction data as an example	42
Disease- and gene-specific deep learning for pathogenicity prediction of rare missense variants in cancer predisposition genes	40
circGPAcorr: an integrative tool for functional annotation of circular RNAs using expression data	40
Polygenic risk modeling of tumor stage and survival in bladder cancer	31
Comparing new tools of artificial intelligence to the authentic intelligence of our global health students	29
Ten simple rules for providing bioinformatics support within a hospital	28
Neural network methods for diagnosing patient conditions from cardiopulmonary exercise testing data	27
Machine learning approaches to identify systemic lupus erythematosus in anti-nuclear antibody-positive patients using genomic data and electronic health records	25
Skin in the game: a review of computational models of the skin	24
Unsupervised clustering based coronary artery segmentation	22
The biomedical knowledge graph of symptom phenotype in coronary artery plaque: machine learning-based analysis of real-world clinical data	22
AI-Driven SaO2 prediction from pulse oximetry and electronic health records	21
TASC: a time-aware sequence clustering framework with uncertainty quantification for electronic health record trajectories	20
Discovery of postoperative clinical states linked to cardiac surgery-associated acute kidney injury	20
Decoding dynamic miRNA:ceRNA interactions unveils therapeutic insights and targets across predominant cancer landscapes	19

Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning	18
Multi-omics analysis of genetic drivers linking aortic stenosis and left ventricular diastolic dysfunction in heart failure	18
Genetics and precision health: the ecological fallacy and artificial intelligence solutions	18
Early differentiation between paroxysmal and persistent atrial fibrillation based on interpretable machine learning: a multicenter retrospective study	17
FISM: harnessing deep learning and reinforcement learning for precision detection of microaneurysms and retinal exudates for early diabetic retinopathy diagnosis	17
Multi-output LSTM-based prediction of postoperative delirium: integrating baseline and perioperative data for enhanced risk stratification in older spine surgery patients	16
Supervised multiple kernel learning approaches for multi-omics data integration	15
Machine learning analysis of Drosophila testis transcriptomic data reveals potential regulatory sequences	14
Mapping the evolving trend of research on efferocytosis: a comprehensive data-mining-based study	14
FARFOOD: a database of potential interactions between food compounds and drugs	14
Correction: Motif clustering and digital biomarker extraction for free-living physical activity analysis	14
Using GPT-4 to write a scientific review article: a pilot evaluation study	13
A biology-based quality-diversity algorithm for drug repurposing in Alzheimer’s disease using automated machine learning	13
TLEUDS: a cascade Dual-Transfer learning system with quality- and knowledge-enhanced for precise fetal CHD screening	13
Deep learning multi-omics integration identifies new molecular subtypes of lung cancer	12
Tree-based ensemble learning models for protein-protein interactions detection: a review and experimental evaluation	12
Advancing preeclampsia prediction: a tailored machine learning pipeline integrating resampling and ensemble models for handling imbalanced medical data	12
Multimodal deep learning for survival prediction and biomarker discovery in non-small cell lung cancer	12
Effective hybrid feature selection using different bootstrap enhances cancers classification performance	11
Motif clustering and digital biomarker extraction for free-living physical activity analysis	11
Predictive modeling of ALS progression: an XGBoost approach using clinical features	10
Interpreting drug synergy in breast cancer with deep learning using target-protein inhibition profiles	10
m1A-Ensem: accurate identification of 1-methyladenosine sites through ensemble models	10
From COVID-19 to monkeypox: a novel predictive model for emerging infectious diseases	10
Ensemble feature selection and tabular data augmentation with generative adversarial networks to enhance cutaneous melanoma identification and interpretability	9
MediNet: ensemble transfer learning approach for classification of medical drugs-related text reviews using significant combined-embeddings	9
Machine learning models for reinjury risk prediction using cardiopulmonary exercise testing (CPET) data: optimizing athlete recovery	9
Disclosing transcriptomics network-based signatures of glioma heterogeneity using sparse methods	9
Assessment of the causal relationship between gut microbiota and cardiovascular diseases: a bidirectional Mendelian randomization analysis	9
An unsupervised image segmentation algorithm for coronary angiography	9
Understanding predictions of drug profiles using explainable machine learning models	9
Reference-free phylogeny from sequencing data	9
Detection of iron deficiency anemia by medical images: a comparative study of machine learning algorithms	8
Open challenges and opportunities in federated foundation models towards biomedical healthcare	8
Learning a distance for the clustering of patients with amyotrophic lateral sclerosis	8
Computational prediction of cellular elastic modulus from mechanosensitive gene expression at multiple biological levels	8
Harnessing machine learning with auditory tests and demographic factors to forecast children’s reading abilities in children living with and without HIV	8
Deep learning-based Emergency Department In-hospital Cardiac Arrest Score (Deep EDICAS) for early prediction of cardiac arrest and cardiopulmonary resuscitation in the emergency department	8
Saliency-driven explainable deep learning in medical imaging: bridging visual explainability and statistical quantitative analysis	8
A machine learning approach using conditional normalizing flow to address extreme class imbalance problems in personal health records	8
Light-XAI: a CADx for explainable cervical cancer detection via attention-based lightweight convolutional neural networks and layer-wise feature fusion	8
Changing word meanings in biomedical literature reveal pandemics and new technologies	7
Optimizing accuracy and dimensionality: a swarm intelligence strategy for robust cancer genomics classification	7
Decoding ancestry-specific genetic risk: interpretable deep feature selection reveals prostate cancer SNP disparities in diverse populations	7
Optimizing age-related hearing risk predictions: an advanced machine learning integration with HHIE-S	7
A crisis of overconfidence: Why confidence, not accuracy, is the real risk in clinical AI	7
Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families	7
6mA-StackingCV: an improved stacking ensemble model for predicting DNA N6-methyladenine site	7
Identification of immune-associated biomarkers of diabetes nephropathy tubulointerstitial injury based on machine learning: a bioinformatics multi-chip integrated analysis	7
ChatGPT and large language models in academia: opportunities and challenges	6

A multi-metric evaluation of readability in psychiatric discharge summaries	6
A Gated Recurrent Unit based architecture for recognizing ontology concepts from biological literature	6
Clustering-based low-rank matrix approximation for multimodal medical image compression	6
Evaluation of network-guided random forest for disease gene discovery	6
An explainable machine learning model for predicting postoperative cholangitis in pediatric surgical patients with pancreaticobiliary maljunction	6
Revealing third-order interactions through the integration of machine learning and entropy methods in genomic studies	6
Multi-domain feature fusion with variational mode decomposition and hybrid LightGBM-Logistic Regression for multi-class seizure classification	6
TGNet: tensor-based graph convolutional networks for multimodal brain network analysis	6
The Matthews correlation coefficient (MCC) should replace the ROC AUC as the standard metric for assessing binary classification	6
Using artificial intelligence (AI) to model clinical variant reporting for next generation sequencing (NGS) oncology assays	6
Endoscopy-based IBD identification by a quantized deep learning pipeline	6
Network-based multi-omics integrative analysis methods in drug discovery: a systematic review	6
MultiChem: predicting chemical properties using multi-view graph attention network	6
Correction: A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma	6
DAG-VAERL: a novel causal inference method for building causal gene regulatory networks	6
Exo-Tox: Identifying Exotoxins from secreted bacterial proteins	6
Machine Learning Algorithms for understanding the determinants of under-five Mortality	5
A regularized Cox hierarchical model for incorporating annotation information in predictive omic studies	5
Cross-regional radiomics: a novel framework for relationship-based feature extraction with validation in Parkinson’s disease motor subtyping	5
ScInfoVAE: interpretable dimensional reduction of single cell transcription data with variational autoencoders and extended mutual information regularization	5
Machine-learning-based models to predict cardiovascular risk using oculomics and clinic variables in KNHANES	5
The ethics of data mining in healthcare: challenges, frameworks, and future directions	5
QIGTD: identifying critical genes in the evolution of lung adenocarcinoma with tensor decomposition	5
EMMA-STRAT: a multi-omics based machine learning framework for stratification of endometrial carcinoma molecular subtypes and MSI status	5
Analysis of risk factors progression of preterm delivery using electronic health records	5
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences	5
Algorithm-based detection of acute kidney injury according to full KDIGO criteria including urine output following cardiac surgery: a descriptive analysis	5
Deciphering the tissue-specific functional effect of Alzheimer risk SNPs with deep genome annotation	5
Construction and application of medication reminder system: intelligent generation of universal medication schedule	5
Enhancing hepatopathy clinical trial efficiency: a secure, large language model-powered pre-screening pipeline	4
Deep vision in agriculture: assessing the function of YOLO in the classification of plant leaf diseases (PLDs)	4
Network analysis of longitudinal electronic health records using linear mixed models	4
MPGR-Net: multi-scale patch graph reasoning for weakly supervised pathological image segmentation	4
Towards a potential pan-cancer prognostic signature for gene expression based on probesets and ensemble machine learning	4
Machine learning based study for the classification of Type 2 diabetes mellitus subtypes	4
Prognostic biomarker discovery in pancreatic cancer through hybrid ensemble feature selection and multi-omics data	4
Radio Frequency Tagging–enabled patient monitoring: integrating mobility tracking with early warning systems for enhanced safety	4
Cross-cohort genetic risk prediction for Alzheimer’s disease: a transfer learning approach using GWAS and deep learning models	4
Quantum analysis of squiggle data	4
Electronic medical records imputation by temporal Generative Adversarial Network	4
AVSeg-XAI: Deep learning framework for A/V segmentation with vascular features reveals retinal oculomics as biomarker for cardiovascular disease	4
subMG automates data submission for metagenomics studies	4
ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data	4
Priority-Elastic net for binary disease outcome prediction based on multi-omics data	4
PAGER: A novel genotype encoding strategy for modeling deviations from additivity in complex trait association studies	4
Assessing the limitations of relief-based algorithms in detecting higher-order interactions	3
Early prediction of longitudinal treatment adherence in obstructive sleep apnea using machine learning approaches	3
Deep learning-based approaches for multi-omics data integration and analysis	3
Can open source large language models be used for tumor documentation in Germany?—An evaluation on urological doctors’ notes	3
Coxmos: interpretable survival models for high-dimensional and multi-omic data	3
Comparison of cancer subtype identification methods combined with feature selection methods in omics data analysis	3
Leveraging mixed-effects regression trees for the analysis of high-dimensional longitudinal data to identify the low and high-risk subgroups: simulation study with application to genetic study	3
Agenda setting for health equity assessment through the lenses of social determinants of health using machine learning approach: a framework and preliminary pilot study	3
Hierarchical machine learning models for predicting antenatal care utilisation among Nigerian women: Identifying actionable insights for health policy	3
Inverse problem for parameters identification in a modified SIRD epidemic model using ensemble neural networks	3
Iron homeostasis landscape informs patient survival and neoadjuvant chemotherapy response in cancer	3
Learning the therapeutic targets of acute myeloid leukemia through multiscale human interactome network and community analysis	3
Distinct network patterns emerge from Cartesian and XOR epistasis models: a comparative network science analysis	3
AI as an accelerator for defining new problems that transcends boundaries	3
Enhanced labor pain monitoring using machine learning and ECG waveform analysis for uterine contraction-induced pain	3
Automated quantitative trait locus analysis (AutoQTL)	3
CAUSALRLSTACK: adaptive balancing of deep representation and causal effect estimation with application to HIV-related health data	3
From prompt engineering to agent engineering: expanding the AI toolbox with autonomous agentic AI collaborators for biomedical discovery	3
Deep learning-driven TCR$$\beta$$ repertoire analysis enhances diagnosis and enables mining of immunological biomarkers in systemic lupus erythematosus	3
Short- and long-term weekly patient-reported outcomes prediction undergoing radiotherapy: single-patient time series model vs. transformer-based multi-patient time series model	3
Deep learning based prediction of RNA 5hmC modifications using composite feature representations and comparative benchmarking with transformer models	3
Interpretable machine learning for Parkinson’s disease diagnosis, staging, and biological mechanism exploration: a multicenter analysis	2
Feature graphs for interpretable unsupervised tree ensembles: centrality, interaction, and application in disease subtyping	2
Correction: Predictive modeling of ALS progression: an XGBoost approach using clinical features	2
Construction of an interpretable machine learning model for predicting gestational diabetes mellitus based on 45 dietary nutrients	2
Prognostic feature based on androgen-responsive genes in bladder cancer and screening for potential targeted drugs	2
A novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classification	2
Unsupervised encoding selection through ensemble pruning for biomedical classification	2
KeySDL: sparse dictionary learning for keystone microbe identification from steady-state observations using a dynamical-systems model	2
Cardio-respiratory deep learning model to predict hospital admission from emergency department electrocardiogram images and respiration videos: a prospective study	2
Construction and validation of a machine learning-based model predicting early readmission in patients with decompensated cirrhosis: a prospective two-center cohort study	2
Machine learning-based assessment of the healthy human gut mycobiota landscape using ITS1 DNA metabarcoding data	2
An online non-radiographic osteoporosis prediction calculator constructed using interpretable machine learning	2
Bioinformatics analysis of Rickettsia typhi autoimmune associations and screening of Streptomyces-derived inhibitors	2
Investigating causal effects of HDL-C on cognitive function through cross-sectional and Mendelian randomization analyses: concentration–response patterns and clues for Alzheimer’s disease prevention	2

Overlapping filter bank convolutional neural network for multisubject multicategory motor imagery brain-computer interface	2
Private pathological assessment via machine learning and homomorphic encryption	2
DBSCAN applied to EHRs data from patients with glioblastoma clusters patients based on cytosolic Hsp70 protein, sex, and brain subventricular zone	2
Proteome mining of Yersinia Enterocolitica for drug targets and computational inhibitor identification with ADMET, anti-inflammation potential and formulation characteristics	2
A generative deep neural network for pan-digestive tract cancer survival analysis	2
The Venus score for the assessment of the quality and trustworthiness of biomedical datasets	2
A deep learning approach for classifying and predicting children's nutritional status in Ethiopia using LSTM-FC neural networks	2