Journal of Biomedical Informatics

Article	Citations
From translational bioinformatics computational methodologies to personalized medicine	174
Learning the progression patterns of treatments using a probabilistic generative model	138
A Syntax-enhanced model based on category keywords for biomedical relation extraction	122
Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors	117
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	99
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	97
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	91
Predicting non-coding RNA function using Artificial Intelligence	91
Leveraging heterogeneous tabular of EHRs with prompt learning for clinical prediction	86
CBFI: A multi-layer gene network key node identification algorithm integrating structural-biological features and dynamic regulatory weights	83
Explainable multimodal deep learning models for variable-length sequences in critically ill patients	78
Corrigendum to “A pipeline for harmonising NHS Scotland laboratory data to enable national-level analyses” [J. Biomed. Inform. 2025 Feb;162:104771. https://doi.org/10.1016/j.jbi.2024.104771. Epub 2025	75
Context-Aware adaptive normalization LSTM (CAAN-LSTM) for immunotherapy decision support in cancer clinical data analysis	75
Measuring disease burden with individual cumulative incidence in patients with cirrhosis	72
Joint modeling of mixed outcomes using a rank-based sparse neural network	70
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	69
Discontinuous named entities in clinical text: A systematic literature review	67
A self-supervised language model selection strategy for biomedical question answering	67
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	66
From centralized to ad-hoc knowledge base construction for hypotheses generation	66
Towards Reliable Clinical Data: A Collaborative Data Governance Architecture with Lifecycle Integration	66
TransDiffECG: Semantically controllable ECG synthesis via transformer-based diffusion modeling	65
Towards a unified search: Improving PubMed retrieval with full text	65
Multi-agent norm perception and induction in distributed healthcare	62
Graph-based abstractive biomedical text summarization	59

Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	57
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	56
Causal intervention validation of gene regulatory signals in scGPT	56
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	55
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	53
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	53
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	53
A multimodal machine learning algorithm improved diagnostic accuracy for otitis media in a school aged Aboriginal population	52
Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	51
Cover 1/Spine	51
Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	51
fmi-ii: Table of Contents	50
MDD-MARF: a multimodal depression detection model based on multi-level attention mechanism and residual fusion	50
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	50
A federated learning framework for ethical dynamic treatment allocation across heterogeneous hospitals	49
A study of large language models for patient information extraction: Model architecture, fine-tuning strategy, and multi-task instruction tuning	48
Graph embedding-based link prediction for literature-based discovery in Alzheimer’s Disease	48
Network-based analysis of Alzheimer’s Disease genes using multi-omics network integration with graph diffusion	48
GERNERMED++: Semantic annotation in German medical NLP through transfer-learning, translation and word alignment	45
Clustering-based fusion for medical information retrieval	45
Non-invasive prediction of massive transfusion during surgery using intraoperative hemodynamic monitoring data	44
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications	44
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	44
Vision-language model-based semantic-guided imaging biomarker for lung nodule malignancy prediction	42
How to determine when data incompleteness compromises the correct training of data-enhanced mechanical models of haemodialysis? A data quality criterion	42
Call for papers: agentic AI for real-world evidence life cycle support − scaling trustworthy evaluation of treatment safety and effectiveness	42
Heterogeneous domain adaptation survival analysis with partially observed outcomes via dictionary learning and distribution alignment	41
Natural language processing for clinical notes in dentistry: A systematic review	40
Digital twins in increasing diversity in clinical trials: A systematic review	40
Extracting medication changes in clinical narratives using pre-trained language models	39
Contrastive pre-training and linear interaction attention-based transformer for universal medical reports generation	39
A computational framework for predicting drug-target interactions by fusing gene ontology information with cross attention	39
Using a clinical narrative-aware pre-trained language model for predicting emergency department patient disposition and unscheduled return visits	39
Cover 2: Editorial Board	38
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	38
A machine learning approach for automating review of a RxNorm medication mapping pipeline output	38
A framework for longitudinal latent factor modelling of treatment response in clinical trials with applications to Psoriatic Arthritis and Rheumatoid Arthritis	37
Assessing racial bias in healthcare predictive models: Practical lessons from an empirical evaluation of 30-day hospital readmission models	37
Study on multimodal spatially-constrained contrastive learning for knee osteoarthritis severity grading	36
Machine learning applications related to suicide in military and Veterans: A scoping literature review	36
Advancing cancer driver gene identification through an integrative network and pathway approach	36
Large-scale investigation of weakly-supervised deep learning for the fine-grained semantic indexing of biomedical literature	35
Deep learning in surgical process modeling: A systematic review of workflow recognition	35
Extraction of distant recurrence sites for breast cancer patients from free-text clinical notes using large language models	35
A cohort of patients in New York State with an alcohol use disorder and subsequent treatment information – A merging of two administrative data sources	35
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia	35
Deep learning for rare disease: A scoping review	34
Fairness and inclusion methods for biomedical informatics research	34
Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages	34
Temporal attention networks for biomedical hypothesis generation	34

Evaluating and mitigating bias in machine learning models for cardiovascular disease prediction	33
Corrigendum to “Theory of trust and acceptance of artificial intelligence technology (TrAAIT): An instrument to assess clinician trust and acceptance of artificial intelligence” [J. Biomed. Inform. 14	33
A methodology of phenotyping ICU patients from EHR data: High-fidelity, personalized, and interpretable phenotypes estimation	32
Few-shot learning based oral cancer diagnosis using a dual feature extractor prototypical network	32
They May Not Work! An evaluation of eleven sentiment analysis tools on seven social media datasets	32
A multidimensional hierarchical framework for sources of bias in real-world healthcare evidence: a scoping review	32
fmi-ii: Table of Contents	32
Multi-view based heterogeneous graph contrastive learning for drug–target interaction prediction	32
Sentiment analysis of clinical narratives: A scoping review	32
Graph fusion prediction of autism based on attentional mechanisms	31
Interpretable statistical modeling of patient flow in emergency departments	31
JLCRB: A unified multi-view-based joint representation learning for CircRNA binding sites prediction	30
CD-Tron: Leveraging large clinical language model for early detection of cognitive decline from electronic health records	30
Enhancing AI-based diabetic retinopathy screening in low- and middle-income countries with synthetic data	30
Towards a framework for interoperability and reproducibility of predictive models	29
Drug repositioning with metapath guidance and adaptive negative sampling enhancement	29
MPCM-RRG: Multi-modal Prompt Collaboration Mechanism for Radiology Report Generation	29
Improving severity classification of Hebrew PET-CT pathology reports using test-time augmentation	29
Focused digital cohort selection from social media using the metric backbone of biomedical knowledge graphs	28
Multi-modal fusion model for Time-Varying medical Data: Addressing Long-Term dependencies and memory challenges in sequence fusion	28
Learning dynamic binary treatment policies under treatment selection bias: A Conservative Q-Learning approach with representation balancing	28
Identifying cooperating cancer driver genes in individual patients through hypergraph random walk	27
Provision and evaluation of explanations within an automated planning-based approach to solving the multimorbidity problem	27
Emulate randomized clinical trials using heterogeneous treatment effect estimation for personalized treatments: Methodology review and benchmark	27
Joint learning-based causal relation extraction from biomedical literature	27
Adaptable graph neural networks design to support generalizability for clinical event prediction	26
From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare	26
Promoting equity in clinical research: The role of social determinants of health	25
A dual-attention based coupling network for diabetes classification with heterogeneous data	25
Editorial Board	25
fmi-ii: Table of Contents	25
Progress Note Understanding — Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 shared task	25
Learning from multiple data sources for decision making in health care	25
fmi-ii: Table of Contents	25
A new computational workflow to guide personalized drug therapy	24
Scaling up biomedical vision-language models: Fine-tuning, instruction tuning, and multi-modal learning	24
How do others cope? Extracting coping strategies for adverse drug events from social media	24
Behaviour recommendations with a deep learning model and genetic algorithm for health debt characterisation	24
Discovering interpretable medical process models: A case study in trauma resuscitation	24
DC-COX: Data collaboration Cox proportional hazards model for privacy-preserving survival analysis on multiple parties	23
Multi-domain ECG feature extraction enable accurate automated recognition of bipolar disorder, depression and schizophrenia	23
Weakly Semi-supervised phenotyping using Electronic Health records	23
A trajectory-informed model for detecting drug-drug-host interaction from real-world data	23
Unsupervised probabilistic models for sequential Electronic Health Records	23
Resource-efficient instruction tuning of large language models for biomedical named entity recognition	23
Composite pathway-guided Cox modeling for interpretable survival prediction in breast cancer	23
A roadmap to artificial intelligence (AI): Methods for designing and building AI ready data to promote fairness	22
KGiA: Drug repurposing through disease-aware knowledge graph augmentation	22
A novel machine learning-based workflow to capture intra-patient heterogeneity through transcriptional multi-label characterization and clinically relevant classification	22
Examining implementation outcomes in health information exchange systems: A scoping review	22
Machine learning approaches for the discovery of clinical pathways from patient data: A systematic review	22
An interpretable machine learning approach to multimodal stress detection in a simulated office environment	22
A gradient boosting tree model for multi-department venous thromboembolism risk assessment with imbalanced data	21
Early detection of subjective cognitive decline from self-reported symptoms: An interpretable attention-cost fusion approach	21
Technical/Algorithm, Stakeholder, and Society (TASS) barriers to the application of artificial intelligence in medicine: A systematic review	21
How can we reward you? A compliance and reward ontology (CaRO) for eliciting quantitative reward rules for engagement in mHealth app and healthy behaviors	21
Cover 1/Spine	21
Integration of Mendelian randomisation and systems biology models to identify novel blood-based biomarkers for stroke	21
Causal inference for time series datasets with partially overlapping variables	21
Predicting line of therapy transition via similar patient augmentation	21
Real-time prediction of organ failures in patients with acute pancreatitis using longitudinal irregular data	21
CLARUS: An interactive explainable AI platform for manual counterfactuals in graph neural networks	21
UCVA ontology: Standardizing local context factors to support the analysis of unwarranted clinical variation	20
A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare	20
Scalable relevance ranking algorithm via semantic similarity assessment improves efficiency of medical chart review	20
Bidirectional data harmonization across the multiple chronic disease disparities research consortium: A pipeline description of opportunities and challenges	20
Ontology-driven identification of inconsistencies in clinical data: A case study in lung cancer phenotyping	20
GraphFusion: Integrative prediction of drug synergy using multi-scale graph representations and cell line contexts	20
CTKGR: temporal knowledge graph enhanced prediction of in-hospital events for pneumonia patients using electronic health records	20
Enhancing data quality in medical concept normalization through large language models	20
Hybrid visualization-based framework for depressive state detection and characterization of atypical patients	19
Algorithms for evaluation of minimal cut sets	19
Pseudo-labeling and knowledge-guided contrastive learning for radiology report generation	19
Improving the interoperability of drugs terminologies: Infusing local standardization with an international perspective	19
Ontology-grounded knowledge graphs for mitigating hallucinations in large language models for clinical question answering	19
Temporally consistent survival prediction for non-uniform longitudinal data	19
A REDCap advanced randomization module to meet the needs of modern trials	19
A scoping review of natural language processing in addressing medically inaccurate information: Errors, misinformation, and hallucination	19
Augmented intelligence for multimodal virtual biopsy in breast cancer using generative artificial intelligence	19
EGeRepDR: An enhanced genetic-based representation learning for drug repurposing using multiple biomedical sources	19

Tell me something interesting: Clinical utility of machine learning prediction models in the ICU	19
DeepEN: A deep reinforcement learning framework for personalized enteral nutrition in critical care	19
A utility-based machine learning-driven personalized lifestyle recommendation for cardiovascular disease prevention	18
Dual parallel net: A novel deep learning model for rectal tumor segmentation via CNN and transformer with Gaussian Mixture prior	18
Retrieval-augmented in-context learning for multimodal large language models in disease classification	18
A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata	18
Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data	18
Call for Papers: Special Issue on Learning from Multiple Data Sources for Decision Making in Health Care	18
MKCL: Medical Knowledge with Contrastive Learning model for radiology report generation	18
A joint learning framework for analyzing data from national geriatric centralized networks: A new toolbox deciphering real-world complexity	18
Creating an ignorance-base: Exploring known unknowns in the scientific literature	18
Cover 1/Spine	18
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals	18
AI-assisted protocol information extraction for improved accuracy and efficiency in clinical trial workflows	18
Cover 1/Spine	17
Leveraging undecided cases in chart-reviewed phenotypes to enhance EHR-based association studies	17
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias	17
FG-DDI: Functional group-aware graph neural networks for drug–drug interaction prediction	17
Novel evaluation approach for molecular signature-based deconvolution methods	17
Computational frameworks integrating deep learning and statistical models in mining multimodal omics data	17
Selecting a smartwatch for trials involving older adults with neurodegenerative diseases: A researcher’s framework to avoid hidden pitfalls	17
Conceptual framework for prediction models of patient deterioration based on nursing documentation patterns: reproducibility and generalizability with a large number of hospitals across the United Sta	17
An attention-based framework for integrating WSI and genomic data in cancer survival prediction	17
Call for papers: Semantics-enabled biomedical literature analytics	16
Adapting the open-source Gen3 platform and kubernetes for the NIH HEAL IMPOWR and MIRHIQL clinical trial data commons: Customization, cloud transition, and optimization	16
Data-driven overdiagnosis definitions: A scoping review	16
On the role of the UMLS in supporting diagnosis generation proposed by Large Language Models	16
Computational strategies in nutrigenetics: Constructing a reference dataset of nutrition-associated genetic polymorphisms	16
Personalized insulin dose manipulation attack and its detection using interval-based temporal patterns and machine learning algorithms	16
Disentangling the phenotypic patterns of hypertension and chronic hypotension	16
Considerations for using predictive models that include race as an input variable: The case study of lung cancer screening	16
A Multidatabase ExTRaction PipEline (METRE) for facile cross validation in critical care research	16
Taming vision transformers for clinical laryngoscopy assessment	16
Toward the European Health Data Space: The IMPaCT-Data secure infrastructure for EHR-based precision medicine research	15
The crisis of biomedical foundation models	15
MedKA: A knowledge graph-augmented approach to improve factuality in medical Large Language Models	15
DispFormer: A dual attention transformer with denoising for biomedical irregular time series classification	15
Evaluating accuracy and fairness of clinical decision support algorithms when health care resources are limited	15
Assessing fairness in machine learning models: A study of racial bias using matched counterparts in mortality prediction for patients with chronic diseases	15
Attention-based synthetic data generation for calibration-enhanced survival analysis: A case study for chronic kidney disease using electronic health records	15
Federated causal discovery with missing data in a multicentric study on endometrial cancer	15
Extracting adverse drug events from clinical Notes: A systematic review of approaches used	15
GutGPT: A multidimensional knowledge-enhanced large language model for gastrointestinal medicine	15
Textual emotion detection in health: Advances and applications	15
Discovering clinical drug-drug interactions with known pharmacokinetics mechanisms using spontaneous reporting systems and electronic health records	14
Cover 1/Spine	14
Journal's cover	14
Multisource and temporal variability in Portuguese hospital administrative datasets: Data quality implications	14
Multimodal large language models for medical image diagnosis: Challenges and opportunities	14
Utilization of geospatial distribution in the measurement of study cohort representativeness	14
Contextual information contributes to biomedical named entity normalization	14
PCGMMF: a prediction method for breast cancer prognostic recurrence and metastasis risk based on enhanced multimodal feature fusion	14
Ensemble machine learning model trained on a new synthesized dataset generalizes well for stress prediction using wearable devices	14
Cover 1/Spine	14
A semi-supervised approach to unobtrusively predict abnormality in breathing patterns using hydraulic bed sensor data in older adults aging in place	14
Modeling engagement with a digital behavior change intervention (HeartSteps II): An exploratory system identification approach	14
Exploring the role of reinforcement learning in vision-language models for cardiovascular disease decision support	14
A novel data-driven approach for Personas validation in healthcare using self-supervised machine learning	13
How well do multimodal LLMs interpret CT scans? An auto-evaluation framework for analyses	13
Ontology enrichment using a large language model: Applying lexical, semantic, and knowledge network-based similarity for concept placement	13
A hybrid system to understand the relations between assessments and plans in progress notes	13
PEER: Towards reliable and efficient inference via Patience-Based Early Exiting with Rejection	13
Beyond Fine-Tuning: Leveraging Domain-Aware In-Context learning with large language models for clinical named entity recognition	13
Meaningful time-related aspects of alerts in Clinical Decision Support Systems. A unified framework	13
Transformer-based models for ICD-10 coding of death certificates with Portuguese text	13
Analysis of longitudinal social media for monitoring symptoms during a pandemic	13
Causal knowledge graph construction and evaluation for clinical decision support of diabetic nephropathy	13
Precision Drug Repurposing (PDR): Patient-level modeling and prediction combining foundational knowledge graph with biobank data	13
Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation	13
Heat and hearts: An exposure-anchored computational phenotyping framework for assessing cardiovascular vulnerability during extreme heat	13
Data integration through canonical correlation analysis and its application to OMICs research	13
A systematic mapping study of semantic technologies in multi-omics data integration	13
Promoting smartphone-based keratitis screening using meta-learning: A multicenter study	13
A visual approach to facilitating conversations about supportive care options in the context of cognitive impairment	13
KEBLM: Knowledge-Enhanced Biomedical Language Models	13