Journal of Biomedical Informatics

Article	Citations
A self-supervised language model selection strategy for biomedical question answering	217
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	198
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	129
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	107
Measuring disease burden with individual cumulative incidence in patients with cirrhosis	102
Discontinuous named entities in clinical text: A systematic literature review	98
Leveraging heterogeneous tabular of EHRs with prompt learning for clinical prediction	97
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	81
Multi-agent norm perception and induction in distributed healthcare	80
From translational bioinformatics computational methodologies to personalized medicine	79
A Syntax-enhanced model based on category keywords for biomedical relation extraction	76
Deep neural networks for neuro-oncology: Towards patient individualized design of chemo-radiation therapy for Glioblastoma patients	73
Cover 1/Spine	71
Identifying cancer sub-types from genomic scale data sets using confidence based integration (CBI)	70
Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors	67
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	66
Joint modeling of mixed outcomes using a rank-based sparse neural network	65
A multimodal machine learning algorithm improved diagnostic accuracy for otitis media in a school aged Aboriginal population	62
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	57
Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	57
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	57
Learning the progression patterns of treatments using a probabilistic generative model	56
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	55
Towards a unified search: Improving PubMed retrieval with full text	55
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	55

Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	53
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	52
From centralized to ad-hoc knowledge base construction for hypotheses generation	51
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	51
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	50
TransDiffECG: Semantically controllable ECG synthesis via transformer-based diffusion modeling	50
Graph-based abstractive biomedical text summarization	50
Digital twins in increasing diversity in clinical trials: A systematic review	48
fmi-ii: Table of Contents	48
Cover 1/Spine	48
Predicting pharmacotherapeutic outcomes for type 2 diabetes: An evaluation of three approaches to leveraging electronic health record data from multiple sources	45
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	45
Clustering-based fusion for medical information retrieval	44
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications	44
Using a clinical narrative-aware pre-trained language model for predicting emergency department patient disposition and unscheduled return visits	44
Natural language processing for clinical notes in dentistry: A systematic review	41
MDD-MARF: a multimodal depression detection model based on multi-level attention mechanism and residual fusion	41
Non-invasive prediction of massive transfusion during surgery using intraoperative hemodynamic monitoring data	41
Extracting medication changes in clinical narratives using pre-trained language models	40
Network-based analysis of Alzheimer’s Disease genes using multi-omics network integration with graph diffusion	40
Decision-support systems for managing polypharmacy in the elderly: A scoping review	40
Vision-language model-based semantic-guided imaging biomarker for lung nodule malignancy prediction	40
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	39
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	39
GERNERMED++: Semantic annotation in German medical NLP through transfer-learning, translation and word alignment	39
Leveraging Multi-source knowledge for Chinese clinical named entity recognition via relational graph convolutional network	37
Graph embedding-based link prediction for literature-based discovery in Alzheimer’s Disease	37
Cover 2: Editorial Board	35
A framework for longitudinal latent factor modelling of treatment response in clinical trials with applications to Psoriatic Arthritis and Rheumatoid Arthritis	35
Applications of artificial intelligence to aid early detection of dementia: A scoping review on current capabilities and future directions	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
Contrastive pre-training and linear interaction attention-based transformer for universal medical reports generation	35
Fairness and inclusion methods for biomedical informatics research	34
Advancing cancer driver gene identification through an integrative network and pathway approach	34
Deep learning in surgical process modeling: A systematic review of workflow recognition	33
Multi-view based heterogeneous graph contrastive learning for drug–target interaction 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
Cover 2: Editorial Board	33
Cover 1/Spine	32
Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages	32
Machine learning applications related to suicide in military and Veterans: A scoping literature review	32
Assessing racial bias in healthcare predictive models: Practical lessons from an empirical evaluation of 30-day hospital readmission models	31
Few-shot learning based oral cancer diagnosis using a dual feature extractor prototypical network	31
COVIDSum: A linguistically enriched SciBERT-based summarization model for COVID-19 scientific papers	31
Large-scale investigation of weakly-supervised deep learning for the fine-grained semantic indexing of biomedical literature	31
Sentiment analysis of clinical narratives: A scoping review	31
Multi-view prediction of Alzheimer’s disease progression with end-to-end integrated framework	31
They May Not Work! An evaluation of eleven sentiment analysis tools on seven social media datasets	30
Novel informatics approaches to COVID-19 Research: From methods to applications	30
Temporal attention networks for biomedical hypothesis generation	30

A machine learning approach for automating review of a RxNorm medication mapping pipeline output	30
Evaluating and mitigating bias in machine learning models for cardiovascular disease prediction	30
Study on multimodal spatially-constrained contrastive learning for knee osteoarthritis severity grading	30
Multi-modal fusion model for Time-Varying medical Data: Addressing Long-Term dependencies and memory challenges in sequence fusion	29
A methodology of phenotyping ICU patients from EHR data: High-fidelity, personalized, and interpretable phenotypes estimation	29
fmi-ii: Table of Contents	29
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia	29
Deep learning for rare disease: A scoping review	29
Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer	29
Towards a framework for interoperability and reproducibility of predictive models	28
Joint learning-based causal relation extraction from biomedical literature	28
Interpretable statistical modeling of patient flow in emergency departments	28
Adaptable graph neural networks design to support generalizability for clinical event prediction	28
Provision and evaluation of explanations within an automated planning-based approach to solving the multimorbidity problem	28
MPCM-RRG: Multi-modal Prompt Collaboration Mechanism for Radiology Report Generation	27
Focused digital cohort selection from social media using the metric backbone of biomedical knowledge graphs	27
Class imbalance in out-of-distribution datasets: Improving the robustness of the TextCNN for the classification of rare cancer types	27
Drug repositioning with metapath guidance and adaptive negative sampling enhancement	27
Enhancing AI-based diabetic retinopathy screening in low- and middle-income countries with synthetic data	27
Graph fusion prediction of autism based on attentional mechanisms	27
Emulate randomized clinical trials using heterogeneous treatment effect estimation for personalized treatments: Methodology review and benchmark	27
Identifying cooperating cancer driver genes in individual patients through hypergraph random walk	27
From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare	26
Improving severity classification of Hebrew PET-CT pathology reports using test-time augmentation	26
JLCRB: A unified multi-view-based joint representation learning for CircRNA binding sites prediction	26
fmi-ii: Table of Contents	25
CD-Tron: Leveraging large clinical language model for early detection of cognitive decline from electronic health records	25
Weakly Semi-supervised phenotyping using Electronic Health records	24
KGiA: Drug repurposing through disease-aware knowledge graph augmentation	24
Machine learning approaches for the discovery of clinical pathways from patient data: A systematic review	24
A trajectory-informed model for detecting drug-drug-host interaction from real-world data	24
Discovering interpretable medical process models: A case study in trauma resuscitation	23
Progress Note Understanding — Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 shared task	23
A new computational workflow to guide personalized drug therapy	23
A novel machine learning-based workflow to capture intra-patient heterogeneity through transcriptional multi-label characterization and clinically relevant classification	23
DC-COX: Data collaboration Cox proportional hazards model for privacy-preserving survival analysis on multiple parties	23
fmi-ii: Table of Contents	22
Inferring the patient’s age from implicit age clues in health forum posts	22
Real-time prediction of organ failures in patients with acute pancreatitis using longitudinal irregular data	22
A roadmap to artificial intelligence (AI): Methods for designing and building AI ready data to promote fairness	22
A dual-attention based coupling network for diabetes classification with heterogeneous data	22
Learning from multiple data sources for decision making in health care	22
Scaling up biomedical vision-language models: Fine-tuning, instruction tuning, and multi-modal learning	22
Gene Expression Variation Analysis (GEVA): A new R package to evaluate variations in differential expression in multiple biological conditions	22
Behaviour recommendations with a deep learning model and genetic algorithm for health debt characterisation	22
Promoting equity in clinical research: The role of social determinants of health	22
How do others cope? Extracting coping strategies for adverse drug events from social media	22
Unsupervised probabilistic models for sequential Electronic Health Records	21
Resource-efficient instruction tuning of large language models for biomedical named entity recognition	21
CLARUS: An interactive explainable AI platform for manual counterfactuals in graph neural networks	21
Technical/Algorithm, Stakeholder, and Society (TASS) barriers to the application of artificial intelligence in medicine: A systematic review	21
Integration of Mendelian randomisation and systems biology models to identify novel blood-based biomarkers for stroke	21
An interpretable machine learning approach to multimodal stress detection in a simulated office environment	21
Examining implementation outcomes in health information exchange systems: A scoping review	21
Deep learning for temporal data representation in electronic health records: A systematic review of challenges and methodologies	21
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	20
Continuous-time probabilistic models for longitudinal electronic health records	20
Causal inference for time series datasets with partially overlapping variables	20
A REDCap advanced randomization module to meet the needs of modern trials	20
Early detection of subjective cognitive decline from self-reported symptoms: An interpretable attention-cost fusion approach	20
Predicting line of therapy transition via similar patient augmentation	20
Improving the interoperability of drugs terminologies: Infusing local standardization with an international perspective	20
Cover 1/Spine	20
A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare	20
How can we reward you? A compliance and reward ontology (CaRO) for eliciting quantitative reward rules for engagement in mHealth app and healthy behaviors	20
Explainable process trace classification: An application to stroke	20
Ontology-driven identification of inconsistencies in clinical data: A case study in lung cancer phenotyping	20
Scalable relevance ranking algorithm via semantic similarity assessment improves efficiency of medical chart review	19
Pseudo-labeling and knowledge-guided contrastive learning for radiology report generation	19
GraphFusion: Integrative prediction of drug synergy using multi-scale graph representations and cell line contexts	19
Call for Papers: Special Issue on Learning from Multiple Data Sources for Decision Making in Health Care	19
Machine learning algorithm for feature space clustering of mixed data with missing information based on molecule similarity	19
A scoping review of natural language processing in addressing medically inaccurate information: Errors, misinformation, and hallucination	19
A gradient boosting tree model for multi-department venous thromboembolism risk assessment with imbalanced data	19
Augmented intelligence for multimodal virtual biopsy in breast cancer using generative artificial intelligence	19
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals	19
CODER: Knowledge-infused cross-lingual medical term embedding for term normalization	19
Question-aware transformer models for consumer health question summarization	19
Tell me something interesting: Clinical utility of machine learning prediction models in the ICU	19

Algorithms for evaluation of minimal cut sets	19
A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata	18
Multi-level process mining methodology for exploring disease-specific care processes	18
Cover 1/Spine	18
Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria’s impact on patient count and safety	18
Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data	18
fmi-ii: Table of Contents	18
An attention-based framework for integrating WSI and genomic data in cancer survival prediction	18
EGeRepDR: An enhanced genetic-based representation learning for drug repurposing using multiple biomedical sources	18
Cover 2: Editorial Board	18
Creating an ignorance-base: Exploring known unknowns in the scientific literature	17
Computational frameworks integrating deep learning and statistical models in mining multimodal omics data	17
MKCL: Medical Knowledge with Contrastive Learning model for radiology report generation	17
Multimodal large language models for medical image diagnosis: Challenges and opportunities	17
Dual parallel net: A novel deep learning model for rectal tumor segmentation via CNN and transformer with Gaussian Mixture prior	17
A utility-based machine learning-driven personalized lifestyle recommendation for cardiovascular disease prevention	17
A joint learning framework for analyzing data from national geriatric centralized networks: A new toolbox deciphering real-world complexity	17
Cover 1/Spine	17
Considerations for using predictive models that include race as an input variable: The case study of lung cancer screening	17
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias	17
Cover 1/Spine	17
An efficient model selection for linear discriminant function-based recursive feature elimination	17
Toward the European Health Data Space: The IMPaCT-Data secure infrastructure for EHR-based precision medicine research	17
Assessing fairness in machine learning models: A study of racial bias using matched counterparts in mortality prediction for patients with chronic diseases	16
Attention-based synthetic data generation for calibration-enhanced survival analysis: A case study for chronic kidney disease using electronic health records	16
Evaluating accuracy and fairness of clinical decision support algorithms when health care resources are limited	16
GutGPT: A multidimensional knowledge-enhanced large language model for gastrointestinal medicine	16
Disentangling the phenotypic patterns of hypertension and chronic hypotension	16
Leveraging undecided cases in chart-reviewed phenotypes to enhance EHR-based association studies	16
Federated causal discovery with missing data in a multicentric study on endometrial cancer	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
fmi-ii: Table of Contents	16
Computational strategies in nutrigenetics: Constructing a reference dataset of nutrition-associated genetic polymorphisms	16
Selecting a smartwatch for trials involving older adults with neurodegenerative diseases: A researcher’s framework to avoid hidden pitfalls	16
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	16
Taming vision transformers for clinical laryngoscopy assessment	16
Call for papers: Semantics-enabled biomedical literature analytics	16
Novel evaluation approach for molecular signature-based deconvolution methods	16
Stratifying individuals into non-alcoholic fatty liver disease risk levels using time series machine learning models	15
MedKA: A knowledge graph-augmented approach to improve factuality in medical Large Language Models	15
Extracting adverse drug events from clinical Notes: A systematic review of approaches used	15
Personalized insulin dose manipulation attack and its detection using interval-based temporal patterns and machine learning algorithms	15
Data-driven overdiagnosis definitions: A scoping review	15
A Multidatabase ExTRaction PipEline (METRE) for facile cross validation in critical care research	15
The crisis of biomedical foundation models	15
A simple neural vector space model for medical concept normalization using concept embeddings	15
Discovering clinical drug-drug interactions with known pharmacokinetics mechanisms using spontaneous reporting systems and electronic health records	15
On the role of the UMLS in supporting diagnosis generation proposed by Large Language Models	15
Textual emotion detection in health: Advances and applications	14
Cover 1/Spine	14
PCGMMF: a prediction method for breast cancer prognostic recurrence and metastasis risk based on enhanced multimodal feature fusion	14
A hybrid system to understand the relations between assessments and plans in progress notes	14
The RareDis corpus: A corpus annotated with rare diseases, their signs and symptoms	14
Cover 1/Spine	14
Transformer-based models for ICD-10 coding of death certificates with Portuguese text	14
Utilization of geospatial distribution in the measurement of study cohort representativeness	14
Process data analytics for hospital case-mix planning	14
Ensemble machine learning model trained on a new synthesized dataset generalizes well for stress prediction using wearable devices	14
Implementation of specialised attention mechanisms: ICD-10 classification of Gastrointestinal discharge summaries in English, Spanish and Swedish	14
Identifying task groupings for multi-task learning using pointwise V-usable information	14
Multisource and temporal variability in Portuguese hospital administrative datasets: Data quality implications	13
A visual approach to facilitating conversations about supportive care options in the context of cognitive impairment	13
A novel data-driven approach for Personas validation in healthcare using self-supervised machine learning	13
Meaningful time-related aspects of alerts in Clinical Decision Support Systems. A unified framework	13
How well do multimodal LLMs interpret CT scans? An auto-evaluation framework for analyses	13
KEBLM: Knowledge-Enhanced Biomedical Language Models	13
Evaluation of ChatGPT-generated medical responses: A systematic review and meta-analysis	13
Ontology enrichment using a large language model: Applying lexical, semantic, and knowledge network-based similarity for concept placement	13
Precision Drug Repurposing (PDR): Patient-level modeling and prediction combining foundational knowledge graph with biobank data	13
fmi-ii: Table of Contents	13
fmi-ii: Table of Contents	13
A systematic mapping study of semantic technologies in multi-omics data integration	13
Signal from the noise: A mixed graphical and quantitative process mining approach to evaluate care pathways applied to emergency stroke care	13
Causal knowledge graph construction and evaluation for clinical decision support of diabetic nephropathy	13
An annotated corpus from biomedical articles to construct a drug-food interaction database	13
Analysis of longitudinal social media for monitoring symptoms during a pandemic	13
Disease evolution and risk-based disease trajectories in congestive heart failure patients	13
Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation	13
Promoting smartphone-based keratitis screening using meta-learning: A multicenter study	13
Modeling engagement with a digital behavior change intervention (HeartSteps II): An exploratory system identification approach	13
Contextual information contributes to biomedical named entity normalization	13
Data integration through canonical correlation analysis and its application to OMICs research	13
SynthMedic: Utilizing large language models for synthetic discharge summary generation, correction and validation	12
Cover 1/Spine	12
Call for Papers: Data Generation in Healthcare Environments	12
PLRTE: Progressive learning for biomedical relation triplet extraction using large language models	12
Cover 2: Editorial Board	12
Privacy preserving collaborative learning of generalized linear mixed model	12
Negation-based transfer learning for improving biomedical Named Entity Recognition and Relation Extraction	12
Principled estimation and evaluation of treatment effect heterogeneity: A case study application to dabigatran for patients with atrial fibrillation	12
Variational temporal deconfounder network for individualized treatment effect estimation with longitudinal observational data	12
Temporal information extraction with the scalable cross-sentence context for electronic health records	12
Medication event extraction in clinical notes: Contribution of the WisPerMed team to the n2c2 2022 challenge	12
Identifying progression subphenotypes of Alzheimer’s disease from large-scale electronic health records with machine learning	12
Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration	12