Journal of Biomedical Informatics

Article	Citations
Towards a unified search: Improving PubMed retrieval with full text	150
From translational bioinformatics computational methodologies to personalized medicine	145
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	114
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	110
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	106
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	93
Discontinuous named entities in clinical text: A systematic literature review	83
Graph-based abstractive biomedical text summarization	83
A self-supervised language model selection strategy for biomedical question answering	82
Learning the progression patterns of treatments using a probabilistic generative model	76
Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	73
A Syntax-enhanced model based on category keywords for biomedical relation extraction	68
Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors	67
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	66
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	66
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	66
Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	65
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	61
Predicting non-coding RNA function using Artificial Intelligence	61
Multi-agent norm perception and induction in distributed healthcare	61
From centralized to ad-hoc knowledge base construction for hypotheses generation	60
A multimodal machine learning algorithm improved diagnostic accuracy for otitis media in a school aged Aboriginal population	58
Leveraging heterogeneous tabular of EHRs with prompt learning for clinical prediction	58
Explainable multimodal deep learning models for variable-length sequences in critically ill patients	56
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	56

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	52
Context-Aware adaptive normalization LSTM (CAAN-LSTM) for immunotherapy decision support in cancer clinical data analysis	52
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	52
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	51
Joint modeling of mixed outcomes using a rank-based sparse neural network	51
Measuring disease burden with individual cumulative incidence in patients with cirrhosis	51
TransDiffECG: Semantically controllable ECG synthesis via transformer-based diffusion modeling	50
Cover 1/Spine	50
Extracting medication changes in clinical narratives using pre-trained language models	48
fmi-ii: Table of Contents	48
A computational framework for predicting drug-target interactions by fusing gene ontology information with cross attention	47
Decision-support systems for managing polypharmacy in the elderly: A scoping review	46
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	46
Contrastive pre-training and linear interaction attention-based transformer for universal medical reports generation	46
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	45
Vision-language model-based semantic-guided imaging biomarker for lung nodule malignancy prediction	44
A federated learning framework for ethical dynamic treatment allocation across heterogeneous hospitals	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	44
MDD-MARF: a multimodal depression detection model based on multi-level attention mechanism and residual fusion	44
A study of large language models for patient information extraction: Model architecture, fine-tuning strategy, and multi-task instruction tuning	43
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications	43
Network-based analysis of Alzheimer’s Disease genes using multi-omics network integration with graph diffusion	41
Graph embedding-based link prediction for literature-based discovery in Alzheimer’s Disease	41
GERNERMED++: Semantic annotation in German medical NLP through transfer-learning, translation and word alignment	40
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	40
Non-invasive prediction of massive transfusion during surgery using intraoperative hemodynamic monitoring data	40
Clustering-based fusion for medical information retrieval	40
Digital twins in increasing diversity in clinical trials: A systematic review	39
Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer	37
Fairness and inclusion methods for biomedical informatics research	37
Cover 2: Editorial Board	37
Study on multimodal spatially-constrained contrastive learning for knee osteoarthritis severity grading	36
Cover 2: Editorial Board	36
Assessing racial bias in healthcare predictive models: Practical lessons from an empirical evaluation of 30-day hospital readmission models	36
A multidimensional hierarchical framework for sources of bias in real-world healthcare evidence: a scoping review	36
Advancing cancer driver gene identification through an integrative network and pathway approach	36
Machine learning applications related to suicide in military and Veterans: A scoping literature review	36
Evaluating and mitigating bias in machine learning models for cardiovascular disease prediction	35
Large-scale investigation of weakly-supervised deep learning for the fine-grained semantic indexing of biomedical literature	35
Few-shot learning based oral cancer diagnosis using a dual feature extractor prototypical network	35
Deep learning in surgical process modeling: A systematic review of workflow recognition	34
A framework for longitudinal latent factor modelling of treatment response in clinical trials with applications to Psoriatic Arthritis and Rheumatoid Arthritis	34
A methodology of phenotyping ICU patients from EHR data: High-fidelity, personalized, and interpretable phenotypes estimation	34
They May Not Work! An evaluation of eleven sentiment analysis tools on seven social media datasets	34
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia	34
Extraction of distant recurrence sites for breast cancer patients from free-text clinical notes using large language models	33
Temporal attention networks for biomedical hypothesis generation	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 cohort of patients in New York State with an alcohol use disorder and subsequent treatment information – A merging of two administrative data sources	32

Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages	32
Sentiment analysis of clinical narratives: A scoping review	31
A machine learning approach for automating review of a RxNorm medication mapping pipeline output	31
Deep learning for rare disease: A scoping review	31
Multi-view based heterogeneous graph contrastive learning for drug–target interaction prediction	31
fmi-ii: Table of Contents	30
Interpretable statistical modeling of patient flow in emergency departments	30
Identifying cooperating cancer driver genes in individual patients through hypergraph random walk	30
Provision and evaluation of explanations within an automated planning-based approach to solving the multimorbidity problem	30
JLCRB: A unified multi-view-based joint representation learning for CircRNA binding sites prediction	29
Graph fusion prediction of autism based on attentional mechanisms	29
Improving severity classification of Hebrew PET-CT pathology reports using test-time augmentation	28
Drug repositioning with metapath guidance and adaptive negative sampling enhancement	28
Multi-modal fusion model for Time-Varying medical Data: Addressing Long-Term dependencies and memory challenges in sequence fusion	27
Adaptable graph neural networks design to support generalizability for clinical event prediction	27
Joint learning-based causal relation extraction from biomedical literature	27
CD-Tron: Leveraging large clinical language model for early detection of cognitive decline from electronic health records	27
Enhancing AI-based diabetic retinopathy screening in low- and middle-income countries with synthetic data	27
Towards a framework for interoperability and reproducibility of predictive models	26
MPCM-RRG: Multi-modal Prompt Collaboration Mechanism for Radiology Report Generation	26
From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare	26
Learning dynamic binary treatment policies under treatment selection bias: A Conservative Q-Learning approach with representation balancing	26
Focused digital cohort selection from social media using the metric backbone of biomedical knowledge graphs	26
fmi-ii: Table of Contents	25
fmi-ii: Table of Contents	25
Behaviour recommendations with a deep learning model and genetic algorithm for health debt characterisation	25
Progress Note Understanding — Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 shared task	25
Emulate randomized clinical trials using heterogeneous treatment effect estimation for personalized treatments: Methodology review and benchmark	25
A dual-attention based coupling network for diabetes classification with heterogeneous data	25
Editorial Board	25
Discovering interpretable medical process models: A case study in trauma resuscitation	24
Integration of Mendelian randomisation and systems biology models to identify novel blood-based biomarkers for stroke	24
Real-time prediction of organ failures in patients with acute pancreatitis using longitudinal irregular data	24
A roadmap to artificial intelligence (AI): Methods for designing and building AI ready data to promote fairness	24
A new computational workflow to guide personalized drug therapy	24
Examining implementation outcomes in health information exchange systems: A scoping review	24
A novel machine learning-based workflow to capture intra-patient heterogeneity through transcriptional multi-label characterization and clinically relevant classification	24
How do others cope? Extracting coping strategies for adverse drug events from social media	24
Scaling up biomedical vision-language models: Fine-tuning, instruction tuning, and multi-modal learning	24
Unsupervised probabilistic models for sequential Electronic Health Records	24
KGiA: Drug repurposing through disease-aware knowledge graph augmentation	23
Multi-domain ECG feature extraction enable accurate automated recognition of bipolar disorder, depression and schizophrenia	23
A trajectory-informed model for detecting drug-drug-host interaction from real-world data	23
An interpretable machine learning approach to multimodal stress detection in a simulated office environment	23
Weakly Semi-supervised phenotyping using Electronic Health records	23
Composite pathway-guided Cox modeling for interpretable survival prediction in breast cancer	23
CLARUS: An interactive explainable AI platform for manual counterfactuals in graph neural networks	22
Technical/Algorithm, Stakeholder, and Society (TASS) barriers to the application of artificial intelligence in medicine: A systematic review	22
Learning from multiple data sources for decision making in health care	22
Promoting equity in clinical research: The role of social determinants of health	22
Machine learning approaches for the discovery of clinical pathways from patient data: A systematic review	22
DC-COX: Data collaboration Cox proportional hazards model for privacy-preserving survival analysis on multiple parties	22
Augmented intelligence for multimodal virtual biopsy in breast cancer using generative artificial intelligence	21
Cover 1/Spine	21
Continuous-time probabilistic models for longitudinal electronic health records	21
Resource-efficient instruction tuning of large language models for biomedical named entity recognition	21
Pseudo-labeling and knowledge-guided contrastive learning for radiology report generation	21
Improving the interoperability of drugs terminologies: Infusing local standardization with an international perspective	20
A gradient boosting tree model for multi-department venous thromboembolism risk assessment with imbalanced data	20
Tell me something interesting: Clinical utility of machine learning prediction models in the ICU	20
Scalable relevance ranking algorithm via semantic similarity assessment improves efficiency of medical chart review	20
Predicting line of therapy transition via similar patient augmentation	20
GraphFusion: Integrative prediction of drug synergy using multi-scale graph representations and cell line contexts	20
Early detection of subjective cognitive decline from self-reported symptoms: An interpretable attention-cost fusion approach	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
A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare	20
Hybrid visualization-based framework for depressive state detection and characterization of atypical patients	20
Bidirectional data harmonization across the multiple chronic disease disparities research consortium: A pipeline description of opportunities and challenges	19
A REDCap advanced randomization module to meet the needs of modern trials	19
Causal inference for time series datasets with partially overlapping variables	19
Enhancing data quality in medical concept normalization through large language models	19
CTKGR: temporal knowledge graph enhanced prediction of in-hospital events for pneumonia patients using electronic health records	19
Algorithms for evaluation of minimal cut sets	19
Ontology-driven identification of inconsistencies in clinical data: A case study in lung cancer phenotyping	19
UCVA ontology: Standardizing local context factors to support the analysis of unwarranted clinical variation	19
A scoping review of natural language processing in addressing medically inaccurate information: Errors, misinformation, and hallucination	19
Ontology-grounded knowledge graphs for mitigating hallucinations in large language models for clinical question answering	19
Cover 1/Spine	18
EGeRepDR: An enhanced genetic-based representation learning for drug repurposing using multiple biomedical sources	18
Computational frameworks integrating deep learning and statistical models in mining multimodal omics data	18

Creating an ignorance-base: Exploring known unknowns in the scientific literature	18
Temporally consistent survival prediction for non-uniform longitudinal data	18
Cover 1/Spine	18
Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data	18
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals	18
A joint learning framework for analyzing data from national geriatric centralized networks: A new toolbox deciphering real-world complexity	18
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
An attention-based framework for integrating WSI and genomic data in cancer survival prediction	18
Retrieval-augmented in-context learning for multimodal large language models in disease classification	17
Cover 1/Spine	17
Attention-based synthetic data generation for calibration-enhanced survival analysis: A case study for chronic kidney disease using electronic health records	17
Computational strategies in nutrigenetics: Constructing a reference dataset of nutrition-associated genetic polymorphisms	17
A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata	17
fmi-ii: Table of Contents	17
Adapting the open-source Gen3 platform and kubernetes for the NIH HEAL IMPOWR and MIRHIQL clinical trial data commons: Customization, cloud transition, and optimization	17
Disentangling the phenotypic patterns of hypertension and chronic hypotension	17
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias	17
Call for Papers: Special Issue on Learning from Multiple Data Sources for Decision Making in Health Care	17
Call for papers: Semantics-enabled biomedical literature analytics	17
FG-DDI: Functional group-aware graph neural networks for drug–drug interaction prediction	17
A Multidatabase ExTRaction PipEline (METRE) for facile cross validation in critical care research	17
MKCL: Medical Knowledge with Contrastive Learning model for radiology report generation	17
Personalized insulin dose manipulation attack and its detection using interval-based temporal patterns and machine learning algorithms	16
Textual emotion detection in health: Advances and applications	16
On the role of the UMLS in supporting diagnosis generation proposed by Large Language Models	16
Novel evaluation approach for molecular signature-based deconvolution methods	16
The crisis of biomedical foundation models	16
Considerations for using predictive models that include race as an input variable: The case study of lung cancer screening	16
Ensemble machine learning model trained on a new synthesized dataset generalizes well for stress prediction using wearable devices	16
Data-driven overdiagnosis definitions: A scoping review	16
Assessing fairness in machine learning models: A study of racial bias using matched counterparts in mortality prediction for patients with chronic diseases	16
Selecting a smartwatch for trials involving older adults with neurodegenerative diseases: A researcher’s framework to avoid hidden pitfalls	16
Evaluating accuracy and fairness of clinical decision support algorithms when health care resources are limited	15
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	15
Toward the European Health Data Space: The IMPaCT-Data secure infrastructure for EHR-based precision medicine research	15
A simple neural vector space model for medical concept normalization using concept embeddings	15
MedKA: A knowledge graph-augmented approach to improve factuality in medical Large Language Models	15
Taming vision transformers for clinical laryngoscopy assessment	15
Multimodal large language models for medical image diagnosis: Challenges and opportunities	15
GutGPT: A multidimensional knowledge-enhanced large language model for gastrointestinal medicine	15
A semi-supervised approach to unobtrusively predict abnormality in breathing patterns using hydraulic bed sensor data in older adults aging in place	14
Leveraging undecided cases in chart-reviewed phenotypes to enhance EHR-based association studies	14
Cover 1/Spine	14
Promoting smartphone-based keratitis screening using meta-learning: A multicenter study	14
PEER: Towards reliable and efficient inference via Patience-Based Early Exiting with Rejection	14
Discovering clinical drug-drug interactions with known pharmacokinetics mechanisms using spontaneous reporting systems and electronic health records	14
Utilization of geospatial distribution in the measurement of study cohort representativeness	14
A hybrid system to understand the relations between assessments and plans in progress notes	14
Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation	14
Federated causal discovery with missing data in a multicentric study on endometrial cancer	14
Cover 1/Spine	14
Extracting adverse drug events from clinical Notes: A systematic review of approaches used	14
A visual approach to facilitating conversations about supportive care options in the context of cognitive impairment	14
Heat and hearts: An exposure-anchored computational phenotyping framework for assessing cardiovascular vulnerability during extreme heat	13
Beyond Fine-Tuning: Leveraging Domain-Aware In-Context learning with large language models for clinical named entity recognition	13
Modeling engagement with a digital behavior change intervention (HeartSteps II): An exploratory system identification approach	13
Transformer-based models for ICD-10 coding of death certificates with Portuguese text	13
Data integration through canonical correlation analysis and its application to OMICs research	13
Ontology enrichment using a large language model: Applying lexical, semantic, and knowledge network-based similarity for concept placement	13
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
Evaluation of ChatGPT-generated medical responses: A systematic review and meta-analysis	13
KEBLM: Knowledge-Enhanced Biomedical Language Models	13
Implementation of specialised attention mechanisms: ICD-10 classification of Gastrointestinal discharge summaries in English, Spanish and Swedish	13