Journal of Biomedical Informatics

Article	Citations
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	146
From centralized to ad-hoc knowledge base construction for hypotheses generation	133
Towards a unified search: Improving PubMed retrieval with full text	107
A multimodal machine learning algorithm improved diagnostic accuracy for otitis media in a school aged Aboriginal population	107
From translational bioinformatics computational methodologies to personalized medicine	101
Cover 1/Spine	91
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	82
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	81
Learning the progression patterns of treatments using a probabilistic generative model	77
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	70
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	70
Multi-agent norm perception and induction in distributed healthcare	66
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	66
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	65
Predicting non-coding RNA function using Artificial Intelligence	63
Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	61
TransDiffECG: Semantically controllable ECG synthesis via transformer-based diffusion modeling	61
Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors	60
A Syntax-enhanced model based on category keywords for biomedical relation extraction	60
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	60
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	59
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	56
Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	55
Measuring disease burden with individual cumulative incidence in patients with cirrhosis	53
Joint modeling of mixed outcomes using a rank-based sparse neural network	52

Discontinuous named entities in clinical text: A systematic literature review	51
Context-Aware adaptive normalization LSTM (CAAN-LSTM) for immunotherapy decision support in cancer clinical data analysis	50
Graph-based abstractive biomedical text summarization	50
Explainable multimodal deep learning models for variable-length sequences in critically ill patients	49
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	48
Leveraging heterogeneous tabular of EHRs with prompt learning for clinical prediction	48
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	48
A self-supervised language model selection strategy for biomedical question answering	47
Cover 1/Spine	46
Graph embedding-based link prediction for literature-based discovery in Alzheimer’s Disease	45
fmi-ii: Table of Contents	45
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	44
Decision-support systems for managing polypharmacy in the elderly: A scoping review	44
A computational framework for predicting drug-target interactions by fusing gene ontology information with cross attention	44
Extracting medication changes in clinical narratives using pre-trained language models	44
Predicting pharmacotherapeutic outcomes for type 2 diabetes: An evaluation of three approaches to leveraging electronic health record data from multiple sources	44
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	43
A federated learning framework for ethical dynamic treatment allocation across heterogeneous hospitals	43
Network-based analysis of Alzheimer’s Disease genes using multi-omics network integration with graph diffusion	42
Using a clinical narrative-aware pre-trained language model for predicting emergency department patient disposition and unscheduled return visits	42
Non-invasive prediction of massive transfusion during surgery using intraoperative hemodynamic monitoring data	42
MDD-MARF: a multimodal depression detection model based on multi-level attention mechanism and residual fusion	41
Clustering-based fusion for medical information retrieval	41
GERNERMED++: Semantic annotation in German medical NLP through transfer-learning, translation and word alignment	40
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications	40
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	40
Digital twins in increasing diversity in clinical trials: A systematic review	39
Contrastive pre-training and linear interaction attention-based transformer for universal medical reports generation	39
Vision-language model-based semantic-guided imaging biomarker for lung nodule malignancy prediction	38
Cover 2: Editorial Board	37
Natural language processing for clinical notes in dentistry: A systematic review	37
A cohort of patients in New York State with an alcohol use disorder and subsequent treatment information – A merging of two administrative data sources	36
Fairness and inclusion methods for biomedical informatics research	36
Novel informatics approaches to COVID-19 Research: From methods to applications	35
Machine learning applications related to suicide in military and Veterans: A scoping literature review	35
Large-scale investigation of weakly-supervised deep learning for the fine-grained semantic indexing of biomedical literature	35
Cover 2: Editorial Board	35
Sentiment analysis of clinical narratives: A scoping review	35
Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages	34
A methodology of phenotyping ICU patients from EHR data: High-fidelity, personalized, and interpretable phenotypes estimation	34
A multidimensional hierarchical framework for sources of bias in real-world healthcare evidence: a scoping review	34
Temporal attention networks for biomedical hypothesis generation	34
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia	34
Study on multimodal spatially-constrained contrastive learning for knee osteoarthritis severity grading	33
Deep learning for rare disease: A scoping review	32
Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer	32
Assessing racial bias in healthcare predictive models: Practical lessons from an empirical evaluation of 30-day hospital readmission models	32
Multi-view based heterogeneous graph contrastive learning for drug–target interaction prediction	32
Advancing cancer driver gene identification through an integrative network and pathway approach	32
Few-shot learning based oral cancer diagnosis using a dual feature extractor prototypical network	31

Deep learning in surgical process modeling: A systematic review of workflow recognition	31
A machine learning approach for automating review of a RxNorm medication mapping pipeline output	31
A framework for longitudinal latent factor modelling of treatment response in clinical trials with applications to Psoriatic Arthritis and Rheumatoid Arthritis	31
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	30
Evaluating and mitigating bias in machine learning models for cardiovascular disease prediction	30
fmi-ii: Table of Contents	30
They May Not Work! An evaluation of eleven sentiment analysis tools on seven social media datasets	30
Learning dynamic binary treatment policies under treatment selection bias: A Conservative Q-Learning approach with representation balancing	29
Towards a framework for interoperability and reproducibility of predictive models	29
Joint learning-based causal relation extraction from biomedical literature	29
Drug repositioning with metapath guidance and adaptive negative sampling enhancement	29
CD-Tron: Leveraging large clinical language model for early detection of cognitive decline from electronic health records	28
Interpretable statistical modeling of patient flow in emergency departments	28
Identifying cooperating cancer driver genes in individual patients through hypergraph random walk	27
Graph fusion prediction of autism based on attentional mechanisms	27
Adaptable graph neural networks design to support generalizability for clinical event prediction	27
JLCRB: A unified multi-view-based joint representation learning for CircRNA binding sites prediction	26
Enhancing AI-based diabetic retinopathy screening in low- and middle-income countries with synthetic data	26
Provision and evaluation of explanations within an automated planning-based approach to solving the multimorbidity problem	26
MPCM-RRG: Multi-modal Prompt Collaboration Mechanism for Radiology Report Generation	26
Improving severity classification of Hebrew PET-CT pathology reports using test-time augmentation	26
From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare	25
Multi-modal fusion model for Time-Varying medical Data: Addressing Long-Term dependencies and memory challenges in sequence fusion	25
fmi-ii: Table of Contents	25
Emulate randomized clinical trials using heterogeneous treatment effect estimation for personalized treatments: Methodology review and benchmark	25
Progress Note Understanding — Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 shared task	25
Focused digital cohort selection from social media using the metric backbone of biomedical knowledge graphs	25
Editorial Board	25
A dual-attention based coupling network for diabetes classification with heterogeneous data	24
Scaling up biomedical vision-language models: Fine-tuning, instruction tuning, and multi-modal learning	24
Gene Expression Variation Analysis (GEVA): A new R package to evaluate variations in differential expression in multiple biological conditions	24
CLARUS: An interactive explainable AI platform for manual counterfactuals in graph neural networks	24
Integration of Mendelian randomisation and systems biology models to identify novel blood-based biomarkers for stroke	24
Behaviour recommendations with a deep learning model and genetic algorithm for health debt characterisation	24
fmi-ii: Table of Contents	24
An interpretable machine learning approach to multimodal stress detection in a simulated office environment	24
Learning from multiple data sources for decision making in health care	24
Technical/Algorithm, Stakeholder, and Society (TASS) barriers to the application of artificial intelligence in medicine: A systematic review	24
A new computational workflow to guide personalized drug therapy	23
Promoting equity in clinical research: The role of social determinants of health	23
How do others cope? Extracting coping strategies for adverse drug events from social media	23
Machine learning approaches for the discovery of clinical pathways from patient data: A systematic review	23
A trajectory-informed model for detecting drug-drug-host interaction from real-world data	22
DC-COX: Data collaboration Cox proportional hazards model for privacy-preserving survival analysis on multiple parties	22
Discovering interpretable medical process models: A case study in trauma resuscitation	22
Examining implementation outcomes in health information exchange systems: A scoping review	22
Resource-efficient instruction tuning of large language models for biomedical named entity recognition	22
KGiA: Drug repurposing through disease-aware knowledge graph augmentation	22
Enhancing data quality in medical concept normalization through large language models	21
Continuous-time probabilistic models for longitudinal electronic health records	21
Real-time prediction of organ failures in patients with acute pancreatitis using longitudinal irregular data	21
Improving the interoperability of drugs terminologies: Infusing local standardization with an international perspective	21
A roadmap to artificial intelligence (AI): Methods for designing and building AI ready data to promote fairness	21
A novel machine learning-based workflow to capture intra-patient heterogeneity through transcriptional multi-label characterization and clinically relevant classification	21
Predicting line of therapy transition via similar patient augmentation	21
Cover 1/Spine	21
Unsupervised probabilistic models for sequential Electronic Health Records	21
Weakly Semi-supervised phenotyping using Electronic Health records	21
A gradient boosting tree model for multi-department venous thromboembolism risk assessment with imbalanced data	20
Causal inference for time series datasets with partially overlapping variables	20
Augmented intelligence for multimodal virtual biopsy in breast cancer using generative artificial intelligence	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
Scalable relevance ranking algorithm via semantic similarity assessment improves efficiency of medical chart review	20
Early detection of subjective cognitive decline from self-reported symptoms: An interpretable attention-cost fusion approach	20
Pseudo-labeling and knowledge-guided contrastive learning for radiology report generation	20
Ontology-grounded knowledge graphs for mitigating hallucinations in large language models for clinical question answering	20
Call for Papers: Special Issue on Learning from Multiple Data Sources for Decision Making in Health Care	19
Ontology-driven identification of inconsistencies in clinical data: A case study in lung cancer phenotyping	19
GraphFusion: Integrative prediction of drug synergy using multi-scale graph representations and cell line contexts	19
Hybrid visualization-based framework for depressive state detection and characterization of atypical patients	19
A scoping review of natural language processing in addressing medically inaccurate information: Errors, misinformation, and hallucination	19
UCVA ontology: Standardizing local context factors to support the analysis of unwarranted clinical variation	19
Tell me something interesting: Clinical utility of machine learning prediction models in the ICU	19
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
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals	19
CTKGR: temporal knowledge graph enhanced prediction of in-hospital events for pneumonia patients using electronic health records	19
A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare	19
A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata	18
Cover 1/Spine	18

An efficient model selection for linear discriminant function-based recursive feature elimination	18
Algorithms for evaluation of minimal cut sets	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
Temporally consistent survival prediction for non-uniform longitudinal data	18
A utility-based machine learning-driven personalized lifestyle recommendation for cardiovascular disease prevention	18
Cover 1/Spine	18
A joint learning framework for analyzing data from national geriatric centralized networks: A new toolbox deciphering real-world complexity	18
An attention-based framework for integrating WSI and genomic data in cancer survival prediction	17
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias	17
Evaluating accuracy and fairness of clinical decision support algorithms when health care resources are limited	17
Assessing fairness in machine learning models: A study of racial bias using matched counterparts in mortality prediction for patients with chronic diseases	17
fmi-ii: Table of Contents	17
Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data	17
MKCL: Medical Knowledge with Contrastive Learning model for radiology report generation	17
GutGPT: A multidimensional knowledge-enhanced large language model for gastrointestinal medicine	17
Federated causal discovery with missing data in a multicentric study on endometrial cancer	17
Cover 1/Spine	17
Creating an ignorance-base: Exploring known unknowns in the scientific literature	17
Call for papers: Semantics-enabled biomedical literature analytics	17
A Multidatabase ExTRaction PipEline (METRE) for facile cross validation in critical care research	17
Toward the European Health Data Space: The IMPaCT-Data secure infrastructure for EHR-based precision medicine research	17
Dual parallel net: A novel deep learning model for rectal tumor segmentation via CNN and transformer with Gaussian Mixture prior	17
Extracting adverse drug events from clinical Notes: A systematic review of approaches used	16
Leveraging undecided cases in chart-reviewed phenotypes to enhance EHR-based association studies	16
Data-driven overdiagnosis definitions: A scoping review	16
A simple neural vector space model for medical concept normalization using concept embeddings	16
Process data analytics for hospital case-mix planning	16
The crisis of biomedical foundation models	16
Multimodal large language models for medical image diagnosis: Challenges and opportunities	16
Attention-based synthetic data generation for calibration-enhanced survival analysis: A case study for chronic kidney disease using electronic health records	16
Disentangling the phenotypic patterns of hypertension and chronic hypotension	16
Textual emotion detection in health: Advances and applications	16
Taming vision transformers for clinical laryngoscopy assessment	16
Considerations for using predictive models that include race as an input variable: The case study of lung cancer screening	15
FG-DDI: Functional group-aware graph neural networks for drug–drug interaction prediction	15
MedKA: A knowledge graph-augmented approach to improve factuality in medical Large Language Models	15
Personalized insulin dose manipulation attack and its detection using interval-based temporal patterns and machine learning algorithms	15
Adapting the open-source Gen3 platform and kubernetes for the NIH HEAL IMPOWR and MIRHIQL clinical trial data commons: Customization, cloud transition, and optimization	15
Novel evaluation approach for molecular signature-based deconvolution methods	15
Ensemble machine learning model trained on a new synthesized dataset generalizes well for stress prediction using wearable devices	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
Computational strategies in nutrigenetics: Constructing a reference dataset of nutrition-associated genetic polymorphisms	15
Discovering clinical drug-drug interactions with known pharmacokinetics mechanisms using spontaneous reporting systems and electronic health records	15
Cover 1/Spine	14
On the role of the UMLS in supporting diagnosis generation proposed by Large Language Models	14
fmi-ii: Table of Contents	14
Multisource and temporal variability in Portuguese hospital administrative datasets: Data quality implications	14
Selecting a smartwatch for trials involving older adults with neurodegenerative diseases: A researcher’s framework to avoid hidden pitfalls	14
Cover 1/Spine	14
A hybrid system to understand the relations between assessments and plans in progress notes	14
PEER: Towards reliable and efficient inference via Patience-Based Early Exiting with Rejection	14
Utilization of geospatial distribution in the measurement of study cohort representativeness	14
A semi-supervised approach to unobtrusively predict abnormality in breathing patterns using hydraulic bed sensor data in older adults aging in place	14
A visual approach to facilitating conversations about supportive care options in the context of cognitive impairment	14
Promoting smartphone-based keratitis screening using meta-learning: A multicenter study	14
Contextual information contributes to biomedical named entity normalization	13
Data integration through canonical correlation analysis and its application to OMICs research	13
Meaningful time-related aspects of alerts in Clinical Decision Support Systems. A unified framework	13
Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation	13
Beyond Fine-Tuning: Leveraging Domain-Aware In-Context learning with large language models for clinical named entity recognition	13
A novel data-driven approach for Personas validation in healthcare using self-supervised machine learning	13
Transformer-based models for ICD-10 coding of death certificates with Portuguese text	13
Modeling engagement with a digital behavior change intervention (HeartSteps II): An exploratory system identification approach	13
Identifying task groupings for multi-task learning using pointwise V-usable information	13
KEBLM: Knowledge-Enhanced Biomedical Language Models	13
Analysis of longitudinal social media for monitoring symptoms during a pandemic	13
Multi-task learning with dynamic re-weighting to achieve fairness in healthcare predictive modeling	12
Extracting drug–drug interactions from no-blinding texts using key semantic sentences and GHM loss	12
Cover 2: Editorial Board	12
PCGMMF: a prediction method for breast cancer prognostic recurrence and metastasis risk based on enhanced multimodal feature fusion	12
Causal knowledge graph construction and evaluation for clinical decision support of diabetic nephropathy	12
Evaluation of ChatGPT-generated medical responses: A systematic review and meta-analysis	12
ADSP: An adaptive sample pooling strategy for diagnostic testing	12
SynthMedic: Utilizing large language models for synthetic discharge summary generation, correction and validation	12
MultiADE: A Multi-domain benchmark for Adverse Drug Event extraction	12
A systematic mapping study of semantic technologies in multi-omics data integration	12
Implementation of specialised attention mechanisms: ICD-10 classification of Gastrointestinal discharge summaries in English, Spanish and Swedish	12
Precision Drug Repurposing (PDR): Patient-level modeling and prediction combining foundational knowledge graph with biobank data	12
ParTRE: A relational triple extraction model of complicated entities and imbalanced relations in Parkinson’s disease	12
Variational temporal deconfounder network for individualized treatment effect estimation with longitudinal observational data	12
PLRTE: Progressive learning for biomedical relation triplet extraction using large language models	12
Ontology enrichment using a large language model: Applying lexical, semantic, and knowledge network-based similarity for concept placement	12
How well do multimodal LLMs interpret CT scans? An auto-evaluation framework for analyses	12
Cover 1/Spine	12
Padé approximant meets federated learning: A nearly lossless, one-shot algorithm for evidence synthesis in distributed research networks with rare outcomes	11
Cover 1/Spine	11
Clinical outcome-guided deep temporal clustering for disease progression subtyping	11
Semisupervised neural biomedical sense disambiguation approach for aspect-based sentiment analysis on social networks	11
BiFDR: Brain-Inspired Federated Diffusion Transformer with Reinforcement for privacy-preserving molecular generation	11
Cover 1/Spine	11
Developing a deep learning natural language processing algorithm for automated reporting of adverse drug reactions	11
Comparative evaluation of the heterozygous variant standard deviation as a quality measure for next-generation sequencing	11
A deep learning approach for Spatio-Temporal forecasting of new cases and new hospital admissions of COVID-19 spread in Reggio Emilia, Northern Italy	11
Cover 2: Editorial Board	11