Journal of Biomedical Informatics

Article	Citations
Leveraging heterogeneous tabular of EHRs with prompt learning for clinical prediction	207
Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	188
A self-supervised language model selection strategy for biomedical question answering	113
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	100
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	95
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	89
A multimodal machine learning algorithm improved diagnostic accuracy for otitis media in a school aged Aboriginal population	86
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	77
Graph-based abstractive biomedical text summarization	74
Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors	67
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	66
Joint modeling of mixed outcomes using a rank-based sparse neural network	65
Measuring disease burden with individual cumulative incidence in patients with cirrhosis	63
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	63
From centralized to ad-hoc knowledge base construction for hypotheses generation	60
Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	58
Discontinuous named entities in clinical text: A systematic literature review	57
Multi-agent norm perception and induction in distributed healthcare	56
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	53
From translational bioinformatics computational methodologies to personalized medicine	53
Deep neural networks for neuro-oncology: Towards patient individualized design of chemo-radiation therapy for Glioblastoma patients	51
A Syntax-enhanced model based on category keywords for biomedical relation extraction	51
Cover 1/Spine	50
Towards a unified search: Improving PubMed retrieval with full text	50
Identifying cancer sub-types from genomic scale data sets using confidence based integration (CBI)	50

Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	49
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	49
Learning the progression patterns of treatments using a probabilistic generative model	49
TransDiffECG: Semantically controllable ECG synthesis via transformer-based diffusion modeling	48
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	47
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	45
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	44
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	44
fmi-ii: Table of Contents	43
Cover 1/Spine	43
Using a clinical narrative-aware pre-trained language model for predicting emergency department patient disposition and unscheduled return visits	40
Digital twins in increasing diversity in clinical trials: A systematic review	39
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications	39
Network-based analysis of Alzheimer’s Disease genes using multi-omics network integration with graph diffusion	39
Leveraging Multi-source knowledge for Chinese clinical named entity recognition via relational graph convolutional network	38
Decision-support systems for managing polypharmacy in the elderly: A scoping review	38
Applications of artificial intelligence to aid early detection of dementia: A scoping review on current capabilities and future directions	37
Predicting pharmacotherapeutic outcomes for type 2 diabetes: An evaluation of three approaches to leveraging electronic health record data from multiple sources	37
Implementation and evaluation of a multivariate abstraction-based, interval-based dynamic time-warping method as a similarity measure for longitudinal medical records	36
Clustering-based fusion for medical information retrieval	36
Natural language processing for clinical notes in dentistry: A systematic review	35
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	35
CASIDE: A data model for interoperable cancer survivorship information based on FHIR	35
Contrastive pre-training and linear interaction attention-based transformer for universal medical reports generation	35
Non-invasive prediction of massive transfusion during surgery using intraoperative hemodynamic monitoring data	34
A cost-effective IoT learning environment for the training and assessment of surgical technical skills with visual learning analytics	33
GERNERMED++: Semantic annotation in German medical NLP through transfer-learning, translation and word alignment	33
Extracting medication changes in clinical narratives using pre-trained language models	33
Graph embedding-based link prediction for literature-based discovery in Alzheimer’s Disease	33
Cover 2: Editorial Board	33
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	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
A framework for longitudinal latent factor modelling of treatment response in clinical trials with applications to Psoriatic Arthritis and Rheumatoid Arthritis	31
Advancing cancer driver gene identification through an integrative network and pathway approach	31
Large-scale investigation of weakly-supervised deep learning for the fine-grained semantic indexing of biomedical literature	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	31
Temporal attention networks for biomedical hypothesis generation	30
A methodology of phenotyping ICU patients from EHR data: High-fidelity, personalized, and interpretable phenotypes estimation	30
Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages	30
Machine learning applications related to suicide in military and Veterans: A scoping literature review	30
Fairness and inclusion methods for biomedical informatics research	30
They May Not Work! An evaluation of eleven sentiment analysis tools on seven social media datasets	29
A machine learning approach for automating review of a RxNorm medication mapping pipeline output	29
Few-shot learning based oral cancer diagnosis using a dual feature extractor prototypical network	29
Deep learning in surgical process modeling: A systematic review of workflow recognition	29
Multi-view based heterogeneous graph contrastive learning for drug–target interaction prediction	29
Assessing racial bias in healthcare predictive models: Practical lessons from an empirical evaluation of 30-day hospital readmission models	28
Cover 2: Editorial Board	28
Novel informatics approaches to COVID-19 Research: From methods to applications	28
Multi-view prediction of Alzheimer’s disease progression with end-to-end integrated framework	28

Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer	28
Deep learning for rare disease: A scoping review	28
COVIDSum: A linguistically enriched SciBERT-based summarization model for COVID-19 scientific papers	28
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia	28
Cover 1/Spine	28
Sentiment analysis of clinical narratives: A scoping review	27
Evaluating and mitigating bias in machine learning models for cardiovascular disease prediction	27
Drug repositioning with metapath guidance and adaptive negative sampling enhancement	26
Multi-modal fusion model for Time-Varying medical Data: Addressing Long-Term dependencies and memory challenges in sequence fusion	26
Provision and evaluation of explanations within an automated planning-based approach to solving the multimorbidity problem	26
fmi-ii: Table of Contents	26
Focused digital cohort selection from social media using the metric backbone of biomedical knowledge graphs	26
Identifying cooperating cancer driver genes in individual patients through hypergraph random walk	25
Adaptable graph neural networks design to support generalizability for clinical event prediction	25
Interpretable statistical modeling of patient flow in emergency departments	25
CD-Tron: Leveraging large clinical language model for early detection of cognitive decline from electronic health records	25
Improving severity classification of Hebrew PET-CT pathology reports using test-time augmentation	24
MPCM-RRG: Multi-modal Prompt Collaboration Mechanism for Radiology Report Generation	24
Towards a framework for interoperability and reproducibility of predictive models	24
Adversarial neural network with sentiment-aware attention for detecting adverse drug reactions	24
Graph fusion prediction of autism based on attentional mechanisms	24
Class imbalance in out-of-distribution datasets: Improving the robustness of the TextCNN for the classification of rare cancer types	23
Cover 2: Editorial Board	23
Estimating redundancy in clinical text	23
A trajectory-informed model for detecting drug-drug-host interaction from real-world data	22
JLCRB: A unified multi-view-based joint representation learning for CircRNA binding sites prediction	22
Resource-efficient instruction tuning of large language models for biomedical named entity recognition	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
Joint learning-based causal relation extraction from biomedical literature	22
From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare	22
fmi-ii: Table of Contents	22
Progress Note Understanding — Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 shared task	22
Emulate randomized clinical trials using heterogeneous treatment effect estimation for personalized treatments: Methodology review and benchmark	22
Integration of Mendelian randomisation and systems biology models to identify novel blood-based biomarkers for stroke	22
Discovering interpretable medical process models: A case study in trauma resuscitation	22
KGiA: Drug repurposing through disease-aware knowledge graph augmentation	21
Real-time prediction of organ failures in patients with acute pancreatitis using longitudinal irregular data	21
GLA-Net: A global-local attention network for automatic cataract classification	21
A roadmap to artificial intelligence (AI): Methods for designing and building AI ready data to promote fairness	21
Learning from multiple data sources for decision making in health care	21
fmi-ii: Table of Contents	21
CLARUS: An interactive explainable AI platform for manual counterfactuals in graph neural networks	21
Machine learning approaches for the discovery of clinical pathways from patient data: A systematic review	21
DC-COX: Data collaboration Cox proportional hazards model for privacy-preserving survival analysis on multiple parties	21
Promoting equity in clinical research: The role of social determinants of health	21
Deep learning for temporal data representation in electronic health records: A systematic review of challenges and methodologies	21
A new computational workflow to guide personalized drug therapy	21
Scaling up biomedical vision-language models: Fine-tuning, instruction tuning, and multi-modal learning	21
Behaviour recommendations with a deep learning model and genetic algorithm for health debt characterisation	20
How do others cope? Extracting coping strategies for adverse drug events from social media	20
A dual-attention based coupling network for diabetes classification with heterogeneous data	20
Gene Expression Variation Analysis (GEVA): A new R package to evaluate variations in differential expression in multiple biological conditions	20
An interpretable machine learning approach to multimodal stress detection in a simulated office environment	20
A practical approach towards causality mining in clinical text using active transfer learning	20
Unsupervised probabilistic models for sequential Electronic Health Records	20
Inferring the patient’s age from implicit age clues in health forum posts	20
Causal inference for time series datasets with partially overlapping variables	19
Technical/Algorithm, Stakeholder, and Society (TASS) barriers to the application of artificial intelligence in medicine: A systematic review	19
How can we reward you? A compliance and reward ontology (CaRO) for eliciting quantitative reward rules for engagement in mHealth app and healthy behaviors	19
Early detection of subjective cognitive decline from self-reported symptoms: An interpretable attention-cost fusion approach	19
Question-aware transformer models for consumer health question summarization	19
Weakly Semi-supervised phenotyping using Electronic Health records	19
Cover 1/Spine	19
Enhancing data quality in medical concept normalization through large language models	18
Ontology-driven identification of inconsistencies in clinical data: A case study in lung cancer phenotyping	18
Hybrid visualization-based framework for depressive state detection and characterization of atypical patients	18
A scoping review of natural language processing in addressing medically inaccurate information: Errors, misinformation, and hallucination	18
Improving the interoperability of drugs terminologies: Infusing local standardization with an international perspective	18
Predicting line of therapy transition via similar patient augmentation	18
GraphFusion: Integrative prediction of drug synergy using multi-scale graph representations and cell line contexts	17
Explainable process trace classification: An application to stroke	17
CODER: Knowledge-infused cross-lingual medical term embedding for term normalization	17
Machine learning algorithm for feature space clustering of mixed data with missing information based on molecule similarity	17
Call for Papers: Special Issue on Learning from Multiple Data Sources for Decision Making in Health Care	17
A REDCap advanced randomization module to meet the needs of modern trials	17
Scalable relevance ranking algorithm via semantic similarity assessment improves efficiency of medical chart review	17
Cover 1/Spine	17
A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare	17
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals	17

Tell me something interesting: Clinical utility of machine learning prediction models in the ICU	17
Continuous-time probabilistic models for longitudinal electronic health records	17
A gradient boosting tree model for multi-department venous thromboembolism risk assessment with imbalanced data	17
An attention-based framework for integrating WSI and genomic data in cancer survival prediction	17
Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data	16
fmi-ii: Table of Contents	16
A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata	16
A utility-based machine learning-driven personalized lifestyle recommendation for cardiovascular disease prevention	16
MKCL: Medical Knowledge with Contrastive Learning model for radiology report generation	16
EGeRepDR: An enhanced genetic-based representation learning for drug repurposing using multiple biomedical sources	16
fmi-ii: Table of Contents	16
Computational frameworks integrating deep learning and statistical models in mining multimodal omics data	16
Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria’s impact on patient count and safety	16
Multi-level process mining methodology for exploring disease-specific care processes	16
Cover 1/Spine	16
An efficient model selection for linear discriminant function-based recursive feature elimination	16
Creating an ignorance-base: Exploring known unknowns in the scientific literature	16
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias	16
Dual parallel net: A novel deep learning model for rectal tumor segmentation via CNN and transformer with Gaussian Mixture prior	16
Cover 1/Spine	15
Toward the European Health Data Space: The IMPaCT-Data secure infrastructure for EHR-based precision medicine research	15
Algorithms for evaluation of minimal cut sets	15
A Multidatabase ExTRaction PipEline (METRE) for facile cross validation in critical care research	15
The RareDis corpus: A corpus annotated with rare diseases, their signs and symptoms	15
Novel evaluation approach for molecular signature-based deconvolution methods	15
Cover 1/Spine	15
Leveraging undecided cases in chart-reviewed phenotypes to enhance EHR-based association studies	15
Textual emotion detection in health: Advances and applications	15
Selecting a smartwatch for trials involving older adults with neurodegenerative diseases: A researcher’s framework to avoid hidden pitfalls	15
Ensemble machine learning model trained on a new synthesized dataset generalizes well for stress prediction using wearable devices	15
Cover 2: Editorial Board	15
Taming vision transformers for clinical laryngoscopy assessment	15
Evaluating accuracy and fairness of clinical decision support algorithms when health care resources are limited	15
Personalized insulin dose manipulation attack and its detection using interval-based temporal patterns and machine learning algorithms	15
The crisis of biomedical foundation models	15
Computational strategies in nutrigenetics: Constructing a reference dataset of nutrition-associated genetic polymorphisms	14
Stratifying individuals into non-alcoholic fatty liver disease risk levels using time series machine learning models	14
Data-driven overdiagnosis definitions: A scoping review	14
Multimodal large language models for medical image diagnosis: Challenges and opportunities	14
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	14
Considerations for using predictive models that include race as an input variable: The case study of lung cancer screening	14
Process data analytics for hospital case-mix planning	14
Federated causal discovery with missing data in a multicentric study on endometrial cancer	14
MedKA: A knowledge graph-augmented approach to improve factuality in medical Large Language Models	14
fmi-ii: Table of Contents	14
Call for papers: Semantics-enabled biomedical literature analytics	14
Assessing fairness in machine learning models: A study of racial bias using matched counterparts in mortality prediction for patients with chronic diseases	14
GutGPT: A multidimensional knowledge-enhanced large language model for gastrointestinal medicine	14
A new methodological framework for hazard detection models in health information technology systems	13
Adapting the open-source Gen3 platform and kubernetes for the NIH HEAL IMPOWR and MIRHIQL clinical trial data commons: Customization, cloud transition, and optimization	13
Cover 1/Spine	13
A semi-supervised approach to unobtrusively predict abnormality in breathing patterns using hydraulic bed sensor data in older adults aging in place	13
Identifying task groupings for multi-task learning using pointwise V-usable information	13
A visual approach to facilitating conversations about supportive care options in the context of cognitive impairment	13
Evaluation of ChatGPT-generated medical responses: A systematic review and meta-analysis	13
A simple neural vector space model for medical concept normalization using concept embeddings	13
Disentangling the phenotypic patterns of hypertension and chronic hypotension	13
Cover 1/Spine	13
On the role of the UMLS in supporting diagnosis generation proposed by Large Language Models	13
Data integration through canonical correlation analysis and its application to OMICs research	13
Contextual information contributes to biomedical named entity normalization	13
Utilization of geospatial distribution in the measurement of study cohort representativeness	13
Extracting adverse drug events from clinical Notes: A systematic review of approaches used	13
Discovering clinical drug-drug interactions with known pharmacokinetics mechanisms using spontaneous reporting systems and electronic health records	13
Analysis of longitudinal social media for monitoring symptoms during a pandemic	13
Promoting smartphone-based keratitis screening using meta-learning: A multicenter study	13
Meaningful time-related aspects of alerts in Clinical Decision Support Systems. A unified framework	13
A systematic mapping study of semantic technologies in multi-omics data integration	13
Causal knowledge graph construction and evaluation for clinical decision support of diabetic nephropathy	12
Transformer-based models for ICD-10 coding of death certificates with Portuguese text	12
PCGMMF: a prediction method for breast cancer prognostic recurrence and metastasis risk based on enhanced multimodal feature fusion	12
fmi-ii: Table of Contents	12
Signal from the noise: A mixed graphical and quantitative process mining approach to evaluate care pathways applied to emergency stroke care	12
How well do multimodal LLMs interpret CT scans? An auto-evaluation framework for analyses	12
Implementation of specialised attention mechanisms: ICD-10 classification of Gastrointestinal discharge summaries in English, Spanish and Swedish	12
Enhancing identification performance of cognitive impairment high-risk based on a semi-supervised learning method	12
Identifying progression subphenotypes of Alzheimer’s disease from large-scale electronic health records with machine learning	12
ParTRE: A relational triple extraction model of complicated entities and imbalanced relations in Parkinson’s disease	12
Multisource and temporal variability in Portuguese hospital administrative datasets: Data quality implications	12
An annotated corpus from biomedical articles to construct a drug-food interaction database	12
Modeling engagement with a digital behavior change intervention (HeartSteps II): An exploratory system identification approach	12
KEBLM: Knowledge-Enhanced Biomedical Language Models	12
A hybrid system to understand the relations between assessments and plans in progress notes	12
Precision Drug Repurposing (PDR): Patient-level modeling and prediction combining foundational knowledge graph with biobank data	12
Federated Bayesian network learning from multi-site data	12
Principled estimation and evaluation of treatment effect heterogeneity: A case study application to dabigatran for patients with atrial fibrillation	12
ADSP: An adaptive sample pooling strategy for diagnostic testing	12
Variational temporal deconfounder network for individualized treatment effect estimation with longitudinal observational data	12
fmi-ii: Table of Contents	12
A novel data-driven approach for Personas validation in healthcare using self-supervised machine learning	12
Ontology enrichment using a large language model: Applying lexical, semantic, and knowledge network-based similarity for concept placement	12
Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation	12
Disease evolution and risk-based disease trajectories in congestive heart failure patients	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	11