Journal of Biomedical Informatics

Article	Citations
Cover 1/Spine	203
Leveraging heterogeneous tabular of EHRs with prompt learning for clinical prediction	184
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	105
Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors	96
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	92
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	85
Joint modeling of mixed outcomes using a rank-based sparse neural network	80
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	72
Measuring disease burden with individual cumulative incidence in patients with cirrhosis	69
Graph-based abstractive biomedical text summarization	65
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	63
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	62
From centralized to ad-hoc knowledge base construction for hypotheses generation	62
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	62
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	59
Deep neural networks for neuro-oncology: Towards patient individualized design of chemo-radiation therapy for Glioblastoma patients	53
Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	52
A self-supervised language model selection strategy for biomedical question answering	50
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	49
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	49
Identifying cancer sub-types from genomic scale data sets using confidence based integration (CBI)	49
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	49
A multimodal machine learning algorithm improved diagnostic accuracy for otitis media in a school aged Aboriginal population	48
A Syntax-enhanced model based on category keywords for biomedical relation extraction	47
Learning the progression patterns of treatments using a probabilistic generative model	47

Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	47
Discontinuous named entities in clinical text: A systematic literature review	46
Multi-agent norm perception and induction in distributed healthcare	46
From translational bioinformatics computational methodologies to personalized medicine	44
Towards a unified search: Improving PubMed retrieval with full text	44
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	43
Cover 1/Spine	42
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	42
fmi-ii: Table of Contents	42
Extracting medication changes in clinical narratives using pre-trained language models	40
Using a clinical narrative-aware pre-trained language model for predicting emergency department patient disposition and unscheduled return visits	38
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications	37
A cost-effective IoT learning environment for the training and assessment of surgical technical skills with visual learning analytics	37
Clustering-based fusion for medical information retrieval	36
Digital twins in increasing diversity in clinical trials: A systematic review	35
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	35
Predicting pharmacotherapeutic outcomes for type 2 diabetes: An evaluation of three approaches to leveraging electronic health record data from multiple sources	35
Decision-support systems for managing polypharmacy in the elderly: A scoping review	35
Network-based analysis of Alzheimer’s Disease genes using multi-omics network integration with graph diffusion	35
Unified concept and assertion detection using contextual multi-task learning in a clinical decision support system	35
Applications of artificial intelligence to aid early detection of dementia: A scoping review on current capabilities and future directions	33
Leveraging Multi-source knowledge for Chinese clinical named entity recognition via relational graph convolutional network	33
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	33
Non-invasive prediction of massive transfusion during surgery using intraoperative hemodynamic monitoring data	33
Long-term prediction for temporal propagation of seasonal influenza using Transformer-based model	33
Implementation and evaluation of a multivariate abstraction-based, interval-based dynamic time-warping method as a similarity measure for longitudinal medical records	32
Natural language processing for clinical notes in dentistry: A systematic review	32
Graph embedding-based link prediction for literature-based discovery in Alzheimer’s Disease	32
GERNERMED++: Semantic annotation in German medical NLP through transfer-learning, translation and word alignment	31
Cover 2: Editorial Board	31
Contrastive pre-training and linear interaction attention-based transformer for universal medical reports generation	31
Machine learning applications related to suicide in military and Veterans: A scoping literature review	31
CASIDE: A data model for interoperable cancer survivorship information based on FHIR	31
fmi-ii: Table of Contents	31
They May Not Work! An evaluation of eleven sentiment analysis tools on seven social media datasets	30
Cover 2: Editorial Board	30
A cohort of patients in New York State with an alcohol use disorder and subsequent treatment information – A merging of two administrative data sources	30
Cover 1/Spine	30
A framework for longitudinal latent factor modelling of treatment response in clinical trials with applications to Psoriatic Arthritis and Rheumatoid Arthritis	29
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	29
A machine learning approach for automating review of a RxNorm medication mapping pipeline output	29
A methodology of phenotyping ICU patients from EHR data: High-fidelity, personalized, and interpretable phenotypes estimation	28
Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages	28
Assessing racial bias in healthcare predictive models: Practical lessons from an empirical evaluation of 30-day hospital readmission models	28
Advancing cancer driver gene identification through an integrative network and pathway approach	28
Temporal attention networks for biomedical hypothesis generation	27
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia	27
Multi-view based heterogeneous graph contrastive learning for drug–target interaction prediction	27
Deep learning in surgical process modeling: A systematic review of workflow recognition	27
Novel informatics approaches to COVID-19 Research: From methods to applications	27

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

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