Journal of Biomedical Informatics

Article	Citations
Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	177
Deep neural networks for neuro-oncology: Towards patient individualized design of chemo-radiation therapy for Glioblastoma patients	167
Learning the progression patterns of treatments using a probabilistic generative model	150
A multimodal machine learning algorithm improved diagnostic accuracy for otitis media in a school aged Aboriginal population	127
Identifying cancer sub-types from genomic scale data sets using confidence based integration (CBI)	79
A Syntax-enhanced model based on category keywords for biomedical relation extraction	79
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	74
Cover 1/Spine	73
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	69
A self-supervised language model selection strategy for biomedical question answering	59
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	57
An effective feature extraction method based on GDS for atrial fibrillation detection	56
From translational bioinformatics computational methodologies to personalized medicine	55
Predicting treatment recommendations in postmenopausal osteoporosis	55
Discontinuous named entities in clinical text: A systematic literature review	52
Towards a unified search: Improving PubMed retrieval with full text	50
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	50
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	50
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	49
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	47
Knowledge discovery from emergency ambulance dispatch during COVID-19: A case study of Nagoya City, Japan	46
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	46
Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	45
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	44
Improving broad-coverage medical entity linking with semantic type prediction and large-scale datasets	44

Graph-based abstractive biomedical text summarization	44
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	41
Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors	40
Pupillary light reflex as a diagnostic aid from computational viewpoint: A systematic literature review	39
From centralized to ad-hoc knowledge base construction for hypotheses generation	39
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	39
Unified concept and assertion detection using contextual multi-task learning in a clinical decision support system	37
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	36
Applications of artificial intelligence to aid early detection of dementia: A scoping review on current capabilities and future directions	36
CASIDE: A data model for interoperable cancer survivorship information based on FHIR	36
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications	36
Long-term prediction for temporal propagation of seasonal influenza using Transformer-based model	35
A cost-effective IoT learning environment for the training and assessment of surgical technical skills with visual learning analytics	35
Decision-support systems for managing polypharmacy in the elderly: A scoping review	34
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	34
Using a clinical narrative-aware pre-trained language model for predicting emergency department patient disposition and unscheduled return visits	34
Predicting pharmacotherapeutic outcomes for type 2 diabetes: An evaluation of three approaches to leveraging electronic health record data from multiple sources	33
Cover 1/Spine	32
Network-based analysis of Alzheimer’s Disease genes using multi-omics network integration with graph diffusion	31
fmi-ii: Table of Contents	31
Extracting medication changes in clinical narratives using pre-trained language models	30
Building an OMOP common data model-compliant annotated corpus for COVID-19 clinical trials	30
Non-invasive prediction of massive transfusion during surgery using intraoperative hemodynamic monitoring data	29
Natural language processing for clinical notes in dentistry: A systematic review	29
Graph embedding-based link prediction for literature-based discovery in Alzheimer’s Disease	29
GERNERMED++: Semantic annotation in German medical NLP through transfer-learning, translation and word alignment	28
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	27
Novel informatics approaches to COVID-19 Research: From methods to applications	27
Letter to Editor: An argument for a universal health record	27
Contrastive pre-training and linear interaction attention-based transformer for universal medical reports generation	27
Implementation and evaluation of a multivariate abstraction-based, interval-based dynamic time-warping method as a similarity measure for longitudinal medical records	27
fmi-ii: Table of Contents	27
Cover 2: Editorial Board	27
Leveraging Multi-source knowledge for Chinese clinical named entity recognition via relational graph convolutional network	27
Clustering-based fusion for medical information retrieval	27
Cover 1/Spine	27
COVIDSum: A linguistically enriched SciBERT-based summarization model for COVID-19 scientific papers	26
Cover 2: Editorial Board	26
Evaluating and mitigating bias in machine learning models for cardiovascular disease prediction	26
They May Not Work! An evaluation of eleven sentiment analysis tools on seven social media datasets	26
Deep learning for rare disease: A scoping review	26
Clinical decision-making framework against over-testing based on modeling implicit evaluation criteria	26
Multi-view prediction of Alzheimer’s disease progression with end-to-end integrated framework	25
Assessing racial bias in healthcare predictive models: Practical lessons from an empirical evaluation of 30-day hospital readmission models	25
Temporal attention networks for biomedical hypothesis generation	25
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia	25
Methods and measures to quantify ICU patient heterogeneity	25
A methodology of phenotyping ICU patients from EHR data: High-fidelity, personalized, and interpretable phenotypes estimation	25
Large-scale investigation of weakly-supervised deep learning for the fine-grained semantic indexing of biomedical literature	25
Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer	25

Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages	25
A framework for longitudinal latent factor modelling of treatment response in clinical trials with applications to Psoriatic Arthritis and Rheumatoid Arthritis	25
Provision and evaluation of explanations within an automated planning-based approach to solving the multimorbidity problem	24
Few-shot learning based oral cancer diagnosis using a dual feature extractor prototypical network	24
Deep learning in surgical process modeling: A systematic review of workflow recognition	24
Sentiment analysis of clinical narratives: A scoping review	24
Fairness and inclusion methods for biomedical informatics research	24
Advancing cancer driver gene identification through an integrative network and pathway approach	24
Pulse of the pandemic: Iterative topic filtering for clinical information extraction from social media	24
Biomedical named entity recognition using BERT in the machine reading comprehension framework	24
A cohort of patients in New York State with an alcohol use disorder and subsequent treatment information – A merging of two administrative data sources	24
Adversarial neural network with sentiment-aware attention for detecting adverse drug reactions	23
Cover 2: Editorial Board	23
Estimating redundancy in clinical text	23
fmi-ii: Table of Contents	23
Adaptable graph neural networks design to support generalizability for clinical event prediction	23
From GPT to DeepSeek: Significant gaps remain in realizing AI in healthcare	22
Joint learning-based causal relation extraction from biomedical literature	22
Multi-modal fusion model for Time-Varying medical Data: Addressing Long-Term dependencies and memory challenges in sequence fusion	22
A knowledge base of clinical trial eligibility criteria	22
JLCRB: A unified multi-view-based joint representation learning for CircRNA binding sites prediction	22
Identifying cooperating cancer driver genes in individual patients through hypergraph random walk	21
Graph fusion prediction of autism based on attentional mechanisms	21
Examining implementation outcomes in health information exchange systems: A scoping review	21
Emulate randomized clinical trials using heterogeneous treatment effect estimation for personalized treatments: Methodology review and benchmark	21
DC-COX: Data collaboration Cox proportional hazards model for privacy-preserving survival analysis on multiple parties	21
Improving severity classification of Hebrew PET-CT pathology reports using test-time augmentation	21
Towards a framework for interoperability and reproducibility of predictive models	21
Class imbalance in out-of-distribution datasets: Improving the robustness of the TextCNN for the classification of rare cancer types	21
Machine learning research towards combating COVID-19: Virus detection, spread prevention, and medical assistance	21
Gene Expression Variation Analysis (GEVA): A new R package to evaluate variations in differential expression in multiple biological conditions	20
Behaviour recommendations with a deep learning model and genetic algorithm for health debt characterisation	20
Cover 1/Spine	20
Inferring the patient’s age from implicit age clues in health forum posts	20
Unsupervised probabilistic models for sequential Electronic Health Records	20
A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases	20
fmi-ii: Table of Contents	20
A dual-attention based coupling network for diabetes classification with heterogeneous data	19
Discovering interpretable medical process models: A case study in trauma resuscitation	19
Learning Drug-Disease-Target Embedding (DDTE) from knowledge graphs to inform drug repurposing hypotheses	19
Progress Note Understanding — Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 shared task	19
How do others cope? Extracting coping strategies for adverse drug events from social media	19
Predictive models of aging of the human eye based on ocular anterior segment morphology	19
A scoring model to detect abusive medical institutions based on patient classification system: Diagnosis-related group and ambulatory patient group	19
A new computational workflow to guide personalized drug therapy	19
Integration of Mendelian randomisation and systems biology models to identify novel blood-based biomarkers for stroke	19
Tracking and analysis of discourse dynamics and polarity during the early Corona pandemic in Iran	19
Machine learning approaches for the discovery of clinical pathways from patient data: A systematic review	19
Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive	19
fmi-ii: Table of Contents	19
A practical approach towards causality mining in clinical text using active transfer learning	19
Real-time prediction of organ failures in patients with acute pancreatitis using longitudinal irregular data	18
Promoting equity in clinical research: The role of social determinants of health	18
Technical/Algorithm, Stakeholder, and Society (TASS) barriers to the application of artificial intelligence in medicine: A systematic review	18
An interpretable machine learning approach to multimodal stress detection in a simulated office environment	18
De-novo FAIRification via an Electronic Data Capture system by automated transformation of filled electronic Case Report Forms into machine-readable data	18
Weakly Semi-supervised phenotyping using Electronic Health records	18
Implementation of stacking based ARIMA model for prediction of Covid-19 cases in India	18
A roadmap to artificial intelligence (AI): Methods for designing and building AI ready data to promote fairness	18
Cover 2: Editorial Board	17
Machine learning algorithm for feature space clustering of mixed data with missing information based on molecule similarity	17
CLARUS: An interactive explainable AI platform for manual counterfactuals in graph neural networks	17
Explainable process trace classification: An application to stroke	17
Scalable relevance ranking algorithm via semantic similarity assessment improves efficiency of medical chart review	17
Cover 1/Spine	17
How can we reward you? A compliance and reward ontology (CaRO) for eliciting quantitative reward rules for engagement in mHealth app and healthy behaviors	17
FeARH: Federated machine learning with anonymous random hybridization on electronic medical records	17
Improving the interoperability of drugs terminologies: Infusing local standardization with an international perspective	17
Question-aware transformer models for consumer health question summarization	17
Cover 1/Spine	17
Predicting line of therapy transition via similar patient augmentation	17
Deep learning for temporal data representation in electronic health records: A systematic review of challenges and methodologies	17
Cover 1/Spine	17
GLA-Net: A global-local attention network for automatic cataract classification	17
A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare	16
CODER: Knowledge-infused cross-lingual medical term embedding for term normalization	16
A gradient boosting tree model for multi-department venous thromboembolism risk assessment with imbalanced data	16
Multi-level process mining methodology for exploring disease-specific care processes	16
Safety-driven design of machine learning for sepsis treatment	16
Early detection of subjective cognitive decline from self-reported symptoms: An interpretable attention-cost fusion approach	16

Ontology-driven identification of inconsistencies in clinical data: A case study in lung cancer phenotyping	16
Hybrid visualization-based framework for depressive state detection and characterization of atypical patients	16
Tell me something interesting: Clinical utility of machine learning prediction models in the ICU	16
Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data	16
Cover 2: Editorial Board	16
Enhancing data quality in medical concept normalization through large language models	16
Machine learning enabled identification of potential SARS-CoV-2 3CLpro inhibitors based on fixed molecular fingerprints and Graph-CNN neural representations	16
Continuous-time probabilistic models for longitudinal electronic health records	16
Creating an ignorance-base: Exploring known unknowns in the scientific literature	16
fmi-ii: Table of Contents	16
MKCL: Medical Knowledge with Contrastive Learning model for radiology report generation	15
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals	15
Cover 2: Editorial Board	15
A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata	15
Identification of pediatric respiratory diseases using a fine-grained diagnosis system	15
fmi-ii: Table of Contents	15
Cover 1/Spine	15
EGeRepDR: An enhanced genetic-based representation learning for drug repurposing using multiple biomedical sources	15
Algorithms for evaluation of minimal cut sets	15
Cover 1/Spine	15
Computational frameworks integrating deep learning and statistical models in mining multimodal omics data	14
Augmented reality in robotic assisted orthopaedic surgery: A pilot study	14
Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria’s impact on patient count and safety	14
Call for papers: Semantics-enabled biomedical literature analytics	14
Process data analytics for hospital case-mix planning	14
Dual parallel net: A novel deep learning model for rectal tumor segmentation via CNN and transformer with Gaussian Mixture prior	14
Predicting future state for adaptive clinical pathway management	14
A utility-based machine learning-driven personalized lifestyle recommendation for cardiovascular disease prevention	14
Call for Papers: Special Issue on Learning from Multiple Data Sources for Decision Making in Health Care	14
A simple neural vector space model for medical concept normalization using concept embeddings	14
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias	14
Longitudinal K-means approaches to clustering and analyzing EHR opioid use trajectories for clinical subtypes	14
An efficient model selection for linear discriminant function-based recursive feature elimination	14
fmi-ii: Table of Contents	14
The RareDis corpus: A corpus annotated with rare diseases, their signs and symptoms	14
Assessing fairness in machine learning models: A study of racial bias using matched counterparts in mortality prediction for patients with chronic diseases	13
Information handoffs in critical care and their implications for information quality: A socio-technical network approach	13
Evaluating accuracy and fairness of clinical decision support algorithms when health care resources are limited	13
Toward the European Health Data Space: The IMPaCT-Data secure infrastructure for EHR-based precision medicine research	13
The Envirome Web Service: Patient context at the point of care	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
Disentangling the phenotypic patterns of hypertension and chronic hypotension	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 comparative analysis of system features used in the TREC-COVID information retrieval challenge	13
On the role of the UMLS in supporting diagnosis generation proposed by Large Language Models	13
A Multidatabase ExTRaction PipEline (METRE) for facile cross validation in critical care research	13
Ensemble machine learning model trained on a new synthesized dataset generalizes well for stress prediction using wearable devices	13
Taming vision transformers for clinical laryngoscopy assessment	13
Selecting a smartwatch for trials involving older adults with neurodegenerative diseases: A researcher’s framework to avoid hidden pitfalls	13
Considerations for using predictive models that include race as an input variable: The case study of lung cancer screening	13
Extracting adverse drug events from clinical Notes: A systematic review of approaches used	13
Novel evaluation approach for molecular signature-based deconvolution methods	13
fmi-ii: Table of Contents	12
Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation	12
A semi-supervised approach to unobtrusively predict abnormality in breathing patterns using hydraulic bed sensor data in older adults aging in place	12
A visual approach to facilitating conversations about supportive care options in the context of cognitive impairment	12
fmi-ii: Table of Contents	12
Data-driven overdiagnosis definitions: A scoping review	12
Cover 1/Spine	12
Implementation of specialised attention mechanisms: ICD-10 classification of Gastrointestinal discharge summaries in English, Spanish and Swedish	12
Disease evolution and risk-based disease trajectories in congestive heart failure patients	12
Signal from the noise: A mixed graphical and quantitative process mining approach to evaluate care pathways applied to emergency stroke care	12
Promoting smartphone-based keratitis screening using meta-learning: A multicenter study	12
Personalized insulin dose manipulation attack and its detection using interval-based temporal patterns and machine learning algorithms	12
Leveraging undecided cases in chart-reviewed phenotypes to enhance EHR-based association studies	12
A hybrid system to understand the relations between assessments and plans in progress notes	12
Textual emotion detection in health: Advances and applications	12
Precision Drug Repurposing (PDR): Patient-level modeling and prediction combining foundational knowledge graph with biobank data	12
Utilization of geospatial distribution in the measurement of study cohort representativeness	12
Multisource and temporal variability in Portuguese hospital administrative datasets: Data quality implications	12
A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19	12
Discovering clinical drug-drug interactions with known pharmacokinetics mechanisms using spontaneous reporting systems and electronic health records	12
An annotated corpus from biomedical articles to construct a drug-food interaction database	11
Data integration through canonical correlation analysis and its application to OMICs research	11
Modeling engagement with a digital behavior change intervention (HeartSteps II): An exploratory system identification approach	11
Transformer-based models for ICD-10 coding of death certificates with Portuguese text	11
Improving Chinese electronic medical record retrieval by field weight assignment, negation detection, and re-ranking	11
Enhancing identification performance of cognitive impairment high-risk based on a semi-supervised learning method	11
A strategy for validation of variables derived from large-scale electronic health record data	11
A generalized kernel machine approach to identify higher-order composite effects in multi-view datasets, with application to adolescent brain development and osteoporosis	11
Analysis of longitudinal social media for monitoring symptoms during a pandemic	11
Causal knowledge graph construction and evaluation for clinical decision support of diabetic nephropathy	11
Meaningful time-related aspects of alerts in Clinical Decision Support Systems. A unified framework	11
Population stratification enables modeling effects of reopening policies on mortality and hospitalization rates	11
Contextual information contributes to biomedical named entity normalization	11
A systematic mapping study of semantic technologies in multi-omics data integration	11
Cover 1/Spine	11
Face mask detection using deep learning: An approach to reduce risk of Coronavirus spread	11
A novel data-driven approach for Personas validation in healthcare using self-supervised machine learning	11
Cover 2: Editorial Board	11
Federated Bayesian network learning from multi-site data	11
KEBLM: Knowledge-Enhanced Biomedical Language Models	11
Cover 1/Spine	11