Journal of Biomedical Informatics

Article	Citations
Clinical research text summarization method based on fusion of domain knowledge	167
DOME: Directional medical embedding vectors from Electronic Health Records	164
From translational bioinformatics computational methodologies to personalized medicine	149
A pipeline for harmonising NHS Scotland laboratory data to enable national-level analyses	126
Discontinuous named entities in clinical text: A systematic literature review	92
Machine learning based predictive model for the analysis of sequence activity relationships using protein spectra and protein descriptors	78
Dual-level diagnostic feature learning with recurrent neural networks for treatment sequence recommendation	73
Towards a unified search: Improving PubMed retrieval with full text	73
MedGCN: Medication recommendation and lab test imputation via graph convolutional networks	71
Few-shot learning for medical text: A review of advances, trends, and opportunities	70
DAS-DDI: A dual-view framework with drug association and drug structure for drug–drug interaction prediction	67
Identification of pediatric respiratory diseases using a fine-grained diagnosis system	54
Coherence and comprehensibility: Large language models predict lay understanding of health-related content	54
Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	54
Improving non-invasive hemoglobin measurement accuracy using nonparametric models	53
Augmented reality in robotic assisted orthopaedic surgery: A pilot study	53
Generalized and transferable patient language representation for phenotyping with limited data	51
ConceptWAS: A high-throughput method for early identification of COVID-19 presenting symptoms and characteristics from clinical notes	50
French FastContext: A publicly accessible system for detecting negation, temporality and experiencer in French clinical notes	49
Predicting future state for adaptive clinical pathway management	48
BioPREP: Deep learning-based predicate classification with SemMedDB	47
Evaluation of an automated phenotyping algorithm for rheumatoid arthritis	44
Improving broad-coverage medical entity linking with semantic type prediction and large-scale datasets	44
Knowledge discovery from emergency ambulance dispatch during COVID-19: A case study of Nagoya City, Japan	44
ICD2Vec: Mathematical representation of diseases	43

From centralized to ad-hoc knowledge base construction for hypotheses generation	42
Efficient strabismus diagnosis from small samples: Harnessing spatial features for improved accuracy	42
Automated annotation of disease subtypes	42
RadioBERT: A deep learning-based system for medical report generation from chest X-ray images using contextual embeddings	41
An efficient model selection for linear discriminant function-based recursive feature elimination	39
Integrated rapid-cycle comparative effectiveness trials using flexible point of care randomisation in electronic health record systems	38
Clinical comparison between trial participants and potentially eligible patients using electronic health record data: A generalizability assessment method	38
ADPG: Biomedical entity recognition based on Automatic Dependency Parsing Graph	37
FIRLA: a Fast Incremental Record Linkage Algorithm	37
LGTRL-DE: Local and Global Temporal Representation Learning with Demographic Embedding for in-hospital mortality prediction	36
Augmenting biomedical named entity recognition with general-domain resources	35
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	35
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	35
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	35
Nonstationary multivariate Gaussian processes for electronic health records	34
Privacy-preserving model evaluation for logistic and linear regression using homomorphically encrypted genotype data	34
Triple and quadruple optimization for feature selection in cancer biomarker discovery	34
Algorithms for evaluation of minimal cut sets	34
fmi-ii: Table of Contents	33
Safety-driven design of machine learning for sepsis treatment	31
Large-scale neural biomedical entity linking with layer overwriting	31
New JBI policy emphasizes clinically-meaningful novel machine learning methods	30
Identifying cancer sub-types from genomic scale data sets using confidence based integration (CBI)	30
Cover 1/Spine	30
Cover 1/Spine	30
Cover 2: Editorial Board	29
Cover 2: Editorial Board	29
fmi-ii: Table of Contents	29
Cover 1/Spine	28
fmi-ii: Table of Contents	27
Creating an ignorance-base: Exploring known unknowns in the scientific literature	27
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	27
Cover 1/Spine	27
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	27
fmi-ii: Table of Contents	27
fmi-ii: Table of Contents	27
Query bot for retrieving patients’ clinical history: A COVID-19 use-case	27
fmi-ii: Table of Contents	27
Representation of time-varying and time-invariant EMR data and its application in modeling outcome prediction for heart failure patients	26
Cover 1/Spine	26
Multi-level process mining methodology for exploring disease-specific care processes	25
Exploring the potential impact of multi-factor precision interventions in Alzheimer’s disease with system dynamics	25
Cover 2: Editorial Board	25
An effective feature extraction method based on GDS for atrial fibrillation detection	25
An omics data analysis method based on feature linear relationship and graph convolutional network	25
Cover 2: Editorial Board	24
A deep learning approach for transgender and gender diverse patient identification in electronic health records	24
Predicting Alzheimer’s Disease from Spoken and Written Language Using Fusion-Based Stacked Generalization	24
Large Language Models, scientific knowledge and factuality: A framework to streamline human expert evaluation	24
MTDCNet: A 3D multi-threading dilated convolutional network for brain tumor automatic segmentation	24

GENA: A knowledge graph for nutrition and mental health	24
Opportunities for incorporating intersectionality into biomedical informatics	24
Cross-domain visual prompting with spatial proximity knowledge distillation for histological image classification	24
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	24
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	24
Call for Papers: Special Issue on Learning from Multiple Data Sources for Decision Making in Health Care	24
Deep neural networks for neuro-oncology: Towards patient individualized design of chemo-radiation therapy for Glioblastoma patients	23
Graph neural networks for clinical risk prediction based on electronic health records: A survey	23
Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions	23
Learning the progression patterns of treatments using a probabilistic generative model	23
A utility-based machine learning-driven personalized lifestyle recommendation for cardiovascular disease prevention	23
ALLERDET: A novel web app for prediction of protein allergenicity	23
Improved screening of fall risk using free-living based accelerometer data	23
Graph-based abstractive biomedical text summarization	23
Supporting SNOMED CT postcoordination with knowledge graph embeddings	23
Fine-tuning coreference resolution for different styles of clinical narratives	22
Dual parallel net: A novel deep learning model for rectal tumor segmentation via CNN and transformer with Gaussian Mixture prior	22
Evaluation of clinical practice guideline-derived clinical decision support systems using a novel quality model	22
A Syntax-enhanced model based on category keywords for biomedical relation extraction	22
Updating and recalibrating causal probabilistic models on a new target population	22
Data Management Plans in the genomics research revolution of Africa: Challenges and recommendations	22
A multimodal machine learning algorithm improved diagnostic accuracy for otitis media in a school aged Aboriginal population	21
Longitudinal K-means approaches to clustering and analyzing EHR opioid use trajectories for clinical subtypes	21
Developing libraries of semantically-augmented graphics as visual standards for biomedical information systems	21
A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata	21
Enhancing clinical data warehousing with provenance data to support longitudinal analyses and large file management: The gitOmmix approach for genomic and image data	21
Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data	20
Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	20
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals	20
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias	20
Adversarial reinforcement learning for dynamic treatment regimes	20
Explainable artificial intelligence in high-throughput drug repositioning for subgroup stratifications with interventionable potential	20
Multimodal model with text and drug embeddings for adverse drug reaction classification	20
Personalization in mHealth: Innovative informatics methods to improve patient experience and health outcome	19
Pixel-wise body composition prediction with a multi-task conditional generative adversarial network	19
Integrating differential expression, co-expression and gene network analysis for the identification of common genes associated with tumor angiogenesis deregulation	19
EHR-QC: A streamlined pipeline for automated electronic health records standardisation and preprocessing to predict clinical outcomes	19
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	19
Aligned deep neural network for integrative analysis with high-dimensional input	19
Evaluation of OMOP CDM, i2b2 and ICGC ARGO for supporting data harmonization in a breast cancer use case of a multicentric European AI project	19
EGeRepDR: An enhanced genetic-based representation learning for drug repurposing using multiple biomedical sources	19
Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria’s impact on patient count and safety	19
Development of comprehensive annotation criteria for patients’ states from clinical texts	19
A novel deep interval type-2 fuzzy LSTM (DIT2FLSTM) model applied to COVID-19 pandemic time-series prediction	18
Computational frameworks integrating deep learning and statistical models in mining multimodal omics data	18
PRIMIS: Privacy-preserving medical image sharing via deep sparsifying transform learning with obfuscation	18
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	18
Longitudinal deep learning clustering of Type 2 Diabetes Mellitus trajectories using routinely collected health records	18
Corrigendum to “Letter to Editor: Consistent Reporting of Reusable PhenX CDEs in the NIH Common Data Elements Repository” [J. Biomed. Inf. 120 (2021) 103845]	18
SurvMaximin: Robust federated approach to transporting survival risk prediction models	18
Predicting treatment recommendations in postmenopausal osteoporosis	18
HLA amino acid Mismatch-Based risk stratification of kidney allograft failure using a novel Machine learning algorithm	18
Cross-Modal self-supervised vision language pre-training with multiple objectives for medical visual question answering	18
Left ventricle segmentation combining deep learning and deformable models with anatomical constraints	17
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	17
A self-supervised language model selection strategy for biomedical question answering	17
AdaDiag: Adversarial Domain Adaptation of Diagnostic Prediction with Clinical Event Sequences	17
AutoScore-Imbalance: An interpretable machine learning tool for development of clinical scores with rare events data	17
Criteria2Query 3.0: Leveraging generative large language models for clinical trial eligibility query generation	17
Analysis of security and privacy challenges for DNA-genomics applications and databases	17
Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature	17
Overview of the 2022 n2c2 shared task on contextualized medication event extraction in clinical notes	17
Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors	16
Data mining and machine learning in cancer survival research: An overview and future recommendations	16
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	16
A probabilistic model for co-occurrence analysis in bibliometrics	16
Diagnosis of COVID-19 via acoustic analysis and artificial intelligence by monitoring breath sounds on smartphones	16
A deep learning approach for inpatient length of stay and mortality prediction	16
A fusion of data science and feed-forward neural network-based modelling of COVID-19 outbreak forecasting in IRAQ	16
TransforMED: End-to-Εnd Transformers for Evidence-Based Medicine and Argument Mining in medical literature	16
Pupillary light reflex as a diagnostic aid from computational viewpoint: A systematic literature review	16
REDCap on FHIR: Clinical Data Interoperability Services	16
A deep attention model to forecast the Length Of Stay and the in-hospital mortality right on admission from ICD codes and demographic data	16
Evaluating pointwise reliability of machine learning prediction	15
Personalized insulin dose manipulation attack and its detection using interval-based temporal patterns and machine learning algorithms	15
Language inference-based learning for Low-Resource Chinese clinical named entity recognition using language model	15
Comparative study of machine learning methods for COVID-19 transmission forecasting	15
Extracting adverse drug events from clinical Notes: A systematic review of approaches used	15
Enhancing generalization of medical image segmentation via game theory-based domain selection	15
MKCL: Medical Knowledge with Contrastive Learning model for radiology report generation	15

Network-based analysis of Alzheimer’s Disease genes using multi-omics network integration with graph diffusion	15
fmi-ii: Table of Contents	15
Long-term prediction for temporal propagation of seasonal influenza using Transformer-based model	15
Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants	15
Critical carE Database for Advanced Research (CEDAR): An automated method to support intensive care units with electronic health record data	15
Applying generative AI with retrieval augmented generation to summarize and extract key clinical information from electronic health records	15
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	15
Clinical narrative-aware deep neural network for emergency department critical outcome prediction	15
Integration of persuasive elements into exergames: Application in the development of a novel gait rehabilitation system for children with musculoskeletal conditions	15
A Multidatabase ExTRaction PipEline (METRE) for facile cross validation in critical care research	15
Valley-Forecast: Forecasting Coccidioidomycosis incidence via enhanced LSTM models trained on comprehensive meteorological data	14
Fair patient model: Mitigating bias in the patient representation learned from the electronic health records	14
Evaluation of the key active ingredients of ‘Radix Astragali and Rehmanniae Radix Mixture’ and related signaling pathways involved in ameliorating diabetic foot ulcers from the perspective of TCM-rela	14
Evaluating accuracy and fairness of clinical decision support algorithms when health care resources are limited	14
Process data analytics for hospital case-mix planning	14
Generalized genomic data sharing for differentially private federated learning	14
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	14
Cover 2: Editorial Board	14
Leveraging Multi-source knowledge for Chinese clinical named entity recognition via relational graph convolutional network	14
Identifying acute kidney injury subphenotypes using an outcome-driven deep-learning approach	14
Taming vision transformers for clinical laryngoscopy assessment	14
A weakly supervised model for the automated detection of adverse events using clinical notes	14
Automating medical simulations	14
Cover 1/Spine	14
Selecting a smartwatch for trials involving older adults with neurodegenerative diseases: A researcher’s framework to avoid hidden pitfalls	14
Development of a generalizable natural language processing pipeline to extract physician-reported pain from clinical reports: Generated using publicly-available datasets and tested on institutional cl	14
Modeling repeated measurements data using the multilevel Bayesian network: A case of child morbidity	13
Cover 1/Spine	13
A cost-effective IoT learning environment for the training and assessment of surgical technical skills with visual learning analytics	13
fmi-ii: Table of Contents	13
Cover 2: Editorial Board	13
Interpretability of time-series deep learning models: A study in cardiovascular patients admitted to Intensive care unit	13
Cover 2: Editorial Board	13
Call for papers: Semantics-enabled biomedical literature analytics	13
A compartment modeling approach to reconstruct and analyze gender and age-grouped CoViD-19 Italian data for decision-making strategies	13
Cover 1/Spine	13
fmi-ii: Table of Contents	13
Cover 1/Spine	13
Machine learning for holistic visualization of STEMI registry data	13
fmi-ii: Table of Contents	12
Cover 2: Editorial Board	12
Cover 2: Editorial Board	12
Using information theory to optimize a diagnostic threshold to match physician-ordering practice	12
On learning disentangled representations for individual treatment effect estimation	12
Confederated learning in healthcare: Training machine learning models using disconnected data separated by individual, data type and identity for Large-Scale health system Intelligence	12
Graph-based clinical recommender: Predicting specialists procedure orders using graph representation learning	12
Cover 1/Spine	12
Letter to Editor: An Argument for a Universal Health Record	12
Diagnosis clarification by generalization to patient-friendly terms and definitions: Validation study	12
AutoScore-Survival: Developing interpretable machine learning-based time-to-event scores with right-censored survival data	12
A maintenance hemodialysis mortality prediction model based on anomaly detection using longitudinal hemodialysis data	12
Inductive database to support iterative data mining: Application to biomarker analysis on patient data in the Fight-HF project	12
Efficient verification for outsourced genome-wide association studies	12
Novel evaluation approach for molecular signature-based deconvolution methods	12
Unified concept and assertion detection using contextual multi-task learning in a clinical decision support system	12
Call for Papers: Special Issue on Fairness and Inclusion in Biomedical Informatics Research: Technical and Social Perspectives	12
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	12
Automated interpretable discovery of heterogeneous treatment effectiveness: A COVID-19 case study	12
Phenotyping coronavirus disease 2019 during a global health pandemic: Lessons learned from the characterization of an early cohort	12
Towards quality improvement of vaccine concept mappings in the OMOP vocabulary with a semi-automated method	12
Cover 2: Editorial Board	12
Toward the European Health Data Space: The IMPaCT-Data secure infrastructure for EHR-based precision medicine research	11
Cost prediction for ischemic heart disease hospitalization: Interpretable feature extraction using network analysis	11
Supporting rural public health practice to address local-level social determinants of health across Northwest states: Development of an interactive visualization dashboard	11
Integration of incomplete multi-omics data using Knowledge Distillation and Supervised Variational Autoencoders for disease progression prediction	11
Natural language processing for clinical notes in dentistry: A systematic review	11
Non-invasive prediction of massive transfusion during surgery using intraoperative hemodynamic monitoring data	11
Fully automated detection of formal thought disorder with Time-series Augmented Representations for Detection of Incoherent Speech (TARDIS)	11
Lessons learned to enable question answering on knowledge graphs extracted from scientific publications: A case study on the coronavirus literature	11
A novel hierarchical machine learning model for hospital-acquired venous thromboembolism risk assessment among multiple-departments	11
Automatic categorization of self-acknowledged limitations in randomized controlled trial publications	11
Rich learning representations for human activity recognition: How to empower deep feature learning for biological time series	11
Extracting experimental parameter entities from scientific articles	11
Causal inference for observational longitudinal studies using deep survival models	11
Benefit-aware early prediction of health outcomes on multivariate EEG time series	11
A voice-based digital assistant for intelligent prompting of evidence-based practices during ICU rounds	11
Disentangling the phenotypic patterns of hypertension and chronic hypotension	11
Assessing fairness in machine learning models: A study of racial bias using matched counterparts in mortality prediction for patients with chronic diseases	11
Identify and mitigate bias in electronic phenotyping: A comprehensive study from computational perspective	11
A new methodological framework for hazard detection models in health information technology systems	11
A simple neural vector space model for medical concept normalization using concept embeddings	10
Cover 2: Editorial Board	10
Adaptation of an NLP system to a new healthcare environment to identify social determinants of health	10
Predicting pharmacotherapeutic outcomes for type 2 diabetes: An evaluation of three approaches to leveraging electronic health record data from multiple sources	10
Adapting the open-source Gen3 platform and kubernetes for the NIH HEAL IMPOWR and MIRHIQL clinical trial data commons: Customization, cloud transition, and optimization	10
Sparse modelling of cancer patients’ survival based on genomic copy number alterations	10
Clustering-based fusion for medical information retrieval	10
Detection of emerging drugs involved in overdose via diachronic word embeddings of substances discussed on social media	10
Cover 1/Spine	10
Temporal patterns selection for All-Cause Mortality prediction in T2D with ANNs	10
Early multi-cancer detection through deep learning: An anomaly detection approach using Variational Autoencoder	10
View-independent gait events detection using CNN-transformer hybrid network	10
Dynamic deformable attention network (DDANet) for COVID-19 lesions semantic segmentation	10
Representing and utilizing clinical textual data for real world studies: An OHDSI approach	10
Infrastructure platform for privacy-preserving distributed machine learning development of computer-assisted theragnostics in cancer	10