Journal of Biomedical Informatics

Article	Citations
Clinical research text summarization method based on fusion of domain knowledge	150
From translational bioinformatics computational methodologies to personalized medicine	136
Creating a computer assisted ICD coding system: Performance metric choice and use of the ICD hierarchy	135
Machine learning based predictive model for the analysis of sequence activity relationships using protein spectra and protein descriptors	126
PRIMIS: Privacy-preserving medical image sharing via deep sparsifying transform learning with obfuscation	123
fmi-ii: Table of Contents	120
Large-scale neural biomedical entity linking with layer overwriting	80
Cover 1/Spine	74
Safety-driven design of machine learning for sepsis treatment	70
Cover 1/Spine	69
Identifying cancer sub-types from genomic scale data sets using confidence based integration (CBI)	67
New JBI policy emphasizes clinically-meaningful novel machine learning methods	65
Cover 1/Spine	64
Cover 2: Editorial Board	55
Cover 2: Editorial Board	53
Cover 1/Spine	52
fmi-ii: Table of Contents	52
fmi-ii: Table of Contents	51
fmi-ii: Table of Contents	49
Query bot for retrieving patients’ clinical history: A COVID-19 use-case	46
Cover 1/Spine	45
Realistic 3D infant head surfaces augmentation to improve AI-based diagnosis of cranial deformities	43
Creating an ignorance-base: Exploring known unknowns in the scientific literature	41
Predicting relations between SOAP note sections: The value of incorporating a clinical information model	41
fmi-ii: Table of Contents	40

fmi-ii: Table of Contents	39
Representation of time-varying and time-invariant EMR data and its application in modeling outcome prediction for heart failure patients	37
Cover 2: Editorial Board	36
Cover 1/Spine	36
Multi-level process mining methodology for exploring disease-specific care processes	35
An effective feature extraction method based on GDS for atrial fibrillation detection	35
Exploring the potential impact of multi-factor precision interventions in Alzheimer’s disease with system dynamics	33
Predicting Alzheimer’s Disease from Spoken and Written Language Using Fusion-Based Stacked Generalization	32
An omics data analysis method based on feature linear relationship and graph convolutional network	32
Analysis of security and privacy challenges for DNA-genomics applications and databases	32
Opportunities for incorporating intersectionality into biomedical informatics	32
Cover 2: Editorial Board	32
Large Language Models, scientific knowledge and factuality: A framework to streamline human expert evaluation	31
Call for Papers: Special Issue on Learning from Multiple Data Sources for Decision Making in Health Care	31
Longitudinal K-means approaches to clustering and analyzing EHR opioid use trajectories for clinical subtypes	30
ALLERDET: A novel web app for prediction of protein allergenicity	30
Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions	30
Improved screening of fall risk using free-living based accelerometer data	30
Deep neural networks for neuro-oncology: Towards patient individualized design of chemo-radiation therapy for Glioblastoma patients	29
A fusion of data science and feed-forward neural network-based modelling of COVID-19 outbreak forecasting in IRAQ	29
Supporting SNOMED CT postcoordination with knowledge graph embeddings	27
DOME: Directional medical embedding vectors from Electronic Health Records	27
Dual parallel net: A novel deep learning model for rectal tumor segmentation via CNN and transformer with Gaussian Mixture prior	27
A utility-based machine learning-driven personalized lifestyle recommendation for cardiovascular disease prevention	26
Detection of valvular heart diseases combining orthogonal non-negative matrix factorization and convolutional neural networks in PCG signals	26
A Syntax-enhanced model based on category keywords for biomedical relation extraction	26
Evaluating pointwise reliability of machine learning prediction	26
Adversarial reinforcement learning for dynamic treatment regimes	26
Data Management Plans in the genomics research revolution of Africa: Challenges and recommendations	26
GENA: A knowledge graph for nutrition and mental health	26
Explainable artificial intelligence in high-throughput drug repositioning for subgroup stratifications with interventionable potential	26
A deep learning approach for transgender and gender diverse patient identification in electronic health records	24
EGeRepDR: An enhanced genetic-based representation learning for drug repurposing using multiple biomedical sources	24
Personalization in mHealth: Innovative informatics methods to improve patient experience and health outcome	24
Data mining and machine learning in cancer survival research: An overview and future recommendations	24
Evaluation of OMOP CDM, i2b2 and ICGC ARGO for supporting data harmonization in a breast cancer use case of a multicentric European AI project	24
Applying generative AI with retrieval augmented generation to summarize and extract key clinical information from electronic health records	24
EHR-QC: A streamlined pipeline for automated electronic health records standardisation and preprocessing to predict clinical outcomes	24
Fine-tuning coreference resolution for different styles of clinical narratives	23
A self-supervised language model selection strategy for biomedical question answering	23
Evaluation of clinical practice guideline-derived clinical decision support systems using a novel quality model	23
Introducing the BlendedICU dataset, the first harmonized, international intensive care dataset	23
MAM: Flexible Monte-Carlo Agent based model for modelling COVID-19 spread	23
Integrating differential expression, co-expression and gene network analysis for the identification of common genes associated with tumor angiogenesis deregulation	22
Updating and recalibrating causal probabilistic models on a new target population	22
Random forest swarm optimization-based for heart diseases diagnosis	22
Aligned deep neural network for integrative analysis with high-dimensional input	22
Overview of the 2022 n2c2 shared task on contextualized medication event extraction in clinical notes	22
Pupillary light reflex as a diagnostic aid from computational viewpoint: A systematic literature review	22
MKCL: Medical Knowledge with Contrastive Learning model for radiology report generation	22

A novel deep interval type-2 fuzzy LSTM (DIT2FLSTM) model applied to COVID-19 pandemic time-series prediction	22
Pixel-wise body composition prediction with a multi-task conditional generative adversarial network	21
Nonstationary multivariate Gaussian processes for electronic health records	21
A deep attention model to forecast the Length Of Stay and the in-hospital mortality right on admission from ICD codes and demographic data	21
MedGCN: Medication recommendation and lab test imputation via graph convolutional networks	21
MTDCNet: A 3D multi-threading dilated convolutional network for brain tumor automatic segmentation	21
Critical carE Database for Advanced Research (CEDAR): An automated method to support intensive care units with electronic health record data	21
DAS-DDI: A dual-view framework with drug association and drug structure for drug–drug interaction prediction	21
Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria’s impact on patient count and safety	20
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias	20
Development of comprehensive annotation criteria for patients’ states from clinical texts	20
Criteria2Query 3.0: Leveraging generative large language models for clinical trial eligibility query generation	20
Graph neural networks for clinical risk prediction based on electronic health records: A survey	20
Dual-level diagnostic feature learning with recurrent neural networks for treatment sequence recommendation	19
BioPREP: Deep learning-based predicate classification with SemMedDB	19
Coherence and comprehensibility: Large language models predict lay understanding of health-related content	19
Augmented reality in robotic assisted orthopaedic surgery: A pilot study	19
French FastContext: A publicly accessible system for detecting negation, temporality and experiencer in French clinical notes	19
Generalized and transferable patient language representation for phenotyping with limited data	19
TransforMED: End-to-Εnd Transformers for Evidence-Based Medicine and Argument Mining in medical literature	19
Improving non-invasive hemoglobin measurement accuracy using nonparametric models	19
Predicting future state for adaptive clinical pathway management	19
REDCap on FHIR: Clinical Data Interoperability Services	19
Identification of pediatric respiratory diseases using a fine-grained diagnosis system	19
Diagnosis of COVID-19 via acoustic analysis and artificial intelligence by monitoring breath sounds on smartphones	18
AdaDiag: Adversarial Domain Adaptation of Diagnostic Prediction with Clinical Event Sequences	18
Multimodal model with text and drug embeddings for adverse drug reaction classification	18
Improving broad-coverage medical entity linking with semantic type prediction and large-scale datasets	18
Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes	18
From centralized to ad-hoc knowledge base construction for hypotheses generation	18
Towards a unified search: Improving PubMed retrieval with full text	18
A deep learning approach for inpatient length of stay and mortality prediction	18
Evaluation of an automated phenotyping algorithm for rheumatoid arthritis	18
Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature	18
Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?	17
RadioBERT: A deep learning-based system for medical report generation from chest X-ray images using contextual embeddings	17
Efficient strabismus diagnosis from small samples: Harnessing spatial features for improved accuracy	17
Exploration of text matching methods in Chinese disease Q&A systems: A method using ensemble based on BERT and boosted tree models	17
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences	17
Automated annotation of disease subtypes	17
Left ventricle segmentation combining deep learning and deformable models with anatomical constraints	17
An efficient model selection for linear discriminant function-based recursive feature elimination	17
Few-shot learning for medical text: A review of advances, trends, and opportunities	16
Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data	16
Hypothesis-driven modeling of the human lung–ventilator system: A characterization tool for Acute Respiratory Distress Syndrome research	16
FIRLA: a Fast Incremental Record Linkage Algorithm	16
AutoScore-Imbalance: An interpretable machine learning tool for development of clinical scores with rare events data	16
One-shot distributed algorithms for addressing heterogeneity in competing risks data across clinical sites	16
LGTRL-DE: Local and Global Temporal Representation Learning with Demographic Embedding for in-hospital mortality prediction	16
Clinical comparison between trial participants and potentially eligible patients using electronic health record data: A generalizability assessment method	16
Computational frameworks integrating deep learning and statistical models in mining multimodal omics data	16
ADPG: Biomedical entity recognition based on Automatic Dependency Parsing Graph	16
Augmenting biomedical named entity recognition with general-domain resources	16
Integrated rapid-cycle comparative effectiveness trials using flexible point of care randomisation in electronic health record systems	16
Privacy-preserving model evaluation for logistic and linear regression using homomorphically encrypted genotype data	15
ConceptWAS: A high-throughput method for early identification of COVID-19 presenting symptoms and characteristics from clinical notes	15
Knowledge discovery from emergency ambulance dispatch during COVID-19: A case study of Nagoya City, Japan	15
Triple and quadruple optimization for feature selection in cancer biomarker discovery	15
ICD2Vec: Mathematical representation of diseases	15
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals	15
Learning the progression patterns of treatments using a probabilistic generative model	15
A probabilistic model for co-occurrence analysis in bibliometrics	15
Longitudinal deep learning clustering of Type 2 Diabetes Mellitus trajectories using routinely collected health records	15
Algorithms for evaluation of minimal cut sets	15
Predicting treatment recommendations in postmenopausal osteoporosis	15
A robust phenotype-driven likelihood ratio analysis approach assisting interpretable clinical diagnosis of rare diseases	15
HLA amino acid Mismatch-Based risk stratification of kidney allograft failure using a novel Machine learning algorithm	15
Cross-domain visual prompting with spatial proximity knowledge distillation for histological image classification	14
A pipeline for harmonising NHS Scotland laboratory data to enable national-level analyses	14
Personalized insulin dose manipulation attack and its detection using interval-based temporal patterns and machine learning algorithms	14
Integrating longitudinal clinical and microbiome data to predict growth faltering in preterm infants	14
Automating medical simulations	14
Corrigendum to “Letter to Editor: Consistent Reporting of Reusable PhenX CDEs in the NIH Common Data Elements Repository” [J. Biomed. Inf. 120 (2021) 103845]	14
Digital Phenotyping of Mental Health using multimodal sensing of multiple situations of interest: A Systematic Literature Review	14
Developing libraries of semantically-augmented graphics as visual standards for biomedical information systems	14
Evaluating gender bias in ML-based clinical risk prediction models: A study on multiple use cases at different hospitals	14
A Multidatabase ExTRaction PipEline (METRE) for facile cross validation in critical care research	14
Cover 1/Spine	14
SurvMaximin: Robust federated approach to transporting survival risk prediction models	14
Cross-Modal self-supervised vision language pre-training with multiple objectives for medical visual question answering	14

Discontinuous named entities in clinical text: A systematic literature review	14
Enhancing clinical data warehousing with provenance data to support longitudinal analyses and large file management: The gitOmmix approach for genomic and image data	14
Clustering-based fusion for medical information retrieval	14
Fine-tuning BERT for automatic ADME semantic labeling in FDA drug labeling to enhance product-specific guidance assessment	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
Graph-based abstractive biomedical text summarization	14
Process data analytics for hospital case-mix planning	13
A weakly supervised model for the automated detection of adverse events using clinical notes	13
Automatic detection of COVID-19 vaccine misinformation with graph link prediction	13
Applications of artificial intelligence to aid early detection of dementia: A scoping review on current capabilities and future directions	13
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	13
Representing and utilizing clinical textual data for real world studies: An OHDSI approach	13
Integration of persuasive elements into exergames: Application in the development of a novel gait rehabilitation system for children with musculoskeletal conditions	13
Ensemble machine learning model trained on a new synthesized dataset generalizes well for stress prediction using wearable devices	13
Fair patient model: Mitigating bias in the patient representation learned from the electronic health records	13
Machine learning-based demand forecasting in cancer palliative care home hospitalization	13
A compartment modeling approach to reconstruct and analyze gender and age-grouped CoViD-19 Italian data for decision-making strategies	13
Evaluating accuracy and fairness of clinical decision support algorithms when health care resources are limited	13
Cover 2: Editorial Board	13
Generalized genomic data sharing for differentially private federated learning	13
fmi-ii: Table of Contents	12
Cover 1/Spine	12
fmi-ii: Table of Contents	12
Machine learning for holistic visualization of STEMI registry data	12
Learning prognostic models using a mixture of biclustering and triclustering: Predicting the need for non-invasive ventilation in Amyotrophic Lateral Sclerosis	12
Causal feature selection using a knowledge graph combining structured knowledge from the biomedical literature and ontologies: A use case studying depression as a risk factor for Alzheimer’s disease	12
GHS-NET a generic hybridized shallow neural network for multi-label biomedical text classification	12
Cover 1/Spine	12
A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19	12
Cover 2: Editorial Board	12
Cover 2: Editorial Board	12
Leveraging Multi-source knowledge for Chinese clinical named entity recognition via relational graph convolutional network	12
Extracting medication changes in clinical narratives using pre-trained language models	12
Early diagnosis of Parkinson's disease using Continuous Convolution Network: Handwriting recognition based on off-line hand drawing without template	12
Information handoffs in critical care and their implications for information quality: A socio-technical network approach	12
A cost-effective IoT learning environment for the training and assessment of surgical technical skills with visual learning analytics	12
Identifying acute kidney injury subphenotypes using an outcome-driven deep-learning approach	12
Modeling repeated measurements data using the multilevel Bayesian network: A case of child morbidity	12
Letter to Editor: An Argument for a Universal Health Record	11
The IeDEA harmonist data toolkit: A data quality and data sharing solution for a global HIV research consortium	11
Unified concept and assertion detection using contextual multi-task learning in a clinical decision support system	11
fmi-ii: Table of Contents	11
Long-term prediction for temporal propagation of seasonal influenza using Transformer-based model	11
Using information theory to optimize a diagnostic threshold to match physician-ordering practice	11
Graph-based clinical recommender: Predicting specialists procedure orders using graph representation learning	11
Cover 2: Editorial Board	11
Cover 2: Editorial Board	11
fmi-ii: Table of Contents	11
Call for papers: Semantics-enabled biomedical literature analytics	11
Novel evaluation approach for molecular signature-based deconvolution methods	11
Comparative study of machine learning methods for COVID-19 transmission forecasting	11
AutoScore-Survival: Developing interpretable machine learning-based time-to-event scores with right-censored survival data	11
A fuzzy-based framework for diagnosing esophageal mobility disorder using high-resolution manometry	11
Diagnosis clarification by generalization to patient-friendly terms and definitions: Validation study	11
An informatics-driven intelligent system to improve healthcare accessibility for vulnerable populations	11
Cover 1/Spine	11
Cover 1/Spine	11
Cover 2: Editorial Board	11
Incorporating multi-level CNN and attention mechanism for Chinese clinical named entity recognition	11
Call for Papers: Special Issue on Fairness and Inclusion in Biomedical Informatics Research: Technical and Social Perspectives	11
Toward the European Health Data Space: The IMPaCT-Data secure infrastructure for EHR-based precision medicine research	10
Cost prediction for ischemic heart disease hospitalization: Interpretable feature extraction using network analysis	10
Building an OMOP common data model-compliant annotated corpus for COVID-19 clinical trials	10
KeMRE: Knowledge-enhanced medical relation extraction for Chinese medicine instructions	10
Decision-support systems for managing polypharmacy in the elderly: A scoping review	10
Automated classification of cancer morphology from Italian pathology reports using Natural Language Processing techniques: A rule-based approach	10
Implementation and evaluation of a multivariate abstraction-based, interval-based dynamic time-warping method as a similarity measure for longitudinal medical records	10
On learning disentangled representations for individual treatment effect estimation	10
Automated interpretable discovery of heterogeneous treatment effectiveness: A COVID-19 case study	10
Providing clinical context to the spatio-temporal analysis of 4D CT perfusion to predict acute ischemic stroke lesion outcomes	10
Lessons learned to enable question answering on knowledge graphs extracted from scientific publications: A case study on the coronavirus literature	10
Multimodal learning on graphs for disease relation extraction	10
Supporting rural public health practice to address local-level social determinants of health across Northwest states: Development of an interactive visualization dashboard	10
Phenotyping coronavirus disease 2019 during a global health pandemic: Lessons learned from the characterization of an early cohort	10
Stratifying individuals into non-alcoholic fatty liver disease risk levels using time series machine learning models	10
A scalable approach for developing clinical risk prediction applications in different hospitals	10
Confederated learning in healthcare: Training machine learning models using disconnected data separated by individual, data type and identity for Large-Scale health system Intelligence	10
Generative adversarial networks for biomedical time series forecasting and imputation	10
Topological data analysis in biomedicine: A review	10
A novel hierarchical machine learning model for hospital-acquired venous thromboembolism risk assessment among multiple-departments	10
Retrieve and rerank for automated ICD coding via Contrastive Learning	10
A voice-based digital assistant for intelligent prompting of evidence-based practices during ICU rounds	10
Considerations for using predictive models that include race as an input variable: The case study of lung cancer screening	10
Fully automated detection of formal thought disorder with Time-series Augmented Representations for Detection of Incoherent Speech (TARDIS)	10
Language inference-based learning for Low-Resource Chinese clinical named entity recognition using language model	10
A conceptual framework for external validity	10
A maintenance hemodialysis mortality prediction model based on anomaly detection using longitudinal hemodialysis data	10
Inductive database to support iterative data mining: Application to biomarker analysis on patient data in the Fight-HF project	10
Efficient verification for outsourced genome-wide association studies	10
Traditional Chinese medicine symptom normalization approach leveraging hierarchical semantic information and text matching with attention mechanism	10
Towards quality improvement of vaccine concept mappings in the OMOP vocabulary with a semi-automated method	10
Temporal patterns selection for All-Cause Mortality prediction in T2D with ANNs	10
Annotated dataset creation through large language models for non-english medical NLP	10
Hierarchical label-wise attention transformer model for explainable ICD coding	10
Benefit-aware early prediction of health outcomes on multivariate EEG time series	10