2025
Medical foundation large language models for comprehensive text analysis and beyond
Xie Q, Chen Q, Chen A, Peng C, Hu Y, Lin F, Peng X, Huang J, Zhang J, Keloth V, Zhou X, Qian L, He H, Shung D, Ohno-Machado L, Wu Y, Xu H, Bian J. Medical foundation large language models for comprehensive text analysis and beyond. Npj Digital Medicine 2025, 8: 141. PMID: 40044845, PMCID: PMC11882967, DOI: 10.1038/s41746-025-01533-1.Peer-Reviewed Original ResearchText analysis tasksAnalysis tasksLanguage modelDomain-specific knowledgeZero-ShotHuman evaluationSupervised settingTask-specific instructionsClinical data sourcesSpecialized medical knowledgeChatGPTText analysisPretrainingTaskData sourcesMedical applicationsMedical knowledgeEnhanced performanceTextPerformance
2024
Improving large language models for clinical named entity recognition via prompt engineering
Hu Y, Chen Q, Du J, Peng X, Keloth V, Zuo X, Zhou Y, Li Z, Jiang X, Lu Z, Roberts K, Xu H. Improving large language models for clinical named entity recognition via prompt engineering. Journal Of The American Medical Informatics Association 2024, 31: 1812-1820. PMID: 38281112, PMCID: PMC11339492, DOI: 10.1093/jamia/ocad259.Peer-Reviewed Original ResearchClinical NER tasksNER taskTask-specific promptsEntity recognitionLanguage modelTraining samplesState-of-the-art modelsFew-shot learningState-of-the-artMinimal training dataTask-specific knowledgeF1-socreAnnotated samplesConcept extractionModel performanceAnnotated datasetsTraining dataF1 scoreTask descriptionFormat specificationsComplex clinical dataOptimal performanceTaskEvaluation schemaGPT model
2018
Extended Analysis of Topological-Pattern-Based Ontology Enrichment
He Z, Keloth V, Chen Y, Geller J. Extended Analysis of Topological-Pattern-Based Ontology Enrichment. 2023 IEEE International Conference On Bioinformatics And Biomedicine (BIBM) 2018, 00: 1641-1648. PMID: 30854243, PMCID: PMC6402505, DOI: 10.1109/bibm.2018.8621564.Peer-Reviewed Original ResearchUnified Medical Language SystemTarget ontologyNational Cancer Institute ThesaurusMaintenance of biomedical ontologiesPairs of ontologiesMedical Language SystemHuman expertsCross-ontologyReference ontologyBiomedical ontologiesOntologyLanguage systemExpert resourcesHierarchical relationshipsTheoretical analysisApproximate locationTopological patternsThesaurusReference conceptTaskConceptClassificationMethodUnified
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