2024
Ensemble pretrained language models to extract biomedical knowledge from literature
Li Z, Wei Q, Huang L, Li J, Hu Y, Chuang Y, He J, Das A, Keloth V, Yang Y, Diala C, Roberts K, Tao C, Jiang X, Zheng W, Xu H. Ensemble pretrained language models to extract biomedical knowledge from literature. Journal Of The American Medical Informatics Association 2024, 31: 1904-1911. PMID: 38520725, PMCID: PMC11339500, DOI: 10.1093/jamia/ocae061.Peer-Reviewed Original ResearchNatural language processingNatural language processing systemsLanguage modelExpansion of biomedical literatureZero-shot settingManually annotated corpusKnowledge graph developmentTask-specific modelsDomain-specific modelsZero-ShotEntity recognitionBillion parametersEnsemble learningLocation informationKnowledge basesBiomedical entitiesLanguage processingFree textGraph developmentBiomedical conceptsAutomated techniqueBiomedical literatureDetection methodPredictive performanceBiomedical knowledge
2011
Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases.
Xu H, Fu Z, Shah A, Chen Y, Peterson N, Chen Q, Mani S, Levy M, Dai Q, Denny J. Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases. AMIA Annual Symposium Proceedings 2011, 2011: 1564-72. PMID: 22195222, PMCID: PMC3243156.Peer-Reviewed Original ResearchConceptsEntire electronic health recordElectronic health recordsNatural language processingHealth recordsStructured EHR dataMachine learningText dataNarrative text dataF-measureLanguage processingClinical narrativesEHR dataSuch tasksColorectal cancerDetection methodConcept identificationCohort of patientsColorectal cancer casesVanderbilt University HospitalCase detection methodsClinical notesCRC patientsCRC casesUniversity HospitalCancer cases
2007
A study of abbreviations in clinical notes.
Xu H, Stetson P, Friedman C. A study of abbreviations in clinical notes. AMIA Annual Symposium Proceedings 2007, 2007: 821-5. PMID: 18693951, PMCID: PMC2655910.Peer-Reviewed Original ResearchConceptsUnified Medical Language SystemNatural language processing systemsLanguage processing systemNarrative clinical notesDetection methodClinical notesDifferent knowledge sourcesSense inventoryDomain expertsNLP systemsCorrect sensesDecision supportText corporaKnowledge sourcesError detectionProcessing systemBiomedical literatureStudy of abbreviationsLanguage systemPatient informationAmbiguity rateBetter detection methodsDatabaseAnnotationAbbreviations