2021
Leveraging a health information exchange for analyses of COVID-19 outcomes including an example application using smoking history and mortality
Tortolero G, Brown M, Sharma S, de Oliveira Otto M, Yamal J, Aguilar D, Gunther M, Mofleh D, Harris R, John J, de Vries P, Ramphul R, Serbo D, Kiger J, Banerjee D, Bonvino N, Merchant A, Clifford W, Mikhail J, Xu H, Murphy R, Wei Q, Vahidy F, Morrison A, Boerwinkle E. Leveraging a health information exchange for analyses of COVID-19 outcomes including an example application using smoking history and mortality. PLOS ONE 2021, 16: e0247235. PMID: 34081724, PMCID: PMC8174716, DOI: 10.1371/journal.pone.0247235.Peer-Reviewed Original ResearchConceptsBody mass indexCOVID-19 patientsRisk factorsTobacco useCOVID-19 fatalitiesHealth information exchangeRace/ethnicityCOVID-19Laboratory risk factorsNumber of comorbiditiesCOVID-19 cohortMultivariable logistic regressionImportant risk factorPotential risk factorsCOVID-19 outcomesFormer tobacco usersTobacco use historyLarge health information exchangeMass indexElectronic health record systemsUnfavorable outcomeClinical dataTobacco usersOutcome analysisElectronic health information
2020
Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies
Rasmy L, Tiryaki F, Zhou Y, Xiang Y, Tao C, Xu H, Zhi D. Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. Journal Of The American Medical Informatics Association 2020, 27: 1593-1599. PMID: 32930711, PMCID: PMC7647355, DOI: 10.1093/jamia/ocaa180.Peer-Reviewed Original ResearchConceptsUnified Medical Language SystemRecurrent neural networkNeural networkPrediction performanceLogistic regressionPredictive modelingDeep learningData aggregationElectronic health record dataMachine learningRisk predictionBetter prediction performanceDengue hemorrhagic feverHealth record dataEHR dataCancer predictionLarge vocabularyDifferent tasksPredictive modelHeart failureDiabetes patientsPancreatic cancerClinical dataHemorrhagic feverICD-9
2018
Toward a normalized clinical drug knowledge base in China—applying the RxNorm model to Chinese clinical drugs
Wang L, Zhang Y, Jiang M, Wang J, Dong J, Liu Y, Tao C, Jiang G, Zhou Y, Xu H. Toward a normalized clinical drug knowledge base in China—applying the RxNorm model to Chinese clinical drugs. Journal Of The American Medical Informatics Association 2018, 25: 809-818. PMID: 29635469, PMCID: PMC7647010, DOI: 10.1093/jamia/ocy020.Peer-Reviewed Original ResearchConceptsChinese patent drugDrug knowledge basePatent drugsClinical drugsChemical drugsChinese drugsManual reviewChinese patent medicineElectronic health record systemsClinical dataChina's health insurance systemHealth record systemsDrug AdministrationHealth insurance systemDrug informationDrugsPatent medicineDrug namesRecord systemPharmacy system
2017
Psychiatric symptom recognition without labeled data using distributional representations of phrases and on-line knowledge
Zhang Y, Zhang O, Wu Y, Lee H, Xu J, Xu H, Roberts K. Psychiatric symptom recognition without labeled data using distributional representations of phrases and on-line knowledge. Journal Of Biomedical Informatics 2017, 75: s129-s137. PMID: 28624644, PMCID: PMC5705397, DOI: 10.1016/j.jbi.2017.06.014.Peer-Reviewed Original ResearchConceptsPsychiatric symptomsCandidate symptomMental disordersPsychiatric notesList of symptomsMayo ClinicClinical dataSymptom recognitionPatient experiencePersonalized preventionSymptomsAmerican Psychiatric AssociationAbstractTextClinical conceptsPsychiatric AssociationPhenotypic classificationDisordersClinical textMIMIC-IIHealthcare knowledgeConclusionSubjective descriptionsClinicDiseaseDiagnosisA hybrid approach to automatic de-identification of psychiatric notes
Lee H, Wu Y, Zhang Y, Xu J, Xu H, Roberts K. A hybrid approach to automatic de-identification of psychiatric notes. Journal Of Biomedical Informatics 2017, 75: s19-s27. PMID: 28602904, PMCID: PMC5705430, DOI: 10.1016/j.jbi.2017.06.006.Peer-Reviewed Original ResearchConceptsPsychiatric notesCEGS N-GRIDNatural language processing systemsRule-based componentTask Track 1Language processing systemRule-based approachDe-identificationDomain adaptationRich featuresProcessing systemHybrid approachN gridTrack 1Clinical dataTest setSystem performanceMachineHealth informationHybrid systemSystemClinical applicationTaskInformationDataLiterature-Based Discovery of Confounding in Observational Clinical Data.
Malec S, Wei P, Xu H, Bernstam E, Myneni S, Cohen T. Literature-Based Discovery of Confounding in Observational Clinical Data. AMIA Annual Symposium Proceedings 2017, 2016: 1920-1929. PMID: 28269951, PMCID: PMC5333204.Peer-Reviewed Original Research
2014
Chapter 12 Linking Genomic and Clinical Data for Discovery and Personalized Care
Denny J, Xu H. Chapter 12 Linking Genomic and Clinical Data for Discovery and Personalized Care. 2014, 395-424. DOI: 10.1016/b978-0-12-401678-1.00012-9.Peer-Reviewed Original ResearchElectronic health recordsEHR dataNatural language processingSuch algorithmsLanguage processingDecision supportPhenotype algorithmsIdeal repositoryHealth recordsNumber of challengesRepositoryAlgorithmClinical notesClinical careClinical documentationGenomic dataResult dataAccurate caseDNA biobanksEarly demonstration projectsHealth care qualityClinical recordsMedication recordsClinical dataTool
2010
An automated approach to calculating the daily dose of tacrolimus in electronic health records.
Xu H, Doan S, Birdwell K, Cowan J, Vincz A, Haas D, Basford M, Denny J. An automated approach to calculating the daily dose of tacrolimus in electronic health records. AMIA Joint Summits On Translational Science Proceedings 2010, 2010: 71-5. PMID: 21347153, PMCID: PMC3041548.Peer-Reviewed Original ResearchElectronic health recordsUnstructured clinical dataNatural language processingHealth recordsTime-consuming taskUnstructured formatClinical textLanguage processingAutomated ApproachDaily doseData setsTest casesDetailed drug informationDrug mentionsDaily dosesClinical dataMedication informationClinical researchMedication namesDrug informationInformationTacrolimusMedicationsDoseTaskMedEx: a medication information extraction system for clinical narratives
Xu H, Stenner S, Doan S, Johnson K, Waitman L, Denny J. MedEx: a medication information extraction system for clinical narratives. Journal Of The American Medical Informatics Association 2010, 17: 19-24. PMID: 20064797, PMCID: PMC2995636, DOI: 10.1197/jamia.m3378.Peer-Reviewed Original ResearchConceptsClinic visit notesVisit notesMedication informationClinical notesDischarge summariesElectronic medical record dataMedical record dataElectronic medical recordsMedication dataMedical recordsClinical dataClinical researchRecord dataHealthcare safetyDrug namesMedexF-measureClinical narrativesNatural language processing systemsInformation extraction system