2024
Develop and validate a computable phenotype for the identification of Alzheimer's disease patients using electronic health record data
He X, Wei R, Huang Y, Chen Z, Lyu T, Bost S, Tong J, Li L, Zhou Y, Li Z, Guo J, Tang H, Wang F, DeKosky S, Xu H, Chen Y, Zhang R, Xu J, Guo Y, Wu Y, Bian J. Develop and validate a computable phenotype for the identification of Alzheimer's disease patients using electronic health record data. Alzheimer's & Dementia Diagnosis Assessment & Disease Monitoring 2024, 16: e12613. PMID: 38966622, PMCID: PMC11220631, DOI: 10.1002/dad2.12613.Peer-Reviewed Original ResearchElectronic health record dataElectronic health recordsComputable phenotypeHealth record dataManual chart reviewHealth recordsAlzheimer's diseaseDiagnosis codesRecord dataChart reviewUTHealthAlzheimer's disease patientsUniversity of MinnesotaAD diagnosisAD identificationDisease patientsPatientsAlzheimerAD patientsDemographicsDiagnosisDiseaseCodeDataUniversityMapping Study Variables to Common Data Elements Using GPT for Sheets: Towards Standardized Data Collection and Sharing
Ram P, Hong N, Xu H, Jiang X. Mapping Study Variables to Common Data Elements Using GPT for Sheets: Towards Standardized Data Collection and Sharing. 2024, 00: 320-325. DOI: 10.1109/ichi61247.2024.00048.Peer-Reviewed Original ResearchKamino: A Scalable Architecture to Support Medical AI Research Using Large Real World Data
Lin F, Young P, He H, Huang J, Gagne R, Rice D, Price N, Byron W, Hu Y, Felker D, Button W, Meeker D, Hsiao A, Xu H, Torre C, Schulz W. Kamino: A Scalable Architecture to Support Medical AI Research Using Large Real World Data. 2024, 00: 500-504. DOI: 10.1109/ichi61247.2024.00072.Peer-Reviewed Original ResearchElectronic health recordsAI researchNatural language processing tasksElectronic health record dataLanguage processing tasksComputing resource managementLarge-scale data retrievalMedical AI researchLeveraging electronic health recordsStandard data modelKubernetes orchestratorScalable architectureProcessing tasksResource allocation systemsSecurity considerationsAccess managementData retrievalData modelArchitectural solutionsOMOP CDMReal World DataWorld DataHealth recordsOMOPData
2023
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia
Ohno-Machado L, Jiang X, Kuo T, Tao S, Chen L, Ram P, Zhang G, Xu H. A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia. Journal Of Biomedical Informatics 2023, 139: 104322. PMID: 36806328, PMCID: PMC10975485, DOI: 10.1016/j.jbi.2023.104322.Peer-Reviewed Original ResearchConceptsPrivacy of individualsAppropriate privacy protectionData-driven modelsPrivacy protectionPrivacy risksData Coordination CenterData hubData repositoryHierarchical strategyPrivacyBiomedical discoveryData setsRecord linkageData Coordinating CenterRepositoryComplex strategiesCoordination centerTechnologyTechniqueDataPartiesSetHierarchy
2017
A 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 applicationTaskInformationDataFinding useful data across multiple biomedical data repositories using DataMed
Ohno-Machado L, Sansone S, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj A, Bell E, Soysal E, Zong N, Kim H. Finding useful data across multiple biomedical data repositories using DataMed. Nature Genetics 2017, 49: 816-819. PMID: 28546571, PMCID: PMC6460922, DOI: 10.1038/ng.3864.Peer-Reviewed Original ResearchConceptsBiomedical data repositoriesHealth big dataData setsKnowledge discoveryBig dataMultiple repositoriesSearch enginesData indexFAIR principlesDataMedData repositoryService providersKnowledge initiativesKnowledge expertsBiomedical research communityResearch communityRepositoryScience landscapeUseful dataInteroperabilityMetadataFindabilitySetEngineData
2013
DTMBIO 2013
Butte A, Lee D, Xu H, Song M. DTMBIO 2013. 2013, 2555-2556. DOI: 10.1145/2505515.2505814.Peer-Reviewed Original Research
2012
DTMBIO 2012
Song M, Lee D, Xu H, Ananiadou S. DTMBIO 2012. 2012, 2766-2767. DOI: 10.1145/2396761.2398758.Peer-Reviewed Original Research
2011
Data from clinical notes: a perspective on the tension between structure and flexible documentation
Rosenbloom S, Denny J, Xu H, Lorenzi N, Stead W, Johnson K. Data from clinical notes: a perspective on the tension between structure and flexible documentation. Journal Of The American Medical Informatics Association 2011, 18: 181-186. PMID: 21233086, PMCID: PMC3116264, DOI: 10.1136/jamia.2010.007237.Peer-Reviewed Original ResearchConceptsReusable dataElectronic health record system adoptionStructured documentationComputer-based documentation systemsClinical notesClinical documentationStructured dataText processingSystem adoptionRecord systemSuch systemsDocumentation systemWorkflowContent needsProvidersUsabilityDocumentationExpressivitySystemHealthcare providersPatient careDataProcessingMajor goalAdoption