2023
Patient Dietary Supplements Use: Do Results from Natural Language Processing of Clinical Notes Agree with Survey Data?
Redd D, Workman T, Shao Y, Cheng Y, Tekle S, Garvin J, Brandt C, Zeng-Treitler Q. Patient Dietary Supplements Use: Do Results from Natural Language Processing of Clinical Notes Agree with Survey Data? Medical Sciences 2023, 11: 37. PMID: 37367736, PMCID: PMC10304046, DOI: 10.3390/medsci11020037.Peer-Reviewed Original ResearchConceptsSelf-reported supplement useSupplement useClinical notesStructured medical recordsUnstructured clinical notesPrescription medicationsClinical recordsMedical recordsPhysician guidanceDietary supplementsNatural language processing toolsPatientsNatural language processingFolic acidHealthcare facilitiesLanguage processing toolsSupplementsF1 scoreLanguage processingPotential interactionsNLP performanceProcessing toolsNLP extractionExtra informationMedicationsDeveloping Validated Tools to Identify Pulmonary Embolism in Electronic Databases: Rationale and Design of the PE-EHR+ Study
Bikdeli B, Lo Y, Khairani C, Bejjani A, Jimenez D, Barco S, Mahajan S, Caraballo C, Secemsky E, Klok F, Hunsaker A, Aghayev A, Muriel A, Wang Y, Hussain M, Appah-Sampong A, Lu Y, Lin Z, Aneja S, Khera R, Goldhaber S, Zhou L, Monreal M, Krumholz H, Piazza G. Developing Validated Tools to Identify Pulmonary Embolism in Electronic Databases: Rationale and Design of the PE-EHR+ Study. Thrombosis And Haemostasis 2023, 123: 649-662. PMID: 36809777, PMCID: PMC11200175, DOI: 10.1055/a-2039-3222.Peer-Reviewed Original ResearchConceptsElectronic health recordsNLP algorithmNatural language processing toolsLanguage processing toolsPrincipal discharge diagnosisICD-10 codesDischarge diagnosisNLP toolsChart reviewHealth systemProcessing toolsYale New Haven Health SystemPatient identificationElectronic databasesHealth recordsData validationHigh-risk PEPulmonary Embolism ResearchSecondary discharge diagnosisIdentification of patientsManual chart reviewNegative predictive valueCodeRadiology reportsAlgorithm
2022
Multiscale Decompositions of Hardy Spaces
Coifman R, Peyrière J. Multiscale Decompositions of Hardy Spaces. Applied And Numerical Harmonic Analysis 2022, 445-462. DOI: 10.1007/978-3-030-45847-8_20.Peer-Reviewed Original Research
2021
Feasibility of capturing real-world data from health information technology systems at multiple centers to assess cardiac ablation device outcomes: A fit-for-purpose informatics analysis report
Jiang G, Dhruva SS, Chen J, Schulz WL, Doshi AA, Noseworthy PA, Zhang S, Yu Y, Young H, Brandt E, Ervin KR, Shah ND, Ross JS, Coplan P, Drozda JP. Feasibility of capturing real-world data from health information technology systems at multiple centers to assess cardiac ablation device outcomes: A fit-for-purpose informatics analysis report. Journal Of The American Medical Informatics Association 2021, 28: 2241-2250. PMID: 34313748, PMCID: PMC8449615, DOI: 10.1093/jamia/ocab117.Peer-Reviewed Original ResearchConceptsReal-world dataHealth information technology systemsInformation technology systemsUnique device identifiersMaturity modelNatural language processing toolsTechnology systemsUnstructured data elementsNatural language processingCommon data modelData quality frameworkLanguage processing toolsComputable phenotypeInformatics approachElectronic health recordsClinical data systemsData modelLanguage processingDevice identifiersStandardized codesData elementsProcessing toolsInformatics technologiesData captureHealth recordsCOVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model
Wang J, Abu-El-Rub N, Gray J, Pham H, Zhou Y, Manion F, Liu M, Song X, Xu H, Rouhizadeh M, Zhang Y. COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model. Journal Of The American Medical Informatics Association 2021, 28: 1275-1283. PMID: 33674830, PMCID: PMC7989301, DOI: 10.1093/jamia/ocab015.Peer-Reviewed Original ResearchConceptsNatural language processing toolsCommon data modelLanguage processing toolsElectronic health recordsClinical natural language processing toolsData modelDeep learning-based modelProcessing toolsOMOP Common Data ModelPattern-based rulesObservational Medical Outcomes Partnership Common Data ModelLearning-based modelsSpecific information needsUse casesNLP toolsClinical textFree textExtensive evaluationDownloadable packageInformation needsHybrid approachResearch communityHealth recordsData sourcesHigh performance
2020
Opioid2FHIR: A system for extracting FHIR-compatible opioid prescriptions from clinical text
Wang J, Mathews W, Pham H, Xu H, Zhang Y. Opioid2FHIR: A system for extracting FHIR-compatible opioid prescriptions from clinical text. 2020, 00: 1748-1751. DOI: 10.1109/bibm49941.2020.9313258.Peer-Reviewed Original ResearchFast Healthcare Interoperability ResourcesInformation extractionNatural language processing techniquesLanguage processing techniquesMedical concept normalizationOpioid informationPost-processing rulesClinical decision supportManual effortConcept normalizationClinical textF-measureNLP applicationsPrescription recordsClinical data standardsData standardsDecision supportFree textProcessing toolsPrescription drug monitoring programsNational public health emergencyProcessing techniquesPrescription opioid overdoseDrug monitoring programsDrug overdose deathsEfficient and Accurate Extracting of Unstructured EHRs on Cancer Therapy Responses for the Development of RECIST Natural Language Processing Tools: Part I, the Corpus
Li Y, Luo Y, Wampfler J, Rubinstein S, Tiryaki F, Ashok K, Warner J, Xu H, Yang P. Efficient and Accurate Extracting of Unstructured EHRs on Cancer Therapy Responses for the Development of RECIST Natural Language Processing Tools: Part I, the Corpus. JCO Clinical Cancer Informatics 2020, 4: cci.19.00147. PMID: 32364754, PMCID: PMC7265793, DOI: 10.1200/cci.19.00147.Peer-Reviewed Original ResearchConceptsNatural language processing toolsElectronic health recordsLanguage processing toolsGold standard dataUnstructured electronic health recordsProcessing toolsAmount of dataClinical notesStandard dataMayo Clinic electronic health recordsClinic's electronic health recordEnvironment toolsAccurate annotationHealth recordsInformatics toolsEffective analysisData setsTextual sourcesCorpusToolInformationData extractionSetExtractingAnnotation
2019
Development of a Natural Language Processing Tool to Extract Radiation Treatment Sites
Walker G, Soysal E, Xu H. Development of a Natural Language Processing Tool to Extract Radiation Treatment Sites. Cureus 2019, 11: e6010. PMID: 31815074, PMCID: PMC6881088, DOI: 10.7759/cureus.6010.Peer-Reviewed Original Research
2014
Identifying plausible adverse drug reactions using knowledge extracted from the literature
Shang N, Xu H, Rindflesch T, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. Journal Of Biomedical Informatics 2014, 52: 293-310. PMID: 25046831, PMCID: PMC4261011, DOI: 10.1016/j.jbi.2014.07.011.Peer-Reviewed Original ResearchConceptsPredication-based Semantic IndexingReflective Random IndexingLBD methodsNatural language processing toolsBiomedical literatureDrug-adverse event associationsLanguage processing toolsSemantic indexingElectronic health recordsRandom IndexingHuman reviewVast repositoryDiscovery methodsVolume of knowledgeProcessing toolsEvaluation setHealth recordsData sourcesEvent associationsIndexingDrug-effect relationshipsRepositoryLarge volumesADR associationsReasoning pathwaysOpen Source Clinical NLP - More than Any Single System.
Masanz J, Pakhomov S, Xu H, Wu S, Chute C, Liu H. Open Source Clinical NLP - More than Any Single System. AMIA Joint Summits On Translational Science Proceedings 2014, 2014: 76-82. PMID: 25954581, PMCID: PMC4419764.Peer-Reviewed Original ResearchClinical NLPNLP systemsNatural language processing toolsOpen source softwareLanguage processing toolsInformation technology practicesPluggable componentsSource softwareNLP softwareProcessing capabilitiesProcessing toolsResearch communityNLPCollaborative communitySingle systemSoftwareTechnology practicesNLP activityUIMAAnnotatorsSystemApacheOngoing activityFrameworkCapabilityPhenDisco: phenotype discovery system for the database of genotypes and phenotypes
Doan S, Lin K, Conway M, Ohno-Machado L, Hsieh A, Feupe S, Garland A, Ross M, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim H. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. Journal Of The American Medical Informatics Association 2014, 21: 31-36. PMID: 23989082, PMCID: PMC3912702, DOI: 10.1136/amiajnl-2013-001882.Peer-Reviewed Original ResearchConceptsNew information retrieval systemInformation retrieval systemsInformation retrieval toolsDatabase of GenotypesText processing toolsRetrieval systemSearch scenariosDiscovery systemRetrieval toolsAuthorized usersNon-standardized wayCross-study validationSearch comparisonProcessing toolsPromising performanceUsersPhenotype informationDatabaseInformationBiotechnology InformationQueriesMetadataEntrezResourcesSystem
2013
Using automatic alignment to analyze endangered language data: Testing the viability of untrained alignment
DiCanio C, Nam H, Whalen D, Bunnell H, Amith J, García R. Using automatic alignment to analyze endangered language data: Testing the viability of untrained alignment. The Journal Of The Acoustical Society Of America 2013, 134: 2235-2246. PMID: 23967953, PMCID: PMC5392066, DOI: 10.1121/1.4816491.Peer-Reviewed Original ResearchConceptsPhonetic analysisLanguage dataForced alignmentPhone setDocument endangered languagesSpeech processing toolsEndangered languagesCorpus dataTarget languageTraining languageSmall corpusLanguageCorpusDocument corpusAutomatic alignmentProcess of segmentationSegmentation taskAlignment systemAllophonesEnglishSpeechMixtecData setsProcessing toolsContextualAnalyzing differences between chinese and english clinical text: a cross-institution comparison of discharge summaries in two languages.
Wu Y, Lei J, Wei W, Tang B, Denny J, Rosenbloom S, Miller R, Giuse D, Zheng K, Xu H. Analyzing differences between chinese and english clinical text: a cross-institution comparison of discharge summaries in two languages. 2013, 192: 662-6. PMID: 23920639, PMCID: PMC4957806.Peer-Reviewed Original ResearchConceptsNatural language processing toolsEnglish clinical textClinical textLanguage processing toolsChinese clinical textCultural differencesMajor clinical componentsTextWestern institutionsInpatient discharge summariesCross-country collaborationDocument levelProcessing toolsClinical documentsLanguageUS institutionsUsesUnprecedented amountValuable insightsInstitutionsDocumentsChinaWorldwide adoptionEMR dataCollaboration
2006
A natural language processing (NLP) tool to assist in the curation of the laboratory Mouse Tumor Biology Database.
Xu H, Krupke D, Blake J, Friedman C. A natural language processing (NLP) tool to assist in the curation of the laboratory Mouse Tumor Biology Database. AMIA Annual Symposium Proceedings 2006, 2006: 1150. PMID: 17238769, PMCID: PMC1839428.Peer-Reviewed Original ResearchConceptsMouse Genome Informatics groupNatural language processing toolsModel organism databaseMouse Tumor Biology DatabaseLanguage processing toolsBiology databasesOrganism databasesGenomic informationBiological communitiesProcessing toolsSpecific organismsInformatics GroupOrganismsKey informationDatabaseInformationSubstantial effortCurationTool
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