2024
NLP Applications—Other Biomedical Texts
Roberts K, Xu H, Demner Fushman D. NLP Applications—Other Biomedical Texts. Cognitive Informatics In Biomedicine And Healthcare 2024, 429-444. DOI: 10.1007/978-3-031-55865-8_15.Peer-Reviewed Original Research
2022
IMI-CDE: an interactive interface for collaborative mapping of study variables to common data elements
Tao S, Chou W, Li J, Du J, Ram P, Abeysinghe R, Xu H, Jiang X, Rose P, Ohno-Machado L, Zhang G. IMI-CDE: an interactive interface for collaborative mapping of study variables to common data elements. 2022, 00: 465-468. DOI: 10.1109/ichi54592.2022.00070.Peer-Reviewed Original Research
2020
Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents
Amith M, Lin R, Cui L, Wang D, Zhu A, Xiong G, Xu H, Roberts K, Tao C. Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents. BMC Medical Informatics And Decision Making 2020, 20: 259. PMID: 33317519, PMCID: PMC7734717, DOI: 10.1186/s12911-020-01267-y.Peer-Reviewed Original ResearchConceptsDialogue engineUser-centric systemOntology-based systemQuestion-answering systemManagement engineSoftware engineQuestion AnsweringConversational agentsDialogue interactionCompetency questionsContextual informationConsumer usersCore taskAccuracy scoresConsumer questionsEngineConversational flowHealth informationSimulation trialsInformationUsersFuture plansNext stepOntologyWizard
2019
Cost-aware active learning for named entity recognition in clinical text
Wei Q, Chen Y, Salimi M, Denny J, Mei Q, Lasko T, Chen Q, Wu S, Franklin A, Cohen T, Xu H. Cost-aware active learning for named entity recognition in clinical text. Journal Of The American Medical Informatics Association 2019, 26: 1314-1322. PMID: 31294792, PMCID: PMC6798575, DOI: 10.1093/jamia/ocz102.Peer-Reviewed Original ResearchConceptsAnnotation costUser studyActive learningAL methodsAL algorithmCost-CAUSEReal-world environmentsAnnotation taskAnnotation timeAnnotation accuracyEntity recognitionClinical textAnnotation dataPassive learningInformative examplesCurve scoreMost approachesSimulation areaUsersSyntactic featuresLearningCost measuresAlgorithmCostAnnotation
2018
Clinical text annotation - what factors are associated with the cost of time?
Wei Q, Franklin A, Cohen T, Xu H. Clinical text annotation - what factors are associated with the cost of time? AMIA Annual Symposium Proceedings 2018, 2018: 1552-1560. PMID: 30815201, PMCID: PMC6371268.Peer-Reviewed Original ResearchConceptsAnnotation timeClinical textNatural language processing modelsClinical corpusIndividual user behaviorEntity recognition taskLanguage processing modelsPractice of annotationCharacteristics of sentencesClinical Text AnnotationText annotationsUser behaviorIndividual usersCost of timeActive learning researchRecognition taskLearning researchProcessing modelCost modelAnnotationUsersLimited workCorpusTextTask
2017
User needs analysis and usability assessment of DataMed – a biomedical data discovery index
Dixit R, Rogith D, Narayana V, Salimi M, Gururaj A, Ohno-Machado L, Xu H, Johnson T. User needs analysis and usability assessment of DataMed – a biomedical data discovery index. Journal Of The American Medical Informatics Association 2017, 25: 337-344. PMID: 29202203, PMCID: PMC7378884, DOI: 10.1093/jamia/ocx134.Peer-Reviewed Original ResearchData discoveryUsability evaluationInformation needsUser interfaceBiomedical dataIterative usability evaluationsInformation retrieval toolsUser interface needsHigh-quality metadataResearchers informationCommon search enginesDiscovery systemRetrieval toolsDataMedUser studyRelevance judgmentsSearch enginesUser needsDataset explorationUsability assessmentRetrieval techniquesNew retrieval techniqueIncomplete metadataMetadataUsersAn active learning-enabled annotation system for clinical named entity recognition
Chen Y, Lask T, Mei Q, Chen Q, Moon S, Wang J, Nguyen K, Dawodu T, Cohen T, Denny J, Xu H. An active learning-enabled annotation system for clinical named entity recognition. BMC Medical Informatics And Decision Making 2017, 17: 82. PMID: 28699546, PMCID: PMC5506567, DOI: 10.1186/s12911-017-0466-9.Peer-Reviewed Original ResearchConceptsNovel AL algorithmAL algorithmAnnotation timeUser studyEntity recognitionAnnotation systemNatural language processing modelsLanguage processing modelsAnnotation costMedical domainAnnotation processDifferent usersNER modelProcessing modelAlgorithmAL methodsResultsThe simulation resultsUsersSimulation resultsInformation contentFuture workRecognitionLarge numberSystemReal-life setting
2015
Ease of adoption of clinical natural language processing software: An evaluation of five systems
Zheng K, Vydiswaran V, Liu Y, Wang Y, Stubbs A, Uzuner Ö, Gururaj A, Bayer S, Aberdeen J, Rumshisky A, Pakhomov S, Liu H, Xu H. Ease of adoption of clinical natural language processing software: An evaluation of five systems. Journal Of Biomedical Informatics 2015, 58: s189-s196. PMID: 26210361, PMCID: PMC4974203, DOI: 10.1016/j.jbi.2015.07.008.Peer-Reviewed Original ResearchConceptsClinical NLP systemsNLP systemsNatural language processing softwareThird-party componentsUsability testing toolGroup of usersLanguage processing softwareEase of adoptionExpert evaluatorsSoftware distributionBiomedical softwareComputer scienceEnd usersUsability assessmentI2b2 challengeTesting toolsEvaluation showHuman evaluatorsSystem submissionsEase of useHealth informaticsProcessing softwareAdoption issuesUsersSpecial track
2014
PhenDisco: 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