2024
Ascle—A Python Natural Language Processing Toolkit for Medical Text Generation: Development and Evaluation Study
Yang R, Zeng Q, You K, Qiao Y, Huang L, Hsieh C, Rosand B, Goldwasser J, Dave A, Keenan T, Ke Y, Hong C, Liu N, Chew E, Radev D, Lu Z, Xu H, Chen Q, Li I. Ascle—A Python Natural Language Processing Toolkit for Medical Text Generation: Development and Evaluation Study. Journal Of Medical Internet Research 2024, 26: e60601. PMID: 39361955, PMCID: PMC11487205, DOI: 10.2196/60601.Peer-Reviewed Original ResearchConceptsNatural language processingNatural language processing toolkitQuestion-answering taskLanguage modelText generationText processingDomain-specific language modelsNatural language processing functionsMinimal programming expertiseText generation tasksMedical knowledge graphMachine translation tasksROUGE-L scoreDomain-specific challengesAll-in-one solutionROUGE-LText summarizationBLEU scoreKnowledge graphMachine translationUnstructured textQuestion-answeringHugging FaceProcessing toolkitLanguage processing
2021
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers
Zhang Y, Yao X, Zhou H, Wu X, Tian J, Zeng J, Yan L, Duan C, Liu H, Li H, Chen K, Hu Z, Ye Z, Xu H. OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. Nucleic Acids Research 2021, 50: d1340-d1347. PMID: 34554251, PMCID: PMC8728274, DOI: 10.1093/nar/gkab851.Peer-Reviewed Original ResearchConceptsAlternative splicingCancer-specific splicing eventsDifferential alternative splicingHuman cancersTCGA tumor samplesSplicing differencesSplicing eventsProtein complexityAdjacent normal samplesSplicingGene expressionSplicing dataNormal samplesAbnormal splicingIntegrative viewMRNA levelsDifferential analysisTumor samplesTranscripts
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
Recognizing software names in biomedical literature using machine learning
Wei Q, Zhang Y, Amith M, Lin R, Lapeyrolerie J, Tao C, Xu H. Recognizing software names in biomedical literature using machine learning. Health Informatics Journal 2019, 26: 21-33. PMID: 31566474, PMCID: PMC7334865, DOI: 10.1177/1460458219869490.Peer-Reviewed Original ResearchConceptsSoftware namesF-measureNatural language processing methodsBiomedical literatureWord representation featuresLanguage processing methodsEntity recognition systemSoftware catalogSoftware repositoriesFeature engineeringBiomedical softwareRecognition systemSoftware toolsBiomedical domainRepresentation featuresMEDLINE abstractsWord embeddingsKnowledge featuresManual curationSoftwareMachineProcessing methodsBest systemRepositorySystem
2017
Finding 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 dataInteroperabilityMetadataFindabilitySetEngineDataSemantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features.
Zhang Y, Jiang M, Wang J, Xu H. Semantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features. AMIA Annual Symposium Proceedings 2017, 2016: 1283-1292. PMID: 28269926, PMCID: PMC5333340.Peer-Reviewed Original ResearchExpressing Biomedical Ontologies in Natural Language for Expert Evaluation.
Amith M, Manion F, Harris M, Zhang Y, Xu H, Tao C. Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. 2017, 245: 838-842. PMID: 29295217, PMCID: PMC6644701.Peer-Reviewed Original Research
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
2012
Identifying the status of genetic lesions in cancer clinical trial documents using machine learning
Wu Y, Levy M, Micheel C, Yeh P, Tang B, Cantrell M, Cooreman S, Xu H. Identifying the status of genetic lesions in cancer clinical trial documents using machine learning. BMC Genomics 2012, 13: s21. PMID: 23282337, PMCID: PMC3535695, DOI: 10.1186/1471-2164-13-s8-s21.Peer-Reviewed Original ResearchDTome: a web-based tool for drug-target interactome construction
Sun J, Wu Y, Xu H, Zhao Z. DTome: a web-based tool for drug-target interactome construction. BMC Bioinformatics 2012, 13: s7. PMID: 22901092, PMCID: PMC3372450, DOI: 10.1186/1471-2105-13-s9-s7.Peer-Reviewed Original ResearchConceptsWeb-based toolUser-friendly web interfaceWeb-based queriesRich data sourceDifferent knowledge basesDatabase schemaWeb interfaceVisualization processKnowledge basesComputational workflowDiscovery processData sourcesNetworkDrug-target interactionsDrugs' primary targetsDrug-target networkWorkflowEarly-stage drug discoveryNetwork analysisQueriesToolPromising approachDrug discovery processSchemaDetailed network analysis
2007
Using contextual and lexical features to restructure and validate the classification of biomedical concepts
Fan J, Xu H, Friedman C. Using contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics 2007, 8: 264. PMID: 17650333, PMCID: PMC2014782, DOI: 10.1186/1471-2105-8-264.Peer-Reviewed Original ResearchConceptsUnified Medical Language SystemString-based approachesMean reciprocal rankReciprocal rankNatural language processingError rateContextual featuresLexical featuresIntegration of dataLow error rateReasoning systemAutomatic approachComplementary classifiersLanguage processingClassification approachBiomedical terminologiesClassification errorOntological conceptsBiomedical conceptsOntological termsSyntactic approachLanguage systemClassifierSyntactic featuresOntology
2006
Natural language processing and visualization in the molecular imaging domain
Tulipano P, Tao Y, Millar W, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier Y, Friedman C. Natural language processing and visualization in the molecular imaging domain. Journal Of Biomedical Informatics 2006, 40: 270-281. PMID: 17084109, DOI: 10.1016/j.jbi.2006.08.002.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineComputational BiologyDatabases, BibliographicDatabases, GeneticDiagnostic ImagingGenomicsHumansInformation Storage and RetrievalNatural Language ProcessingPhenotypeProgramming LanguagesSoftwareSystems IntegrationTerminology as TopicUser-Computer InterfaceVocabulary, ControlledConceptsImaging domainNatural language processing systemsNatural language processingLanguage processing systemJava viewerNLP systemsFormal evaluation studiesLanguage processingInformation resourcesProcessing systemMedical imagingIndex imagesSystem performanceBiological informationInformationImagesVisualizationBioMedLEEPerformanceNLPEvaluation studyDomainGenomics literatureSystemSimultaneous visualization