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 processingExtracting Systemic Anticancer Therapy and Response Information From Clinical Notes Following the RECIST Definition
Zuo X, Kumar A, Shen S, Li J, Cong G, Jin E, Chen Q, Warner J, Yang P, Xu H. Extracting Systemic Anticancer Therapy and Response Information From Clinical Notes Following the RECIST Definition. JCO Clinical Cancer Informatics 2024, 8: e2300166. PMID: 38885475, DOI: 10.1200/cci.23.00166.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsData MiningDeep LearningElectronic Health RecordsHumansMachine LearningNatural Language ProcessingNeoplasmsResponse Evaluation Criteria in Solid TumorsConceptsNatural language processingDomain-specific language modelsNatural language processing systemsInformation extraction systemRule-based moduleNarrative clinical textsNLP tasksEntity recognitionText normalizationAssertion classificationLanguage modelInformation extractionClinical textElectronic health recordsLearning-basedClinical notesLanguage processingTest setSystem performanceHealth recordsResponse extractionTime-consumingAnticancer therapyInformationAssessment information
2023
AutoCriteria: a generalizable clinical trial eligibility criteria extraction system powered by large language models
Datta S, Lee K, Paek H, Manion F, Ofoegbu N, Du J, Li Y, Huang L, Wang J, Lin B, Xu H, Wang X. AutoCriteria: a generalizable clinical trial eligibility criteria extraction system powered by large language models. Journal Of The American Medical Informatics Association 2023, 31: 375-385. PMID: 37952206, PMCID: PMC10797270, DOI: 10.1093/jamia/ocad218.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsEligibility DeterminationFemaleHumansInformation Storage and RetrievalLanguageNatural Language ProcessingConceptsLanguage modelInformation extraction systemOverall F1 scoreCriteria informationF1 scoreManual annotationScalable solutionContextual informationComplex scenariosContextual attributesExtraction systemReal-world settingsSystem evaluationModeling capabilitiesClinical trial protocol documentsInformationProtocol documentsRepresenting and utilizing clinical textual data for real world studies: An OHDSI approach
Keloth V, Banda J, Gurley M, Heider P, Kennedy G, Liu H, Liu F, Miller T, Natarajan K, V Patterson O, Peng Y, Raja K, Reeves R, Rouhizadeh M, Shi J, Wang X, Wang Y, Wei W, Williams A, Zhang R, Belenkaya R, Reich C, Blacketer C, Ryan P, Hripcsak G, Elhadad N, Xu H. Representing and utilizing clinical textual data for real world studies: An OHDSI approach. Journal Of Biomedical Informatics 2023, 142: 104343. PMID: 36935011, PMCID: PMC10428170, DOI: 10.1016/j.jbi.2023.104343.Peer-Reviewed Original ResearchMeSH KeywordsData ScienceElectronic Health RecordsHumansMedical InformaticsNarrationNatural Language ProcessingConceptsNatural language processingCommon data modelTextual dataNLP solutionObservational Health Data SciencesOMOP Common Data ModelSpecific use casesObservational Medical Outcomes Partnership Common Data ModelHealth Data SciencesRepresentation of informationUse casesElectronic health recordsReal-world evidence generationData scienceClinical textData modelClinical notesLanguage processingHealth recordsLoad dataClinical documentationCurrent applicationsInformationWorkflowEvidence generation
2022
Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer’s disease and related dementias
Chen Z, Zhang H, Yang X, Wu S, He X, Xu J, Guo J, Prosperi M, Wang F, Xu H, Chen Y, Hu H, DeKosky S, Farrer M, Guo Y, Wu Y, Bian J. Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer’s disease and related dementias. International Journal Of Medical Informatics 2022, 170: 104973. PMID: 36577203, PMCID: PMC11325083, DOI: 10.1016/j.ijmedinf.2022.104973.Peer-Reviewed Original ResearchMeSH KeywordsAlzheimer DiseaseBiomarkersDocumentationElectronic Health RecordsHumansNatural Language ProcessingConceptsElectronic health recordsPatients' electronic health recordsCognitive testsCognitive test scoresFlorida health systemSeverity categoriesHealth recordsAD-related dementiaAD/ADRD researchAD/ADRDPatient levelAlzheimer's diseaseClinical narrativesHealth systemBiomarkersDifferent severityDiseaseSeverityPatientsADRD researchStandardized approachDementiaTest scoresPopulation characteristicsScoresA comparative study of pre-trained language models for named entity recognition in clinical trial eligibility criteria from multiple corpora
Li J, Wei Q, Ghiasvand O, Chen M, Lobanov V, Weng C, Xu H. A comparative study of pre-trained language models for named entity recognition in clinical trial eligibility criteria from multiple corpora. BMC Medical Informatics And Decision Making 2022, 22: 235. PMID: 36068551, PMCID: PMC9450226, DOI: 10.1186/s12911-022-01967-7.Peer-Reviewed Original ResearchMeSH KeywordsClinical Trials as TopicEligibility DeterminationHumansInformation Storage and RetrievalLanguageMedicineNamesNatural Language ProcessingConceptsPre-trained language modelsNER taskUnstructured textEntity recognitionLanguage modelNatural language processing techniquesClinical trial eligibility criteriaLanguage processing techniquesData augmentation resultsData augmentation approachDomain-specific corpusBetter performanceTransformer modelCross-validation showMultiple data sourcesEligibility criteria textBiomedical domainEmbedding modelsNER performanceAugmentation approachContextual embeddingsMeaningful informationEvaluation resultsSuch documentsProcessing techniquesAssessment of Electronic Health Record for Cancer Research and Patient Care Through a Scoping Review of Cancer Natural Language Processing
Wang L, Fu S, Wen A, Ruan X, He H, Liu S, Moon S, Mai M, Riaz I, Wang N, Yang P, Xu H, Warner J, Liu H. Assessment of Electronic Health Record for Cancer Research and Patient Care Through a Scoping Review of Cancer Natural Language Processing. JCO Clinical Cancer Informatics 2022, 6: e2200006. PMID: 35917480, PMCID: PMC9470142, DOI: 10.1200/cci.22.00006.Peer-Reviewed Original ResearchDiscovering novel drug-supplement interactions using SuppKG generated from the biomedical literature
Schutte D, Vasilakes J, Bompelli A, Zhou Y, Fiszman M, Xu H, Kilicoglu H, Bishop J, Adam T, Zhang R. Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature. Journal Of Biomedical Informatics 2022, 131: 104120. PMID: 35709900, PMCID: PMC9335448, DOI: 10.1016/j.jbi.2022.104120.Peer-Reviewed Original ResearchMeSH KeywordsDietary SupplementsNatural Language ProcessingPubMedSemanticsUnified Medical Language SystemConceptsUnified Medical Language SystemComprehensive knowledge graphDomain terminologyKnowledge graphSemantic relationsNatural language processing technologyLanguage processing technologyNLP toolsDownstream tasksF1 scoreSemantic relationshipsDiscovery patternsPubMed abstractsLimited coverageBiomedical literatureProcessing technologyLanguage systemSemRepDietary supplement informationManual reviewNovel methodologyGraphNodesDomainTaskCombining human and machine intelligence for clinical trial eligibility querying
Fang Y, Idnay B, Sun Y, Liu H, Chen Z, Marder K, Xu H, Schnall R, Weng C. Combining human and machine intelligence for clinical trial eligibility querying. Journal Of The American Medical Informatics Association 2022, 29: 1161-1171. PMID: 35426943, PMCID: PMC9196697, DOI: 10.1093/jamia/ocac051.Peer-Reviewed Original ResearchMeSH KeywordsArtificial IntelligenceCOVID-19Eligibility DeterminationHumansNatural Language ProcessingPatient SelectionConceptsNegation scope detectionCohort queriesScope detectionHealth Information Technology Usability Evaluation ScaleHuman-computer collaborationValue normalizationNatural language processingMachine intelligenceDomain expertsEligibility criteria textUsability evaluationLearnability scoreF1 scoreUser interventionLanguage processingHuman intelligenceUsability scoreQueriesError correctionEngagement featuresIntelligenceDisease trialsFrequent modificationsEnhanced modulesCOVID-19 clinical trials
2021
Are synthetic clinical notes useful for real natural language processing tasks: A case study on clinical entity recognition
Li J, Zhou Y, Jiang X, Natarajan K, Pakhomov S, Liu H, Xu H. Are synthetic clinical notes useful for real natural language processing tasks: A case study on clinical entity recognition. Journal Of The American Medical Informatics Association 2021, 28: 2193-2201. PMID: 34272955, PMCID: PMC8449609, DOI: 10.1093/jamia/ocab112.Peer-Reviewed Original ResearchPrivacy-protecting, reliable response data discovery using COVID-19 patient observations
Kim J, Neumann L, Paul P, Day M, Aratow M, Bell D, Doctor J, Hinske L, Jiang X, Kim K, Matheny M, Meeker D, Pletcher M, Schilling L, SooHoo S, Xu H, Zheng K, Ohno-Machado L, Anderson D, Anderson N, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bernstam E, Carter W, Chau N, Choi Y, Covington S, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hu Z, Ir D, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Mou Z, Murphy R, Neumann L, Nguyen N, Niedermayer S, Park E, Perkins A, Post K, Rieder C, Scherer C, Soares A, Soysal E, Tep B, Toy B, Wang B, Wu Z, Zhou Y, Zucker R. Privacy-protecting, reliable response data discovery using COVID-19 patient observations. Journal Of The American Medical Informatics Association 2021, 28: 1765-1776. PMID: 34051088, PMCID: PMC8194878, DOI: 10.1093/jamia/ocab054.Peer-Reviewed Original ResearchA Discrete Joint Model for Entity and Relation Extraction from Clinical Notes.
Ji Z, Ghiasvand O, Wu S, Xu H. A Discrete Joint Model for Entity and Relation Extraction from Clinical Notes. AMIA Joint Summits On Translational Science Proceedings 2021, 2021: 315-324. PMID: 34457146, PMCID: PMC8378610.Peer-Reviewed Original ResearchConceptsRelation classificationPipeline architectureClinical natural language processingNatural language processingEntity recognitionBeam searchRelation extractionClinical notesLanguage processingClassification stepEntity pairsStructured perceptronFundamental taskClinical narrativesTraditional solutionsRecognition stepError propagationArchitectureJoint modelTaskSubtasksPerceptronClinical conceptsEntitiesClassificationA Comparison between Human and NLP-based Annotation of Clinical Trial Eligibility Criteria Text Using The OMOP Common Data Model.
Li X, Liu H, Kury F, Yuan C, Butler A, Sun Y, Ostropolets A, Xu H, Weng C. A Comparison between Human and NLP-based Annotation of Clinical Trial Eligibility Criteria Text Using The OMOP Common Data Model. AMIA Joint Summits On Translational Science Proceedings 2021, 2021: 394-403. PMID: 34457154, PMCID: PMC8378608.Peer-Reviewed Original ResearchCOVID-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 ResearchMeSH KeywordsCOVID-19Deep LearningElectronic Health RecordsHumansInformation Storage and RetrievalNatural Language ProcessingSymptom AssessmentConceptsNatural 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
The UMLS knowledge sources at 30: indispensable to current research and applications in biomedical informatics
Humphreys B, Del Fiol G, Xu H. The UMLS knowledge sources at 30: indispensable to current research and applications in biomedical informatics. Journal Of The American Medical Informatics Association 2020, 27: 1499-1501. PMID: 33059366, PMCID: PMC7647371, DOI: 10.1093/jamia/ocaa208.Peer-Reviewed Original ResearchTime event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events
Li F, Du J, He Y, Song H, Madkour M, Rao G, Xiang Y, Luo Y, Chen H, Liu S, Wang L, Liu H, Xu H, Tao C. Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. Journal Of The American Medical Informatics Association 2020, 27: 1046-1056. PMID: 32626903, PMCID: PMC7647306, DOI: 10.1093/jamia/ocaa058.Peer-Reviewed Original ResearchMeSH KeywordsBiological OntologiesDecision Support Systems, ClinicalElectronic Health RecordsHumansNatural Language ProcessingSemantic WebTimeConceptsTime Event OntologyComplex temporal relationsEvent ontologyNatural language processing fieldTemporal relationsTime-related queriesInformation annotationProcessing fieldTemporal informationData propertiesRelation representationClinical narrativesSemantic representationElectronic health record dataRich setHealth record dataOntologyStrong capabilityReasoningSetQueriesOrder relationRecord dataRepresentationPrimitivesEfficient 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 ResearchMeSH KeywordsElectronic Health RecordsHumansNatural Language ProcessingNeoplasmsResponse Evaluation Criteria in Solid TumorsConceptsNatural 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 extractionSetExtractingAnnotationAchievability to Extract Specific Date Information for Cancer Research.
Wang L, Wampfler J, Dispenzieri A, Xu H, Yang P, Liu H. Achievability to Extract Specific Date Information for Cancer Research. AMIA Annual Symposium Proceedings 2020, 2019: 893-902. PMID: 32308886, PMCID: PMC7153063.Peer-Reviewed Original ResearchRelation Extraction from Clinical Narratives Using Pre-trained Language Models.
Wei Q, Ji Z, Si Y, Du J, Wang J, Tiryaki F, Wu S, Tao C, Roberts K, Xu H. Relation Extraction from Clinical Narratives Using Pre-trained Language Models. AMIA Annual Symposium Proceedings 2020, 2019: 1236-1245. PMID: 32308921, PMCID: PMC7153059.Peer-Reviewed Original ResearchMeSH KeywordsDatasets as TopicHumansInformation Storage and RetrievalMachine LearningNarrationNatural Language ProcessingSemanticsConceptsPre-trained language modelsNatural language processingLanguage modelRE tasksNLP tasksClinical narrativesRecent deep learning methodsDeep learning methodsClinical NLP tasksRelation extraction taskTraditional word embeddingsTraditional machineExtraction taskArt performanceRelation extractionBERT modelLanguage processingLearning methodsWord embeddingsShared TaskPrevious stateBiomedical literatureDifferent implementationsTaskOpen domain
2019
Editorial: The second international workshop on health natural language processing (HealthNLP 2019)
Wang Y, Xu H, Uzuner O. Editorial: The second international workshop on health natural language processing (HealthNLP 2019). BMC Medical Informatics And Decision Making 2019, 19: 233. PMID: 31801516, PMCID: PMC6894102, DOI: 10.1186/s12911-019-0930-9.Peer-Reviewed Original Research