2024
Deep-Transfer-Learning–Based Natural Language Processing of Serial Free-Text Computed Tomography Reports for Predicting Survival of Patients With Pancreatic Cancer
Kim S, Kim S, Kim E, Cecchini M, Park M, Choi J, Kim S, Hwang H, Kang C, Choi H, Shin S, Kang J, Lee C. Deep-Transfer-Learning–Based Natural Language Processing of Serial Free-Text Computed Tomography Reports for Predicting Survival of Patients With Pancreatic Cancer. JCO Clinical Cancer Informatics 2024, 8: e2400021. PMID: 39151114, DOI: 10.1200/cci.24.00021.Peer-Reviewed Original ResearchConceptsArea under the receiver operating characteristic curveSurvival of patientsCT reportsPancreatic cancerNatural language processingC-indexPredicting SurvivalOverall survival of patientsTertiary hospitalPredicting 1-year survivalPredicting survival of patientsImproved C-indexSurvival informationPancreatic cancer survivalReceiver operating characteristic curveInternal test data setNLP modelsComputed tomography reportsLanguage processingKorean tertiary hospitalOverall survivalConsecutive patientsActual survivalConcordance indexPatientsA taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction
Fu S, Wang L, He H, Wen A, Zong N, Kumari A, Liu F, Zhou S, Zhang R, Li C, Wang Y, St Sauver J, Liu H, Sohn S. A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction. Journal Of The American Medical Informatics Association 2024, 31: 1493-1502. PMID: 38742455, PMCID: PMC11187420, DOI: 10.1093/jamia/ocae101.Peer-Reviewed Original ResearchNatural language processingClinical concept extractionElectronic health recordsConcept extractionClinical natural language processingConcept extraction taskNatural language processing modelsElectronic health record settingsDomain-specific knowledgeError taxonomyHeterogeneity of electronic health recordsReal-world dataAnalysis processExtraction taskOWL formatAnnotated examplesError analysisNLP modelsCommunity feedbackLanguage processingMulti-site settingConduct error analysisError classesError typesError analysis process
2023
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C)
Liu S, Wen A, Wang L, He H, Fu S, Miller R, Williams A, Harris D, Kavuluru R, Liu M, Abu-el-Rub N, Schutte D, Zhang R, Rouhizadeh M, Osborne J, He Y, Topaloglu U, Hong S, Saltz J, Schaffter T, Pfaff E, Chute C, Duong T, Haendel M, Fuentes R, Szolovits P, Xu H, Liu H. An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). Journal Of The American Medical Informatics Association 2023, 30: 2036-2040. PMID: 37555837, PMCID: PMC10654844, DOI: 10.1093/jamia/ocad134.Peer-Reviewed Original ResearchConceptsNatural language processingNLP modelsClinical natural language processingNatural language processing frameworkEHR-based clinical researchMulti-site settingSymptom extractionProcessing frameworkNLP frameworkLanguage processingNLP solutionMulti-site dataAlgorithm robustnessMethodology advancementsResearch communityTranslational research communityNational COVID Cohort CollaborativeCase demonstrationProcess heterogeneityFrameworkAnnotationCOVID cohortDetecting Ground Glass Opacity Features in Patients With Lung Cancer: Automated Extraction and Longitudinal Analysis via Deep Learning–Based Natural Language Processing
Lee K, Liu Z, Chandran U, Kalsekar I, Laxmanan B, Higashi M, Jun T, Ma M, Li M, Mai Y, Gilman C, Wang T, Ai L, Aggarwal P, Pan Q, Oh W, Stolovitzky G, Schadt E, Wang X. Detecting Ground Glass Opacity Features in Patients With Lung Cancer: Automated Extraction and Longitudinal Analysis via Deep Learning–Based Natural Language Processing. JMIR AI 2023, 2: e44537. PMID: 38875565, PMCID: PMC11041451, DOI: 10.2196/44537.Peer-Reviewed Original ResearchNatural language processingDeep learning-based natural language processingNLP pipelineElectronic health recordsLanguage processingBidirectional long short-term memoryLong short-term memoryRadiology notesNatural language processing pipelineGranular featuresHealth recordsShort-term memoryNLP modelsAutomated extractionNodule featuresAutomatically
2022
Getting More Out of Large Databases and EHRs with Natural Language Processing and Artificial Intelligence
Khosravi B, Rouzrokh P, Erickson B. Getting More Out of Large Databases and EHRs with Natural Language Processing and Artificial Intelligence. Journal Of Bone And Joint Surgery 2022, 104: 51-55. PMID: 36260045, DOI: 10.2106/jbjs.22.00567.Peer-Reviewed Original ResearchConceptsNatural language processingElectronic health recordsNLP modelsLanguage processingDeep learning-based NLP modelsNatural language processing projectMethod of information extractionClinical natural language processingNatural language processing methodsExtract meaningful relationshipsExtract structural informationInformation extractionClinical textArtificial intelligenceElectronic health record dataHealth recordsStructural informationInformationIntelligenceClinical patient encountersArtificialInfluence patient outcomesTechnical aspectsMethodModelDevelopment and Validation of a Model to Identify Critical Brain Injuries Using Natural Language Processing of Text Computed Tomography Reports
Torres-Lopez VM, Rovenolt GE, Olcese AJ, Garcia GE, Chacko SM, Robinson A, Gaiser E, Acosta J, Herman AL, Kuohn LR, Leary M, Soto AL, Zhang Q, Fatima S, Falcone GJ, Payabvash MS, Sharma R, Struck AF, Sheth KN, Westover MB, Kim JA. Development and Validation of a Model to Identify Critical Brain Injuries Using Natural Language Processing of Text Computed Tomography Reports. JAMA Network Open 2022, 5: e2227109. PMID: 35972739, PMCID: PMC9382443, DOI: 10.1001/jamanetworkopen.2022.27109.Peer-Reviewed Original ResearchConceptsNatural language processingF-scoreTest data setsLanguage processingIndependent test data setsData setsBidirectional Encoder RepresentationsAcute brain injuryLarge data setsHead CTBrain injuryNLP toolsF1 scoreNER modelTransformer architectureClinical textEncoder RepresentationsNLP algorithmNLP modelsCT reportsCustom dictionaryTraining setCross-validation performancePerformance metricsAvailable new tools
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