2024
Ensemble pretrained language models to extract biomedical knowledge from literature
Li Z, Wei Q, Huang L, Li J, Hu Y, Chuang Y, He J, Das A, Keloth V, Yang Y, Diala C, Roberts K, Tao C, Jiang X, Zheng W, Xu H. Ensemble pretrained language models to extract biomedical knowledge from literature. Journal Of The American Medical Informatics Association 2024, 31: 1904-1911. PMID: 38520725, PMCID: PMC11339500, DOI: 10.1093/jamia/ocae061.Peer-Reviewed Original ResearchNatural language processingNatural language processing systemsLanguage modelExpansion of biomedical literatureZero-shot settingManually annotated corpusKnowledge graph developmentTask-specific modelsDomain-specific modelsZero-ShotEntity recognitionBillion parametersEnsemble learningLocation informationKnowledge basesBiomedical entitiesLanguage processingFree textGraph developmentBiomedical conceptsAutomated techniqueBiomedical literatureDetection methodPredictive performanceBiomedical knowledge
2021
From Tokenization to Self-Supervision: Building a High-Performance Information Extraction System for Chemical Reactions in Patents
Wang J, Ren Y, Zhang Z, Xu H, Zhang Y. From Tokenization to Self-Supervision: Building a High-Performance Information Extraction System for Chemical Reactions in Patents. Frontiers In Research Metrics And Analytics 2021, 6: 691105. PMID: 35005421, PMCID: PMC8727901, DOI: 10.3389/frma.2021.691105.Peer-Reviewed Original ResearchEvent extractionEntity recognitionNatural language processing techniquesAccurate information extractionInformation extraction systemLanguage processing techniquesKnowledge-based rulesInformation extractionAutomatic toolEnd systemArt resultsSemantic rolesLanguage modelSelf-SupervisionFree textChemical patentsSubtask 1Reaction extractionDifferent semantic rolesHybrid approachEvent triggersProcessing techniquesSubtasksTokenizationHigh performanceCOVID-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 deaths
2015
Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network.
Wu Y, Jiang M, Lei J, Xu H. Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network. 2015, 216: 624-8. PMID: 26262126, PMCID: PMC4624324.Peer-Reviewed Original ResearchConceptsDeep neural networksLarge unlabeled corpusNamed Entity RecognitionWord embeddingsUnlabeled corpusUnsupervised learningEntity recognitionNeural networkNatural language processing technologyNovel deep learning methodLanguage processing technologyDeep learning methodsUnsupervised feature learningFeature engineering approachImportant healthcare informationChinese clinical textTypes of entitiesFeature learningNER taskClinical textLearning methodsClinical documentsCRF modelHealthcare informationFree text