2024
A Study of Biomedical Relation Extraction Using GPT Models.
Zhang J, Wibert M, Zhou H, Peng X, Chen Q, Keloth V, Hu Y, Zhang R, Xu H, Raja K. A Study of Biomedical Relation Extraction Using GPT Models. AMIA Joint Summits On Translational Science Proceedings 2024, 2024: 391-400. PMID: 38827097, PMCID: PMC11141827.Peer-Reviewed Original ResearchPrompt Tuning in Biomedical Relation Extraction
He J, Li F, Li J, Hu X, Nian Y, Xiang Y, Wang J, Wei Q, Li Y, Xu H, Tao C. Prompt Tuning in Biomedical Relation Extraction. Journal Of Healthcare Informatics Research 2024, 8: 206-224. PMID: 38681754, PMCID: PMC11052745, DOI: 10.1007/s41666-024-00162-9.Peer-Reviewed Original ResearchFew-shot scenariosBiomedical relation extractionNatural language processingBiomedical RERelation extractionPrompt tuningState-of-the-art performanceText mining applicationsTuning modelBioCreative VISemEval-2013Knowledge graphLanguage modelMining applicationsBiomedical textOriginal inputComputational resourcesLanguage processingExternal knowledgeSpecific textsSuperior performanceDatasetEfficient approachTaskModel performance
2021
A 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 conceptsEntitiesClassification
2020
Relation 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 ResearchConceptsPre-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
Deep learning in clinical natural language processing: a methodical review
Wu S, Roberts K, Datta S, Du J, Ji Z, Si Y, Soni S, Wang Q, Wei Q, Xiang Y, Zhao B, Xu H. Deep learning in clinical natural language processing: a methodical review. Journal Of The American Medical Informatics Association 2019, 27: 457-470. PMID: 31794016, PMCID: PMC7025365, DOI: 10.1093/jamia/ocz200.Peer-Reviewed Original ResearchConceptsNatural language processingClinical natural language processingDeep learningLanguage processingComputing Machinery Digital LibraryInformation extraction tasksMedical informatics communityComputational Linguistics anthologyRecurrent neural networkDigital librariesText classificationElectronic health recordsExtraction taskEntity recognitionWord2vec embeddingsNeural networkRelation extractionNLP communityNLP researchInformatics communitySpecific tasksHealth recordsNLP problemLearningClinical domainsExtracting entities with attributes in clinical text via joint deep learning
Shi X, Yi Y, Xiong Y, Tang B, Chen Q, Wang X, Ji Z, Zhang Y, Xu H. Extracting entities with attributes in clinical text via joint deep learning. Journal Of The American Medical Informatics Association 2019, 26: 1584-1591. PMID: 31550346, PMCID: PMC7647140, DOI: 10.1093/jamia/ocz158.Peer-Reviewed Original ResearchConceptsBidirectional long short-term memoryShort-term memoryLong short-term memoryNatural language processingEntity recognitionChinese corpusBest F1English corpusLanguage processingJoint deep learningTaskConditional Random FieldsRelation extractionAttribute recognitionMemorySequential subtasksDeep learning methodsClinical textA study of deep learning approaches for medication and adverse drug event extraction from clinical text
Wei Q, Ji Z, Li Z, Du J, Wang J, Xu J, Xiang Y, Tiryaki F, Wu S, Zhang Y, Tao C, Xu H. A study of deep learning approaches for medication and adverse drug event extraction from clinical text. Journal Of The American Medical Informatics Association 2019, 27: 13-21. PMID: 31135882, PMCID: PMC6913210, DOI: 10.1093/jamia/ocz063.Peer-Reviewed Original ResearchConceptsDeep learning-based approachDeep learning approachLearning-based approachTraditional machineLearning approachNational NLP Clinical ChallengesAdverse drug event extractionOutperform traditional machineDifferent ensemble approachesConditional Random FieldsSequence labeling approachMIMIC-III databaseEvent extractionMedical domainEntity recognitionClassification componentF1 scoreClinical textRelation extractionClinical documentsVector machineEnd evaluationEnsemble approachClinical corpusMachineIntegrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text
Li Z, Yang Z, Shen C, Xu J, Zhang Y, Xu H. Integrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text. BMC Medical Informatics And Decision Making 2019, 19: 22. PMID: 30700301, PMCID: PMC6354333, DOI: 10.1186/s12911-019-0736-9.Peer-Reviewed Original ResearchConceptsShortest dependency pathConvolutional neural networkNeural network architectureNatural language processingSentence sequenceRelation extractionClinical relation extractionTarget entityNetwork architectureClinical textNeural networkRepresentation moduleDependency pathsDeep learning-based approachNew neural network architectureBidirectional long short-term memory networkLong short-term memory networkDeep learning frameworkDeep neural networksShort-term memory networkLearning-based approachNovel neural approachRelation extraction datasetBi-LSTM networkSyntactic features
2017
Towards Practical Temporal Relation Extraction from Clinical Notes: An Analysis of Direct Temporal Relations
Lee H, Zhang Y, Xu J, Tao C, Xu H, Jiang M. Towards Practical Temporal Relation Extraction from Clinical Notes: An Analysis of Direct Temporal Relations. 2017, 1272-1275. DOI: 10.1109/bibm.2017.8217842.Peer-Reviewed Original ResearchDirect temporal relationsTemporal information extraction methodsTemporal relationsTemporal relation extractionInformation extraction methodRelation extraction systemTemporal relation identificationImplicit relationsClinical textRelation extractionRelation identificationTemporal informationEvent mentionsSource documents
2016
CD-REST: a system for extracting chemical-induced disease relation in literature
Xu J, Wu Y, Zhang Y, Wang J, Lee H, Xu H. CD-REST: a system for extracting chemical-induced disease relation in literature. Database 2016, 2016: baw036. PMID: 27016700, PMCID: PMC4808251, DOI: 10.1093/database/baw036.Peer-Reviewed Original ResearchConceptsChemical-induced disease relationsWeb servicesBiomedical literatureEntity recognitionMachine learning-based approachLearning-based approachHTTP POST requestRelation extraction systemVector space modelConditional Random FieldsSupport vector machineRelation extraction moduleVast biomedical literatureDisease relation extractionChemical-induced disease relation extractionExtraction moduleDisease relationsAutomatic extractionEnd systemPOST requestRelation extractionNormalization moduleVector machineBioCreative VDemonstration system