2017
CNN-based ranking for biomedical entity normalization
Li H, Chen Q, Tang B, Wang X, Xu H, Wang B, Huang D. CNN-based ranking for biomedical entity normalization. BMC Bioinformatics 2017, 18: 385. PMID: 28984180, PMCID: PMC5629610, DOI: 10.1186/s12859-017-1805-7.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBiomedical ResearchDatabases as TopicHumansNeural Networks, ComputerReference StandardsSemanticsConceptsBiomedical entity normalizationEntity normalizationSemantic informationCNN architectureNovel convolutional neural network architectureConvolutional neural network architectureTraditional rule-based methodsNeural network architectureRule-based systemRanking methodRule-based methodNetwork architectureBiomedical entitiesBenchmark datasetsArt performanceEntity mentionsRanking problemCNNNormalization systemArchitectureMorphological informationComparison resultsInformationDatasetSystem
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
2011
Data from clinical notes: a perspective on the tension between structure and flexible documentation
Rosenbloom S, Denny J, Xu H, Lorenzi N, Stead W, Johnson K. Data from clinical notes: a perspective on the tension between structure and flexible documentation. Journal Of The American Medical Informatics Association 2011, 18: 181-186. PMID: 21233086, PMCID: PMC3116264, DOI: 10.1136/jamia.2010.007237.Peer-Reviewed Original ResearchConceptsReusable dataElectronic health record system adoptionStructured documentationComputer-based documentation systemsClinical notesClinical documentationStructured dataText processingSystem adoptionRecord systemSuch systemsDocumentation systemWorkflowContent needsProvidersUsabilityDocumentationExpressivitySystemHealthcare providersPatient careDataProcessingMajor goalAdoption