2021
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review
Guo Y, Zhang Y, Lyu T, Prosperi M, Wang F, Xu H, Bian J. The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. Journal Of The American Medical Informatics Association 2021, 28: 2050-2067. PMID: 34151987, PMCID: PMC8344463, DOI: 10.1093/jamia/ocab098.Peer-Reviewed Original ResearchConceptsAI applicationsArtificial intelligenceData integrationHeterogeneous dataSocial media data analysisMost AI applicationsHeterogeneous data sourcesMedia data analysisProteomics data analysisAI algorithmsAI frameworkElectronic health recordsHeterogenous dataBiased algorithmsHealth recordsCOVID-19 researchData analysisSingle-source approachResearch topicData sourcesResearch areaIntelligenceSurveillance systemDifferent sourcesAlgorithm
2019
Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison
Zhang Y, Tiryaki F, Jiang M, Xu H. Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison. BMC Medical Informatics And Decision Making 2019, 19: 77. PMID: 30943955, PMCID: PMC6448179, DOI: 10.1186/s12911-019-0783-2.Peer-Reviewed Original Research
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
2006
A natural language processing (NLP) tool to assist in the curation of the laboratory Mouse Tumor Biology Database.
Xu H, Krupke D, Blake J, Friedman C. A natural language processing (NLP) tool to assist in the curation of the laboratory Mouse Tumor Biology Database. AMIA Annual Symposium Proceedings 2006, 2006: 1150. PMID: 17238769, PMCID: PMC1839428.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDatabases as TopicDisease Models, AnimalInformation Storage and RetrievalMiceNatural Language ProcessingNeoplasmsConceptsMouse Genome Informatics groupNatural language processing toolsModel organism databaseMouse Tumor Biology DatabaseLanguage processing toolsBiology databasesOrganism databasesGenomic informationBiological communitiesProcessing toolsSpecific organismsInformatics GroupOrganismsKey informationDatabaseInformationSubstantial effortCurationTool