2019
A 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 corpusMachine
2018
Toward a normalized clinical drug knowledge base in China—applying the RxNorm model to Chinese clinical drugs
Wang L, Zhang Y, Jiang M, Wang J, Dong J, Liu Y, Tao C, Jiang G, Zhou Y, Xu H. Toward a normalized clinical drug knowledge base in China—applying the RxNorm model to Chinese clinical drugs. Journal Of The American Medical Informatics Association 2018, 25: 809-818. PMID: 29635469, PMCID: PMC7647010, DOI: 10.1093/jamia/ocy020.Peer-Reviewed Original ResearchConceptsChinese patent drugDrug knowledge basePatent drugsClinical drugsChemical drugsChinese drugsManual reviewChinese patent medicineElectronic health record systemsClinical dataChina's health insurance systemHealth record systemsDrug AdministrationHealth insurance systemDrug informationDrugsPatent medicineDrug namesRecord systemPharmacy system
2016
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning
Zhang Y, Xu J, Chen H, Wang J, Wu Y, Prakasam M, Xu H. Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. Database 2016, 2016: baw049. PMID: 27087307, PMCID: PMC4834204, DOI: 10.1093/database/baw049.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputational BiologyData MiningDatabases, ChemicalPatents as TopicPattern Recognition, AutomatedPharmaceutical PreparationsUnsupervised Machine LearningConceptsMachine learning-based systemsLearning-based systemConditional Random FieldsDomain knowledgeEntity recognitionMatthews correlation coefficientDrug Named Entity RecognitionBioCreative V challengeInformation extraction systemWord representation featuresUnsupervised feature learningUnsupervised learning algorithmNamed Entity RecognitionSemantic type informationSupport vector machinePrecision-recall curveBrown clusteringFeature learningFeature engineeringUnsupervised featureIndividual subtasksMining systemNER taskLearning algorithmCPD taskExtracting drug-enzyme relation from literature as evidence for drug drug interaction
Zhang Y, Wu H, Du J, Xu J, Wang J, Tao C, Li L, Xu H. Extracting drug-enzyme relation from literature as evidence for drug drug interaction. Journal Of Biomedical Semantics 2016, 7: 11. PMID: 26955465, PMCID: PMC4780188, DOI: 10.1186/s13326-016-0052-6.Peer-Reviewed Original ResearchBiological OntologiesData MiningDrug InteractionsEnzymesMachine LearningPharmaceutical PreparationsProtein Binding
2015
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case
Huang L, Soysal E, Zheng W, Zhao Z, Xu H, Sun J. A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. BMC Systems Biology 2015, 9: s2. PMID: 26100720, PMCID: PMC4474536, DOI: 10.1186/1752-0509-9-s4-s2.Peer-Reviewed Original ResearchA comparative study of disease genes and drug targets in the human protein interactome
Sun J, Zhu K, Zheng W, Xu H. A comparative study of disease genes and drug targets in the human protein interactome. BMC Bioinformatics 2015, 16: s1. PMID: 25861037, PMCID: PMC4402590, DOI: 10.1186/1471-2105-16-s5-s1.Peer-Reviewed Original ResearchMeSH KeywordsCluster AnalysisComputational BiologyDiseaseGene Expression RegulationGenome-Wide Association StudyHumansPharmaceutical PreparationsProtein Interaction MapsProteinsConceptsGenome-wide association studiesDisease genesDrug targetsHuman protein-coding genesHuman protein-protein interaction networkProtein-protein interaction networkProtein-coding genesHuman protein interactomeComplex diseasesNovel drug targetsProtein interactomeAnatomical Therapeutic Chemical (ATC) classificationInteraction networksDisease proteinAssociation studiesGenesDisease categoriesInteractomeProteinMajor disease categoriesDifferent disease categoriesFirst comprehensive comparisonTargetTreatment efficacyHigh betweenness
2013
Development and evaluation of an ensemble resource linking medications to their indications
Wei W, Cronin R, Xu H, Lasko T, Bastarache L, Denny J. Development and evaluation of an ensemble resource linking medications to their indications. Journal Of The American Medical Informatics Association 2013, 20: 954-961. PMID: 23576672, PMCID: PMC3756263, DOI: 10.1136/amiajnl-2012-001431.Peer-Reviewed Original ResearchMeSH KeywordsDictionaries as TopicDrug TherapyElectronic Health RecordsInternetMedlinePlusNatural Language ProcessingPharmaceutical PreparationsRxNorm
2012
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs
Liu M, Wu Y, Chen Y, Sun J, Zhao Z, Chen X, Matheny M, Xu H. Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. Journal Of The American Medical Informatics Association 2012, 19: e28-e35. PMID: 22718037, PMCID: PMC3392844, DOI: 10.1136/amiajnl-2011-000699.Peer-Reviewed Original ResearchConceptsAdverse drug reactionsPost-marketing phaseDrug reactionsSevere adverse drug reactionsImportant adverse drug reactionsWithdrawal of rofecoxibPotential adverse drug reactionsPost-marketing surveillanceADR predictionPatient morbidityClinical trialsMajor causeLarge-scale studiesDrugsMolecular pathwaysDrug developmentPhenotypic featuresSignificant improvementPhenotypic characteristicsEarly stagesRecognition of medication information from discharge summaries using ensembles of classifiers
Doan S, Collier N, Xu H, Duy P, Phuong T. Recognition of medication information from discharge summaries using ensembles of classifiers. BMC Medical Informatics And Decision Making 2012, 12: 36. PMID: 22564405, PMCID: PMC3502425, DOI: 10.1186/1472-6947-12-36.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceDecision Support TechniquesFemaleHumansInformation Storage and RetrievalInstitutional Management TeamsMaleMedication SystemsNatural Language ProcessingPatient DischargePattern Recognition, AutomatedPharmaceutical PreparationsReproducibility of ResultsSemanticsSoftware DesignSupport Vector MachineConceptsConditional Random FieldsNatural language processingClinical natural language processingSupport vector machineBest F-scoreEnsemble classifierF-scoreClinical textIndividual classifiersVoting methodMajority votingLocal support vector machineSupervised machine learning methodsClinical entity recognitionClinical NLP systemsDifferent voting strategiesEntity recognition systemRule-based systemEnsemble of classifiersMachine learning methodsRule-based methodI2b2 NLP challengeEntity recognitionRecognition systemNLP systems
2011
The Emerging Role of Electronic Medical Records in Pharmacogenomics
Wilke R, Xu H, Denny J, Roden D, Krauss R, McCarty C, Davis R, Skaar T, Lamba J, Savova G. The Emerging Role of Electronic Medical Records in Pharmacogenomics. Clinical Pharmacology & Therapeutics 2011, 89: 379-386. PMID: 21248726, PMCID: PMC3204342, DOI: 10.1038/clpt.2010.260.Peer-Reviewed Original ResearchMeSH KeywordsDecision Support TechniquesElectronic Health RecordsGenetic Association StudiesGenomicsGenotypeHumansPharmaceutical PreparationsPharmacogeneticsResearch Design
2010
Integrating existing natural language processing tools for medication extraction from discharge summaries
Doan S, Bastarache L, Klimkowski S, Denny J, Xu H. Integrating existing natural language processing tools for medication extraction from discharge summaries. Journal Of The American Medical Informatics Association 2010, 17: 528-531. PMID: 20819857, PMCID: PMC2995674, DOI: 10.1136/jamia.2010.003855.Peer-Reviewed Original Research