2022
A comparative study of pre-trained language models for named entity recognition in clinical trial eligibility criteria from multiple corpora
Li J, Wei Q, Ghiasvand O, Chen M, Lobanov V, Weng C, Xu H. A comparative study of pre-trained language models for named entity recognition in clinical trial eligibility criteria from multiple corpora. BMC Medical Informatics And Decision Making 2022, 22: 235. PMID: 36068551, PMCID: PMC9450226, DOI: 10.1186/s12911-022-01967-7.Peer-Reviewed Original ResearchMeSH KeywordsClinical Trials as TopicEligibility DeterminationHumansInformation Storage and RetrievalLanguageMedicineNamesNatural Language ProcessingConceptsPre-trained language modelsNER taskUnstructured textEntity recognitionLanguage modelNatural language processing techniquesClinical trial eligibility criteriaLanguage processing techniquesData augmentation resultsData augmentation approachDomain-specific corpusBetter performanceTransformer modelCross-validation showMultiple data sourcesEligibility criteria textBiomedical domainEmbedding modelsNER performanceAugmentation approachContextual embeddingsMeaningful informationEvaluation resultsSuch documentsProcessing techniques
2019
Discovery of Noncancer Drug Effects on Survival in Electronic Health Records of Patients With Cancer: A New Paradigm for Drug Repurposing
Wu Y, Warner J, Wang L, Jiang M, Xu J, Chen Q, Nian H, Dai Q, Du X, Yang P, Denny J, Liu H, Xu H. Discovery of Noncancer Drug Effects on Survival in Electronic Health Records of Patients With Cancer: A New Paradigm for Drug Repurposing. JCO Clinical Cancer Informatics 2019, 3: cci.19.00001. PMID: 31141421, PMCID: PMC6693869, DOI: 10.1200/cci.19.00001.Peer-Reviewed Original ResearchMeSH KeywordsClinical Trials as TopicData MiningDrug DevelopmentDrug RepositioningElectronic Health RecordsHumansNeoplasmsPrognosisRegistriesReproducibility of ResultsTreatment OutcomeConceptsVanderbilt University Medical CenterCancer survivalMayo ClinicDrug repurposingNoncancer drugsElectronic health record dataCancer registry dataEHR dataClinical trial evaluationOverall cancer survivalUniversity Medical CenterHealth record dataElectronic health recordsTreatment of cancerClinical trialsDrug classesRegistry dataMedical CenterDrug effectsSignificant associationLongitudinal EHRNew indicationsPatientsCancerHealth records
2017
CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice
Soysal E, Lee H, Zhang Y, Huang L, Chen X, Wei Q, Zheng W, Chang J, Cohen T, Sun J, Xu H. CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice. CPT Pharmacometrics & Systems Pharmacology 2017, 6: 188-196. PMID: 28296354, PMCID: PMC5351410, DOI: 10.1002/psp4.12174.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsBiomedical ResearchClinical Trials as TopicDatabases, FactualDrug DiscoveryHumansKnowledge BasesNeoplasmsPrecision Medicine
2016
Automated identification of molecular effects of drugs (AIMED)
Fathiamini S, Johnson A, Zeng J, Araya A, Holla V, Bailey A, Litzenburger B, Sanchez N, Khotskaya Y, Xu H, Meric-Bernstam F, Bernstam E, Cohen T. Automated identification of molecular effects of drugs (AIMED). Journal Of The American Medical Informatics Association 2016, 23: 758-765. PMID: 27107438, PMCID: PMC4926748, DOI: 10.1093/jamia/ocw030.Peer-Reviewed Original ResearchExtracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov
Xu J, Lee H, Zeng J, Wu Y, Zhang Y, Huang L, Johnson A, Holla V, Bailey A, Cohen T, Meric-Bernstam F, Bernstam E, Xu H. Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov. Journal Of The American Medical Informatics Association 2016, 23: 750-757. PMID: 27013523, PMCID: PMC4926744, DOI: 10.1093/jamia/ocw009.Peer-Reviewed Original ResearchMeSH KeywordsClinical Trials as TopicData MiningDatabases, FactualDNA, NeoplasmHumansKnowledge BasesMutationNatural Language ProcessingNeoplasmsPrecision MedicineConceptsCancer treatment trials
2015
Citation Sentiment Analysis in Clinical Trial Papers.
Xu J, Zhang Y, Wu Y, Wang J, Dong X, Xu H. Citation Sentiment Analysis in Clinical Trial Papers. AMIA Annual Symposium Proceedings 2015, 2015: 1334-41. PMID: 26958274, PMCID: PMC4765697.Peer-Reviewed Original Research
2012
Identifying the status of genetic lesions in cancer clinical trial documents using machine learning
Wu Y, Levy M, Micheel C, Yeh P, Tang B, Cantrell M, Cooreman S, Xu H. Identifying the status of genetic lesions in cancer clinical trial documents using machine learning. BMC Genomics 2012, 13: s21. PMID: 23282337, PMCID: PMC3535695, DOI: 10.1186/1471-2164-13-s8-s21.Peer-Reviewed Original Research