2024
Augmenting biomedical named entity recognition with general-domain resources
Yin Y, Kim H, Xiao X, Wei C, Kang J, Lu Z, Xu H, Fang M, Chen Q. Augmenting biomedical named entity recognition with general-domain resources. Journal Of Biomedical Informatics 2024, 159: 104731. PMID: 39368529, DOI: 10.1016/j.jbi.2024.104731.Peer-Reviewed Original ResearchBioNER datasetsMulti-task learningNER datasetsEntity typesBiomedical datasetsBaseline modelGeneral domain datasetsBiomedical language modelNeural network-basedYield performance improvementsBioNER modelsEntity recognitionBiomedical corporaHuman annotatorsLabel ambiguityLanguage modelTransfer learningF1 scoreBioNERHuman effortNetwork-basedBiomedical resourcesPerformance improvementDatasetSuperior performance
2018
DataMed – an open source discovery index for finding biomedical datasets
Chen X, Gururaj A, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim H, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone S, Fore I, Ohno-Machado L, Grethe J, Xu H. DataMed – an open source discovery index for finding biomedical datasets. Journal Of The American Medical Informatics Association 2018, 25: 300-308. PMID: 29346583, PMCID: PMC7378878, DOI: 10.1093/jamia/ocx121.Peer-Reviewed Original ResearchIngestion pipelineBiomedical datasetsSearch enginesBiomedical domainAdvanced natural language processingRelevant datasetsUser-entered queryData discovery systemUnified metadata modelData ingestion pipelinesNatural language processingOpen-source packageRetrieval engineTerminology servicesMetadata modelMetadata informationDiscovery systemData reuseDataMedBenchmark datasetsBiomedical dataData indexAverage precisionLanguage processingSource package
2017
Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge
Roberts K, Gururaj A, Chen X, Pournejati S, Hersh W, Demner-Fushman D, Ohno-Machado L, Cohen T, Xu H. Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge. Database 2017, 2017: bax068. DOI: 10.1093/database/bax068.Peer-Reviewed Original ResearchBiomedical datasetsRetrieval challengesInformation retrieval techniquesAdvanced query processingBiomedical data repositoriesAdvanced retrieval methodsQuery processingInformation retrievalTest queriesRetrieval systemRank frameworkRetrieval approachRetrieval techniquesData repositoryRetrieval methodTop precisionDatasetQueriesRepositoryChallengesRetrievalTaskLearningSystemCorpus