2023
A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia
Ohno-Machado L, Jiang X, Kuo T, Tao S, Chen L, Ram P, Zhang G, Xu H. A hierarchical strategy to minimize privacy risk when linking “De-identified” data in biomedical research consortia. Journal Of Biomedical Informatics 2023, 139: 104322. PMID: 36806328, PMCID: PMC10975485, DOI: 10.1016/j.jbi.2023.104322.Peer-Reviewed Original ResearchConceptsPrivacy of individualsAppropriate privacy protectionData-driven modelsPrivacy protectionPrivacy risksData Coordination CenterData hubData repositoryHierarchical strategyPrivacyBiomedical discoveryData setsRecord linkageData Coordinating CenterRepositoryComplex strategiesCoordination centerTechnologyTechniqueDataPartiesSetHierarchy
2022
The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition
Kuo T, Jiang X, Tang H, Wang X, Harmanci A, Kim M, Post K, Bu D, Bath T, Kim J, Liu W, Chen H, Ohno-Machado L. The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition. Journal Of The American Medical Informatics Association 2022, 29: 2182-2190. PMID: 36164820, PMCID: PMC9667175, DOI: 10.1093/jamia/ocac165.Peer-Reviewed Original ResearchConceptsSensitive personal informationGenomic data analysisPotential future research directionsPersonal informationSecurity concernsGenomics data repositoryData repositoryReport lessonsProtection techniquesFuture research directionsPrivacyResearch directionsData usePractical challengesGenomic dataData analysisAnonymizationCommunity effortsRepositorySecurityBiomedical researchInformationDataChallenges
2017
DATS, the data tag suite to enable discoverability of datasets
Sansone S, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe J, Xu H, Fore I, Lyle J, Gururaj A, Chen X, Kim H, Zong N, Li Y, Liu R, Ozyurt I, Ohno-Machado L. DATS, the data tag suite to enable discoverability of datasets. Scientific Data 2017, 4: 170059. PMID: 28585923, PMCID: PMC5460592, DOI: 10.1038/sdata.2017.59.Peer-Reviewed Original ResearchFinding useful data across multiple biomedical data repositories using DataMed
Ohno-Machado L, Sansone S, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj A, Bell E, Soysal E, Zong N, Kim H. Finding useful data across multiple biomedical data repositories using DataMed. Nature Genetics 2017, 49: 816-819. PMID: 28546571, PMCID: PMC6460922, DOI: 10.1038/ng.3864.Peer-Reviewed Original ResearchConceptsBiomedical data repositoriesHealth big dataData setsKnowledge discoveryBig dataMultiple repositoriesSearch enginesData indexFAIR principlesDataMedData repositoryService providersKnowledge initiativesKnowledge expertsBiomedical research communityResearch communityRepositoryScience landscapeUseful dataInteroperabilityMetadataFindabilitySetEngineDataInformation 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
2013
Identifying inference attacks against healthcare data repositories.
Vaidya J, Shafiq B, Jiang X, Ohno-Machado L. Identifying inference attacks against healthcare data repositories. AMIA Joint Summits On Translational Science Proceedings 2013, 2013: 262-6. PMID: 24303279, PMCID: PMC3845790.Peer-Reviewed Original Research
2012
A collaborative framework for Distributed Privacy-Preserving Support Vector Machine learning.
Que J, Jiang X, Ohno-Machado L. A collaborative framework for Distributed Privacy-Preserving Support Vector Machine learning. AMIA Annual Symposium Proceedings 2012, 2012: 1350-9. PMID: 23304414, PMCID: PMC3540462.Peer-Reviewed Original ResearchConceptsSupport vector machineVector machinePrivacy-preserving collaborative learningSensitive raw dataPrivacy-preserving mannerEfficient information exchangeDistributed PrivacyLocal repositoryPrivacy concernsCentralized repositoryCollaborative frameworkDecision supportMultiple participantsInformation exchangeRaw dataSVM modelIntermediary resultsMachineCollaborative learningPrivacyPopular toolRepositoryTraditional wayPatient dataServerGrid Binary LOgistic REgression (GLORE): building shared models without sharing data
Wu Y, Jiang X, Kim J, Ohno-Machado L. Grid Binary LOgistic REgression (GLORE): building shared models without sharing data. Journal Of The American Medical Informatics Association 2012, 19: 758-764. PMID: 22511014, PMCID: PMC3422844, DOI: 10.1136/amiajnl-2012-000862.Peer-Reviewed Original ResearchConceptsIntegrity of communicationCentralized data sourcesTraditional LR modelCentral repositoryComputational costData sourcesData setsSame formatPatient dataComputationGenomic dataRare patternRelevant dataLR modelPrediction valueSetRepositoryPartial elementsFormatClassificationCommunicationModelDataPatient setPerformData Locked Inside Databases: A Text Classification In The Database Of Genotypes And Phenotypes (dbGaP) To Address Challenges In Retrieving Clinical Information From Public Data Repositories
Ross M, Kim J, Lin K, Ohno-Machado L, Finn P, Kim H. Data Locked Inside Databases: A Text Classification In The Database Of Genotypes And Phenotypes (dbGaP) To Address Challenges In Retrieving Clinical Information From Public Data Repositories. 2012, a5777-a5777. DOI: 10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5777.Peer-Reviewed Original Research
2004
A primer on gene expression and microarrays for machine learning researchers
Kuo W, Kim E, Trimarchi J, Jenssen T, Vinterbo S, Ohno-Machado L. A primer on gene expression and microarrays for machine learning researchers. Journal Of Biomedical Informatics 2004, 37: 293-303. PMID: 15465482, DOI: 10.1016/j.jbi.2004.07.002.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsNew algorithmSupervised learning modelUCI machineLearning modelMicroarray data analysisAlgorithmic developmentsTypes of dataMachineData setsMain challengesGene expression dataMain motivationAlgorithmData analysisBiomedical experimentsLarge numberExpression dataMicroarray dataResearchersRepositoryWebMicroarray experimentsNew waveDataSet
1999
Using Boolean reasoning to anonymize databases
Øhrn A, Ohno-Machado L. Using Boolean reasoning to anonymize databases. Artificial Intelligence In Medicine 1999, 15: 235-254. PMID: 10206109, DOI: 10.1016/s0933-3657(98)00056-6.Peer-Reviewed Original ResearchConceptsBoolean reasoningMedical data repositoriesMeasure of anonymitySensitive dataPrivacy issuesDatabase fieldAmount of trustConfidential informationDegree of anonymityData repositoryDeterministic inferenceIndividual objectsAnonymityParticular pieceAlgorithmElectronic medical recordsSpecific needsReasoningDatabasePossible misuseAnonymizationInformationRepositoryOutside worldIssues
1997
A virtual repository approach to clinical and utilization studies: application in mammography as alternative to a national database.
Ohno-Machado L, Boxwala A, Ehresman J, Smith D, Greenes R. A virtual repository approach to clinical and utilization studies: application in mammography as alternative to a national database. AMIA Annual Symposium Proceedings 1997, 369-73. PMID: 9357650, PMCID: PMC2233552.Peer-Reviewed Original ResearchConceptsMammography databaseVisualization of resultsHeterogeneous databasesFederated databasesCentralized architectureExploratory analysis toolLegacy systemsCommon queriesPrototype systemQueriesVirtual repositoryAlternative architecturesImmediate displayDifferent databasesArchitectureAnalysis toolsMammography dataUse of dataRepositoryMammography reportsDatabaseUsersDownloadSystemVisualization