2024
Biomedical blockchain with practical implementations and quantitative evaluations: a systematic review
Lacson R, Yu Y, Kuo T, Ohno-Machado L. Biomedical blockchain with practical implementations and quantitative evaluations: a systematic review. Journal Of The American Medical Informatics Association 2024, 31: 1423-1435. PMID: 38726710, PMCID: PMC11105130, DOI: 10.1093/jamia/ocae084.Peer-Reviewed Original ResearchConceptsElectronic health recordsSystematic reviewData sharingMedical data sharingSpeed metricsPreferred Reporting ItemsCertificate storageDecentralized InternetNetwork permissionsBlockchain platformBlockchain applicationsEvaluation metricsBiomedical domainBlockchainBiomedical data managementHealth recordsData managementData storageReporting ItemsHealth sectorQuantitative metricsMedical facilitiesMetricsTrial managementClinical trial managementEarly prediction of long hospital stay for Intensive Care units readmission patients using medication information
Zhang M, Kuo T. Early prediction of long hospital stay for Intensive Care units readmission patients using medication information. Computers In Biology And Medicine 2024, 174: 108451. PMID: 38603899, PMCID: PMC11385457, DOI: 10.1016/j.compbiomed.2024.108451.Peer-Reviewed Original ResearchConceptsIntensive care unitProlonged ICU LOSAverage doseICU LOSLonger hospital stayReceiver operating characteristic curveLogistic regressionPredicting intensive care unitMedical informationExpected Calibration ErrorSummed dosePatient ageHospital staySupport vector machineCare unitMIMIC-IV databasePatient complicationsCharacteristic curveMedicationRandom forestDosePatient recordsAdmissionReadmission patients
2023
Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions
Kuo T, Pham A, Edelson M, Kim J, Chan J, Gupta Y, Ohno-Machado L, Anderson D, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bell D, Bernstam E, Ngan C, Day M, Doctor J, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hinske L, Hu Z, Ir D, Jiang X, Kim K, Kim J, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Matheny M, Meeker D, Mou Z, Neumann L, Nguyen N, Nick A, Ohno-Machado L, Park E, Paul P, Pletcher M, Post K, Rieder C, Scherer C, Schilling L, Soares A, SooHoo S, Soysal E, Steven C, Tep B, Toy B, Wang B, Wu Z, Xu H, Yong C, Zheng K, Zhou Y, Zucker R. Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions. Journal Of The American Medical Informatics Association 2023, 30: 1167-1178. PMID: 36916740, PMCID: PMC10198529, DOI: 10.1093/jamia/ocad049.Peer-Reviewed Original ResearchConceptsFederated data analysisUser activity logsSmart contract deploymentRun-time efficiencyData analysis systemData analysis activitiesActivity logsData discoveryQuerying timeBlockchain systemBlockchain technologyNetwork transactionsCOVID-19 data analysisMultiple institutionsLow deploymentBlockchainGitHub repositoryMultiple nodesLarge networksQueriesAnalysis activitiesHigh availabilityLanguage codeBaseline solutionData analysisA 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
Quorum-based model learning on a blockchain hierarchical clinical research network using smart contracts
Kuo T, Pham A. Quorum-based model learning on a blockchain hierarchical clinical research network using smart contracts. International Journal Of Medical Informatics 2022, 169: 104924. PMID: 36402113, PMCID: PMC9984225, DOI: 10.1016/j.ijmedinf.2022.104924.Peer-Reviewed Original ResearchConceptsSmart contractsPrivacy-preserving modelHierarchical learning algorithmBlockchain smart contractsProtect patient privacyLearning algorithmsNetwork of networksConsensus protocolModeling processPatient privacyQuorum mechanismHierarchical networkAvailability issuesNetworkPrediction correctnessIterative phasesPrediction modelPrivacyImmutabilityCapabilityHealthcare institutionsAlgorithmDatasetIterationLearning continuity
2021
Previewable Contract-Based On-Chain X-Ray Image Sharing Framework for Clinical Research
Li M, Kuo T. Previewable Contract-Based On-Chain X-Ray Image Sharing Framework for Clinical Research. International Journal Of Medical Informatics 2021, 156: 104599. PMID: 34628257, PMCID: PMC8479449, DOI: 10.1016/j.ijmedinf.2021.104599.Peer-Reviewed Original ResearchConceptsSharing frameworkPreview featureSoftware consistBlockchain-based frameworkChest X-ray imagesBlockchain networkSoftware inconsistencySmart contractsMerging functionView imagesBlockchainImprove sharingX-ray imagesFrameworkImagesLatencyInteroperabilityImmutabilityNetworkFeaturesData analysisSoftwareCodePreviewDownstream data analysisBenchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track
Kuo T, Bath T, Ma S, Pattengale N, Yang M, Cao Y, Hudson C, Kim J, Post K, Xiong L, Ohno-Machado L. Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track. International Journal Of Medical Informatics 2021, 154: 104559. PMID: 34474309, PMCID: PMC9933142, DOI: 10.1016/j.ijmedinf.2021.104559.Peer-Reviewed Original ResearchConceptsSecure genome analysis competitionData retrieval queriesBlockchain-based methodData sharing methodReal-world problemsQuery indexType of sharingRetrieval queriesBlockchain technologyLedger technologySource codeBlockchain utilizationBlockchain strategyHealthcare applicationsInteraction recordsSharing methodTest datasetSharing recordsBiomedical research applicationsConsortium resourcesNew platformPatient recordsBlockchainQueriesTechnologyHypertension prevalence in the All of Us Research Program among groups traditionally underrepresented in medical research
Chandler P, Clark C, Zhou G, Noel N, Achilike C, Mendez L, Ramirez A, Loperena-Cortes R, Mayo K, Cohn E, Ohno-Machado L, Boerwinkle E, Cicek M, Qian J, Schully S, Ratsimbazafy F, Mockrin S, Gebo K, Dedier J, Murphy S, Smoller J, Karlson E. Hypertension prevalence in the All of Us Research Program among groups traditionally underrepresented in medical research. Scientific Reports 2021, 11: 12849. PMID: 34158555, PMCID: PMC8219813, DOI: 10.1038/s41598-021-92143-w.Peer-Reviewed Original ResearchConceptsPrevalence of hypertensionHTN prevalenceUs Research ProgramMajor public health concernBlood pressure medicationsPopulation-based studyNutrition Examination SurveyBlood pressure measurementsPopulation-based surveyEHR dataPatient measurementsPublic health concernAntihypertensive medicationsEHR cohortHTN medicationsHypertension prevalenceCrude prevalenceHypertension casesHypertension treatmentExamination SurveyNational HealthHypertensionBilling codesMedicationsCohortPrivacy-protecting, reliable response data discovery using COVID-19 patient observations
Kim J, Neumann L, Paul P, Day M, Aratow M, Bell D, Doctor J, Hinske L, Jiang X, Kim K, Matheny M, Meeker D, Pletcher M, Schilling L, SooHoo S, Xu H, Zheng K, Ohno-Machado L, Anderson D, Anderson N, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bernstam E, Carter W, Chau N, Choi Y, Covington S, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hu Z, Ir D, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Mou Z, Murphy R, Neumann L, Nguyen N, Niedermayer S, Park E, Perkins A, Post K, Rieder C, Scherer C, Soares A, Soysal E, Tep B, Toy B, Wang B, Wu Z, Zhou Y, Zucker R. Privacy-protecting, reliable response data discovery using COVID-19 patient observations. Journal Of The American Medical Informatics Association 2021, 28: 1765-1776. PMID: 34051088, PMCID: PMC8194878, DOI: 10.1093/jamia/ocab054.Peer-Reviewed Original ResearchPredictive Analytics for Glaucoma Using Data From the All of Us Research Program
Baxter S, Saseendrakumar B, Paul P, Kim J, Bonomi L, Kuo T, Loperena R, Ratsimbazafy F, Boerwinkle E, Cicek M, Clark C, Cohn E, Gebo K, Mayo K, Mockrin S, Schully S, Ramirez A, Ohno-Machado L, Investigators A. Predictive Analytics for Glaucoma Using Data From the All of Us Research Program. American Journal Of Ophthalmology 2021, 227: 74-86. PMID: 33497675, PMCID: PMC8184631, DOI: 10.1016/j.ajo.2021.01.008.Peer-Reviewed Original ResearchConceptsGlaucoma surgeryPrimary open-angle glaucomaOphthalmic researchSingle-center cohortElectronic health record dataMultivariable logistic regressionSingle-center dataOpen-angle glaucomaHealth record dataMean ageClaims dataUs Research ProgramLogistic regressionSurgeryRecord dataOphthalmic imagingCharacteristic curveExternal validationGlaucomaCohortAUCSingle-center model
2020
iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching
Kuo T, Jiang X, Tang H, Wang X, Bath T, Bu D, Wang L, Harmanci A, Zhang S, Zhi D, Sofia H, Ohno-Machado L. iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching. BMC Medical Genomics 2020, 13: 98. PMID: 32693816, PMCID: PMC7372776, DOI: 10.1186/s12920-020-0715-0.Peer-Reviewed Original ResearchEXpectation Propagation LOgistic REgRession on permissioned blockCHAIN (ExplorerChain): decentralized online healthcare/genomics predictive model learning
Kuo T, Gabriel R, Cidambi K, Ohno-Machado L. EXpectation Propagation LOgistic REgRession on permissioned blockCHAIN (ExplorerChain): decentralized online healthcare/genomics predictive model learning. Journal Of The American Medical Informatics Association 2020, 27: 747-756. PMID: 32364235, PMCID: PMC7309256, DOI: 10.1093/jamia/ocaa023.Peer-Reviewed Original ResearchConceptsBlockchain technologyCentral serverServer-based methodBenefits of blockchainData protection policiesCentralized serverArtificial intelligenceModel learningDecentralized approachSmall datasetsBlockchainServerComputation strategySingle pointGeneralizable modelCost of efficiencyGenomic datasetsDatasetDistributed modelTechnologyGenomic dataMultiple institutionsDiscrimination powerIntelligencePotential advantages/disadvantagesComparison of Smart Contract Blockchains for Healthcare Applications.
Yu H, Sun H, Wu D, Kuo T. Comparison of Smart Contract Blockchains for Healthcare Applications. AMIA Annual Symposium Proceedings 2020, 2019: 1266-1275. PMID: 32308924, PMCID: PMC7153130.Peer-Reviewed Original ResearchConceptsHealthcare applicationsSmart contract blockchainHyperledger FabricBlockchain networkHealthcare blockchainHealthcare domainSmart contractsBlockchain technologyBlockchainFeatures of platformsPlatformHyperledgerEthereumImplementationTechnologyApplicationsNetworkHealthcareTutorialPragmatic comparison
2019
Machine Learning-Based Predictive Modeling of Surgical Intervention in Glaucoma Using Systemic Data From Electronic Health Records
Baxter S, Marks C, Kuo T, Ohno-Machado L, Weinreb R. Machine Learning-Based Predictive Modeling of Surgical Intervention in Glaucoma Using Systemic Data From Electronic Health Records. American Journal Of Ophthalmology 2019, 208: 30-40. PMID: 31323204, PMCID: PMC6888922, DOI: 10.1016/j.ajo.2019.07.005.Peer-Reviewed Original ResearchConceptsPrimary open-angle glaucomaElectronic health recordsMultivariable logistic regressionSurgical interventionGlaucoma surgeryPOAG patientsSystemic dataHigher mean systolic blood pressureMean systolic blood pressureNon-opioid analgesic medicationsLogistic regressionCertain medication classesEye-specific dataHealth recordsRisk of progressionSystolic blood pressureOpen-angle glaucomaSingle academic institutionAnti-hyperlipidemic medicationsAnalgesic medicationMedication classesProgressive diseaseBlood pressureCalcium blockersOphthalmic medications‘Fit-for-purpose?’ – challenges and opportunities for applications of blockchain technology in the future of healthcare
Mackey T, Kuo T, Gummadi B, Clauson K, Church G, Grishin D, Obbad K, Barkovich R, Palombini M. ‘Fit-for-purpose?’ – challenges and opportunities for applications of blockchain technology in the future of healthcare. BMC Medicine 2019, 17: 68. PMID: 30914045, PMCID: PMC6436239, DOI: 10.1186/s12916-019-1296-7.Peer-Reviewed Original ResearchConceptsApplication of blockchain technologyHealthcare-related dataBlockchain approachBusiness processesHealth blockchainBlockchain technologyData architectureBlockchainData managementTransform healthcareMultidisciplinary groups of practitionersImprove patient outcomesHealthcare stakeholdersHealthcare needsGroup of practitionersHealth sectorMultidisciplinary groupDesign elementsDataHealthcarePatient outcomesPerspective of consumersTechnologyEnhance complianceLow costFair compute loads enabled by blockchain: sharing models by alternating client and server roles
Kuo T, Gabriel R, Ohno-Machado L. Fair compute loads enabled by blockchain: sharing models by alternating client and server roles. Journal Of The American Medical Informatics Association 2019, 26: 392-403. PMID: 30892656, PMCID: PMC7787356, DOI: 10.1093/jamia/ocy180.Peer-Reviewed Original Research
2018
Identifying and characterizing highly similar notes in big clinical note datasets
Gabriel R, Kuo T, McAuley J, Hsu C. Identifying and characterizing highly similar notes in big clinical note datasets. Journal Of Biomedical Informatics 2018, 82: 63-69. PMID: 29679685, DOI: 10.1016/j.jbi.2018.04.009.Peer-Reviewed Original ResearchConceptsClinical note datasetsDe-duplication algorithmMIMIC-III datasetElectronic health recordsJaccard similarityDe-duplicationLocality sensitive hashingMIMIC-IIINear-duplicatesScalable algorithmMeasure similarityAccurate statistical modelsSources of duplicationClustering methodDatasetAlgorithmApproximation algorithmHealth recordsDisjoint setsInstitutional datasetComparison of notesPairs of notesHashPairwise comparisonsPairwise
2017
Ensembles of NLP Tools for Data Element Extraction from Clinical Notes.
Kuo T, Rao P, Maehara C, Doan S, Chaparro J, Day M, Farcas C, Ohno-Machado L, Hsu C. Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. AMIA Annual Symposium Proceedings 2017, 2016: 1880-1889. PMID: 28269947, PMCID: PMC5333200.Peer-Reviewed Original ResearchConceptsNatural language processingNLP toolsElectronic health recordsData elementsConcept extractionLanguage processingEnsemble methodDiverse conceptsEvaluation resultsHealth recordsElement extractionClinical notesPlausible solutionToolPipelineExtractionPerformanceEnsembleExtraction performanceConceptNarrative textProcessingText
2016
Weakly supervised learning of biomedical information extraction from curated data
Jain S, R. K, Kuo T, Bhargava S, Lin G, Hsu C. Weakly supervised learning of biomedical information extraction from curated data. BMC Bioinformatics 2016, 17: s1. PMID: 26817711, PMCID: PMC4847485, DOI: 10.1186/s12859-015-0844-1.Peer-Reviewed Original ResearchConceptsTraining examplesInformation extractionGenome-wide association studiesCommittee of weak classifiersCurated dataInformation extraction tasksBiomedical information extractionWeakly supervised learningCost-sensitive learningBiomedical text miningSupervised machine learningNoisy labelsWeak classifiersExtraction taskInformation extractorExpert annotationsBig dataMachine learningText miningBaseline counterpartExperimental resultsAssociation studiesTarget phenotypeBiomedical databasesTask