2023
Guiding Principles to Address the Impact of Algorithm Bias on Racial and Ethnic Disparities in Health and Health Care
Chin M, Afsar-Manesh N, Bierman A, Chang C, Colón-Rodríguez C, Dullabh P, Duran D, Fair M, Hernandez-Boussard T, Hightower M, Jain A, Jordan W, Konya S, Moore R, Moore T, Rodriguez R, Shaheen G, Snyder L, Srinivasan M, Umscheid C, Ohno-Machado L. Guiding Principles to Address the Impact of Algorithm Bias on Racial and Ethnic Disparities in Health and Health Care. JAMA Network Open 2023, 6: e2345050. PMID: 38100101, PMCID: PMC11181958, DOI: 10.1001/jamanetworkopen.2023.45050.Peer-Reviewed Original ResearchSimulating complex patient populations with hierarchical learning effects to support methods development for post-market surveillance
Davis S, Ssemaganda H, Koola J, Mao J, Westerman D, Speroff T, Govindarajulu U, Ramsay C, Sedrakyan A, Ohno-Machado L, Resnic F, Matheny M. Simulating complex patient populations with hierarchical learning effects to support methods development for post-market surveillance. BMC Medical Research Methodology 2023, 23: 89. PMID: 37041457, PMCID: PMC10088292, DOI: 10.1186/s12874-023-01913-9.Peer-Reviewed Original ResearchConceptsSynthetic datasetsData characteristicsFeature distributionGround truthMIMIC-III dataReal-world dataData generation processComplex simulation studiesData relationshipsUser definitionSmall datasetsSimulation requirementsCorrelated featuresWorld dataCustomizable optionsReal-world complexitySynthetic patientsNew algorithmDatasetGeneration processLearningAlgorithmData simulation techniquesLearning effectGeneralizable framework
2021
Privacy-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 ResearchCalibrating predictive model estimates in a distributed network of patient data
Huang Y, Jiang X, Gabriel R, Ohno-Machado L. Calibrating predictive model estimates in a distributed network of patient data. Journal Of Biomedical Informatics 2021, 117: 103758. PMID: 33811986, DOI: 10.1016/j.jbi.2021.103758.Peer-Reviewed Original ResearchConceptsData privacyRecalibration modelHigh-performance predictive modelsIntegration of dataPatient dataPredictive model estimatesDistributed networkExpected calibration errorMaximum calibration errorPrivacyClinical informaticsCalibration errorsComputational efficiencyPredictive analysisAlgorithmBuilding modelsModel buildingImportant issuePerformance measuresPredictive modelMultiple health systemsLarge numberIsotonic regressionInformaticsSystem
2020
EXpectation 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/disadvantages
2019
Fair 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
2017
Blockchain distributed ledger technologies for biomedical and health care applications
Kuo T, Kim H, Ohno-Machado L. Blockchain distributed ledger technologies for biomedical and health care applications. Journal Of The American Medical Informatics Association 2017, 24: 1211-1220. PMID: 29016974, PMCID: PMC6080687, DOI: 10.1093/jamia/ocx068.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHealth care domainHealth care applicationsBlockchain technologyLedger technologyCare domainFeatures of blockchainBenefits of blockchainCare applicationsFamous BitcoinInformatics researchersBlockchainTechnologyApplicationsCovered topicsBitcoinDomainLatest applicationsPotential challengesDatabase
2015
VERTIcal Grid lOgistic regression (VERTIGO)
Li Y, Jiang X, Wang S, Xiong H, Ohno-Machado L. VERTIcal Grid lOgistic regression (VERTIGO). Journal Of The American Medical Informatics Association 2015, 23: 570-579. PMID: 26554428, PMCID: PMC4901373, DOI: 10.1093/jamia/ocv146.Peer-Reviewed Original ResearchConceptsFederated data analysisReal-world medical classification problemsMedical classification problemsLogistic regression algorithmAccurate global modelData setsReal data setsClassification problemExchange of informationLR problemTime complexityComputational complexityExpensive operationRegression algorithmComputational costData analysisAlgorithmDual optimizationTechnical challengesLarge amountComplexityPatient recordsLR modelNovel techniqueHessian matrixWebDISCO: a web service for distributed cox model learning without patient-level data sharing
Lu C, Wang S, Ji Z, Wu Y, Xiong L, Jiang X, Ohno-Machado L. WebDISCO: a web service for distributed cox model learning without patient-level data sharing. Journal Of The American Medical Informatics Association 2015, 22: 1212-1219. PMID: 26159465, PMCID: PMC5009917, DOI: 10.1093/jamia/ocv083.Peer-Reviewed Original Research
2014
Privacy Preserving RBF Kernel Support Vector Machine
Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy Preserving RBF Kernel Support Vector Machine. BioMed Research International 2014, 2014: 827371. PMID: 25013805, PMCID: PMC4071990, DOI: 10.1155/2014/827371.Peer-Reviewed Original ResearchConceptsPrivate dataPrivacy-preserving data disseminationKernel support vector machineRBF kernel support vector machinePublic dataSupport vector machineSupport vector machine modelVector machine modelData disseminationData sharingBiomedical dataPrivacy standardsVector machineRBF kernelPerformance metricsSVMMachine modelFull usePrivacyFinal outputSeparable caseAvailable informationMachineSharingMetricsGAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda
Wang S, Kim J, Jiang X, Brunner S, Ohno-Machado L. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda. BMC Medical Genomics 2014, 7: s9. PMID: 25077821, PMCID: PMC4101446, DOI: 10.1186/1755-8794-7-s1-s9.Peer-Reviewed Original ResearchConceptsCompute Unified Device ArchitectureGraphics processing unitsHigh performance computeParallel computingNVIDIA Compute Unified Device ArchitectureUnified Device ArchitectureMultiple test datasetsGiga cell updatesTimes performance gainsSmith-Waterman algorithmGPU developersSW implementationSource codeExecution timeGHz CPUIntel XeonLong reference sequencesProcessing unitTarget identification algorithmCell updatesTest datasetProjects/Such large scalePerformance gainsBiomedical research communityDifferentially private distributed logistic regression using private and public data
Ji Z, Jiang X, Wang S, Xiong L, Ohno-Machado L. Differentially private distributed logistic regression using private and public data. BMC Medical Genomics 2014, 7: s14. PMID: 25079786, PMCID: PMC4101668, DOI: 10.1186/1755-8794-7-s1-s14.Peer-Reviewed Original ResearchConceptsPrivate dataDifferential privacyPublic datasetsPublic dataRigorous privacy guaranteeData privacy researchPrivate data setsData mining modelsData setsProvable privacyPrivacy guaranteesMining modelPrivacy researchDifferent data setsArt frameworksMedical informaticsPrivacyAmount of noisePrivate methodsAuxiliary informationBetter utilityNew algorithmUpdate stepAvailable public dataAlgorithmHUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads
Li P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L. HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. Journal Of The American Medical Informatics Association 2014, 21: 363-373. PMID: 24368726, PMCID: PMC3932469, DOI: 10.1136/amiajnl-2013-002147.Peer-Reviewed Original ResearchConceptsBase quality valuesCompression algorithmStorage savingsGenome compressionSequence Alignment/Map (SAM) formatCompression ratioNovel compression algorithmComparable compression ratioCompression mechanismK-means clusteringDifferent reference genomesQuality valuesDecompression qualityLossless compressionExecution timeCompression rateAligned readsMap formatAlgorithmBiomedical communityDifferent quality valuesExperimental datasetsAdaptive schemeStorage capabilityArchivingPhenDisco: phenotype discovery system for the database of genotypes and phenotypes
Doan S, Lin K, Conway M, Ohno-Machado L, Hsieh A, Feupe S, Garland A, Ross M, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim H. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. Journal Of The American Medical Informatics Association 2014, 21: 31-36. PMID: 23989082, PMCID: PMC3912702, DOI: 10.1136/amiajnl-2013-001882.Peer-Reviewed Original ResearchConceptsNew information retrieval systemInformation retrieval systemsInformation retrieval toolsDatabase of GenotypesText processing toolsRetrieval systemSearch scenariosDiscovery systemRetrieval toolsAuthorized usersNon-standardized wayCross-study validationSearch comparisonProcessing toolsPromising performanceUsersPhenotype informationDatabaseInformationBiotechnology InformationQueriesMetadataEntrezResourcesSystem
2013
Recent trends in biomedical informatics: a study based on JAMIA articles
Jiang X, Tse K, Wang S, Doan S, Kim H, Ohno-Machado L. Recent trends in biomedical informatics: a study based on JAMIA articles. Journal Of The American Medical Informatics Association 2013, 20: e198-e205. PMID: 24214018, PMCID: PMC3861936, DOI: 10.1136/amiajnl-2013-002429.Peer-Reviewed Original ResearchDNA-COMPACT: DNA COMpression Based on a Pattern-Aware Contextual Modeling Technique
Li P, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X. DNA-COMPACT: DNA COMpression Based on a Pattern-Aware Contextual Modeling Technique. PLOS ONE 2013, 8: e80377. PMID: 24282536, PMCID: PMC3840021, DOI: 10.1371/journal.pone.0080377.Peer-Reviewed Original ResearchConceptsReference-free compressionDisk storage capacityCompression algorithmDecompression costData transferringArt algorithmsCompression performanceFile sizeGenome compressionCompression rateBit rateAlgorithmDNA compressionBiomedical researchersPerformance advantagesGenome dataModeling techniquesContextual modelImportant concernResearch purposesCompressionPerformanceStorage capacityBitsReference sequenceNatural language processing: algorithms and tools to extract computable information from EHRs and from the biomedical literature
Ohno-Machado L, Nadkarni P, Johnson K. Natural language processing: algorithms and tools to extract computable information from EHRs and from the biomedical literature. Journal Of The American Medical Informatics Association 2013, 20: 805-805. PMID: 23935077, PMCID: PMC3756279, DOI: 10.1136/amiajnl-2013-002214.Commentaries, Editorials and LettersComparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis.
Thawait S, Kim J, Klufas R, Morrison W, Flanders A, Carrino J, Ohno-Machado L. Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis. American Journal Of Roentgenology 2013, 200: 493-502. PMID: 23436836, DOI: 10.2214/ajr.11.7192.Peer-Reviewed Original ResearchAdultAgedAged, 80 and overAlgorithmsCohort StudiesComputer SimulationDiagnosis, DifferentialFemaleFractures, CompressionHumansImage EnhancementImage Interpretation, Computer-AssistedMagnetic Resonance ImagingMaleMiddle AgedModels, BiologicalNeoplasmsPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificitySpinal FracturesYoung AdultNucleotide sequence alignment using sparse coding and belief propagation
Roozgard A, Barzigar N, Wang S, Jiang X, Ohno-Machado L, Cheng S. Nucleotide sequence alignment using sparse coding and belief propagation. Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2013, 2013: 588-591. PMID: 24109755, PMCID: PMC3909563, DOI: 10.1109/embc.2013.6609568.Peer-Reviewed Original Research
2012
Privacy-preserving heterogeneous health data sharing
Mohammed N, Jiang X, Chen R, Fung B, Ohno-Machado L. Privacy-preserving heterogeneous health data sharing. Journal Of The American Medical Informatics Association 2012, 20: 462-469. PMID: 23242630, PMCID: PMC3628047, DOI: 10.1136/amiajnl-2012-001027.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsConfidentialityData MiningDatabases, FactualFemaleHumansInformation DisseminationMalePrivacyConceptsSet-valued dataDifferential privacyNoise additionPrivacy-preserving mannerAdversary's background knowledgeStrong privacy guaranteesBackground knowledgeHealth data sharingPrivacy modelPrivacy guaranteesSensitive dataData sharingHealthcare dataPrivate mannerAlgorithm designPrivacyRaw dataSynthetic dataAlgorithmHealth dataProbabilistic wayDiscriminative analysisExperimental resultsUseful informationClassification analysis