2023
Dual-Domain Iterative Network with Adaptive Data Consistency for Joint Denoising and Few-Angle Reconstruction of Low-Dose Cardiac SPECT
Chen X, Zhou B, Xie H, Guo X, Liu Q, Sinusas A, Liu C. Dual-Domain Iterative Network with Adaptive Data Consistency for Joint Denoising and Few-Angle Reconstruction of Low-Dose Cardiac SPECT. Lecture Notes In Computer Science 2023, 14307: 49-59. DOI: 10.1007/978-3-031-44917-8_5.Peer-Reviewed Original ResearchIterative networkAuxiliary modulesJoint denoisingLow reconstruction accuracySource codeData consistencyNetwork performanceAblation studiesReconstruction accuracyCardiac SPECTConsistency moduleHardware expensePrediction accuracyAngle reconstructionNetworkDenoisingImage noiseAngle projectionsModuleADC moduleAccuracyReconstructionImagesMPI dataCode
2022
Insights from incorporating quantum computing into drug design workflows
Lau B, Emani P, Chapman J, Yao L, Lam T, Merrill P, Warrell J, Gerstein M, Lam H. Insights from incorporating quantum computing into drug design workflows. Bioinformatics 2022, 39: btac789. PMID: 36477833, PMCID: PMC9825754, DOI: 10.1093/bioinformatics/btac789.Peer-Reviewed Original ResearchConceptsQuantum machine learningComputer-aided drug designMachine-learning moduleQuantum computing methodsCommercial quantum computersMachine learningJupyter notebooksNeural networkComputing methodClassical baselinesDesign workflowQML modelsQuantum hardwarePython codeAcademic useSupplementary dataQuantum computerWorkflowJudicious partitioningModuleHardwareGitHubClassical counterpartCase studyComputerMCP-Net: Inter-frame Motion Correction with Patlak Regularization for Whole-body Dynamic PET
Guo X, Zhou B, Chen X, Liu C, Dvornek N. MCP-Net: Inter-frame Motion Correction with Patlak Regularization for Whole-body Dynamic PET. Lecture Notes In Computer Science 2022, 13434: 163-172. PMID: 38464686, PMCID: PMC10923180, DOI: 10.1007/978-3-031-16440-8_16.Peer-Reviewed Original ResearchConvolutional long short-term memory (ConvLSTM) layersLong short-term memory layersMotion estimation moduleShort-term memory layersDeep learning benchmarksEnhanced network performanceImage registration problemMotion correction frameworkMotion correctionU-NetNetwork performanceLearning benchmarksSimilarity measurementEstimation moduleRegistration problemGradient lossMemory layerLoss functionDynamic frameDynamic positron emission tomographyFitting errorSpatial alignmentSpatial misalignmentPatient motionModule
2021
Graph‐based risk assessment and error detection in radiation therapy
Munbodh R, Bowles JK, Zaveri HP. Graph‐based risk assessment and error detection in radiation therapy. Medical Physics 2021, 48: 965-977. PMID: 33340128, DOI: 10.1002/mp.14666.Peer-Reviewed Original ResearchConceptsGraph traversalConstraint satisfaction problemsSoftware entitiesConstraint programmingDetection of errorsActivity diagramsHardware systemSatisfaction problemsLogical formulasError detectionTractable unitsQuality assuranceConstraint violationsModular approachGraph theoryPlanning systemGraphTraversalModuleQA processVerify systemForms of inconsistencyLogical inconsistenciesAnatomical contoursAssurance
2019
IMPROVING THE PERSONAL CARE ASSISTANT WORKFORCE THROUGH TRAINING, DATA, AND TECHNOLOGY
Abujarad F, Swierenga S, Luz C, Hanson K, Curtin C, Luo Z, Swanson-Aprill L. IMPROVING THE PERSONAL CARE ASSISTANT WORKFORCE THROUGH TRAINING, DATA, AND TECHNOLOGY. Innovation In Aging 2019, 3: s667-s667. PMCID: PMC6841470, DOI: 10.1093/geroni/igz038.2467.Peer-Reviewed Original ResearchData platformMain user interfaceUser acceptance testingUser interfaceUsability evaluationOnline systemAdministration functionsResource allocationAcceptance testingDevelopment phasePlatformTechnology platformDesign approachInnovative systemCore componentPCATechnologyIntegrated modelUsersPCA trainingTrackingTrainingSystemModuleAllocationDeveloping Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP
Soysal E, Warner J, Wang J, Jiang M, Harvey K, Jain S, Dong X, Song H, Siddhanamatha H, Wang L, Dai Q, Chen Q, Du X, Tao C, Yang P, Denny J, Liu H, Xu H. Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. Studies In Health Technology And Informatics 2019, 264: 1041-1045. PMID: 31438083, PMCID: PMC7359882, DOI: 10.3233/shti190383.Peer-Reviewed Original ResearchConceptsElectronic health recordsNLP solutionNatural language processing technologyInformation extraction moduleLanguage processing technologyInformation extraction tasksUser-friendly interfaceBest F-measureInformation extractionExtraction moduleExtraction taskCustomizable modulesNLP systemsF-measureAcademic useHealth recordsComparable performanceProcessing technologyVanderbilt University Medical CenterModuleDiverse typesInformationNLPSubstantial effortSystem
2017
exprso: an R-package for the rapid implementation of machine learning algorithms
Quinn T, Tylee D, Glatt S. exprso: an R-package for the rapid implementation of machine learning algorithms. F1000Research 2017, 5: 2588. PMID: 29560250, PMCID: PMC5832912, DOI: 10.12688/f1000research.9893.2.Peer-Reviewed Original ResearchNon-expert programmersObject-oriented frameworkMulti-class classificationHigh-dimensional dataMachine learningEnsemble classificationIntuitive machineCross-validation schemeR packageFeature selectionNew R packageProgrammersInterchangeable modulesGeneralizable modelMachineClassificationRapid implementationModuleAlgorithmLearningImplementationPipelineSchemeFrameworkPrediction
2016
exprso: an R-package for the rapid implementation of machine learning algorithms
Quinn T, Tylee D, Glatt S. exprso: an R-package for the rapid implementation of machine learning algorithms. F1000Research 2016, 5: 2588. DOI: 10.12688/f1000research.9893.1.Peer-Reviewed Original ResearchNon-expert programmersObject-oriented frameworkMulti-class classificationHigh-dimensional dataNative supportMachine learningEnsemble classificationIntuitive machineCross-validation schemeR packageFeature selectionBinary classifierNew R packageSimplicity of useProgrammersInterchangeable modulesMachineGeneralizable modelClassificationRapid implementationModuleClassifierSuiteAlgorithmLearning
2014
Improving the Quality of Thyroid Cancer Care: How Does the Thyroid Cancer Care Collaborative Cross the Institute of Medicine's Quality Chasm?
Mehra S, Tuttle RM, Bergman D, Bernet V, Brett E, Cobin R, Doherty G, Klopper J, Lee S, Machac J, Milas M, Mechanick JI, Orloff L, Randolph G, Ross DS, Smallridge R, Terris D, Tufano R, Alon E, Clain J, Dos Reis L, Scherl S, Urken ML. Improving the Quality of Thyroid Cancer Care: How Does the Thyroid Cancer Care Collaborative Cross the Institute of Medicine's Quality Chasm? Thyroid 2014, 24: 615-624. PMID: 24512449, DOI: 10.1089/thy.2013.0441.Peer-Reviewed Original ResearchConceptsThyroid Cancer Care CollaborativeInformation technologyInstitute of MedicineDecision-making modulePortability of dataThyroid cancer careWorkflow integrationCancer careQuality ChasmIOM recommendationsHealthcare deliveryCancer care deliveryThyroid cancer managementVirtual tumor boardsCare CollaborativeTumor boardCancer managementHealthcare organizationsCare processesScoring systemCare deliveryWeb-based programCurrent systemModuleClinicians
2012
A study of transportability of an existing smoking status detection module across institutions.
Liu M, Shah A, Jiang M, Peterson N, Dai Q, Aldrich M, Chen Q, Bowton E, Liu H, Denny J, Xu H. A study of transportability of an existing smoking status detection module across institutions. AMIA Annual Symposium Proceedings 2012, 2012: 577-86. PMID: 23304330, PMCID: PMC3540509.Peer-Reviewed Original ResearchConceptsDetection moduleNatural language processing systemsKnowledge Extraction SystemEMR dataRule-based classifierClinical Text AnalysisHighest F-measureLanguage processing systemElectronic medical recordsF-measureLevels of classificationProcessing systemSpecific tasksText analysisClassifierDesirable performanceModuleModest effortExtraction systemCTAKESSmoking moduleMachineSystemTaskClassification
2011
The dChip survival analysis module for microarray data
Amin S, Shah P, Yan A, Adamia S, Minvielle S, Avet-Loiseau H, Munshi N, Li C. The dChip survival analysis module for microarray data. BMC Bioinformatics 2011, 12: 72. PMID: 21388547, PMCID: PMC3068974, DOI: 10.1186/1471-2105-12-72.Peer-Reviewed Original ResearchConceptsAnalysis moduleUser-friendly wayDemonstration dataMicroarray data analysisAnalysis functionsFast computationSoftware packageSoftwareSignificant chromosome regionsMicroarray dataMinimal learning curveGene expressionDChip softwareModuleGenome-wide copy number alterationsData analysisSNP array dataSurvival gene signaturesCopy number dataChromosome displayContext of genesUsersCopy number alterationsChromosome regionsClustering
2006
The BioImage Suite Datatree Tool: Enabling Flexible Realtime Surgical Visualizations
DiStasio M, Vives K, Papademetris X. The BioImage Suite Datatree Tool: Enabling Flexible Realtime Surgical Visualizations. Insight Journal 2006 DOI: 10.54294/f0fw56.Peer-Reviewed Original ResearchCytoAccess, a relational laboratory information management system for a clinical cytogenetics laboratory.
Xiang B, Li P, Hemingway SS, Qumsiyeh M. CytoAccess, a relational laboratory information management system for a clinical cytogenetics laboratory. Journal Of The Association Of Genetic Technologists 2006, 32: 168-70. PMID: 17130662.Peer-Reviewed Original ResearchEntry moduleManagement systemLaboratory information management systemData entry moduleInformation management systemLaboratory management systemMicrosoft Access softwareData miningAdministrative moduleMaintenance moduleAccess softwareCode tableData processingData linkFunctional modulesPatient informationReport templateModuleUsersQuality managementMiningSystemSoftwareBilling formsUpdating
2005
LIFEBRIDGE: A Portable, Modular, Rapidly Available “Plug-and-Play” Mechanical Circulatory Support System
Mehlhorn U, Brieske M, Fischer U, Ferrari M, Brass P, Fischer J, Zerkowski H. LIFEBRIDGE: A Portable, Modular, Rapidly Available “Plug-and-Play” Mechanical Circulatory Support System. The Annals Of Thoracic Surgery 2005, 80: 1887-1892. PMID: 16242474, DOI: 10.1016/j.athoracsur.2005.03.040.Peer-Reviewed Original ResearchConceptsExperimental safety evaluationMechanical circulatory support systemsPower supplyCirculatory support systemsPeripheral cannulationControl moduleAir embolizationTransport conditionsModular designCardiopulmonary bypass circuitBase modulePump flowModular constructionCentral cannulationAdequate perfusionPlugAir bolusBypass circuitElimination programModuleLifebridgeCannulationInitial evaluationDoppler devicePatient module
2001
NEOSIM: Portable large-scale plug and play modelling
Goddard N, Hood G, Howell F, Hines M, De Schutter E. NEOSIM: Portable large-scale plug and play modelling. Neurocomputing 2001, 38: 1657-1661. DOI: 10.1016/s0925-2312(01)00528-8.Peer-Reviewed Original ResearchSet of interfacesData analysis moduleParallel simulation toolsNew simulation frameworkAdditional modelling effortSimulation frameworkAnalysis moduleSimulation moduleLarge-scale plugSimulation toolManageable levelModuleFrameworkLarge scaleComputerArchitectureNEOSIMModelling effortsVisualisationDetailed modelSetPlugInterfaceProtocolToolGeneration of dynamically configured check lists for intra-operative problems using a set of covering algorithms.
Sawa T, Ohno-Machado L. Generation of dynamically configured check lists for intra-operative problems using a set of covering algorithms. AMIA Annual Symposium Proceedings 2001, 593-7. PMID: 11837218, PMCID: PMC2243696.Peer-Reviewed Original Research
1998
Automatic query mapping among genomic databases: a pilot exploration.
Cheung KH, Nadkarni P, Miller P, Shin DG. Automatic query mapping among genomic databases: a pilot exploration. AMIA Annual Symposium Proceedings 1998, 942-6. PMID: 9929357, PMCID: PMC2232293.Peer-Reviewed Original Research
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