2024
Tumor response assessment in hepatocellular carcinoma treated with immunotherapy: imaging biomarkers for clinical decision-making
Sobirey R, Matuschewski N, Gross M, Lin M, Kao T, Kasolowsky V, Strazzabosco M, Stein S, Savic L, Gebauer B, Jaffe A, Duncan J, Madoff D, Chapiro J. Tumor response assessment in hepatocellular carcinoma treated with immunotherapy: imaging biomarkers for clinical decision-making. European Radiology 2024, 1-11. PMID: 39033181, DOI: 10.1007/s00330-024-10955-6.Peer-Reviewed Original ResearchMedian overall survivalTumor response criteriaTumor response assessmentHepatocellular carcinoma patientsHepatocellular carcinomaTumor responseOverall survivalResponse criteriaResponse assessmentNon-respondersPoorer median overall survivalPrediction of tumor responsePredictive valueHepatocellular carcinoma immunotherapyDisease controlPrognostic of survivalClinical baseline parametersLog-rank testKaplan-Meier curvesMultivariate Cox regressionPredicting overall survivalCox regression modelsSurvival benefitStratify patientsMRI pre-Medical image registration via neural fields
Sun S, Han K, You C, Tang H, Kong D, Naushad J, Yan X, Ma H, Khosravi P, Duncan J, Xie X. Medical image registration via neural fields. Medical Image Analysis 2024, 97: 103249. PMID: 38963972, DOI: 10.1016/j.media.2024.103249.Peer-Reviewed Original ResearchLearning-based methodsNeural fieldsNeural networkImage registrationMedical image analysis tasksMini-batch gradient descentImage analysis tasksDeep neural networksMedical image registrationDiffeomorphic image registrationImage registration frameworkOptimization-based methodDomain shiftAnalysis tasksGradient descentCompetitive performanceImage pairsRegistration taskOptimal deformationShort computation timeRegistration frameworkDesign choicesDisplacement vector fieldComputation timeModel optimizationHigh‐resolution extracellular pH imaging of liver cancer with multiparametric MR using Deep Image Prior
Dong S, Shewarega A, Chapiro J, Cai Z, Hyder F, Coman D, Duncan J. High‐resolution extracellular pH imaging of liver cancer with multiparametric MR using Deep Image Prior. NMR In Biomedicine 2024, 37: e5145. PMID: 38488205, DOI: 10.1002/nbm.5145.Peer-Reviewed Original ResearchDeep Image PriorU-NetUnsupervised deep learning techniquesU-Net parametersDeep learning techniquesHigh-resolution ground truthU-Net architectureSuper-resolution imagingImage priorsSuper-resolutionGround truthMean absolute errorDeepSpatial resolutionPostprocessing methodDeep imagingAbsolute errorImagesAnatomical MR imagesMR spectroscopic imagingAnatomical informationSpectroscopic imagingInformationAcquisition timeErrorGrand Challenges at the Interface of Engineering and Medicine
Subramaniam S, Akay M, Anastasio M, Bailey V, Boas D, Bonato P, Chilkoti A, Cochran J, Colvin V, Desai T, Duncan J, Epstein F, Fraley S, Giachelli C, Grande-Allen K, Green J, Guo X, Hilton I, Humphrey J, Johnson C, Karniadakis G, King M, Kirsch R, Kumar S, Laurencin C, Li S, Lieber R, Lovell N, Mali P, Margulies S, Meaney D, Ogle B, Palsson B, Peppas N, Perreault E, Rabbitt R, Setton L, Shea L, Shroff S, Shung K, Tolias A, van der Meulen M, Varghese S, Vunjak-Novakovic G, White J, Winslow R, Zhang J, Zhang K, Zukoski C, Miller M. Grand Challenges at the Interface of Engineering and Medicine. IEEE Open Journal Of Engineering In Medicine And Biology 2024, 5: 1-13. PMID: 38415197, PMCID: PMC10896418, DOI: 10.1109/ojemb.2024.3351717.Peer-Reviewed Original ResearchEffect of Incomplete Cryoablation and Matrix Metalloproteinase Inhibition on Intratumoral CD8+ T-Cell Infiltration in Murine Hepatocellular Carcinoma.
Shewarega A, Santana J, Nam D, Berz A, Tefera J, Kahl V, Mishra S, Coman D, Duncan J, Roberts S, Wetter A, Madoff D, Chapiro J. Effect of Incomplete Cryoablation and Matrix Metalloproteinase Inhibition on Intratumoral CD8+ T-Cell Infiltration in Murine Hepatocellular Carcinoma. Radiology 2024, 310: e232365. PMID: 38349244, PMCID: PMC10902598, DOI: 10.1148/radiol.232365.Peer-Reviewed Original ResearchConceptsT cell infiltrationCD8<sup>+</sup> T cellsMatrix metalloproteinase inhibitionT cellsHepatocellular carcinomaMatrix metalloproteinase inhibitorsMatrix metalloproteinasesResidual tumorCXCR3<sup>+</sup> CD8<sup>+</sup> T cellsCytotoxic CD8<sup>+</sup> T cell infiltrationIntratumoral CD8+ T cell infiltrationCD8+ T cell infiltrationCD8<sup>+</sup> T cell infiltrationMouse model of hepatocellular carcinomaEarly-stage hepatocellular carcinomaImage-guided tumor ablationUnpaired Student's <i>t</i> testModel of hepatocellular carcinomaFirst-line therapyMurine hepatocellular carcinomaT cell subsetsTumor-associated macrophagesMurine HCC modelLocal immune responseFemale BALB/c micePatient-Specific Heart Geometry Modeling for Solid Biomechanics Using Deep Learning
Pak D, Liu M, Kim T, Liang L, Caballero A, Onofrey J, Ahn S, Xu Y, McKay R, Sun W, Gleason R, Duncan J. Patient-Specific Heart Geometry Modeling for Solid Biomechanics Using Deep Learning. IEEE Transactions On Medical Imaging 2024, 43: 203-215. PMID: 37432807, PMCID: PMC10764002, DOI: 10.1109/tmi.2023.3294128.Peer-Reviewed Original ResearchConceptsFinite element analysisDeep learning methodsSpatial accuracyElement analysisDeep learningStress estimationLearning methodsSimulation accuracyDeployment simulationHigh spatial accuracyThin structuresMesh generationVolumetric meshingDeformation energyGeometry modelingVolumetric meshMesh qualityElement qualitySimultaneous optimizationMain noveltyBiomechanics studiesMeshModeling characteristicsAccuracyDownstream analysis
2023
Unsupervised Domain Adaptation by Cross-Prototype Contrastive Learning for Medical Image Segmentation
Cai Z, Xin J, Dong S, You C, Shi P, Zeng T, Zhang J, Onofrey J, Zheng N, Duncan J. Unsupervised Domain Adaptation by Cross-Prototype Contrastive Learning for Medical Image Segmentation. 2023, 00: 819-824. DOI: 10.1109/bibm58861.2023.10386055.Peer-Reviewed Original ResearchUnsupervised domain adaptationDistribution alignmentDomain adaptationContrastive learningUnsupervised domain adaptation methodsMedical image segmentation tasksDomain distribution alignmentGlobal distribution alignmentContrastive learning methodDomain adaptation performanceIntra-class distancePixel-level featuresImage segmentation tasksInter-class distancePublic cardiac datasetsCategory centroidDiscrimination of classesClass prototypesSegmentation taskSource domainTarget domainCardiac datasetsLearning methodsGlobal prototypesCentroid alignmentRethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective.
You C, Dai W, Min Y, Liu F, Clifton D, Zhou S, Staib L, Duncan J. Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective. Advances In Neural Information Processing Systems 2023, 36: 9984-10021. PMID: 38813114, PMCID: PMC11136570.Peer-Reviewed Original ResearchMedical image segmentationContrastive learningImage segmentationSemi-supervised medical image segmentationSemi-supervised contrastive learningSelf-supervised objectiveSemantic segmentation datasetsSemi-supervised methodGround-truth labelsQuality of visual representationSafety-critical tasksSegmentation datasetTail classesSegmentation taskLabel setsTruth labelsCL frameworkNegative examplesModel collapseVariance-reductionVariance-reduction techniquesVisual representationTaskLearningPairs of samples
2022
DuDoUFNet: Dual-Domain Under-to-Fully-Complete Progressive Restoration Network for Simultaneous Metal Artifact Reduction and Low-Dose CT Reconstruction
Zhou B, Chen X, Xie H, Zhou S, Duncan JS, Liu C. DuDoUFNet: Dual-Domain Under-to-Fully-Complete Progressive Restoration Network for Simultaneous Metal Artifact Reduction and Low-Dose CT Reconstruction. IEEE Transactions On Medical Imaging 2022, 41: 3587-3599. PMID: 35816532, PMCID: PMC9812027, DOI: 10.1109/tmi.2022.3189759.Peer-Reviewed Original ResearchFlow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging
Dong S, Hangel G, Chen E, Sun S, Bogner W, Widhalm G, You C, Onofrey J, de Graaf R, Duncan J. Flow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging. Lecture Notes In Computer Science 2022, 13609: 3-13. DOI: 10.1007/978-3-031-18576-2_1.Peer-Reviewed Original ResearchAdversarial networkVisual qualityDeep learning-based super-resolution methodsLearning-based super-resolution methodsFlow-based modelImage visual qualityGenerative adversarial networkHigh visual qualitySuper-resolution methodSuper-resolved imagesGenerative modelHigh-resolution imagesImage modalitiesFlow-based methodNetworkLow spatial resolutionUncertainty estimationImagesPromising resultsEnhancer networkAnatomical informationHigh fidelityEssential toolDatasetQuality adjustmentIncremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation
You C, Xiang J, Su K, Zhang X, Dong S, Onofrey J, Staib L, Duncan J. Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation. Lecture Notes In Computer Science 2022, 13573: 3-16. PMID: 37415747, PMCID: PMC10323962, DOI: 10.1007/978-3-031-18523-6_1.Peer-Reviewed Original ResearchIncremental learningMedical image segmentation tasksMulti-site datasetImage segmentation tasksMedical image segmentationProstate MRI SegmentationComputation resourcesMedical datasetsSegmentation taskImage segmentationSegmentation frameworkEmbedding featuresBenchmark datasetsMRI segmentationTraining dataTarget domainLearning approachPractical deploymentDomain-specific expertiseCompetitive performanceDatasetTraining schemePrior workSegmentationSingle modelMulti-scale Super-Resolution Magnetic Resonance Spectroscopic Imaging with Adjustable Sharpness
Dong S, Hangel G, Bogner W, Widhalm G, Rössler K, Trattnig S, You C, de Graaf R, Onofrey J, Duncan J. Multi-scale Super-Resolution Magnetic Resonance Spectroscopic Imaging with Adjustable Sharpness. Lecture Notes In Computer Science 2022, 13436: 410-420. DOI: 10.1007/978-3-031-16446-0_39.Peer-Reviewed Original ResearchMomentum Contrastive Voxel-Wise Representation Learning for Semi-supervised Volumetric Medical Image Segmentation
You C, Zhao R, Staib L, Duncan J. Momentum Contrastive Voxel-Wise Representation Learning for Semi-supervised Volumetric Medical Image Segmentation. Lecture Notes In Computer Science 2022, 13434: 639-652. PMID: 37465615, PMCID: PMC10352821, DOI: 10.1007/978-3-031-16440-8_61.Peer-Reviewed Original ResearchSimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation
You C, Zhou Y, Zhao R, Staib L, Duncan JS. SimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation. IEEE Transactions On Medical Imaging 2022, 41: 2228-2237. PMID: 35320095, PMCID: PMC10325835, DOI: 10.1109/tmi.2022.3161829.Peer-Reviewed Original ResearchConceptsMedical image segmentationImage segmentationSemi-supervised medical image segmentationRobust Medical Image SegmentationMedical image analysisUnsupervised training strategyAtrial Segmentation ChallengeLearning-based approachMedical image synthesisAverage Dice scoreSemi-supervised approachPair-wise similarityContrastive objectiveData augmentationSegmentation challengePopular datasetsDice scoreSemantic informationDistillation frameworkSegmentation accuracyDownstream tasksImage synthesisPrevious best resultSupervised counterpartMedical dataFederated Transfer Learning for Low-Dose PET Denoising: A Pilot Study With Simulated Heterogeneous Data
Zhou B, Miao T, Mirian N, Chen X, Xie H, Feng Z, Guo X, Li X, Zhou S, Duncan J, Liu C. Federated Transfer Learning for Low-Dose PET Denoising: A Pilot Study With Simulated Heterogeneous Data. IEEE Transactions On Radiation And Plasma Medical Sciences 2022, 7: 284-295. PMID: 37789946, PMCID: PMC10544830, DOI: 10.1109/trpms.2022.3194408.Peer-Reviewed Original ResearchLow-dose PETMedical data privacy regulationsFederated learning algorithmLarge domain shiftTransfer learning frameworkData privacy regulationsHigh-quality reconstructionFederated transferData privacyHeterogeneous dataDomain shiftLearning frameworkLearning algorithmPrivacy regulationsData distributionCollaborative trainingLow-dose dataPET reconstructionPrevious methodsFL methodEfficient wayLocal dataSuperior performanceExperimental resultsDenoisingDual-domain self-supervised learning for accelerated non-Cartesian MRI reconstruction
Zhou B, Schlemper J, Dey N, Mohseni Salehi SS, Sheth K, Liu C, Duncan JS, Sofka M. Dual-domain self-supervised learning for accelerated non-Cartesian MRI reconstruction. Medical Image Analysis 2022, 81: 102538. PMID: 35926336, DOI: 10.1016/j.media.2022.102538.Peer-Reviewed Original ResearchConceptsNon-Cartesian MRI reconstructionMRI reconstructionUndersampled dataPrevious baseline methodsSelf-supervised approachSelf-supervised learningHigh-quality reconstructionReconstruction networkAppearance consistencyDataset demonstrateBaseline methodsImage domainDisjoint partitionsSupervised trainingPractical adoptionReconstruction accuracyDomain partitionImproved image qualityImage qualityDDSSSampling patternK-spaceExperimental resultsNetworkMotion robustnessUsing Adversarial Images to Assess the Robustness of Deep Learning Models Trained on Diagnostic Images in Oncology
Joel MZ, Umrao S, Chang E, Choi R, Yang DX, Duncan JS, Omuro A, Herbst R, Krumholz HM, Aneja S. Using Adversarial Images to Assess the Robustness of Deep Learning Models Trained on Diagnostic Images in Oncology. JCO Clinical Cancer Informatics 2022, 6: e2100170. PMID: 35271304, PMCID: PMC8932490, DOI: 10.1200/cci.21.00170.Peer-Reviewed Original ResearchCineCT platform for in vivo and ex vivo measurement of 3D high resolution Lagrangian strains in the left ventricle following myocardial infarction and intramyocardial delivery of theranostic hydrogel
Midgett D, Thorn S, Ahn S, Uman S, Avendano R, Melvinsdottir I, Lysyy T, Kim J, Duncan J, Humphrey J, Papademetris X, Burdick J, Sinusas A. CineCT platform for in vivo and ex vivo measurement of 3D high resolution Lagrangian strains in the left ventricle following myocardial infarction and intramyocardial delivery of theranostic hydrogel. Journal Of Molecular And Cellular Cardiology 2022, 166: 74-90. PMID: 35227737, PMCID: PMC9035115, DOI: 10.1016/j.yjmcc.2022.02.004.Peer-Reviewed Original ResearchSimultaneous Segmentation and Motion Estimation of Left Ventricular Myocardium in 3D Echocardiography Using Multi-task Learning
Ta K, Ahn SS, Stendahl JC, Langdon J, Sinusas AJ, Duncan JS. Simultaneous Segmentation and Motion Estimation of Left Ventricular Myocardium in 3D Echocardiography Using Multi-task Learning. Lecture Notes In Computer Science 2022, 13131: 123-131. PMID: 35759335, PMCID: PMC9221412, DOI: 10.1007/978-3-030-93722-5_14.Peer-Reviewed Original ResearchMotion estimationMulti-task learning networkMedical image analysis literatureMulti-task learningSingle-task learningMotion estimation techniqueImage analysis literatureComputer visionDecoding branchesFeature encoderLearning frameworkLearning networkLatent featuresAccurate segmentationSimultaneous segmentationEstimate motionImage pairsTask learningRealistic motion patternsVolumetric segmentationSegmentationMotion patternsTaskUnique taskLearning
2021
Quantitative Automated Segmentation of Lipiodol Deposits on Cone-Beam CT Imaging Acquired during Transarterial Chemoembolization for Liver Tumors: A Deep Learning Approach
Malpani R, Petty CW, Yang J, Bhatt N, Zeevi T, Chockalingam V, Raju R, Petukhova-Greenstein A, Santana JG, Schlachter TR, Madoff DC, Chapiro J, Duncan J, Lin M. Quantitative Automated Segmentation of Lipiodol Deposits on Cone-Beam CT Imaging Acquired during Transarterial Chemoembolization for Liver Tumors: A Deep Learning Approach. Journal Of Vascular And Interventional Radiology 2021, 33: 324-332.e2. PMID: 34923098, PMCID: PMC8972393, DOI: 10.1016/j.jvir.2021.12.017.Peer-Reviewed Original Research