2024
Regulating Explainability in Machine Learning Applications -- Observations from a Policy Design Experiment
Nahar N, Rowlett J, Bray M, Omar Z, Papademetris X, Menon A, Kästner C. Regulating Explainability in Machine Learning Applications -- Observations from a Policy Design Experiment. 2024, 2101-2112. DOI: 10.1145/3630106.3659028.Peer-Reviewed Original ResearchAI applicationsArtificial intelligenceEU General Data Protection RegulationGeneral Data Protection RegulationMachine learning applicationsData Protection RegulationHuman subject studiesAI-onlyLearning applicationsProtection RegulationExplainabilityExecution orderEU AI ActAI ActContinuous collaborationDesign processEvidence of compliancePrivacyApplicationsSecurityIntelligenceMachineIterationFairnessTeam of researchersMultimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization
Vafaii H, Mandino F, Desrosiers-Grégoire G, O’Connor D, Markicevic M, Shen X, Ge X, Herman P, Hyder F, Papademetris X, Chakravarty M, Crair M, Constable R, Lake E, Pessoa L. Multimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization. Nature Communications 2024, 15: 229. PMID: 38172111, PMCID: PMC10764905, DOI: 10.1038/s41467-023-44363-z.Peer-Reviewed Original Research
2023
Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity analyses
Jin D, Neelakantan U, Lacadie C, Chen T, Rooney B, Liu Y, Wu W, Wang Z, Papademetris X, Hoffman E. Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping: A pipeline for whole-brain structural and activity analyses. STAR Protocols 2023, 4: 102647. PMID: 37897734, PMCID: PMC10641303, DOI: 10.1016/j.xpro.2023.102647.Peer-Reviewed Original ResearchHigh-throughput functional analysis of autism genes in zebrafish identifies convergence in dopaminergic and neuroimmune pathways
Mendes H, Neelakantan U, Liu Y, Fitzpatrick S, Chen T, Wu W, Pruitt A, Jin D, Jamadagni P, Carlson M, Lacadie C, Enriquez K, Li N, Zhao D, Ijaz S, Sakai C, Szi C, Rooney B, Ghosh M, Nwabudike I, Gorodezky A, Chowdhury S, Zaheer M, McLaughlin S, Fernandez J, Wu J, Eilbott J, Vander Wyk B, Rihel J, Papademetris X, Wang Z, Hoffman E. High-throughput functional analysis of autism genes in zebrafish identifies convergence in dopaminergic and neuroimmune pathways. Cell Reports 2023, 42: 112243. PMID: 36933215, PMCID: PMC10277173, DOI: 10.1016/j.celrep.2023.112243.Peer-Reviewed Original ResearchConceptsGene lossFunctional analysisHigh-throughput functional analysisZebrafish mutantsGene discoverySelect mutantsASD genesAutism genesKey pathwaysASD biologyBrain size differencesMutantsGenesSize differencesPathwayGlobal increaseRelevant mechanismsBiologyCentral challengeNeuroimmune dysfunctionRegionFunctionDiscoveryAutism spectrum disorderClustering of KOR PET images separates people with AUD into distinct responses to naltrexone
Hoye J, Key J, de Laat B, Cosgrove K, Krishnan-Sarin S, Papademetris X, Morris E. Clustering of KOR PET images separates people with AUD into distinct responses to naltrexone. Brain Imaging And Behavior 2023, 17: 367-371. PMID: 36695971, DOI: 10.1007/s11682-023-00758-6.Peer-Reviewed Original Research
2022
HALO: A software tool for real‐time head alignment in the MR scanner
Zhao Z, Galiana G, Zillo C, Camarro T, Qiu M, Papademetris X, Hampson M. HALO: A software tool for real‐time head alignment in the MR scanner. Magnetic Resonance In Medicine 2022, 89: 1506-1513. PMID: 36426774, PMCID: PMC10753491, DOI: 10.1002/mrm.29535.Peer-Reviewed Original ResearchHigh-resolution cortical parcellation based on conserved brain landmarks for localization of multimodal data to the nearest centimeter
McGrath H, Zaveri H, Collins E, Jafar T, Chishti O, Obaid S, Ksendzovsky A, Wu K, Papademetris X, Spencer D. High-resolution cortical parcellation based on conserved brain landmarks for localization of multimodal data to the nearest centimeter. Scientific Reports 2022, 12: 18778. PMID: 36335146, PMCID: PMC9637135, DOI: 10.1038/s41598-022-21543-3.Peer-Reviewed Original ResearchConceptsEpilepsy surgery cohortStandardized brain regionsBrain structure-function relationshipsSurgery cohortClinical usefulnessBrain metricsAnatomical locationBrain regionsBrain localizationCortical parcellationOwn unique benefitsIntracranial electroencephalographyAnatomical designationBrain anatomyHuman brain anatomyHuman brainBrain atlasBrain landmarksBrain atlasesParcellationMagnetic resonanceNearest centimeterAnatomical featuresAnatomyCortical localizationFunctional network properties derived from wide-field calcium imaging differ with wakefulness and across cell type
O’Connor D, Mandino F, Shen X, Horien C, Ge X, Herman P, Hyder F, Crair M, Papademetris X, Lake E, Constable. Functional network properties derived from wide-field calcium imaging differ with wakefulness and across cell type. NeuroImage 2022, 264: 119735. PMID: 36347441, PMCID: PMC9808917, DOI: 10.1016/j.neuroimage.2022.119735.Peer-Reviewed Original ResearchIntroduction to Medical Software
Papademetris X, Quraishi A, Licholai G. Introduction to Medical Software. 2022 DOI: 10.1017/9781009091725.BooksMedical softwareJunior software engineersSoftware lifecycle processesReal-world case studySoftware engineeringSoftware processSoftware engineersSoftware designDigital health entrepreneursHardware devicesMachine learningData scienceComputer scienceLifecycle processManagement systemSoftwareOnline resourcesIndustry standardsEssential topicHealth entrepreneursRisk management systemElectrical engineeringSuccinct coverageCybersecurityEngineeringCineCT 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 Research
2021
Multiple-Shooting Adjoint Method for Whole-Brain Dynamic Causal Modeling
Zhuang J, Dvornek N, Tatikonda S, Papademetris X, Ventola P, Duncan J. Multiple-Shooting Adjoint Method for Whole-Brain Dynamic Causal Modeling. Lecture Notes In Computer Science 2021, 12729: 58-70. DOI: 10.1007/978-3-030-78191-0_5.Peer-Reviewed Original ResearchOrdinary differential equationsAdjoint methodNoisy observationsMultiple shooting methodNon-linear systemsLarge scale continuous systemsLarge-scale systemsParameter value estimationDifferential equationsAccurate gradient estimationExpectation-maximization algorithmNon-linear modelParameter estimationBayesian frameworkGradient estimationContinuous systemToy exampleLarge systemsReal fMRI dataEstimationValue estimationAlgorithmGood accuracyCausal modelingModel changes
2018
Deep-learned placental vessel segmentation for intraoperative video enhancement in fetoscopic surgery
Sadda P, Imamoglu M, Dombrowski M, Papademetris X, Bahtiyar MO, Onofrey J. Deep-learned placental vessel segmentation for intraoperative video enhancement in fetoscopic surgery. International Journal Of Computer Assisted Radiology And Surgery 2018, 14: 227-235. PMID: 30484115, PMCID: PMC6438174, DOI: 10.1007/s11548-018-1886-4.Peer-Reviewed Original ResearchDeep Learning Retinal Vessel Segmentation from a Single Annotated Example: An Application of Cyclic Generative Adversarial Neural Networks
Sadda P, Onofrey J, Papademetris X. Deep Learning Retinal Vessel Segmentation from a Single Annotated Example: An Application of Cyclic Generative Adversarial Neural Networks. Lecture Notes In Computer Science 2018, 11043: 82-91. DOI: 10.1007/978-3-030-01364-6_10.Peer-Reviewed Original ResearchGenerative adversarial neural networksAdversarial neural networkGround truth segmentationNeural networkTruth segmentationMedical image segmentation tasksImage segmentation tasksConvolutional neural networkDeep learning methodsRetinal vessel segmentationConvolutional networkSegmentation taskTraining examplesAnnotated examplesTraining dataLearning methodsVessel segmentationSegmentationSynthetic examplesNetworkLarge amountDatasetTaskExampleAccuracyBetter Feature Matching for Placental Panorama Construction
Sadda P, Onofrey J, Bahtiyar M, Papademetris X. Better Feature Matching for Placental Panorama Construction. Lecture Notes In Computer Science 2018, 11076: 128-137. DOI: 10.1007/978-3-030-00807-9_13.Peer-Reviewed Original ResearchOnly definitive treatmentPlacental vascular diseaseTwin transfusion syndromeSurgical cauterizationDefinitive treatmentTransfusion syndromeTwin pregnanciesPlacental vesselsVascular diseaseIntrauterine environmentPlacental surfaceSurgical proceduresActual surgical procedureVascular formationVisual distractorsEndoscopeVivo imagesPregnancySurgerySyndromeCauterizationPlacentaSegmenting the Brain Surface From CT Images With Artifacts Using Locally Oriented Appearance and Dictionary Learning
Onofrey JA, Staib LH, Papademetris X. Segmenting the Brain Surface From CT Images With Artifacts Using Locally Oriented Appearance and Dictionary Learning. IEEE Transactions On Medical Imaging 2018, 38: 596-607. PMID: 30176584, PMCID: PMC6476428, DOI: 10.1109/tmi.2018.2868045.Peer-Reviewed Original ResearchA Fetal FMRI Specific Motion Correction Algorithm Using 2ND Order Edge Features
Scheinost* D, Onofrey J, Kwon S, Cross S, Sze G, Ment L, Papademetris X. A Fetal FMRI Specific Motion Correction Algorithm Using 2ND Order Edge Features. 2018, 1288-1292. DOI: 10.1109/isbi.2018.8363807.Peer-Reviewed Original Research
2017
The Generalized Steiner Cable-Trench Problem with Application to Error Correction in Vascular Image Analysis
Landquist E, Vasko F, Kresge G, Tal A, Jiang Y, Papademetris X. The Generalized Steiner Cable-Trench Problem with Application to Error Correction in Vascular Image Analysis. Operations Research Proceedings 2017, 391-397. DOI: 10.1007/978-3-319-55702-1_52.Peer-Reviewed Original ResearchRADIOTRACER IMAGING ALLOWS FOR ASSESSMENT OF SERIAL CHANGES IN ANGIOSOME FOOT PERFUSION FOLLOWING REVASCULARIZATION AND PREDICTS LIMB SALVAGE OUTCOMES IN PATIENTS WITH CRITICAL LIMB ISCHEMIA
Buckley J, Mena-Hurtado C, Jeon S, Papademetris X, Blume P, Sumpio B, Sinusas A, Stacy M. RADIOTRACER IMAGING ALLOWS FOR ASSESSMENT OF SERIAL CHANGES IN ANGIOSOME FOOT PERFUSION FOLLOWING REVASCULARIZATION AND PREDICTS LIMB SALVAGE OUTCOMES IN PATIENTS WITH CRITICAL LIMB ISCHEMIA. Journal Of The American College Of Cardiology 2017, 69: 1393. DOI: 10.1016/s0735-1097(17)34782-4.Peer-Reviewed Original ResearchRADIOTRACER IMAGING OF ANGIOSOME FOOT PERFUSION CORRELATES WITH ANKLE-BRACHIAL INDEX AND DIFFERENTIATES CRITICAL LIMB ISCHEMIA PATIENTS FROM HEALTHY SUBJECTS
Buckley J, Papademetris X, Mena-Hurtado C, Blume P, Sumpio B, Sinusas A, Stacy M. RADIOTRACER IMAGING OF ANGIOSOME FOOT PERFUSION CORRELATES WITH ANKLE-BRACHIAL INDEX AND DIFFERENTIATES CRITICAL LIMB ISCHEMIA PATIENTS FROM HEALTHY SUBJECTS. Journal Of The American College Of Cardiology 2017, 69: 1518. DOI: 10.1016/s0735-1097(17)34907-0.Peer-Reviewed Original ResearchUsing connectome-based predictive modeling to predict individual behavior from brain connectivity
Shen X, Finn ES, Scheinost D, Rosenberg MD, Chun MM, Papademetris X, Constable RT. Using connectome-based predictive modeling to predict individual behavior from brain connectivity. Nature Protocols 2017, 12: 506-518. PMID: 28182017, PMCID: PMC5526681, DOI: 10.1038/nprot.2016.178.Peer-Reviewed Original Research