biomedical data science at vanderbilt...informatics big picture • department of biomedical...
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BiomedicalDataScienceatVanderbilt
December13,2017
BradleyMalin,Ph.D.ViceChairforResearch,DepartmentofBiomedicalInformaticsProfessorofBiomedicalInformatics,Biostatistics,&ComputerScienceVanderbiltUniversity
InformaticsBigPicture
• DepartmentofBiomedicalInformaticssituatedintheSchoolofMedicine• Over40primaryfacultyand40secondaryfaculty• Approximately40trainees
• MS/PhD• MSACI• ClinicalInformaticsFellows• Undergraduateandhighschoolinterns
• NLMT15(withdatasciencesupplement)• NLMT32(bigdatascience)
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T15PrincipleInvestigatorsBradleyMalin,Ph.D.
BiomedicalInformatics,Biostatistics&ComputerScience
CindyGadd,Ph.D.BiomedicalInformatics
GretchenPurcellJacks,M.D.,Ph.D.BiomedicalInformatics&Surgery
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Vanderbilt BIDS:Big Biomedical
Data Science Training Program
BradleyMalin,Ph.D.BiomedicalInformatics,
Biostatistics&ComputerScience
JeffreyBlume,Ph.D.Biostatistics
CindyGadd,Ph.D.BiomedicalInformatics
https://news.vanderbilt.edu/2016/04/21/new-doctoral-track-focuses-on-big-biomedical-data-science/
https://www.vumc.org/dbmi/vanderbilt-big-biomedical-data-science-bids-program
HealthDataScienceCenter
https://www.vumc.org/heads/
10labsinSchoolofMedicine,Engineering,andArts&Sciences
Providesguidanceandsupportfordatascienceactivitiesandinterests
EnablesahomeforT32students
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PrimaryBIDSFacultyAppointments
• Anesthesiology• Biochemistry• BiomedicalInformatics• Biostatistics• CancerBiology• Genetics• HealthPolicy• Medicine• MolecularPhysiology&Biophysics• Hematology/Oncology
• BiomedicalEngineering• ComputerEngineering• ComputerScience• ElectricalEngineering
• Biology• Chemistry
SchoolofMedicine SchoolofEngineering
SchoolofArts&Sciences
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3FormalLevelsofEducation
• Ph.D.inBiomedicalInformatics:DataScienceTrack(DST)• 5yearcommitment
• Ph.D.inAnotherField: M.S.inDST• 2-3yearcommitment
• Ph.D.inAnotherField: Course&ResearchSponsorship• 1yearrenewable(butcompetitive)
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2016– 2017
• Ph.D.inBiomedicalInformatics:DataScienceTrack(DST)
• Ph.D.inAnotherField: M.S.inDST
• Ph.D.inAnotherField: Course&ResearchSponsorship
MaryLaurenBenton
EvolutionaryGenomics
NickStrayer(Ph.D.StudentinBiostats)
VisualizationofBigStatistics
LucyD’Agustino(Ph.D.StudentinBiostats)
NewApproachestoSignificanceScoring
MichaelPritchard(Ph.D.StudentinCS)
AdversarialLearning for(Anti-)ViralSystems
RohitVenkat(Ph.D.StudentinMolecularPhysiology&Biophysics)
BigMathModelsofCellularSignaling
AndrewPlassard(Ph.D.StudentinCS)
BigBrainImageProcessing
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2017– 2018
• Ph.D.inBiomedicalInformatics:DataScienceTrack(DST)
• Ph.D.inAnotherField: M.S.inDST
• Ph.D.inAnotherField: Course&ResearchSponsorship
MaryLaurenBenton
EvolutionaryGenomics
NickStrayer(Ph.D.StudentinBiostats)
VisualizationofBigStatistics
MichaelPritchard(Ph.D.StudentinCS)
AdversarialLearning for(Anti-)ViralSystems
SarahMaddox(Ph.D.StudentinBiochemistry)
PhenotypicHeterogeneityinSmallCellLungCancer
GraysonRuhl
DataPrivacy
KimKondratieff
Phenomics
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T15Supplement– DataPrivacyCourse(http://hiplab.mc.vanderbilt.edu/courses/BMIF380/)
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DataPrivacyCourseExtensions:Personnel&Timeline
BradleyMalin,Ph.D.BiomedicalInformatics,
Biostatistics&ComputerScience
YouChen,Ph.D.BiomedicalInformatics
DanielFabbri,Ph.D.BiomedicalInformatics&
ComputerScience
ShuangWang,Ph.D.BiomedicalInformatics
XiaoqianJiang,Ph.D.BiomedicalInformatics
LucilaOhno-Machado,M.D.,Ph.D.BiomedicalInformatics&Medicine
Vand
erbilt
UCSD
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T15Supplement– DataPrivacy(http://hiplab.mc.vanderbilt.edu/courses/BMIF380/)
• Philosophy,Law,Policy,&Ethics
• AccessControlandAuditing
• NLPforde-identification
• Re-identificationmethods
• Formalanonymizationalgorithms
• Advancedanonymization(e.g.,differentialprivacy)
• Securemultipartycomputation
• Casestudiesinbiosurveillance,genomics,andmedicalrecordlinkage
CurrentCourse
• ElectronicConsent
• CasestudiesbasedontheiDASH PrivacyChallenge/Workshops(2015,2016,&2018)
• Securehardwareforbiomedicaldataanalytics
• Privacypreservingdistributeddataanalytics(e.g.,gridlogisticregression)
• Migrationtoanonlineenvironment
Extensions
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T15Supplement:CaseStudiesasEducationalTools
• Introducethecomplexityandmultidisciplinarynatureofbiomedicalinformaticsprojects
• Presentemergingissuesanddevelopingmethodologiesinevolvingareasofthefield
• Provideopportunitiestoidentifysocialandethicalissuesabouthealthdataandtechnology
• Illustrategeneralizablelessons,whichcanbeappliedtootherproblemsinthefield
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CaseStudiesasEducationalTools:CurriculumandEducationalGoals
• Formalizethestructureofbiomedicaldatasciencecasestudies
• Createaninitialseriesinavarietyofopensourceformats,includingprint,onlinetext,andvideolectures
• MakecasestudiesavailableforsharingacrossNLMtrainingprograms
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CaseStudiesasEducationalTools:ProposedCases
Case Study Faculty
Building the infrastructure to support the precision medicine initiativePaulHarris,Ph.D.
JoshuaDenny,M.D.,M.S.
Learning new computational phenotypes from population-scale clinical data ThomasLasko,M.D.,Ph.D.
Predicting suicide attempts in electronic health records ColinWalsh,M.D.,M.A.
Explanation-based electronic medical record auditing DanielFabbri,Ph.D.
Learning organizational structure and collaborative teams through electronicmedical record utilization
YouChen,Ph.D.
NancyLorenzi,Ph.D.
Big data and why privacy does not have to die BradMalin,Ph.D.
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CaseStudiesasEducationalTools:PersonnelandTimeline• CaseSeriesOrganizersandCourseDirectors:
• ProjectManager:CarolynDiehl• Timeline:
• CaseStructure– February2018• FirstCases– April2018• CourseOffering– Summer2018
GretchenPurcellJackson,M.D.,Ph.D.BiomedicalInformatics&Surgery
ColinWalsh,M.D.,M.A.BiomedicalInformatics&Medcine
YouChen,Ph.D.BiomedicalInformatics
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SupplementalTraining(Selected)
• Biomedicaldatasciencemeet-upsonceamonth• Presentationsbyfacultyandstudentsonfinishedandin-progressresearch
• Lessformalsettingtoencourageinteractivelearning
• PizzaandHighPerformanceComputing• http://www.accre.vanderbilt.edu/?page_id=3243• Monthlyseminaronarangeoftopics
• PythonandanalyticsonHPC• ParallelprocessinginR• BigdatatoolsandHadoop• RunningnextgensequencingonHPC
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DataScienceatVanderbilt
• Noofficialprogram
• Provostfundedatransinstitutional program(TIP)tobuildadatasciencecommunity• 5Post-docssponsoredat0.2FTE• Standaloneandjoint-sponsoredseminars• Thinktanks(wherespecificdatasetsarereviewed)• University-wideconference
• Provosthasconvenedtwocommitteestodevelopstrategicplanfor• University-wideinitiative(includesMalin)• M.S.programindatascience,withapplicationfocusareassuchasbiomedicine(includes
BlumeandMalin)
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HealthDataScienceCenterhttps://medschool.vanderbilt.edu/heads/
HealthInformationPrivacyLaboratoryhttp://www.hiplab.org/
CenterforGeneticPrivacy&IdentityinCommunitySettingshttps://medschool.vanderbilt.edu/getprecise/