biomedical data science at vanderbilt...informatics big picture • department of biomedical...

BiomedicalDataScienceatVanderbilt

December13,2017

BradleyMalin,Ph.D.ViceChairforResearch,DepartmentofBiomedicalInformaticsProfessorofBiomedicalInformatics,Biostatistics,&ComputerScienceVanderbiltUniversity

InformaticsBigPicture

• DepartmentofBiomedicalInformaticssituatedintheSchoolofMedicine• Over40primaryfacultyand40secondaryfaculty• Approximately40trainees

• MS/PhD• MSACI• ClinicalInformaticsFellows• Undergraduateandhighschoolinterns

• NLMT15(withdatasciencesupplement)• NLMT32(bigdatascience)

2

T15PrincipleInvestigatorsBradleyMalin,Ph.D.

BiomedicalInformatics,Biostatistics&ComputerScience

CindyGadd,Ph.D.BiomedicalInformatics

GretchenPurcellJacks,M.D.,Ph.D.BiomedicalInformatics&Surgery

3

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

5

PrimaryBIDSFacultyAppointments

• Anesthesiology• Biochemistry• BiomedicalInformatics• Biostatistics• CancerBiology• Genetics• HealthPolicy• Medicine• MolecularPhysiology&Biophysics• Hematology/Oncology

• BiomedicalEngineering• ComputerEngineering• ComputerScience• ElectricalEngineering

• Biology• Chemistry

SchoolofMedicine SchoolofEngineering

SchoolofArts&Sciences

6

3FormalLevelsofEducation

• Ph.D.inBiomedicalInformatics:DataScienceTrack(DST)• 5yearcommitment

• Ph.D.inAnotherField: M.S.inDST• 2-3yearcommitment

• Ph.D.inAnotherField: Course&ResearchSponsorship• 1yearrenewable(butcompetitive)

7

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

8

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

9

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T15Supplement– DataPrivacyCourse(http://hiplab.mc.vanderbilt.edu/courses/BMIF380/)

15

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

16

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

17

T15Supplement:CaseStudiesasEducationalTools

• Introducethecomplexityandmultidisciplinarynatureofbiomedicalinformaticsprojects

• Presentemergingissuesanddevelopingmethodologiesinevolvingareasofthefield

• Provideopportunitiestoidentifysocialandethicalissuesabouthealthdataandtechnology

• Illustrategeneralizablelessons,whichcanbeappliedtootherproblemsinthefield

18

CaseStudiesasEducationalTools:CurriculumandEducationalGoals

• Formalizethestructureofbiomedicaldatasciencecasestudies

• Createaninitialseriesinavarietyofopensourceformats,includingprint,onlinetext,andvideolectures

• MakecasestudiesavailableforsharingacrossNLMtrainingprograms

19

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.

20

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

21

SupplementalTraining(Selected)

• Biomedicaldatasciencemeet-upsonceamonth• Presentationsbyfacultyandstudentsonfinishedandin-progressresearch

• Lessformalsettingtoencourageinteractivelearning

• PizzaandHighPerformanceComputing• http://www.accre.vanderbilt.edu/?page_id=3243• Monthlyseminaronarangeoftopics

• PythonandanalyticsonHPC• ParallelprocessinginR• BigdatatoolsandHadoop• RunningnextgensequencingonHPC

22

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)

23

Questions?b.malin@vanderbilt.edu

HealthDataScienceCenterhttps://medschool.vanderbilt.edu/heads/

HealthInformationPrivacyLaboratoryhttp://www.hiplab.org/

CenterforGeneticPrivacy&IdentityinCommunitySettingshttps://medschool.vanderbilt.edu/getprecise/