biomedical data science at vanderbilt...informatics big picture • department of biomedical...
TRANSCRIPT
![Page 1: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/1.jpg)
BiomedicalDataScienceatVanderbilt
December13,2017
BradleyMalin,Ph.D.ViceChairforResearch,DepartmentofBiomedicalInformaticsProfessorofBiomedicalInformatics,Biostatistics,&ComputerScienceVanderbiltUniversity
![Page 2: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/2.jpg)
InformaticsBigPicture
• DepartmentofBiomedicalInformaticssituatedintheSchoolofMedicine• Over40primaryfacultyand40secondaryfaculty• Approximately40trainees
• MS/PhD• MSACI• ClinicalInformaticsFellows• Undergraduateandhighschoolinterns
• NLMT15(withdatasciencesupplement)• NLMT32(bigdatascience)
2
![Page 3: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/3.jpg)
T15PrincipleInvestigatorsBradleyMalin,Ph.D.
BiomedicalInformatics,Biostatistics&ComputerScience
CindyGadd,Ph.D.BiomedicalInformatics
GretchenPurcellJacks,M.D.,Ph.D.BiomedicalInformatics&Surgery
3
![Page 4: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/4.jpg)
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
![Page 5: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/5.jpg)
HealthDataScienceCenter
https://www.vumc.org/heads/
10labsinSchoolofMedicine,Engineering,andArts&Sciences
Providesguidanceandsupportfordatascienceactivitiesandinterests
EnablesahomeforT32students
5
![Page 6: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/6.jpg)
PrimaryBIDSFacultyAppointments
• Anesthesiology• Biochemistry• BiomedicalInformatics• Biostatistics• CancerBiology• Genetics• HealthPolicy• Medicine• MolecularPhysiology&Biophysics• Hematology/Oncology
• BiomedicalEngineering• ComputerEngineering• ComputerScience• ElectricalEngineering
• Biology• Chemistry
SchoolofMedicine SchoolofEngineering
SchoolofArts&Sciences
6
![Page 7: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/7.jpg)
3FormalLevelsofEducation
• Ph.D.inBiomedicalInformatics:DataScienceTrack(DST)• 5yearcommitment
• Ph.D.inAnotherField: M.S.inDST• 2-3yearcommitment
• Ph.D.inAnotherField: Course&ResearchSponsorship• 1yearrenewable(butcompetitive)
7
![Page 8: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/8.jpg)
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
![Page 9: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/9.jpg)
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
![Page 10: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/10.jpg)
!2+-*?700"'7)7$
(,
![Page 11: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/11.jpg)
8+$G)*+"4%&J,'$/G41+"2
8(JK&LMNNO&J,1/$*7"1+$,&1$&8+$G)*+"4%&J,'$/G41+"2
8(JK&LMPNO&J,1/$*7"1+$,&1$&8+$+,'$/G41+"2
8(JK&LMPQO&()1#$*$%$.+"4%&K$7,*41+$,2&$'&8+$G)*+"4%&J,'$/G41+"2A$
/)A$
GD)
1),"
+)2
-%)"
1+R)2
;S&"$
7/2)
2?
8(JKTMLNO&A%+,+"4%&B)2)4/"#&+,'$/G41+"2
8(JKTMPPO&!521)G2&8+$%$.5
8(JKTMUNO&>414&</+R4"5&+,&8+$G)*+"+,)
8(JK&LMMVO&!"+),1+'+"&A$GG7,+"41+$,
W$7/,4%&A%7X ;K4%%?
B)2)4/"#&A$%%$Y7+7G&;!D/+,.?
8(JKTMSNO&A%+,+"4%&J,'$/G41+$,&!521)G2&3&>414X42)2
![Page 12: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/12.jpg)
(+A$GD71)/&!"+),")
A!&QUZVO&!D)"+4%&[$D+"2&\ 8+.&>414
A!&QVQNO&0%.$/+1#G2
A!&LMLVO&(4"#+,)&6)4/,+,.&
</)/)Y7+2+1)2&;,$1&'$/&./4*741)&"/)*+1?OA!&PPNPO&&</$./4GG+,.&4,*&</$X%)G&!$%R+,.&3&
VVNPO&</$./4G&>)2+.,&4,*&>414&!1/7"17/)2
A$/)
A$G
D)1)
,"+)
2-%
)"1+R
)2;S
&"$7/
2)2?
--A-&LMQUO&]74,1+141+R)&()*+"4%&JG4.)&0,4%52+2
A!&LMLNO&0*R4,")*&0/1+'+"+4%J,1)%%+.),")
A!&LMPNO&0*R4,")*&0%.$/+1#G2
A!&QVTSO&($*)%+,.&4,*&!+G7%41+$,
![Page 13: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/13.jpg)
()()1#$*2
8J^!&LMPPO&</+,"+D%)2&$'&($*)/,&8+$2141+21+"2
8J^!&LMPVO&($*)/,&B)./)22+$,&0,4%52+2
8J^!&TMMNO&B)./)22+$,&($*)%+,.&!1/41).+)2
8J^!&UMLLO&0*R4,")*&!141+21+"4%&A$GD71+,.
A$/)
A$G
D)1)
,"+)
2-%
)"1+R
)2;S
&"$7/
2)2?
8J^!&UMTVO&845)2+4,&()1#$*2
8J^!&TMLVO&!141+21+"4%&6)4/,+,.
8J^!&LMSPO&J,1/$*7"1+$,&1$&</$X4X+%+15&4,*&!141+21+"4%&[#)$/5
8J^!&LMSVO&A$,1)GD$/4/5&!141+21+"4%&J,')/),")
![Page 14: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/14.jpg)
8+$G)*+"4%&!"+),")
JH<&UNNPO&8+$/).7%41+$,&J&
JH<&UNNVO&8+$/).7%41+$,&JJ
9_B!&QMNMO&`7G4,&-FD)/+),")&$'&`)4%1#&3&J%%,)22&0"/$22&1#)&6+')2D4,&JJJ
9_B!&QPNMO&`7G4,&-FD)/+),")&$'&`)4%1#&3&J%%,)22&0"/$22&1#)&6+')2D4,&J
A$/)
A$G
D)1)
,"+)
2-%
)"1+R
)2;S
&"$7/
2)2?
8!AJ&MVTVO&H),$G)&!"+),")
A098&UMSNO&J,1/$*7"1+$,&1$&A4,")/&8+$%$.5
^B
`H-9&FFFFO&>414&J,1)./41+$,&+,&a^G+"2b
![Page 15: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/15.jpg)
T15Supplement– DataPrivacyCourse(http://hiplab.mc.vanderbilt.edu/courses/BMIF380/)
15
![Page 16: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/16.jpg)
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
![Page 17: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/17.jpg)
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
![Page 18: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/18.jpg)
T15Supplement:CaseStudiesasEducationalTools
• Introducethecomplexityandmultidisciplinarynatureofbiomedicalinformaticsprojects
• Presentemergingissuesanddevelopingmethodologiesinevolvingareasofthefield
• Provideopportunitiestoidentifysocialandethicalissuesabouthealthdataandtechnology
• Illustrategeneralizablelessons,whichcanbeappliedtootherproblemsinthefield
18
![Page 19: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/19.jpg)
CaseStudiesasEducationalTools:CurriculumandEducationalGoals
• Formalizethestructureofbiomedicaldatasciencecasestudies
• Createaninitialseriesinavarietyofopensourceformats,includingprint,onlinetext,andvideolectures
• MakecasestudiesavailableforsharingacrossNLMtrainingprograms
19
![Page 20: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/20.jpg)
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
![Page 21: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/21.jpg)
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
![Page 22: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/22.jpg)
SupplementalTraining(Selected)
• Biomedicaldatasciencemeet-upsonceamonth• Presentationsbyfacultyandstudentsonfinishedandin-progressresearch
• Lessformalsettingtoencourageinteractivelearning
• PizzaandHighPerformanceComputing• http://www.accre.vanderbilt.edu/?page_id=3243• Monthlyseminaronarangeoftopics
• PythonandanalyticsonHPC• ParallelprocessinginR• BigdatatoolsandHadoop• RunningnextgensequencingonHPC
22
![Page 23: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/23.jpg)
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
![Page 24: Biomedical Data Science at Vanderbilt...Informatics Big Picture • Department of Biomedical Informatics situated in the School of Medicine • Over 40 primary faculty and 40 secondary](https://reader034.vdocuments.us/reader034/viewer/2022043007/5f9542f997ee265b6f66601b/html5/thumbnails/24.jpg)
HealthDataScienceCenterhttps://medschool.vanderbilt.edu/heads/
HealthInformationPrivacyLaboratoryhttp://www.hiplab.org/
CenterforGeneticPrivacy&IdentityinCommunitySettingshttps://medschool.vanderbilt.edu/getprecise/