Health Informa · Health Informa.cs Lecture 1: Introduc.on Samantha Kleinberg [email protected]

HealthInforma.cs

Lecture1:Introduc.on

[email protected]

Aboutme:SamanthaKleinberg

•  PhDinCS•  Haveworkedinbiomathema.cs,bioinforma.cs/computa.onalbiology,biomedicalinforma.cs

•  Currentresearch– Timeseriesdata,causalinference– Simula.on– Mobilehealth

NICUdataset

•  98pa.entswithsubarachnoidhemorrhage

•  Monitoringincluded– DepthandsurfaceEEG– Microdialysis– Physiologicmeasurements

(nodataonprocedures)

Lotsofdata,butlotsofmissingdata

•  Devicemalfunc.ons•  Deviceconnectedtoperformaprocedure•  Differentmonitorsstartedatdifferent.mes•  Differentrecordingfrequencies

And…

•  Allvariablesmaybemissingatonce(ifmeasuredbysingledevice)– Can’tuseimputa.onmethodsthatassumesomepresentvalues

•  Missingvaluesdependonvariable+othervariables– e.g.BGdependsonitself,aswellasinsulin

•  Variablesarecorrelatedacross.me

Imputa.onw/laggedcorrela.ons

S.A.Rahman,Y.Huang,J.Claassen,N.Heintzman,andS.Kleinberg.CombiningFourierandLaggedk-NearestNeighborImputa.onforBiomedicalTimeSeriesData.JournalofBiomedicalInforma.cs(2015)hbps://github.com/kleinberg-lab/FLK-NN

Differentdata,differentphysiology

ClaassenJ,RahmanSA,HuangY,FreyH,SchmidtM,AlbersD,FaloCM,ParkS,AgarwalS,ConnollyES,KleinbergS(2016)Causalstructureofbrainphysiologyaderbraininjury.PLoSONE.

Regula.onchangesover.me

0-96hrs

96-168hrs

hbp://discoverysedge.mayo.edu/ar.ficial-pancreas/

Causesofchangesinglucose

Cohort:17subjectswithT1DMSensordata(collectedfor>72hours)

– Glucosevalues–  Insulindosage– Ac.vity– Sleepstage– Heartrate– Temperature

WithN.Heintzman(UCSD)http://dial.ucsd.edu/what-we-do.php

Results

veryvigorousexerciseleadstohyperglycemia(fdr<.01)in5-30minutes

– FoundusingbothHR(anaerobicac.vityzone)andMETs

•  Notfoundwithstrictdiscre.za.on•  Supportedbyliterature(MarlissandVranic,2002;RiddellandPerkins,2006)

S.KleinbergandN.Heintzman.Usinguncertaindatafrombody-wornsensorstogaininsightintotype1diabetes.JournalofBiomedicalInforma.cs,2016.

Whyareyouhere?

Whyhealthinforma.cs?

hbps://www.nih.gov/AllofUs-Research-Program

Whatcouldwedowiththis?

•  Who’stheuser?•  Whatproblemdotheyhave?•  HowcanCShelp?

Butwhatdoweneedtoknowfirst?

•  What’sthedataactually?Isitcorrect?•  CanwereallyapplyML/DMmethodstoit?Whatarethechallenges?

•  Canwesharedatafreely?Whynot?•  Howdowepreserveprivacy

(andmuchmore)

Syllabus

Syllabus(con.nued)

Finalprojects

Johnson,A.E.W.etal.MIMIC-III,afreelyaccessiblecri.calcaredatabase.Sci.Data3:160035doi:10.1038/sdata.2016.35(2016).

Administra.via

•  Coursewebsite:hbp://www.skleinberg.org/teaching/HI17/

•  Prerequisites:none•  Textbook:none,ar.cles•  Topics/readingsonsyllabusMAYCHANGE(willmakeannouncementinclass)

•  Workload/grading:midtermpresenta.on(25%),finalproject(50%),par.cipa.on(15%),homework(10%)

Keypolicies

1.  Nolatework.Therearefewdeadlines,butifthedeadline’s11:59pm,worksubmibedat12:01amisn’taccepted(Why?TrysubmiqnganNIHgrant2minuteslate!)

2.

Plagiarism = F

What’splagiarism?

Presen.ngsomeoneelse’sworkasyourown – Copyinganen.repaper– Copyingpartsofotherworks,withoutabribu.on

•  E.g.quoteswithoutcita.ons– Changingafewwords,butkeepingideasandstructure,withoutacknowledgingsource

Easytoavoid!Doyourownworkandacknowledgeallsources.Quotesmustbeinquotes.Don’tsubmitacollage.

1.Quotesbelonginquota.onmarks

•  WRONG!– Blahblah.Textfromotherpapers.BlahBlah.[Cita.on]

– Sec.on1[Cita.on].Quotestextquotes.

•  RightJ– Mytext“Quotefromawesomework.”[cita.on]mytext

3.Nocopying/closeparaphrasing

hbp://researchguides.stevens.edu/plagiarism

Ifyou’rehavingtrouble…

•  Cometoofficehours!Monday2-3inLieb306andbyappointment

•  Emailme

What’shealthinforma.cs?

Biology:

ComputerScience:Theoryandprac.ceof

compu.ngBioinforma.cs

Healthcare:

Informa7onscienceStoring,processing,etcinforma.on

Healthinforma.csBiomedicalinforma.cs

Biomedicalcompu.ng

Transla.onalbioinforma.cs

Anotherdefini.on•  Defini7on:Biomedicalinforma.cs(BMI)istheinterdisciplinaryfieldthatstudies

andpursuestheeffec.veusesofbiomedicaldata,informa.on,andknowledgeforscien.ficinquiry,problemsolving,anddecisionmaking,drivenbyeffortstoimprovehumanhealth.

•  Scopeandbreadthofdiscipline:BMIinves.gatesandsupportsreasoning,modeling,simula.on,experimenta.on,andtransla.onacrossthespectrumfrommoleculestoindividualsandtopopula.ons,frombiologicaltosocialsystems,bridgingbasicandclinicalresearchandprac.ceandthehealthcareenterprise.

•  Theoryandmethodology:BMIdevelops,studies,andappliestheories,methods,andprocessesforthegenera.on,storage,retrieval,use,management,andsharingofbiomedicaldata,informa.on,andknowledge.

•  Technologicalapproach:BMIbuildsonandcontributestocomputer,telecommunica.on,andinforma.onsciencesandtechnologies,emphasizingtheirapplica.oninbiomedicine.

•  Humanandsocialcontext:BMI,recognizingthatpeoplearetheul.mateusersofbiomedicalinforma.on,drawsuponthesocialandbehavioralsciencestoinformthedesignandevalua.onoftechnicalsolu.ons,policies,andtheevolu.onofeconomic,ethical,social,educa.onal,andorganiza.onalsystems.

Kulikowski,C.A.,Shortliffe,E.H.,Currie,L.M.,Elkin,P.L.,Hunter,L.E.,Johnson,T.R.,Kalet,I.J.,Lenert,L.A.,Musen,M.A.,Ozbolt,J.G.,Smith,J.W.,Tarczy-Hornoch,P.Z.&Williamson,J.J.,2012,AMIABoardwhitepaper:defini.onofbiomedicalinforma.csandspecifica.onofcorecompetenciesforgraduateeduca.oninthediscipline,JournaloftheAmericanMedicalInforma7csAssocia7on,pp.amiajnl-2012-001053

Biomedical informatics and its areas of application and practice, spanning the range from molecules to populations and society (adapted from Shortliffe and Blois3).

Kulikowski C A et al. J Am Med Inform Assoc doi:10.1136/amiajnl-2012-001053

Copyright © by the American Medical Informatics Association. All rights reserved.

Mainsubfields

•  (Transla.onal)Bioinforma.cs•  Publichealthinforma.cs•  Healthcare/Clinicalinforma.cs•  Consumer/mHealth

Example:Transla.onalbioinforma.cs

Tatoneq,N.P.,Denny,J.C.,Murphy,S.N.,Fernald,G.H.,Krishnan,G.,Castro,V.,Yue,P.,Tsau,P.S.,Kohane,I.,Roden,D.M.&Altman,R.,2011,Detec.ngdruginterac.onsfromadverse-eventreports:interac.onbetweenparoxe.neandpravasta.nincreasesbloodglucoselevels,ClinicalPharmacology&Therapeu7cs,90(1),pp.133-42

Example:Predic.ngcancerstagefromonlinehealthforumtext

MukundJhaandNoemieElhadad.Cancerstagepredic.onbasedonpa.entonlinediscourse.InProceedingsofthe2010WorkshoponBiomedicalNaturalLanguageProcessing,pages64–71,Uppsala,Sweden,July2010

Example:Clinicalinforma.cs

Consumerinforma.cs

AMIAThemes•  BiomedicalDataVisualiza7on•  ClinicalInforma7cs:findingsrelatedtothedesign,

development,andimplementa.onofstate-of-the-artclinicalsystems

•  ClinicalResearchInforma7cs:addressingthecri.calneedforeffec.veinforma.onmanagementtoaddressthemanychallengesfacingclinicalresearch

•  ClinicalWorkflowandHumanFactors:humanfactorsaspectsofclinicalinforma.onsystemimplementa.onandusethatrevolvesaroundusability,workflow,andpa.entsafety

•  ConsumerInforma7csandPHRs:PersonalHealthRecords(PHRs)andtheconsumerperspec.veintheuseofhealthinforma.onsciencedesignedtoimprovepa.entengagement,medicaloutcomes,andthehealthcaredecision-makingprocess

•  MobileHealth:mHealth,Web2.0,socialmedia,telehealth/telemedicine,andrelatedtopics

•  DataInteroperabilityandInforma7onExchange:methodsthatorganiza.onshaveundertakentodevelopandimplementvariousclinicaldataintegra.onandexchangeac.vi.es

•  DataMining,NLP,Informa7onExtrac7onRetrieval:applica.onofdatamining,naturallanguageprocessing,informa.onextrac.onretrievaltoallareasofbiomedicine

•  AchievingMeaningfulUse:waystopromotethesuccessfulandeffec.vedevelopment,implementa.on,andevalua.onofElectronicHealthRecordsasthena.onworkstoward"meaningfuluse"ofthesesystems

•  GlobaleHealth:GlobaleHealthchallenges

•  Informa7csEduca7onandWorkforceDevelopment:efforttocreateatrainedHITworkforce

•  Informa7csinHealthProfessionalEduca7on:applica.onofinforma.ontechnologyinhealthprofessionaleduca.on

•  Interac7veSystems:human-computerinterac.on(HCI)research,compellingdesigns,orinnova.veinterac.vetechnologies

•  PolicyandEthicalIssues:unprecedentedna.onalHITac.vityandethicalconsidera.onsposedasmoreprac..onersandthepublicinterfacewiththesetechnologies.

•  PublicHealthInforma7csandBiosurveillance:diseasedetec.on,communica.ons,workforcedevelopment,standardsandinteroperability,andbestprac.cestocombinethedomainsofhealthinforma.onscienceandtechnologywiththeprac.ceandscienceofpublichealth

•  ImagingInforma7cs:intersec.onofimagingscience,biomedicalengineeringandbiomedicalinforma.cs,

•  Simula7onandModeling:useofvariouscomputer-basedsimula.onandmodelingmethodologiesandtoolsastheycanbeappliedwithinthefieldofbiomedicalinforma.cs

•  TerminologyandStandardsOntologies:complexissuessurroundingstandardsyntax,seman.cs,andpragma.csofdesign,developmentanduseofvariousapplica.on-specificandgeneralpurposeclinicalterminologiesandontologies

•  Transla7onalBioinforma7csandBiomedicine:opportuni.esinbiomedicalinforma.csthatarisefromthestorage,retrieval,analysis,anddissemina.onofmolecularandgenomicinforma.oninaclinicalseqngcontext

hbp://www.amia.org/amia2013/themes

Stead,W.W.&Lorenzi,N.M.,1999,HealthInforma.csLinkingInvestmenttoValue,JournaloftheAmericanMedicalInforma7csAssocia7on,6(5),pp.341-8.

Goals

Stead,W.W.&Lorenzi,N.M.,1999,HealthInforma.csLinkingInvestmenttoValue,JournaloftheAmericanMedicalInforma7csAssocia7on,6(5),pp.341-8.

An Envisioned Cycle That Ties Patient Care with Knowledge Creation and Dissemination

Providers Caring for Patients

Electronic Health

Records Regional

and National Public

Health and Disease

Registries

Biomedical and

Clinical Research

Information, Decision-Support, and Order-Entry

Systems

Creation of Protocols, Guidelines,

and Educational

Materials

Standards for

Prevention and

Treatment

A �Learning Healthcare System�

SlidebyAMIA

HealthIT

Shortliffe,E.H.&Cimino,J.J.,2013,BiomedicalInforma7cs:ComputerApplica7onsinHealthCareandBiomedicine,SpringerVerla

BMI and HIT

Biomedical InformaticsTraining, Research and

Development•  Academia•  Research Institutes•  Corporate Research Labs

Clinical Systems Companies

Academic Medical Centers

Hospitals, HealthSystems, Practices,Healthcare Industry

Biomedical ResearchCommunity

PEOPLEIDEASSOFTWAREMETHODS

SlidebyAMIA

Personalizedmedicine

Useindividuallevelcharacteris.csandinforma.ontotailortreatment

– Choosingbetweentreatmentsvs.crea.ngindividualtreatment

Personalizedmedicine+informa.cs

•  Using-omicsinclinicalcare•  Decisionsupport•  Findsimilarpa.ents–treatments,outcomes

•  t

Chronicdisease

•  Diabetes•  Obesity•  Asthma•  Epilepsy…

Par.cipatorymedicine

•  Pa.entcentered

hbp://mobilizelabs.org/why-mhealth

Estrin,D.&Sim,I.,2010,OpenmHealtharchitecture:anengineforhealthcareinnova.on,Science(Washington),330(6005),pp.759-60

Challenges/openproblems

•  Data•  Replica.on/valida.on•  Privacy/sharing•  Transla.on

Fornextweek

•  BesuretoreadWicksetal.paperinsyllabus!