Computational Epidemiology

209 Pages·2014·24 MB·English

Computational Epidemiology
Madhav V. Marathe, Naren Ramakrishnan and Anil Kumar Vullikanti
Virginia Tech
Virginia Bioinformatics Institute, Technical Report 14-087, 2014.
Latest full version:
ndssl.vbi.vt.edu/supplementary-info/vskumar/kdd-slides.pdf
August 28, 2014
These slides were presented as a part of the tutorial titled Computational
Epidemiology at KDD 2014, held in New York City, August 24-27, 2014;
http://www.kdd.org/kdd2014/tutorials.html.
We hope to update the slides and supplementary material continually over the
next year.
The current version of the slides can be found at:
ndssl.vbi.vt.edu/supplementary-info/vskumar/kdd-slides.pdf
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Outline
1 Goals, History, Basic Concepts
2 Dynamics and Analysis
3 Inference problems
4 Control and optimization
5 Surveillance and Forecasting
6 Putting it all together: theory to practice
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Goals
Overview and state of the art – emphasis on computing and data
science
Describe open problems and future directions – aim to attract
computing and data scientists to work in this exciting area
Unified framework based on graphical dynamical systems and
associated proof theoretic techniques; e.g. spectral graph theory,
branching processes, mathematical programming, and Bayesian inference.
Computational epidemiology as a multi-disciplinary science
Public health epidemiology as an exemplar of data/computational
science for social good
Does not aim to be extensive; references provided for further exploration.
Important topics not covered
Game theoretic formulations, behavioral modeling, economic impact
Validation, verification and uncertainty quantification (UQ)
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Epidemics and epidemiology in history
Good news: Pandemic of HISTORY OF INFECTIOUS DISEASES
1918 lethality is currently
500-1300 1300-1700 1700-1900 1900-2000 2000-Present
unlikely Governments better
prepared and coordinated :
e.g. SARS epidemic But ..
Planning & response to even
THE MIDDLE AGESTHE RENAISSANCEINDUSTRIAL AGE 20TH CENTURY 21ST CENTURY
a moderate outbreak is
Nearly two-thirds of Rebirth of thinking Industrialization led Discovery of Penicillin.Human Genome
challenging: inadequate the European led to critical to over crowding, Social reform shaped Project completed.
population were observations of poor sanitation and health and human New and
vaccines/anti-virals, affected by the disease outbreaks. subsequent services. emerging diseases:
unknown efficacy, hard plague. Data was studied for epidemics. Increased vaccination SCAhRikSu, nHgu1nNy1a,.
Public health the purpose of Policy makers began aided against Tracking diseases
logistics issues initiatives were understanding health addressing health childhood diseases. through social
developed to stop status. problems and media.
Modern trends complicate the spread of the sanitation.
disease.
planning: increased travel,
immuno-compromised
populations, increased 1918 Pandemic: 50 million deaths in 2 years
urbanization (3-6% world pop) Every country and community
was effected
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What is epidemiology?
Greek words epi = on or upon; demos = people & logos = the study
of.1
Epidemiology: study of the distribution and determinants of
health-related states or events in specified populations, and the
application of this study to the control of health problems.
Now applies to non-communicable diseases as well as social and
behavioral outcomes.
Distribution: concerned about population level effects
Determinants: causes and factors influencing health related events
Application: deals with public health action to reduce the incidence of
disease.
Computational/mathematical epidemiology: deals with the development
of computational/mathematical methods, tools and techniques to
support epidemiology.
1Last JM, ed. Dictionary of Epidemiology.
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Precursors to modern computational
epidemiology
BEGINNINGS OF FORMAL EPIDEMIC MODELING
1796 1854 1897 1946 1981
SMALLPOX // Virus CHOLERA // Bacteria MALARIA // Parasite TUBERCULOSIS // Bacteria HIV // Virus
Edward Jenner’s John Snow was the first to Ronald Ross and George Albert Schatz discovered Luc Montagnier discovered
research led to the link the London cholera Macdonald developed a the antibiotic streptomycin HIV and Robert Gallo
dvaecvceilnoepsm.ent of ewpaitdeerm siocu troc ea. particular mmaotshqeumitoat-ibcoalr nmeo pdaetlh oofg en uSenldmearn t hWe adkirsemcatino.n of dinefetecrtmioiunse adg HenIVt ries stphoen sible
Daniel Bernoulli Disease status today: transmission. Streptomycin was the for AIDS.
mathematical models endemic; occuring in Anderson McKendrick first antibiotic that could The use of social network
demonstrated the benefits poverty-stricken countries. studied with Ross on anti- be used to cure TB. models have been initiated
omfa itnhoecmualatticioanl pfreorsmp eac tive. mpioalnaeriearl inogp emraatniyo ndsis, coveries rDeissiesatasnet s TtaBt usstr taoindsa yp:e drrsuisgt wthieth v itrhues .goal of controlling
Disease status today: eradicated. in stochastic processes. since the 1980s. Disease status
Disease status today: today: no cure.
controlled in US; still
prevalent in Africa, India.
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Modeling before an Modeling during an
EDITORIAL
Epidemic Science in Real Time epidemic epidemic
CREDITS: (LEFT) ED LAUSCH; (RIGHT) JUPITERIMAGES HpoMaGPSapMBscnofrrolaae oseohpdMsrdrosfbotvu yeiicoaeaoedc lsiEnsdalyaalses l,ti loHtoino Vci ezMoSrfitce.a n ncpiPaaAoFbahe rtuli.faett o.on eHbhtttfoeh hle atcilab hesc,lrWn ies v enHIodra inigHlre rcss d aaaootiisllrnftt vuh aitsredFecfmaftsnbitiiwsfrtvbpbcmvomptadaetdaidoaoami*hmnniomronCrleecevvxEcos pgofoeieirilirfucmuidoo.wers ftles a aeeir iere ubWao tmmicetucttlyipmp,aatveeFuemeieeey dn,hrnaehaan IISAStietiiniuluowr pa tngc rllailaalennnnaddany naemkkiaetket teeudpeaeScoct nupmalctscto ars rsrbtt wm tet n itt ,rneirrmisnbIiivnee tcea necetdb fyse oi i ccuo sTaeoaoseroep(htht r cmauloa.ccihletosiid s ikioatea nUh onw sebnnsasyeclnrf fzdoeeltnocsectweite wF uin sipa t ooseaicfhftnaelon agA a wt.tate mealcre whu wthapcoen p tdiiie fyrasinft ,iegaydentTteTn r waio circs e saer aan orialot ainak sndIc r.mi touoaiew c. psodarbs t plratn O hlmodce,osntrc nsgneftahesli it Ivoneenlnyaeuion Dno iSi e., eotrset mi nfeNs encycoisn eaaar.s taierdn,c hcatbeeispa t dnt s cfriw oknnh o eh n n lipniI letrprohrSearsnadbaqe.efaeuaynatiuax a, tf-ie smeasvkfaaesarnh mca r npt fe Telrnlntb l cu nbsdtlo, iM ,oisletna t e sbtiedlecd aciochr aren nvaeeqeicdatulae ssNhiop.e efypgde aasglsrlicnv ioamzteOaevfo cfetot ,itu s ee ntne mrrt inainr1fj r songemiostedteeimndriiamt tmaotaead nauiRe aogahteo1tnt vidueip ihrwrt g r cn i.ub teaeninsenoteatissmoy E ro tunr ne dpsoifroeoncaMwbaetalnttthd.ntetno/ emdrilnsr ot ohn rnh. n l hhJ rdrls ls nwrriDuaftso qneb s ,aeBpasusett ii:ikmobygaeee wT?edt ta yepi aeiic tc cssucmdtyeunftRr aoWdtpva,imce g ryt ra yonee elise1u2i il aeliwTeecrv i sedcAnnlaiee irreemvluale vptrnlp d0 mnet i9bstr ue sro eanuyhmtcns ht Mpdnarhi(icnppyu e0 aaer cia har ePyl1onr eitSSgejeorc aodstatyoci o9ritetteau lrndhloteuuAr,dfeepireda8bnocoisx ee enteanACt nee r recd omlbbefacda (auT an mi it co vea–sia n ds,uptnb1a eapd nktin uteblnIo lntnst IsefitRrdt ditmisclsneC0hi1edssraao luEaoesaamutlmiliasiu hnetitfamcd eeae h. rreu nsoyntnAsh ceS9dfrknrgtm fw1ugc sNhri dliieiH vd reb,af.c wet gy.nyhi soL ecse1t1weidiie) rtavndes asadaesfacayd tlihcn R ib Lu e2 e-. mCs1lnot9 ee isevaei icmyut lnsrie n.mcpoYiimbo,joet6 onrieasgAr riNslmen ne r eucreippertEgncfyduIanaeoeg/rsoopol)rn rtgrio Iastsraet alsna2 treliil a .enm tnLni A1suaiesnicdu uioftoehaanedstss ttvtt irsckc 0itLcwenatoitdAteepDhf essoh eacs otl ctrps fhee eweoi sUve,pe,lsfi0e hdc dnrArrc,p seirteio nceie ,hunum V bpnuna . negraid eaintcnc p2pdiSeaehi eSma to rn r as iwetaelteeen Intncn rnOhreheUtuqTsf –eeo(osyuusaai bi on.lnarpeianccoociHognt dR1hmitdaoe . sepvcu2glste swmmesilficsrp anuapLcatp1iiretlr. aAoT1e c sns ie e 0phiiee1cop s; oukiirsdmeis7r rviestlrviotmoPTma at9 sn–dc3n0oqrnyhtetooe aNsb rnbgo6ov esnlo iEaen lnec,idna 7e clla a 3rcu n2u -p0 els leissloemlfihHyonte i ladi1et ayneeimc-nieay6 ct6Tihocne ,; edsrei 4onhrsmwcad simwn aiil sa asm Hdi2t., oi, etantef noti nipivwfSaeiia h aph l ewhw olrn )sIstnneo enn f fhH odpE t nwv .da etupekvUmifahnteiaa hseroi eopmtefsttda gemanetnhalr k eaneoercrasecselh lo1cScter,2eaerltaoynolnl fsetumlgfh l asqyseyism eir rieAoedpscsiNsmdeboe t o2feuemmascn itcossetvknote r u tutr ooaudL,:tis Vhaexuiu nlre idec- s agn c 1o ee?ggiredaspI cwrseM irrnepm ilpse.hernan n iacEneeiaolzdnp ind ed fhne.atsxhfer eanntaaea OFsmi*otegaeNtie laidneuisica ta gta eantAnotnnp ztanksdl Stelnni inwa.aom ,a)eppi etidsstClherrcnn o fta pt uets Yd, ecegliu s tw nt Frietruiioidalne aoth Eoeeow ettoreanilne tflm fnosfeueo aasatiitroanoe ddte ad ptuvgidt2obniifid wimosh fmeswcmelehOr ea elelx,cdortst n pitele t r g ie 0lot dnmeeahnivc nydrbasedadti titnsip F oneai nroeqiemrebloi nteroubn0s, eazrlpimkeitr,cb r iveotogmeh . rxa clnnuam e i xaieS n eee asi nim9i woee adarnurerlEbpr f rghntvta nwgreae Ceass m iaenieedd d aisnnil i ernpoartmnt e aoesesk rivts m Iaeeoaln,ssowyoe kthp ieicengmdEol iitar udonkbif h,etf ldspeilav pwacidv n tr paeeeumN idhe -f-r--tsrtvsyiocn,txethureaonloalaeoe - lielbshcc e eeseCaM n elmicdeiaatangtdtn. tw llea gep n ianaisarEhtsa,sbtintews t ntamnl ci heotacechl d t hhipb,ew eeloiader Tr1gaim avmtc celffoeef eaoersu ,teryOnyer0 go rt o eiou r eveeprrnt ltt..r oeneimfsio ,eo1eu r aoErhslrroplasl io i xpxPa dedl1air aaam r tftco laet aadpmoarmeiibnOp2lia uineotrt ov f ndtkaskze,nh e6r flslorseUrnhdr Ldhyteuiao na a / lewliisdwaayirirsmtnIfoyg entaalk ybtnjncmtanChetvt,no ysbbegaaim pio esu hgekseecg iYi eunceldj eci nrrenrvpptln.ne dbuot bs ltv eae eyee ttoccnTodhWgi eaoamtr smeidhneeandni adnl Hihfneipint.rf tr.neavnngekc b Wnn1it fia.lnuqatgiiAspdoasS csiu eo 1gemsstItsilgnageumrc Nsroiehn ,in7yn,.ft ser.pca vv gl nnonheai6mt eiragiBuas ns orpaethttteian2sAeteut. nnno hehhceac eunnntiuiir9staid lNtItnddhnoddndneeeeceeass7-----tttt,, 987 on October 7, 2009 www.sciencemag.orgDownloaded from ((rcsueiniosz)qeoneunDtoiao)refimfentpdsemeh,trdomea(icncriiimkant),pleafi(iclenteieaiht,iusee)(itrbiivovciepla)inttlysitbmieoooasnnftlsce (prtaaerinsae)asrtnelaiQ-gdsmtsesuimin,enati(ngeceitireiiissmf)ph,yiiipm(dfntiaeigec)maattnsIirnoudoatlfrnoe(insgirvmpgic)riaestlsiinogn
a pandemic begins interventions.
Epidemic science in real-time
Editorial, Fineberg and Harvey, Science, May 2009: Epidemics Science in
Real-Time
Five areas: (i) Pandemic risk, (ii) vulnerable populations, (iii) available
interventions, (iv) implementation possibilities & (v) pitfalls, and public
understanding.
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Epidemic science in real-time
Editorial, Fineberg and Harvey, Science, May 2009: Epidemics Science in
Real-Time
Five areas: (i) Pandemic risk, (ii) vulnerable populations, (iii) available
interventions, (iv) implementation possibilities & (v) pitfalls, and public
understanding.
Modeling before an Modeling during an
EDITORIAL
Epidemic Science in Real Time epidemic epidemic
CREDITS: (LEFT) ED LAUSCH; (RIGHT) JUPITERIMAGES HpoMaGPSapMBscnofrrolaae oseohpdMsrdrosfbotvu yeiicoaeaoedc lsiEnsdalyaalses l,ti loHtoino Vci ezMoSrfitce.a n ncpiPaaAoFbahe rtuli.faett o.on eHbhtttfoeh hle atcilab hesc,lrWn ies v enHIodra inigHlre rcss d aaaootiisllrnftt vuh aitsredFecfmaftsnbitiiwsfrtvbpbcmvomptadaetdaidoaoami*hmnniomronCrleecevvxEcos pgofoeieirilirfucmuidoo.wers ftles a aeeir iere ubWao tmmicetucttlyipmp,aatveeFuemeieeey dn,hrnaehaan IISAStietiiniuluowr pa tngc rllailaalennnnaddany naemkkiaetket teeudpeaeScoct nupmalctscto ars rsrbtt wm tet n itt ,rneirrmisnbIiivnee tcea necetdb fyse oi i ccuo sTaeoaoseroep(htht r cmauloa.ccihletosiid s ikioatea nUh onw sebnnsasyeclnrf fzdoeeltnocsectweite wF uin sipa t ooseaicfhftnaelon agA a wt.tate mealcre whu wthapcoen p tdiiie fyrasinft ,iegaydentTteTn r waio circs e saer aan orialot ainak sndIc r.mi touoaiew c. psodarbs t plratn O hlmodce,osntrc nsgneftahesli it Ivoneenlnyaeuion Dno iSi e., eotrset mi nfeNs encycoisn eaaar.s taierdn,c hcatbeeispa t dnt s cfriw oknnh o eh n n lipniI letrprohrSearsnadbaqe.efaeuaynatiuax a, tf-ie smeasvkfaaesarnh mca r npt fe Telrnlntb l cu nbsdtlo, iM ,oisletna t e sbtiedlecd aciochr aren nvaeeqeicdatulae ssNhiop.e efypgde aasglsrlicnv ioamzteOaevfo cfetot ,itu s ee ntne mrrt inainr1fj r songemiostedteeimndriiamt tmaotaead nauiRe aogahteo1tnt vidueip ihrwrt g r cn i.ub teaeninsenoteatissmoy E ro tunr ne dpsoifroeoncaMwbaetalnttthd.ntetno/ emdrilnsr ot ohn rnh. n l hhJ rdrls ls nwrriDuaftso qneb s ,aeBpasusett ii:ikmobygaeee wT?edt ta yepi aeiic tc cssucmdtyeunftRr aoWdtpva,imce g ryt ra yonee elise1u2i il aeliwTeecrv i sedcAnnlaiee irreemvluale vptrnlp d0 mnet i9bstr ue sro eanuyhmtcns ht Mpdnarhi(icnppyu e0 aaer cia har ePyl1onr eitSSgejeorc aodstatyoci o9ritetteau lrndhloteuuAr,dfeepireda8bnocoisx ee enteanACt nee r recd omlbbefacda (auT an mi it co vea–sia n ds,uptnb1a eapd nktin uteblnIo lntnst IsefitRrdt ditmisclsneC0hi1edssraao luEaoesaamutlmiliasiu hnetitfamcd eeae h. rreu nsoyntnAsh ceS9dfrknrgtm fw1ugc sNhri dliieiH vd reb,af.c wet gy.nyhi soL ecse1t1weidiie) rtavndes asadaesfacayd tlihcn R ib Lu e2 e-. mCs1lnot9 ee isevaei icmyut lnsrie n.mcpoYiimbo,joet6 onrieasgAr riNslmen ne r eucreippertEgncfyduIanaeoeg/rsoopol)rn rtgrio Iastsraet alsna2 treliil a .enm tnLni A1suaiesnicdu uioftoehaanedstss ttvtt irsckc 0itLcwenatoitdAteepDhf essoh eacs otl ctrps fhee eweoi sUve,pe,lsfi0e hdc dnrArrc,p seirteio nceie ,hunum V bpnuna . negraid eaintcnc p2pdiSeaehi eSma to rn r as iwetaelteeen Intncn rnOhreheUtuqTsf –eeo(osyuusaai bi on.lnarpeianccoociHognt dR1hmitdaoe . sepvcu2glste swmmesilficsrp anuapLcatp1iiretlr. aAoT1e c sns ie e 0phiiee1cop s; oukiirsdmeis7r rviestlrviotmoPTma at9 sn–dc3n0oqrnyhtetooe aNsb rnbgo6ov esnlo iEaen lnec,idna 7e clla a 3rcu n2u -p0 els leissloemlfihHyonte i ladi1et ayneeimc-nieay6 ct6Tihocne ,; edsrei 4onhrsmwcad simwn aiil sa asm Hdi2t., oi, etantef noti nipivwfSaeiia h aph l ewhw olrn )sIstnneo enn f fhH odpE t nwv .da etupekvUmifahnteiaa hseroi eopmtefsttda gemanetnhalr k eaneoercrasecselh lo1cScter,2eaerltaoynolnl fsetumlgfh l asqyseyism eir rieAoedpscsiNsmdeboe t o2feuemmascn itcossetvknote r u tutr ooaudL,:tis Vhaexuiu nlre idec- s agn c 1o ee?ggiredaspI cwrseM irrnepm ilpse.hernan n iacEneeiaolzdnp ind ed fhne.atsxhfer eanntaaea OFsmi*otegaeNtie laidneuisica ta gta eantAnotnnp ztanksdl Stelnni inwa.aom ,a)eppi etidsstClherrcnn o fta pt uets Yd, ecegliu s tw nt Frietruiioidalne aoth Eoeeow ettoreanilne tflm fnosfeueo aasatiitroanoe ddte ad ptuvgidt2obniifid wimosh fmeswcmelehOr ea elelx,cdortst n pitele t r g ie 0lot dnmeeahnivc nydrbasedadti titnsip F oneai nroeqiemrebloi nteroubn0s, eazrlpimkeitr,cb r iveotogmeh . rxa clnnuam e i xaieS n eee asi nim9i woee adarnurerlEbpr f rghntvta nwgreae Ceass m iaenieedd d aisnnil i ernpoartmnt e aoesesk rivts m Iaeeoaln,ssowyoe kthp ieicengmdEol iitar udonkbif h,etf ldspeilav pwacidv n tr paeeeumN idhe -f-r--tsrtvsyiocn,txethureaonloalaeoe - lielbshcc e eeseCaM n elmicdeiaatangtdtn. tw llea gep n ianaisarEhtsa,sbtintews t ntamnl ci heotacechl d t hhipb,ew eeloiader Tr1gaim avmtc celffoeef eaoersu ,teryOnyer0 go rt o eiou r eveeprrnt ltt..r oeneimfsio ,eo1eu r aoErhslrroplasl io i xpxPa dedl1air aaam r tftco laet aadpmoarmeiibnOp2lia uineotrt ov f ndtkaskze,nh e6r flslorseUrnhdr Ldhyteuiao na a / lewliisdwaayirirsmtnIfoyg entaalk ybtnjncmtanChetvt,no ysbbegaaim pio esu hgekseecg iYi eunceldj eci nrrenrvpptln.ne dbuot bs ltv eae eyee ttoccnTodhWgi eaoamtr smeidhneeandni adnl Hihfneipint.rf tr.neavnngekc b Wnn1it fia.lnuqatgiiAspdoasS csiu eo 1gemsstItsilgnageumrc Nsroiehn ,in7yn,.ft ser.pca vv gl nnonheai6mt eiragiBuas ns orpaethttteian2sAeteut. nnno hehhceac eunnntiuiir9staid lNtItnddhnoddndneeeeceeass7-----tttt,, 987 on October 7, 2009 www.sciencemag.orgDownloaded from s(rcu(einiosz)qeoneunDtoiao)refimfentpdsemeh,trdomea(icncriiimkant),pleafi(iclenteieaiht,iusee)(itrbiivovciepla)inttlysitbmieoooasnnftlsce prtaa(erinsae)asrtnelaiQ-gdsmtsesuimin,enati(ngeceitireiiissmf)ph,yiiipm(dfntiaeigec)maattnsIirnoudoatlfrnoe(insgirvmpgic)riaestlsiinogn
a pandemic begins interventions.
8/201
Outline
Compartmental models
Networked Epidemiology
Branching process
Spectral radius characterization
Extensions: threshold models, voter models
Competing contagions
Unifying framework: graph dynamical systems
9/201