The Global Epidemic Simulator Wes Hinsley 1 , Pavlo Minayev 1 Stephen Emmott 2 , Neil Ferguson 1
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Transcript of The Global Epidemic Simulator Wes Hinsley 1 , Pavlo Minayev 1 Stephen Emmott 2 , Neil Ferguson 1
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The Global Epidemic Simulator
Wes Hinsley1, Pavlo Minayev1Stephen Emmott2, Neil Ferguson1
1MRC Centre for Outbreak Analysis and Modelling, Imperial College London 2Microsoft Research, Cambridge
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Aims: To simulate the emergence and spread of an epidemic by explicitly modelling the worlds 6.5 billion people.
A platform for simulating any directly transmitted pathogen e.g. influenza, smallpox, or SARS.
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Previous Work
Strategies for containing an emerging influenza pandemic in Southeast Asia, (Ferguson et al)Nature 437, Sep 2005
Strategies for mitigating an influenza pandemic (Ferguson et al), Nature 442, July 2006
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Challenges:
Computational Performance and Memory
Data availability
Algorithmic Complexity
Statistical Validation or Justification
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Design Create a synthetic population, distributed evenly across different computational nodes. Overlay the world with a grid of patches, and calculate probabilities that people contact each other randomly, from patch-to-patch (rejection/acceptance algorithm) Consider other reasons people may contact each other: households, schools, workplaces, long range travel.
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The Landscan DatasetA grid of 43200x20880 points, (longitude,latitude)Each point is number of people in a region of around 1km23.5 Gb, but mostly sparse so reducible to 600Mb or less if you need
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Decomposition ToolCutting the world into similarly sized sections is not trivial. Writing an data decomposition application made the process (slightly) easier.
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Decomposition ToolThis is how the Europe Node sees the world. Yellow = local (where individuals are stored).Blue = remote patches.
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Decomposition ToolIn more detail Yellow (local) squares are always 20x20 landscan cells. Blue (remote) squares are usually 320x320 landscan cells, but
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Decomposition Toolremote squares can be divided further, if the placing of a border requires them to be. Borders are aligned to a grid, resolution 20x20 landscan cells.
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Decomposition ToolDifferent nodes see the world in differently. But every node knows for every geographical location, which computer has the detailed view.
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Patch k (20x20 landscan cells)Simulation InitialisationAlthough we assign individuals to ~20km patches, we preserve Landscan resolution by assigning more precise longitude and latitude to individuals.
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PopulationNk
Dk,kPatch kPatch k
For each k qk,k = F(Dk,k)NkZk where F is kernel function Zk is normalisation term
Main loop: For each infected individual in patch k Find poisson(R0) contacts, Each contact: sample qk,kPick random individual in kUse ratio of F(Dk,k) and F(ri,j) to adjust for qk,k being an over-estimate.
PopulationNkri,jContact Acceptance/Rejection Algorithm
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Early Results
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Early ResultsFor R0=2.0, incubation ~2 days, infectious ~3 days. Seeded in South America
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653254643
653256276
653257976
653259690
653261254
653262885
653264499
653266167
653267739
653269321
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653272413
653274045
653275732
653277340
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653283821
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653304077
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653346825
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653361448
653362540
653363621
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653367874
Immune
Days
Immune Individuals
america.xls
Total InfectedImmuneNew InfectionsNew contactsRejectionsCon/InfRej/Inf
01105681.21.3333333333
0.2511000000
0.511000000
0.7511000000
111000000
1.2511000000
1.511000000
1.7511000000
211000000
2.251602592.51.8
2.516000000
2.7515100000
314200000
3.2512400000
3.510600000
3.759700000
415736520.8333333333
4.2515700000
4.515700000
4.7515700000
514810000
5.25121000000
5.5141012221
5.75181024822
6181000000
6.25171100000
6.5171100000
6.752413391932.1111111111
727131339313
7.25261400000
7.5261400000
7.75271512221
8261722110.5
8.25271812221
8.5291812723.5
8.75311822211
9311911919
9.2530212110.51
9.531212110.51
9.75292300000
103125141343.25
10.25312611111
10.5322611010
10.75323015851.6
11393027323.54.5714285714
11.25453137142.33333333332
11.55433411902.758.1818181818
11.75543300000
12573424320.75
12.25583411414
12.5603826230.3333333333
12.7561393230.66666666671.5
13604222311.5
13.2560452311.50.3333333333
13.5644615350.6
13.757249512122.41
14745033511.6666666667
14.2583534122532.0833333333
14.5845412020
14.759755614442.33333333333.1428571429
1510459311743.66666666676.7272727273
15.251036637222.33333333333.1428571429
15.51046924822
15.75118737192492.714285714313.1052631579
1613075514322.82.2857142857
16.2513978912741.33333333336.1666666667
16.5139803260.66666666673
16.7514883613252.16666666671.9230769231
1714990482022.5
17.251519436520.8333333333
17.5151105811201.3751.8181818182
17.75160107611401.83333333333.6363636364
18181111926782.88888888893
18.2518211768211.33333333332.625
18.52031221227612.252.2592592593
18.75211130818362.252
1921413558751.69.375
19.252241389141941.555555555613.8571428571
19.52451481233602.751.8181818182
19.75244159710131.42857142861.3
2026116712251702.08333333336.8
20.252681781118931.63636363645.1666666667
20.5274186615142.50.9333333333
20.752971931931981.63157894743.1612903226
2131320312271172.254.3333333333
21.253222121120871.81818181824.35
21.53352241528861.86666666673.0714285714
21.7534923918301771.66666666675.9
223642531530317210.5666666667
22.2538726215321912.13333333335.96875
22.53932761421411.51.9523809524
22.7540629114311052.21428571433.3870967742
234173051226412.16666666671.5769230769
23.2542932617331021.94117647063.0909090909
23.546033620431112.152.5813953488
23.7547734916331152.06253.4848484848
2450436531472581.51612903235.4893617021
24.2552237819321321.68421052634.125
24.554839426452811.73076923086.2444444444
24.7557841227503251.85185185196.5
256034311846932.55555555562.0217391304
25.2561945527424191.55555555569.9761904762
25.5679476428442825.0952380952
25.7571950132663472.06255.2575757576
2674452728581492.07142857142.5689655172
26.2577356032633491.968755.5396825397
26.577858419321601.68421052635
26.7579961929641872.20689655172.921875
2782764937662741.78378378384.1515151515
27.2584968427632112.33333333333.3492063492
27.588870835662321.88571428573.5151515152
27.7593072937673821.81081081085.7014925373
2896476637832632.24324324323.1686746988
28.251039800591236712.08474576275.4552845528
28.5107083434722842.11764705883.9444444444
28.75111987047984442.0851063834.5306122449
29117289938975232.55263157895.3917525773
29.251211948511006351.96078431376.35
29.51314983711586872.22535211274.3481012658
29.7513731024571154942.01754385964.2956521739
3014131075551054851.90909090914.619047619
30.2514901110581355372.32758620693.9777777778
30.515471170621327032.12903225815.3257575758
30.7515861232651246601.90769230775.3225806452
311599129154932061.72222222222.2150537634
31.2516711338651413692.16923076922.6170212766
31.517271400741378671.85135135146.3284671533
31.7517801467791407011.77215189875.0071428571
3218651521931726201.84946236563.6046511628
32.25192415947516312332.17333333337.5644171779
32.5202516519218710692.03260869575.7165775401
32.75211217279619910102.07291666675.0753768844
33220418049920411712.06060606065.7401960784
33.2522801882951808251.89473684214.5833333333
33.523161966851476831.72941176474.6462585034
33.7523932058862029282.34883720934.5940594059
342465216612322512181.82926829275.4133333333
34.252564225311423214332.03508771936.1767241379
34.5264423551192319371.94117647064.0562770563
34.752742244310622810362.15094339624.5438596491
352865253713728114172.05109489055.0427046263
35.252962264912726313372.07086614175.0836501901
35.53072277213628414422.08823529415.0774647887
35.753163287614626213751.79452054795.2480916031
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36.253357310814428925312.00694444448.7577854671
36.53471323314229014442.04225352114.9793103448
36.753536337915228112721.84868421054.5266903915
373644350514330417462.12587412595.7434210526
37.253734364615430423641.9740259747.7763157895
37.53800380615929714731.86792452834.9595959596
37.753926394017434222561.96551724146.5964912281
384097407819639826712.03061224496.7110552764
38.254285423219941021512.06030150755.2463414634
38.54405440219036721251.93157894745.7901907357
38.754600456522646423812.05309734515.1314655172
394707474618838129062.02659574477.6272965879
39.254827491318436421581.97826086965.9285714286
39.54966512221345021872.11267605634.86
39.755122532123748431212.04219409286.4483471074
405204554021841828341.91743119276.7799043062
40.255374572422646434212.05309734517.3728448276
40.55554593125252630262.08730158735.752851711
40.755741612424447529491.94672131156.2084210526
415979636028456729421.99647887325.188712522
41.256248656329060942932.17.0492610837
41.56422680527653938291.95289855077.1038961039
41.756643707028560747102.12982456147.7594728171
426817731927654435141.97101449286.4595588235
42.256959760627454333561.98175182486.1804788214
42.57220786833865738161.94378698225.8082191781
42.757512815433368949512.06906906917.1857764877
437768844130964950662.10032362467.8058551618
43.258069871336470154121.92582417587.7203994294
43.58404901738576450711.98441558446.637434555
43.758649933635667443931.8932584276.5178041543
449040964136780255452.18528610356.9139650873
44.259365996738078256652.05789473687.2442455243
44.597281033243287567512.0254629637.7154285714
44.7599711072339579656982.01518987347.1582914573
45103521106741584968102.04578313258.0212014134
45.25107111145044689156101.99775784756.2962962963
45.5111631184250998673551.93713163067.4594320487
45.751168312232527104769241.98671726766.6131805158
461212512657486100982422.07613168728.1684836472
46.251257913058492984798328.112804878
46.51311413527561113484022.02139037437.4091710758
46.751364214012571117082472.04903677767.0487179487
471420014527618125193152.02427184477.4460431655
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47.751582916076609125482862.05911330056.6076555024
481641716655678134780961.98672566376.010393467
48.251719917232744156299582.09946236566.3751600512
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49.520847205788661740124972.00923787537.182183908
49.7521723212779061776116431.96026490076.5557432432
5022517220479161783117381.94650655026.5832865956
50.25232712289290918181214226.6787678768
50.524187236929911978133481.99596367316.7482305359
50.75251262458310402069140421.98942307696.7868535524
51261512548310762175149902.02137546476.891954023
51.25273842639511852405156262.0295358656.4972972973
51.5286572733212362543160232.05744336576.3008257963
51.75298352828512522476170381.97763578276.8812600969
52310862929812772616172862.04855129216.6077981651
52.25321533042513002533189491.94846153857.4808527438
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52.75346043281714502856199241.96965517246.9761904762
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