Armin R. Mikler Towards Computational Epidemiology Designing an Infectious Disease Outbreak...
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Armin R. Mikler
Towards Computational Epidemiology
Designing an Infectious Disease Outbreak Simulator
Armin R. MiklerDepartment of Computer Science and Engineering
Department of Biological Sciences
University of North Texas
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Armin R. Mikler
Towards Computational Epidemiology
Address broader aspects of EpidemiologyAddress broader aspects of EpidemiologyDisease Tracking, Analysis, and Surveillance
High Performance Computing (HPC)
Simulation
Data visualization.
Design and implement computational tools Design and implement computational tools – investigating Tuberculosis outbreaks and risk assessment
in spatially delineated environments – modeling and simulating details of specific instances of
Tuberculosis occurrences in North Texas – applicable to a wide variety of disease outbreaks in spatially well-defined settings
Contribute towards establishing computational Contribute towards establishing computational epidemiology as a new research domain!!epidemiology as a new research domain!!
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Armin R. Mikler
Disease Outbreak Model
Local Global
• Global – Demography– Socio-economics– Travel
– Transportation
– Geography– Culture
• Local– Delineated space
• Factory, homeless shelter, school
– Airflow– Heating and cooling– Distances in feet– Architectural properties
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Armin R. Mikler
Global Stochastic Cellular Automata Global Stochastic Cellular Automata and the SWARMand the SWARM
Top Layer:Cellular Automata
Global
Middle Layer: Cellular Automata
Regional
Bottom Layer: SWARM
Local
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Armin R. Mikler
The Focus of Study--Locality basedThe Focus of Study--Locality based
This study proposes to model the dynamics of tuberculosis transmission within two facilities in North Texas - a homeless shelter facility providing both long and short-term occupancy with 800 beds, and a factory.
Data was previously collected through interviews during targeted surveillance screening of workers in the factory and homeless people who use the shelter.
Data has been Deidentified !!!
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Armin R. Mikler
Homeless Shelter Data and FindingsHomeless Shelter Data and Findings
For the homeless shelter, the data set comprises screening records for each case including: •Date tested (relative to t0)•Status of tuberculosis•Location in the facility•Length of time spent in the facility•Other variables
Results of initial analysis suggest that TB risk is not uniformly distributed but depends on the location of the sleeping bed and duration and frequency of stay at the night shelter.
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Armin R. Mikler
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Armin R. Mikler
Factory Data and FindingsFactory Data and Findings
In addition to basic screening records as collected for the homeless shelter, other available data for the factory include measures of duration and proximity to infected person such as: • Hours per week in the factory• Hours per week in the same workspace• Hours per week within 3 feet of infected person• Usual work area.
Results of initial analysis indicate that proximity of workspace to infected person was a major determinant of infection.
In fact 100% of those who worked directly in the same space with one infected person were infected with the same strain of TB.
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Armin R. Mikler
Factory LayoutFactory Layout
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Armin R. Mikler
The Paint Area
The Eating AreaAir vent system
The Restroom
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Armin R. Mikler
Modeling ApproachesModeling Approaches
Agent based modeling Level of exposure Emergent behavior defined by individuals’ actions. The average number of bacilli that are emitted (through
coughing, sneezing, etc.) Spatial interaction.
Stochastic Cellular Automata Ambient temperature and airflow Particle Suspension and Dispersion Intrinsically stochastic.
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Armin R. Mikler
From GIS data to Agent-Based From GIS data to Agent-Based SimulationSimulation to Visualization to Visualization
GIS/ Epidemiologic Data
Social Interactions
Visualization
Particle suspension & Airflow
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Armin R. Mikler
Movement and DesireMovement and Desire
Desire Functions
0
1
2
3
4
5
6
7
1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 81 86 91 96
Time (t)
f(x)
Smoking
ThirstSmoking Threshold
Thirst Threshold Example of functions that model different types of desire as a function of time.
A
D
B
CS/D A B C D …A - B C B …B A - C C …C A B - D …D C C C - …… … … … … …Agent at (xi, yi)
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Armin R. Mikler
Particle Suspension and DispersionParticle Suspension and Dispersion
Settling of bacilli
Time
As a function of time, bacilli settle toward the ground and may spread to neighboring cells
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Armin R. Mikler
State of each cell Ci,j depends on Ci,j+1, Ci,j-1, Ci+1,j, Ci-1,j, Ci+1,j-1, Ci+1,j+1, Ci-1,j-1, Ci-1,j+1
The color of a cell changes based on the majority color of its neighbors
T0 T1
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Armin R. Mikler
Visualization--‘Simulated’ ‘Simulated’ SimulationSimulation
Healthy Person Normal
Weaker Person Low/Med TB
Sick Person High TB
Removed Floor
Obstacle
Wall
Pathogen Content
Obstructability
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Armin R. Mikler
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Armin R. Mikler
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Armin R. Mikler
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Armin R. Mikler
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Armin R. Mikler
The Future: Clusters and the GRID
Faster hardware and new high-bandwidth networks demand that we explore new cluster architectures.
Larger, more complex cluster environments make it imperative to invest in new efficient and scalable tools.
Grand Challenge problems will continue to drive the development of computing infrastructure.
Distributed HPC will become common place. (DOE SciDAC)
Management Tools designed for single hosts or small clusters are likely NOT to scale.
New types of Middleware is needed to decouple the underlying distributed infrastructure from the applications.
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Armin R. Mikler
Grid Layers…virtualization
Internet / PrivateNetworks
GridEngine
GridEngine
GridEngine
GridEngine
GridEngine
GridEngine
General Grid Services
Application-Specific Grid Services (APIs)
Applications
Middleware
Grid Access
i.e., ScientificDiscovery throughAdvance Computing
Data Grid
Comp.Grid
BioGrid
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Armin R. Mikler
Matter of Facts….
There is increasing demand for harnessing computational resources Increasing demand for Grid-based computing at the private sector
Computing Power will become a commodity like Water, Gas, etc. As with ISPs, Grid Access Providers (GAPs) will have to guarantee
Quality of Service.
Through Grid Services, we can provide a global computing infrastructure and facilitate services for a large number of application domains at the private and public sector!
Examples: Healthcare, Education, Industrial R&D, Entertainment, Sciences, etc.
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Armin R. Mikler
Cluster SemanticsCluster Semantics
MASTERNODE
NetworkingInterconnect
Cluster Nodes
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Armin R. Mikler
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Armin R. Mikler
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Armin R. Mikler
People Behind - The GroupPeople Behind - The Group
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Armin R. Mikler
A Final Push to Control TB
Because the number of cases of TB in the U.S. are lower than they’ve ever been, we have the opportunity to finally control TB in the U.S.
Recent research suggests that focusing on the dynamics of how TB is transmitted in specific locations is a much-needed final push to TB control.
Homeless shelters and overcrowded areas constitute reservoirs of TB infection.
Yet little research exists on the dynamics of localized TB transmission in homeless shelters.
Little attention has been given to places like factories, warehouses, healthcare facilities, or schools where people work in close proximity for long periods of time.
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Armin R. Mikler
Cray Y-MP & IBM Power4Cray Y-MP & IBM Power4
“Common” supercomputer in early 1990's
~$1 million from Cray Max speed: 2.3 gigaflops (record
speed)
• Pentium III 1Ghz processors. Same processors sold “off the shelf”
• 64 gigaflops• 198th on Top500 list
(http://www.top500.org)
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Armin R. Mikler
Big Mac @ Virginia Tech
Macintosh G5 workstations
Infiniband networking interconnect
3rd fastest supercomputer in the world
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Armin R. Mikler
Cellular Automata (4 Neighbors – von Newman)
State of each cell Ci,j depends on the neighbors Ci,j+1, Ci,j-1, Ci+1,j, Ci-1,j
For example, the color of a cell depends on the majority color of its neighbors
T0 T1