Download Simulation Environments for Viral Epidemics and Simple Ecosystems

ArtVirus and ArtEco
Simulation Environments for Viral
Epidemics and Simple Ecosystems
Zoltan Hascsi 1 and Corneliu Nicolae Zaharia 2
1
"Politehnica" University of Bucharest
2 Institute of Virology - Romanian Academy
[email protected]
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
Summary
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Introduction
The underlying paradigms
The model
Implementation
Conclusions
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
The underlying paradigms
• cellular automata
• multi-agent based system
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
The model:
cellular automaton
north
west
east
south
The cell’s neighborhood
• a bidimensional array of
cells (called niches)
• von Neumann neighborhood
• cell keeps a pointer to the
agent which resides inside
• may have simple properties
encoded in the cell’s state
(food resources, etc.)
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
The model:
agents
• the agents are not encapsulated in the cell’s
state
• agent state is a collection of variables (type,
age, viral state, energy, etc.)
• agent behaviour is implemented through a
set of functions (perception, movement,
etc.)
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
agent: viral state
• based on classic SIR epidemiological model
(S - susceptible, I - infected, R - recovered)
• covers extended epidemiological models,
SIRS, SIER, SEIRS, etc. (E - exposed)
• different types of virus carriers (latent,
acute, chronic and asymptomatic)
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
agent: viral state
susceptible
infected
immune
ArtVirus basic agent states
(simple influenza epidemic model)
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
agent: viral state
susceptible
acute
immune
chronic
asymptom.
carrier
ArtVirus enhanced agent states
(simplified hepatitis B epidemic model)
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
agent: movement
• may be random (ArtVirus, implemented by
the cellular automaton) or decision-based
(ArtEco, implemented by agent functions)
• range of movement defines the agent’s
reachable neighborhood in one step
• movement may be conditioned (age,
available energy, neighbor agents, etc.)
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
agent: movement
n
w
n
e
w
n
e
w
e
s
s
s
a)
b)
c)
a) a potential site of collision between agents; b) all potential collision
sites, empty niches that are in the neighbourhood of more than one
agent, are marked as invalid; c) the agents choose only between the
valid empty niches
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
agent: movement
a)
b)
c)
Possible movement distances: a) in the von Neumann neighbourhood;
b) in the Moore neighbourhood; c) in the von Neumann extended
neighbourhood of radius 2
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
agent: perception
• perception neighbourhood - the cells
(including their agents) that influences the
agent’s decisions and behaviour
• the range of perception is linked to the
agent state (viral state, energy, etc.)
• the perception window may extend farther
than the movement window
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
agent: perception
1
2
2
a)
b)
Perception neighbourhoods: a) of range 1; b) of range 2; The
perception window reaches all cells that lies in the range
according to the Manhattan distance measure.
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
Implementation
• object-oriented programming (OOP)
language
• a very friendly and flexible GUI
• allows users to modify agent and cell
properties during simulation
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
Implementation
• ArtVirus (epidemiological models)
• ArtEco (ecosystem models)
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
Implementation
ecosystem
niche class
cellular automaton
niche 0
niche 1
pagent
. . . .
pagent
other
other
niche
niche
properties properties
cellular automaton
global rules
population
agent 0
agent 1
. . . .
state
state
genotype
genotype
other
agent
properties
other
agent
properties
ECIT 2004
species class
species 0
class
species 1
class
. . . .
species
species
properties properties
and
and
behavior behavior
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
Simulation results for
ArtEco with two types
of agents, predator and
prey, one of a stable
periodic nature, one
chaotic, and the last one
chaotic with extinction.
ECIT 2004
ArtVirus and ArtEco - Simulation Environments for Viral Epidemics and Simple Ecosystems
Conclusions
• We combined cellular automata and multiagent based systems to design a flexible model
for biology and in particular for
epidemiological and ecological studies.
• Our model have been implemented in ArtVirus
and ArtEco simulation environments.
• Despite the model simplicity a range of
complex phenomena emerge in simulations.
ECIT 2004