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Optimization using a host-parasite model with variable-size distributed

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Conference Paper · June 1996

DOI: 10.1109/ICEC.1996.542378 · Source: IEEE Xplore

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 Optimization Using a Host-Parasite Model with
Variable-Size Distributed Populations
Bjorn Olsson
Department of Computer Science
University of Skovde
Box 408, S-541 28, Sweden
bjorne@ida.his.se

Abstract |This paper presents a model of coevolution be-
tween two variable-size, spatially distributed populations,
evolving in an environment with a
ow of resources. The II. Distributed Host-Parasite Coevolution
two populations have a host-parasite relationship where the
host species is dependent on the uptake of resources from
the environment for their reproduction. The parasites seek
to \infect" host organisms and parasitize on their resources
to produce parasite ospring. We show how the approach
can be used for optimization tasks by using instances of the
problem task to determine the outcome of each interaction
between a host and a parasite organism. As an initial test of
the model, we apply it to the problem of designing sorting
networks for several problem sizes: 6, 7, 8, and 9-input.
I. Introduction
We attempt to model the coevolution of host and par-
asite species, where both species have variable size pop-
ulations which evolve in a two-dimensional \world". The
\world" contains resources which are absorbed by host or-
ganisms and used in their reproduction. Parasite organ-
isms attempt to \infect" hosts and make use of the hosts'
resources to produce parasite ospring. Parasites are de-
pendent on hosts, since they have no means of their own to
absorb resources directly from the environment. We show
that this model can be used for optimization by assigning
to one species the task of evolving optimized solutions and
to the other the task of evolving test cases. This idea was
explored successfully by Hillis in [2], which also concerned
optimization using a model of host-parasite coevolution.
Our model is dierent in a number of ways: We let popula-
tions evolve in an environment with explicit resources, we
let interaction between hosts and parasites occur in a less
controlled manner, and we use variable size populations,
allowing parasites to \kill" the hosts they successfully in-
fect. Our model is also dierent in that the use of explicit
for optimization purposes.
A. Overview
The environment consists of a two-dimensional grid
with wrap-around. On this grid we evolve two popula-
tions of \organisms" - a host population and a parasite
population. Host organisms are movable, whereas para-
sites have no ability to move independently. Each host or-
ganism tries to make a one-step movement in a randomly
chosen direction for each time step of the simulation. The
movement succeeds if the adjacent grid cell in the cho-
sen direction is empty, otherwise the host just stays in its
present grid cell until the next time step.
In addition to the environment there is a store of \re-
sources", in the form of a number of \resource particles".
Resources are poured into the environment at a particular
rate and can be absorbed from the environment by host
organisms. A host needs to have absorbed a certain num-
ber of resource particles before it can reproduce. When
reproducing, the host makes a mutated copy of itself and,
in so doing, spends a number of resource particles which
are returned to the store. Parasites have no ability to
take up resources independently. Instead, parasites are
able to \infect" hosts and use up the hosts' resources to
produce parasite ospring. Whenever an organism dies,
all resource particles it contains are returned to the store.
Distribution of particles from the store back to the envi-
ronment are regulated so that a distribution event always
results in the same amount (normally just a single parti-
cle) being distributed to every cell on the grid.
Since reproduction takes place whenever an organism
tness functions has been abandoned altogether. has access to the required resources, population sizes will
There are a number of models in the Articial Life com- vary during the simulation. A number of parameters deal-
munity of distributed agents evolving in an environment ing with resources are used to control the nature of the
with resources. Examples include the Echo [3], LEE [6] population dynamics. The total amount of available re-
and Avida [1] models. We are unaware, however, of any sources, together with the amounts required for reproduc-
work on adapting such models to perform formally dened tion, directly in
uence the environment's carrying capac-
optimization tasks. In this paper, we attempt to show em- ity. As another example, the amount of resources required
pirically that this type of Articial Life model can be used
uence the population dynamics.
In: \Proceedings of the 1996 IEEE International Conference on
Evolutionary Computation", Nagoya, 1996.
for reproduction of a host organism and a parasite organ-
ism, respectively, in
It may be possible to use this model for optimization

1
purposes by assigning to the host population the task of
evolving solutions to an optimization problem. In the ex-
ample application described later in this paper, we have
assigned to the host population the task of evolving sort-
ing networks. We let each host encode a candidate sorting
network and each parasite encode one or more test cases,
i.e. input sequences. Each time a parasite attempts to
infect a host we determine the outcome by testing the
sorting network encoded by the host on the test case en-
coded by the parasite. The probability that the attempt
should return a value for PInf , based on how well the
candidate solution performs on the test cases.
8. For each parasite, p, which is currently infecting a
host h, let p reproduce if h contains a resource amount
 Rp. Parasite reproduction results in the creation
of Op mutated copies of p, the death of p itself, and
the death of h. For each ospring, a random grid
cell within a distance of 10 cells from h and p is cho-
sen. The ospring is placed in the chosen cell unless
the cell already contains a parasite. If no free cell
to infect the host succeeds is determined by counting the
number of misplaced integers in the sequence when it has
been passed through the sorting network.
B. Algorithm
The execution of a simulation consists of the following
steps:
1. Create an initial population of hosts consisting of
Hinit individuals and place these in grid cells cho-
sen at random with the restriction that no cell may
contain more than one host. We have used Hinit =
1; 000.
2. Create an initial population of parasites consisting of
Pinit individuals and place these in grid cells chosen at
random with the restriction that no cell may contain
more than one parasite. We have used Pinit = 1; 000.
3. Fill up the central store of resources C by letting
C = R, where R denotes the total available number
of resource units. We have used R = 2  106 for a grid
of 10,000 cells.
4. Repeat steps 5 to 12 until at least one of the following
is true:
(a) the optimal sorting network for the given task has
been found,
(b) the maximum number of iterations have been ex-
ecuted,
has been found within a xed number of trials, the
ospring dies. We have used Rp = 50 and Op = 5.
9. Let each host \die" with a probability of PdH . A
host that \dies" is removed from the population and
all the resources it contains are returned to C . If the
host is currently infected by a parasite, the parasite
also \dies". We have used PdH = 0:05.
10. Let each parasite \die" with a probability of PdP .
A parasite that \dies" is just removed from the pop-
ulation (it does not contain any resources). We have
used PdP = 0:03.
11. If C >= worldsize, where worldsize denotes the
number of cells in the grid, add one unit of resource
to each grid cell and then set C = C ? worldsize. We
have used worldsize = 10; 000.
12. For each host h which is not infected with a parasite,
let h reproduce if it contains a resource amount  Rh.
Host reproduction results in a single mutated copy of
h, and in splitting of the resources of h so that it keeps
half of the amount for itself and donates the other half
to the ospring. A random grid cell adjacent to h's
cell is chosen and the ospring is placed in the chosen
cell unless it already contains a host. If none of the
cells adjacent to h's cell is unoccupied, the ospring
dies. We have used Rh = 50.
III. Example Application
(c) host population size = 0, In this section, we rst introduce the example prob-
(d) parasite population size = 0.
5. Let each host absorb all resources from the grid cell
which it currently occupies.
6. Let each host make one attempt to move to the ad-
jacent grid cell in a randomly chosen direction. The
move succeeds if the chosen cell is not occupied by
another host, and fails otherwise.
7. For each parasite pi that is occupying the same grid
cell as an uninfected host h, let pi make one at-
lem we have used. We then describe the problem-specic
aspects added to the model in order to apply it to the
example problem, i.e. the representation used for genetic
encoding of candidate solutions and the interaction be-
tween hosts and parasites.
A. Sorting Networks
A sorting network is a sorting algorithm consisting of
tempt at \infecting" h. The probability that the a xed sequence of comparison-swap operations. Such al-
attempt succeeds, PInf (\probability of infection") gorithms are called homogeneous [5] or oblivious [10] since
is determined by executing interaction between host the sequence of comparisons is exactly the same for all in-
and parasite according to the problem-specic inter- puts of a given size. A sorting network for input-sequences
action function. This function should build a candi- of length n can be represented graphically (see gure 1)
date solution to the problem from the host genome as n horizontal lines. Along the horizontal lines, from left
and a set of test cases from the parasite genome. It to right, appears a number of vertical lines, each one con-
necting two horizontal ones. Each vertical line represents

2
a comparator, i.e. a comparison of the two numbers from
the two horizontal lines which it connects. If the upper
number is larger than the lower one, their positions are
switched. Any sequence of n numbers which are input at
the left end of the network should be sorted in increas-
ing order after having passed through to the right end.
The number of steps in the sorting procedure can be re-
duced if we allow adjacent non-overlapping comparisons
to be executed in parallel. A typical optimization prob-
lem in connection with sorting networks is the design of a
minimum-length n-input network, for a given value of n.
By length we mean the number of comparators, whereas
depth refers to the number of steps after parallelization.
appears in gure 2. Since theP set?1 iof, wepossible
on the n-input problem is in=1
comparators
have used genetic
codes of arity 15, 21, 28, and 36 for, respectively, the
6, 7, 8, and 9-input problems. The length of the host
chromosome is equal to the number of comparators used
in the networks which we are trying to evolve, i.e. for the
8-input task, for example, we use host chromosomes with
19 loci. We have left as future work evaluation of possible
advantages of the use of, for example, binary coding to
exploit lower order schemas or building blocks [3].
k b n g c i g m p k d g

The example network in gure 1, which was evolved in
one of our simulations, has length = 19 and depth = 13.
Fig. 1. Evolved 8-input sorting network using 19 comparators.
The problem of designing a minimum-length sorting
network for a given n becomes a formidable task already
for relatively small values of n, due to the large search
space. Consider, for example, the task of designing a 8-
input networkPof length 19. For each of the 19 compara-
tors we have 7i=1 i = 28 ways of connecting two of the
input-lines. This gives a search space of 2819 ' 3  1027
networks. The optimal length of sorting networks is only
known for n  8, whereas for n > 8 new current upper
bounds are still being found. An example is the recent
work of [4], in which a new best network was found for
n = 13. The problem of evolving minimum-length sorting
networks can be approached in dierent ways, as discussed
in [2]. We have chosen to use the lenghts of the currently
known upper bounds (as listed in [4]) and try to evolve
valid sorting networks of these lengths. We have chosen to
5 1
2 2
4 3
3 4
1 5
6 6
Fig. 2. Each character in the host chromosome (top) represents a
comparator. The probability of the parasite (left) \infecting"
the host is a function of the number of misplaced integers in the
output sequence (right). Parasite chromosomes may encode a
number of input sequences.
Mutation of a host ospring consists of replacing the
character in a single locus on the chromosome with an-
other, randomly chosen character. We have chosen to let
each reproduced chromosome be subjected to m point mu-
tations, where m = 0 and m = 1 each have a 0.45 proba-
bility and m > 1 a 0.1 probability. For m > 1, we draw a
random value with uniform distribution in the range 2; ::; l,
where l = chromosome length. Thereafter, m distinct loci
are point mutated. This allows mutation to occasionally
aect a large number of loci simultaneously - something
that is very unlikely to occur in the standard approach
where the probability of more than a few simultaneous
mutations on the same chromosome is negligible.
The genetic coding for parasite chromosomes uses the
integers 1 through n. In the initial parasite population,
each parasite chromosome contains a single permutation
of the integer sequence 1; ::; n. Parasite mutation consists
of exchanging the positions of two integers in the encoded
let evolution work on xed length networks, searching for
the network of given length with highest sorting accuracy.
If the accuracy of the network is perfect, then it is a valid
sorting network of the given length. This is contrary to
the approach in [2] and [4], which allow variable-length
networks during the optimization process.
B. Representations and Genetic Operators
Host chromosomes are sequences of characters, where
each character represents a given comparator. An example
3
sequence. In the simulations discussed below, we used a
parasite mutation probability of 0.1 per locus. This means
that during reproduction each locus had a 0.1 probability
of having its integer value moved to another (random)
locus and replaced by the integer value taken from the
recieving locus.
In addition to mutations, we use a form of recombina-
tion where genetic material is passed from one organism to
another. We hesitate to call the recombination operator
we use \crossover" for two reasons: Firstly, it is a one-
way process where genetic material from one organism is
incorporated into the genome of another - rather than the
mixing of genetic material from two organisms. Secondly,
the recombination does not take place in conjunction with
reproduction. We implement recombination as follows: At
certain intervals (here every 100th time step), each host
organism has a particular probability (here 0.01) of look-
simulations, was able to evolve a 16-input sorting network
of length 61, which is just one comparison more than the
best known network for that problem size. Initial popu-
lations, in Hillis' work, were seeded with 32 comparators
which appear in many of the known 16-input sorting net-
works. Hillis used a Genetic Algorithm with the popu-
lation distributed over a grid. In the non-coevolutionary
ing in its vicinity for another host. If it nds another host, version, tness of each network was determined by testing
it proceeds to copy a portion of its own chromosome. A its sorting accuracy on a number of test cases, of which
random locus is chosen and either the portion preceding
or following after the chosen locus is copied. The copied
section is then introduced into the recipient host, replac-
ing its previous chromosome segment in the corresponding
loci sequence. This form of recombination is more similar
to the conjugation [11] which takes place between bacte-
ria, than to the crossover of higher organisms.
Given the chosen representation, we can design a func-
tion for the interaction between host and parasite individ-
uals, as required in step 7 of the algorithmic description of
the model. We design the function so that, given a para-
site attempting to infect a host, we let the sorting network
encoded by the host sort all the input-sequences encoded
by the parasite. Each output sequence from the network is
then examined and the total number of errors, NrWrong,
counted. An error is a pair of integers nN ; nN +1 in an in-
teger sequence n1 ; ::; nnr inputs such that nN > nN +1 . We
some were xed and some randomly generated. Only the
best scoring half of the population was then allowed to
contribute genetic material to the next generation, with
crossovers taking place between networks located near
each other on the grid. In the coevolutionary version,
a population of parasites were introduced - each parasite
coding for a set of 10 to 20 test cases. Fitness for a sorting
network in a given cell on the grid was then determined
by testing it on the sequences encoded by the parasite lo-
cated in the same grid cell. Fitness for the parasite was
determined by the number of test cases which the sorting
network failed to sort. Selection and reproduction was,
for both populations, carried out in the same way as in
the non-coevolutionary version.
One of the main dierences between our approach and
that of Hillis is that we have altogether abandoned the fa-
miliar Genetic Algorithm concept of explicitly determin-
calculate the probability that the infection attempt suc- ing the tness of each individual and then using a selection
ceeds as PInf = NrWrong n?1 , so that 0  PInf  1 if the mechanism to pick out high-tness individuals for repro-
parasite genome encodes a single input sequence. duction. In our approach, a host organism which encoun-
During a simulation it would be impractical to use ex- ters a parasite runs a risk of being \infected" and \killed"
haustive testing on all input sequences as a tness func- by the parasite, unless it sorts the parasite's input se-
tion due to the large number of possible sequences. In quence(s) correctly. Hosts representing better sorting net-
this work we altogether abandon the idea of using tness works will therefore on the average live longer and produce
functions and let the reproductive success of a host be more ospring, although their tness is never evaluated
implicitly determined by how well it survives interaction
with the parasites it comes across. However, in order to
gather data about the simulation we use a small random
set of input sequences as a screening test applied to all
host ospring and then only exhaustive testing on those
that pass the screening. We thus get an estimate of the
explicitly. We rely instead on endogenous tness evalua-
tion [8] [7]. This form of selection also results in variations
in population size during our simulations. In initial time
steps of our simulations this leads to the pattern of oscil-
lations in population sizes typical of predator-prey coevo-
lution [9]. Population sizes usually become stable towards
average sorting accuracy from the results of the screen-
ing tests and an estimate of the best found solution sofar
from the exhaustive tests. Also, the exhaustive testing on
those that pass the screening guarantees that if there is a
valid sorting network in the population, then we will de-
tect it. Note, however, that these tests are used for gath-
ering statistics only. \Fitness" is determined implicitely
by random interaction between hosts and parasites, where
higher quality hosts have a lower probability of becoming
infected.
C. Comparison with Other Approaches
Hillis [2] focused on the problem of evolving 16-input
sorting networks and, in the host-parasite version of his
4
the end of a simulation, however, as is exemplied in g-
ure 3, although one may hypothesize that there are local
oscillations on the grid also when the global population
sizes appear stable. We have left as future work an eval-
uation of the impact of population size variations on the
evolutionary process.
D. Results
Table 1 shows results from 10 simulation runs each for
the 6, 7, and 8-input problems. The results on the 9-input
problem are from 5 simulation runs only. The length, in
number of comparators, of the sorting networks we tried to
evolve were those listed in [4] as the best currently known;
opt. is the total number of permutations of the input se-
quence (optimumn = n!); avg. best is the number and Population size

percentage of permutations sorted correctly by the best 6000

evolved network, averaged over the 10 (or 5) runs; nr. o.f.

Hosts

4000

stands for number of runs in which an optimal sorting net-

nr.
work (i.e. a valid sorting network of the given length) was
Parasites
2000

found; time is the average number of time steps needed

and nr. sol. the average number of candidate solutions
0
0 200 400 600 800 1000 1200 1400
time

evaluated in those simulations in which the optimum was Sorting accuracy

found. Simulations with n = 6 were allowed to run for a

1

maximum of 5,000 time steps, and this gure was doubled

0.8 Best sofar

prop. correct
for each increment of n, except for n = 9, where a max-
0.6 Average

0.4

imum of 100,000 time steps was allowed. Figure 3 shows 0.2

data from one of the simulations on the 7-input problem. 0

There are initial oscillations in population sizes, which

0 200 400 600 800 1000 1200 1400
time

even out to relatively stable population sizes of 2,000 to
4,000 later in the run. After 1,396 time steps and evalu-
ation of ' 3:3  105 candidate solutions, a valid 7-input
sorting network of length 16 is found. As table 1 shows,
an optimum (a valid sorting network of the given length)
was found in each of the 10 runs on the 6-input problem.
The 8-input problem was the hardest to solve, with only
Fig. 3. Example simulation using = 7. Note that 'best sofar'
n
refers to the best sorting network of those which have passed
a screening test and then been tested on all permutations of
the input sequence, whereas 'average' is based on the results
of the screening tests only. Thus, the average accuracy may
occasionally exceed that of the 'best sofar'.
1 in 10 runs nding a valid sorting network. of evolutionary/adaptive change in the species. There are
few, if any, examples of evolutionary algorithms with vari-
n 6 7 8 9 able population sizes being used for optimization tasks.
length 12 16 19 25 How population dynamics can be exploited to improve
opt. 720 5,040 40,320 362,880 the capacity for optimization is yet to be investigated.
avg 720 5,026 36,703 358,675
best 100% 99.7% 91.0% 98.8% References
nr o.f. 10 9 1 2 [1] Chris Adami and C. Titus Brown. Evolutionary learning in the
2d articial life system "avida". In Articial Life 4, 1994.
nr runs 10 10 10 5 [2] D. Hillis. Co-evolving parasites improve simulated evolution as
time 441 2,706 6,278 29,577 an optimization procedure. In Articial Life II, 1992.
nr sol. 1.0 7.0 13.7 81.6 [3] John H. Holland. Adaptation in Natural and Articial Sys-
tems: An Introductory Analysis with Applications to Biology,
(105) Control, and Articial Intelligence. MIT Press, 2nd edition,
1992.
Table 1 [4] Hugues Juille. Incremental co-evolution of organisms: A new
Results for n =6; ::; 9. approach for optimization and discovery of strategies. In Ad-
vances in Articial Life: Third European Conference on Arti-
IV. Conclusions and Future Work
We have introduced a model of coevolving hosts and
parasites, evolving under spatial distribution in an envi-
ronment with a
ow of resources. We have shown em-
cial Life, 1995.
[5] Donald E. Knuth. The Art of Computer Programming: Volume
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[8] Melanie Mitchell and Stephanie Forrest. Genetic algorithms in
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ecological modeling purposes, can be applied to a formally [9] James D. Murray. Mathematical Biology. Springer-Verlag, 2nd
dened optimization task. Much remains to be done on
how the characteristics of this model can be applied to
other problems. A goal of future analysis is to understand
the eects that the population dynamics caused by coevo-
lutionary relationships have on the evolutionary dynamics.
Population dynamics has been studied extensively using
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View publication stats
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