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RESEARCH PAPER
Evolutionary algorithms to simulate the phylogenesisof a binary artificial immune system
Grazziela P. Figueredo
Æ
Luis A. V. de Carvalho
Æ
Helio J. C. Barbosa
Æ
Nelson F. F. Ebecken
Received: 12 November 2007/Revised: 12 March 2008/Accepted: 13 March 2008/Published online: 29 April 2008
Ó
Springer-Verlag 2008
Abstract
Four binary-encoded models describing someaspects of the phylogenetics evolution in an artificialimmune system have been proposed and analyzed. The firstmodel has focused on the evolution of a paratope’s popu-lation, considering a fixed group of epitopes, to simulate ahypermutation mechanism and observe how the systemwould self-adjust to cover the epitopes. In the secondmodel, the evolution involves a group of antibodies adapt-ing to a given antigenic molecules’ population. The thirdmodel simulated the coevolution between antibodies’ gen-erating gene libraries and antigens. The objective was tosimulate somatic recombination mechanisms to obtain finallibraries apt to produce antibodies to cover any possibleantigen that would appear in the pathogens’ population. Inthe fourth model, the coevolution involves a new populationof self-molecules whose function was to establish restric-tions in the evolution of libraries’ population. For all themodels implemented, evolutionary algorithms (EA) wereused to form adaptive niching inspired in the coevolutionaryshared niching strategy ideas taken from a monopolisticcompetition economic model where ‘‘businessmen’’ locatethemselves among geographically distributed ‘‘clients’’ soas to maximize their profit. Numerical experiments andconclusions are shown. These considerations present manysimilarities to biological immune systems and also someinspirations to solve real-world problems, such as patternrecognition and knowledge discovery in databases.
Keywords
Artificial immune systems
Á
Evolutionary computation
Á
Artificial immune systems models
1 Introduction
The immune system (IS) is able to protect us from a numberof pathogens. It also monitors the organism, searching anddestroying anomalous cells. To perform such tasks, the ISmust recognize a great variety of different compounds anddistinguish, among them, those which can remain in theorganism and those that are to be eliminated. It is believedthat the IS identifies about 10
16
foreign molecules [18],which means that it can identify any molecule [10].The IS pattern recognition task is performed throughsurface receptor molecules of T and B cells. The identifi-cation of antigens in both these types of lymphocytesoccurs differently. B cells recognize antigens throughimmune globulins from its cell surface. T cells recognizeonly antigens presented by an antigen presenting cell(APC). The creation of these receptors and their capabilityto cover all antigens have their origin in a very sophisti-cated genetic mechanism. During the receptor’s formationprocess, the variation is caused by the combinatorialassociations among the receptors codifying genes and thehypermutation mechanism.The hypermutations occur in the lymph nodes’ germi-native centers. Thus, when an APC penetrates the lymph
G. P. Figueredo (
&
)
Á
L. A. V. de Carvalho
Á
N. F. F. EbeckenFederal University of Rio de Janeiro - COPPE,Rio de Janeiro, Brazile-mail: gpfigueredo@gmail.comL. A. V. de Carvalhoe-mail: meucorreioeletronico@gmail.comN. F. F. Ebeckene-mail: nelson@ntt.ufrj.brH. J. C. BarbosaLNCC, MCT, Petro´polis, Brazile-mail: hcbm@lncc.br
 123
Evol. Intel. (2008) 1:133–144DOI 10.1007/s12065-008-0010-z
 
node and shows an antigen to a T cell, or when a B cellfinds a pathogen and identifies it, that means the combi-nation was well succeeded. After the recognizing pattern isestablished, the lymphocyte becomes activated, cloningitself. Clones with high capacity of recognizing a certainantigen tend to proliferate. On the other hand, clones withlow recognizing capacity disappear and are replaced byothers with higher efficiency [19,27]. The analogy between the clonal selection and the Darwinian naturalselection [5] is clearly seen here.After recognizing an antigen by a B cell receptor, fol-lowed by a sequence of other events, a formation of plasmacells clones responsible for the secretion of the samereceptor in its soluble form takes place. This secretedreceptor is the antibody and its function is to catch and bindthe antigen. This binding occurs between the paratope of the antibody and the antigen’s correspondent epitope. Aparatope that presents a strong bind within the epitope has agreater capacity of neutralizing the antigen [6,7]. An antibody is constituted by two equal heavy chainsand two light chains, as it can be seen in Fig.1. The shapeof the molecule is similar to a Y. The base of the Y hasparts of heavy chains and the arms are constituted by bothchains. The antibody’s recognizing site is located at the endof each arm, and is known as V region. The antibody isantigen-specific, and to provide the organism with anti-bodies able to recognize all the antigens, the antibodies’codifying genes suffer somatic recombinations (Fig.2).The variable portion of the light chain requires twodistinct DNA encoding segments. The V one encodes mostof the variable region. The remaining is encoded by a Jsegment. In a non-activated B cell, the V and C regionsencoding DNA sequences are spatially apart from eachother. When B lymphocytes become mature, the somaticrecombination joins genes from segments V, J and C. TheC segment encodes the light chain constant portion of theantibody. This mechanism is illustrated in Fig.2.There are many possible combinations of the availablegene segments, which gives the IS the capability of pro-ducing an enormous number of distinct antibodies.These concepts will be the building blocks of the modelspresented in this work, which simulates the dynamicsbetween paratopes and epitopes, and between antigens andantibodies inside the organism along the evolution of aspecies. This work was inspired by the ideas found in [3,4, 8,10,14–16,21–25,28–30]. Basically, in the above ideas which served as inspirationto the present work, the objective was ‘‘to develop modelsdirected at understanding the pattern recognition process of two aspects of the IS, clonal selection and long term evo-lution of genes.’’ In the works cited above most of themodels work with binary strings evolved by genetic algo-rithms (GAs) [10,14,16,23,28]. Other approaches involving artificial models and citations of many otherArtificial immune systems (AIS) models can be found in[2,9,20,26,36]. No comparison among the models of the present article has been made with the ones previouslycited, because the focus of each work was different.Evolutionary Computation has been chosen to imple-ment the models studied [33]. A coevolutionary geneticalgorithm (CGA) was used to form adaptive niching basedon the ideas of [8]. In that work, in contrast with fixedshared schemes, a niching formation strategy namedcoevolutionary shared niching (CSN) was proposed toallow for the adaptation of the location and the radius of each niche . CSN was inspired by Tullock’s [35] economicmodel of monopolistic competition where ‘‘businessmen’’
Fig. 1
The antibody molecule. Adapted from [19]
Fig. 2
Generation of the antibody’s chains given by somaticrecombinations (adapted from [19])134 Evol. Intel. (2008) 1:133–144
 123
 
locate themselves among geographically distributed ‘‘cli-ents’’ so as to maximize their profit.Four models are described in Sects.2–5, respectively, which also present numerical experiments. The paper endswith Sect.6which discusses the results of our work. It isimportant to make clear that this work does not focus ontheoretical immunology. The main objectives of the fourmodels are to simulate the evolution of an AIS in order tounderstand some aspects of biological IS development inorder to come up with methods and algorithms to solvereal-world engineering problems.Given the great amount of experiments made in all themodels with similar results, it was decided to show only themost important graphs containing the evolution of eachmodel.
2 The first model
In the first model proposed, which represents a simplifi-cation of what happens in biological ISs, there is a group of paratopes that have to adapt through the generations, sothey can optimize the coverage of a fixed given group of epitopes. The aim is to analyze the capability of adaptationof the system in an environment full of aggressive ele-ments, and its behavior due to pattern identification withinthe epitopes structure as well. That is why the simulationsare initially performed with a number of paratopes smallerthan the number of epitopes.It is known that the antibodies are antigen-specific [19],meaningthatitisassumedthatthereisjustoneparatopeableto bind itself to a particular epitope of the antigen molecule.In this model, however, epitopes with slight structural dif-ferences can be inactivated by the same paratope.2.1 The algorithm for the first modelThis sub-section will give details of the first model. Thecorresponding pseudo-code is shown in Algorithm 1. Afterthe algorithm, each part of it is explained in details.
2.1.1 Encoding
In real biological systems, it is known that the constitutingregions of epitopes and paratopes are formed by complexchains of organic compounds. Nevertheless, in this artificialmodel, epitopes and paratopes are represented by binarychains, following [8,10]. Therefore, in the GA context [11, 17], phenotypes and genotypes will be the same.
2.1.2 Initialization
The initialization of paratopes can be made entirely atrandom or, according to [10], by inserting some pre-definedbinary blocks in the chromosome.
2.1.3 Niche distribution
The number of niches is always the same as the paratope’spopulation size. In terms of the CSN, paratopes and epi-topes play the roles of the businessmen and clients,respectively. The distribution of epitopes among the nichesis determined by the smallest distance between them andthe paratopes. Each epitope is compared to a paratope, inorder to establish which paratope is the closest one and,consequently, which niche the epitope will belong to. Theindividuals in the
j
th niche are the epitopes that the
j
thparatope is more apt to neutralize among the current par-atope population. The capability of a paratope to neutralizean epitope is measured by means of a distance computa-tion. Here, distance is understood as a function whichcompares the epitope and paratope chromosomes, alsoknown as
matching function
.There are various types of matching functions [24],however, in this model, the one believed to be most faithfulto biological systems was chosen. The chromosomes arecompared bitwise, and the matching value is determined bythe longest complementary chain between them, as it canbe seen in the following example.Epitope:
000
1
1
11
0101010000
11110Paratope:
111
1
0
11
1010101111
11110
 MatchingValue
¼
10The complementary chains represent the molecular bindbetween a paratope and an epitope. The objective is toreduce the distance between paratopes and epitopes alongthe evolution. The distance will be given by the formula inEq.1:
 Distance
¼
Epitope
0
sChromosomeSize
À
MatchingValue
ð
1
Þ
This distance presented by Eq.1is supposed to beminimized along the process of evolution.
Evol. Intel. (2008) 1:133–144 135
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Sergio Amezcua

Please let me know where are we standing in regard of the epitome string bit manipulation. Is there any interest from the math explanatory group for these theories?

reply04 / 07 / 2012
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