Independent Study Report

Artificial Immune Systems
1. Introduction:
The biological Immune systems is a complex and adaptive system that defends body from the antigens or pathogens from attack. It is possible to differentiate between immune cells as selfcells and non-self cells. It is probable with the aid of the distributed and parallel force that has the intelligence to take appropriate action from local and both global view using its connections of chemical messengers for interactions. There are two majors branches of the immune systems: 1. The innate system is static system which indentify and destroys antigens while; 2. The Adaptive immune system reacts to unknown antigens patterns and develop a reaction to those encountered antigens that can remain within body for longer time.

Such noticeable information processing capability of bio-logical immune system has caught attention of computer engineers around the world for its application in computer security, anomaly detection, fault tolerance, pattern recognition, etc. This field has got its application in robotics and in some cases involves optimization tasks also.

2. Overview of Bio-logical Immune Systems:

The biological immune system has evolved over millions years and it is elaborate defense system. The immune system employs multilevel and overlapping defense in parallel and distributed way although the immune mechanism namely innate and adaptive and processes like humeral and cellular are not known completely.
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The biological immune system respond to attack either to neutralize the antigenic effect or destroy the antigen. Such response is dependent on the way the antigen type and the way it enters.

The crucial features of the biological immune system are: a. Affinity (matching) b. Diversity c. Distributed operation (no central mechanism) Affinity or matching degree refers to the binding between antibody and antigen. Diversity means there should be different number of antibody types that can act as key to antigen locks. Distributed control means that there is no central mechanism to govern the immune response when antigen attacks. There are local interactions between immune cells and antigens.

There are two immune cells that play important role in immune response: 1. B-cells (Bone Marrow), 2. T-cells (Thymus). Both these types of immune cells belongs to bone marrow but T-cells migrate to thymus to get mature and in this way flow in the body through blood. There are three types of T-cells which are mentioned below: a. Helper T-cells These cells are important for the activation of B-cells. b. Killer T-cells

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Such cells are attached to the alien invaders and inject the destroying chemical molecules in to antigens thereby causing their destruction. c. Suppressor T-cells These genre of T-cells suppress the autoimmune interactions between cells. Thereby they contribute to the network stabilization. On the other hand, the B-cells are responsible for the production of antibodies that binds to antigens and cause them to die out. Each B-cell generate only one type of antibody (which numbers in millions). In the figure below, I-II show the invade entering the body and activating T-Cells, which then in IV activate the B-cells, V is the antigen matching, VI the antibody production and VII the antigen‟s destruction.

Figure (1) Immune system Cells [6]
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1. b. 2. 2. destructive enzymes and stomach acids. Cell mediated immunity. Again there are two types of adaptive immunity which are: a. Adaptive immunity (specific ). Thus.From above description one can say that the innate immune system is responsible for the primary response and the adaptive immune system is responsible for secondary response. The sialic acid on foreign molecules make C3b bind to these surfaces for longer time. 4 . Innate immunity (non-specific). pH temperature and chemicals rises unbeneficial living conditions for foreign organisms. Humoral immunity. Adaptive Immunity: It is crucial for learning and memory. The biological immune system composed of skin. respiratory system. the human body is protected against foreign invaders by a multilevel system. MAC is developed that penetrates the cell surface and kill the cell of foreign antigen. Hence. Innate immunity: This immunity is congenital. Extracellular molecules are ingested by macrophages and such process of ingestion is affected by chemical messengers called lymphokines. Such systems affect each other and linked to each other. The immune system is divided into two heads: 1.

Selection 4. Mutation Once we encode. Cytokines secreted by TDH can mediate this kind of cellular immnunity. 3. T-cells are responsible for cell-mediated immunity.1 Initialization and Encoding: In order to implement Artificial Immune System. It involves the interactions between B-cells and antigens.a. Cytotoxic T cells participate in cell-mediated immunity reactions by killing altered self cells. Similarity Measure 3. then a similarity measure is determined in order to calculate degree matching which perform selection and mutation until we reach the stopping criteria. antibody can cross-link the antigen forming the clusters that are more readily ingested by macrophages cells. b. Humoral Immunity This kind of immunity is happened by antibodies molecules contained by fluids within body termed as humors. For instance. the antigen can be destroyed in many ways. Artificial Immune Systems Basic Concepts 3. The subsequent proliferation and formation of memory cells. 5 . there are four parameters which are needed to be considered: 1. When there is an interaction between antibody and antigen. Cell Immunity As the name indicates that it is cell mediated. Encoding 2.

The most common way is string representation. For data mining and intrusion detection. e.5] where 0 indicates not like movie and from 1 to 5 shows the rating of how much the movie is appreciated.. An antigen is target or solution for a given problem.Selection of encoding scheme is very important for algorithm‟s success. 6 . For example. a five variable binary problem can be shown as: (10010) Example: Data Mining: The problem of recommending movies. Similar to Genetic Algorithm. A possible encoding scheme for movie recommendation: ** +* + * ++ … (1) id = identifier score = score to the user. The votes can be binary or it can be 10 integers in a range. there is close relationship between encoding and fitness function of genetic algorithms. the position is variable identifier and the corresponding value of variable. the data to be checked or intrusion in system.g. An antibody is the remaining data. other users in the data set or the network traffic. The encoding deals with representation of user‟s profile with respective to movies seen and the like and respective dislikes. Fitness function is nothing but matching or affinity in artificial immune systems. Now we have to consider two terms namely antigen and antibody. Antigens and antibodies are encoded in the similar way. [0. A list of numbers representing the „vote‟ can turn out to be encoding. where length is number of variables.

there are two different bits at the last. This kind of matching whichever we did is opposite to Hamming Distance technique in which the different bits are needed to changed in order to bring similarity. We can determine the Euclidean distance between two strings. Again consider the strings (00000) and (01010). So. 7 .4]. the score is 3 and for the example second. If we do not want to use the binary representation.200. Once again the score is 3. We can say that the score is 3 depending on the matching between the two strings.Intrusion Detection: The encoding looks like: [<protocol> <source ip> <source port> <destination ip> <destination port>]. 3.12> <25> which represents an incoming data packet send to port 25.2 Similarity or Affinity Measure Matching degree is one of the most important in developing Artificial Immune Systems algorithm.254> <108.111. we identify the continuous number of bits that match and get the length of the longest matching as the similarity measure. example: [<tcp> <113. wildcards like „any port‟ are also often used [2.255. the score is 1. real-valued representation is available. this could be a problem. for the first example. The way in which the matching results is different still the score is 3. Two of the matching algorithm are described below with binary representation: Now consider two strings below: (0 0 0 0 0) and (0 0 0 1 1) It is noticed that by bit-by-bit comparison. So. In these scenarios. In order to avoid such anamoly.112.

whatever we are trying to do is to determine the similarity. the 1 and -1 are the most important. assume that we are finding the users from the data that are same to the main user‟s profile. where the Negative Selection is applied for artificial immune systems implementation. The set of detectors are subjected to matching algorithm that 8 . Let there are two users u and v: ∑ √∑ ( ( ̅)( ̅) ∑ ( ̅) ̅) … (2) n represents the votes for which u and v have voted. One way of solution to such intrusion detection problems is define self set S. Then the set of detectors are randomly initialized. 0 means no correlation.For data mining. the Pearson Correlation Coefficient between the two users. The measure is amended so default to a value of 0 if the two users have no films in common. For data mining. the matching degree is refered to as correlation. Consider the Intrusion Detection. The output ranges from -1 to 1 indicating the strong agreement to strong disagreement. In that situation. In negative selection algorithm. ui is the vote of user for movie i and ū represents the average of user u over entire movies. Now the question arises. If we take the instance of movie recommendation. For this we can use. the element that are matched are eliminated and this shows that the B-cell maturation involves no matching between self molecules or cells.

Hence. negative selection algorithm has been put forward for anomaly detection or fault tolerance. So.4. The negative selection algorithm goes as follows: 1. this is sign of danger or alert. Such detector set is used to continually monitor the network. Generate the set of detectors (M) that detects all the elements not belonging to set P.compares set self. The branch of Computational Intelligence emerged in 1990‟s Artificial Immune Systems is used in computer security. Any matching detector is rejected and we remain with the elements that do not match with self. etc. by taking inspiration from biology. If there is a match. All the matured cells that leave the thymic environment are self-tolerant and they do not identify the self cells. As an inference. pattern recognition.6]. the majority of the biological cells present in thymic environment are self and not non-self. All these non-similar elements are comprising resultant detector set. Biological Immune System Models 4. From information processing view. Define the set that has to be protected and let it be self set (P).1 Negative Selection Principle It‟s been clear that the thymus is responsible for maturation of T-cells and is shielded by the blood barrier which is able to exclude non-self antigens from thymus. [2. negative selection perform pattern recognition by collection important or crucial information about the non-self of the patterns to be identified. the Tcells containing repertoire that recognize the self cells are excluded from the thymus through the biological process termed as Negative Selection. 4. Produce the random elements (C). 9 .

Now the set M is created. The process can be explained as when a B-cell recognizes an antigen with certain degree of affinity. that corresponds to non-self patterns. Figure shows clonal selection. Consider set P‟ to be monitored.2. [12] Figure (2) Negative Selection Principle [12] 4. If the element of set C matches with an element of set P then discard such element or else store it in set M. proliferation and affinity maturation. it is selected to generate high volume of antibodies which binds to antigens and results into their elimination with the aid of other immune 10 . Compare P and C. The set P‟ consists of elements of P and some new patterns or it can be totally new set.2 Clonal Selection It is the theory that is used to describe how an immune response is executed when a non-self pattern is identified by a B-cell complimentary to negative selection. For all the items in set M. detect it whether identifies an element of P‟ and if it does then a non-self pattern is recognized and an action is taken. the next step is to monitor the system for detection of non-self patterns.

An antigen selects immune cells to proliferate. the higher the proliferation. The higher the affinity.cells. 1. This rate of proliferation is directly proportional to affinity. The proliferation process is asexual which is a mitotic process in which cells divide themselves. The mutation rate is inversely proportional to the affinity. The B-cells also become memory cells. The B-cells clones undergo a hyper mutation resulting B-cells with high affinity towards antigens. From the computation point of view. Figure (3) Clonal selection [12] 11 . 2.

Generate a population of patterns (M) randomly. the CLONALG learns to recognize patterns depending on evolutionary like behavior. These are memories of the system. Such criteria are minimum pattern recognition or classification error. the more the number of copies. The more the affinity. 4. until the certain criteria is met. Iterate steps 2 to 5. Hence. then the CLONALG algorithm steps are termed as below: 1. Such algorithm was proposed for pattern recognition and thereafter it was modified for optimization tasks. Identify the individuals of M that have best affinity. However. Produce copies of such elements in proportion to the affinity with the antigen. This very algorithm enables the Artificial Immune Systems to become good at pattern recognition. 3. present each pattern of P to it. CLONALG l algorithm has been proposed to include these properties. Now. So. Determine affinity with each and every element of set M. the lesser the mutation rate. to the population (M). [12] 12 . Mutate all the copies of the element in proportion to the affinity to the input pattern. Suppose the set of patterns given to be P that are to be recognized. 2.Genetic algorithms are similar to clonal selection if cross-over operator is not there. These mutated elements are then added to set M and determine the elements that are matured. The more the affinity. the genetic algorithm has no affinity proportional reproduction and mutation properties. 5. 6.

A network is network of affinities. Now imagine that this antibody Ab1 recognises the idiotope of antibody Ab2. how does it happen? It is proposed the cells and molecules are able to identify each other. We say that the Ab2 is internal image of Ag. Such ideology is modeled by eliminating all but one of the self-recognising cells. In order to explain this theory. assume that there is antibody Ab1 recognises antigen Ag. the molecules that are on the surface of antibodies which are recognized by other antibodies are called idiotopes. such theory is criticized by many immunologist but the computational features of immune network are very important in robotics. So. Such recognition of idiotopes between molecules gives rise to connected cells network. As a result of such interactions. In accordance to this theory. However. The recognition of one antibody by another one results in network suppression. Figure (4) Immune Network [12] 13 . So.3 Immune Network The immune network theory states that the dynamic behavior is still there in immune system even when the antigen is not present.4. Ab1 recognises Ab2 and Ag. a antibody-antibody recognition gives network suppression and antibodyantigen recognition gives rise to network activation and cell proliferation.

1. Combine the remaining elements of step 4 with the remaining elements found for each antigen element presented.1 Shape. 5. For every element in set P. 6. Accept all but those elements from M* that are having threshold more than prescribed. 4. etc. Generate network population randomly. Calculate the matching degree between each and every element of Set M and suppress all but self-recognizing. hydrogen-binding. [12] 5. The concept of Shape-Space is introduced to describe the interactions between immune cell molecules and antigens quantitatively by Perelson and Oster in 1979. The molecules should 14 .Space Model: The interactions between the antibody and antigen is of importance in immune systems. According to this concept. 2. until desired result is attained. allow CLONALG that gives M* (memory cells) and their coordinates for the current antigen. Iterate step 2 to 6. The degree of binding between a antibody and attacking antigen usually involves the short range non-covalent interactions based on electrostatic charge. This gives Set M. 7. Calculate the affinity between elements of M*.Set (P) contains patterns to be recognized. Modeling the Bio-logical Immune Systems 5. the antigens can be recognized within a known region known as recognition region around a antibody. The intent is to eliminate redundancy in the network by suppressing self-recognising elements. 3. van-der Waals force of attractions/repulsions.

the shape space would contain N points. we assume that an antigen can present different types of epitopes and hence a finite number of antibodies can recognize almost infinite numbers of points 15 . Antigenic determinants (epitopes) are characterized by generalized shapes whose complements lie within V as the Ag-Ab interactions are measured via regions of complementarity. The paratopes interacts with almost all the epitopes with Volume V with radius „e‟. charges. They may match with lower affinity. This set of features was called the generalized shape of a molecule [1]. Then a specific point in L-dimensional space called shape-space shows the generalized shape of an attacking molecule of an antigen binding region with relation to its antigen binding properties. width of any bump or groove in the combining site. there is extensive region of complementarity. Each antibody can recognize all types of epitope within recognition region of volume V. The existence of chemical groups as well as the shape and charge distributions are characteristic properties of antigens and antibodies which are crucial in identifying the interactions between these molecules. Imagine that the generalized shape of antibody combining site can be described by L parameters: length. These points would lie in finite volume V of the space because there is only a limited lengths. widths. that an antibody combining site can assume. its charge. It is not necessary that antigen and antibody should match exactly. The confirm numbers of parameters or their values is not desirable. height.interact with each other over sufficient portion of their respective surfaces. etc. etc. Hence. If an organism has a repertoire of N size.

So. This is related to cross-reactivity phenomenon in bio-logical immune systems. Hamming Shape-space [4] 16 . Manhattan shape-space 3. in shape-space model like patterns occupy adajacent regions of the shape space and might be recognized by the same antibody shape as far as „e‟ is provided [6]. there are three ways to represent antibody-antigen pairs and to determine their matching strength: 1. Mathematically.Ab Representations and Affinities: The Ag-Ab representation determine the distance measure that can be used to calculate the degree of interaction between these molecules. 5. Euclidean shape-space 2.2 Ag .Figure (5) Shape-Space Model [6] into volume V.

. ab2. Such sequences can be interpreted as peptides and the different symbols as characteristic properties of amino acids.ag2…. for example in Euclidean or the Manhattan distance. if the coordinates of an antibody are given by <ab1. either antibody or antigen can be represented by a set of real valued coordinates m = <m1.m2. then the distance (D) between them is: √∑ ( ) … (3) √∑ … (4) Eqn (3) is depicts Euclidean distance case and Eqn (4) depicts Manhattan distance case.bols Another shape space is Hamming shape space in which the antigen and antibody are termed as symbol‟s sequences over an alphabet of size k.The generalized shape of a molecule (m). m belongs to L dimensional real valued shapespace. ab3……abL> and the coordinates are given by <ag1. 17 . In the case of Euclidean distance.agL>.…. Shape-spaces that use real valued coordinates and that measure distance in the form of eq (1) are called Euclidean distance shape-spaces and those iin the form of eq (2) are called Manhattan shape-spaces.mL>. In context of artificial immune systems the mapping between shape and sequence are equivalent. The affinity between antibody and antigen is measured by the distance they have between two strings or vectors.

1]. From equation (3) to (5) we see how to determine the affinities between molecules in Euclidean. the distance can be normalized. the molecules have exact complement and their affinity is also maximum. Moreover. recognition region and matching threshold. respectively. over the interval [0. ab = <0 0 1 0 0 1 0> ag = <1 1 0 1 1 0 1> 18 . it is important to coin the relation between distance D. In Euclidean and Manhattan. When the distance between two sequences is maximum. In the universe of bitstring representation the molecular binding takes place only when the bitstrings are complementary to each other. it is good to take into consideration real valued spaces differently than hamming spaces in measuring ag-ab interactions.∑ { … (5) Equation (5) depicts hamming distance measure. In order to study the cross-reactivity. for example. a limit on the magnitude of each shape-space parameter cab be employed. suppose the matching affinity is not maximum. manhattan and hamming shape-spaces. If we assume binary representation of ag-ab interactions then graphical ieraction is clear in hamming shape-space. For example. so that the matching strength also lies in the same range. In other cases.

We can use several activation functions that can give us idea regarding the binding value in proportion to the distances between the ab and ag molecules. the set of all possible antigens is considered as a spaces points. In the hamming shape-space. A bond is established only when the value of the match score is greater than (L – e) in case of the threshold function. where antigenic molecules with similar shapes occupy the adajacent points in the space. In other words.Antibody perfect matching using bit-string representation [6] The affinity between antibody and antigen is the number of bits that are complementary in the representation string. The desired matching strength between two randomly taken bitstrings equals to half of thir length(if they are the same length). The 19 . it means if the antigen is recognized or not by antibody. In continuous case the sigmoid function is good to apply where the „e‟ relies in the inflexion point pf the curve. The way to measure the affinity is by XOR operator.Figure (6) Antigen. A binding value shows whether the molecules are bound or not.

total number of unique antibodies and antigens is bitstring length.6]. 20 . then a perfect match is necessary. e = matching threshold.1) C = coverage of the antibody. L = length of the bitstring. . The number of antigens covered within a region of radius‟e‟ is given by: ∑ ( ) ∑ ( ) …(6. The matching threshold „e‟ determines the coverage provided by a single antibody and in case when e = 0. a given bitstring of length L and an matching threshold e.4. the minimum number of antibody molecules (N) necessary to complete the shape-space coverage can be defined as ( ) … (6.2) ceil is the operator that rounds the value in parenthesis towards its upper nearest integer [2. On the basis of eqn (6). It means that an antibody and antigen must be exacy complement of each other. where k = size of alphabet and L = the A given antibody covers some portion of the shape-space depending on the recognition of some sets of antigens.

0 and 1. Let epitope string and defined as s ≤ min( . Packard is simple enough to simulate on computer but that still contains enough realism to embody characteristic properties of the network. Let the value of the n-th bit of i-th epitope string. Farrner and N. The sequence of amino acids specifying the chemical properties of the epitope and paratope are represented as binary strings. string [1. in this case. ( ) shows the n-th bit value of the j-th paratope 21 . an antibody is represented as (p. The exact string matching is not required. In this model they have left out many crucial features such as T-cells and macrophages which contain the essence of the idiotypic netwok. The sequence of five binary numbers can be corresponded to amino acid. The simplification that is considered here is that each antigen and antibody has only one epitope but in reality one can see antigen or antibody has many different epitopes[5].2].e). The AIS Model The artificial immune system model proposed by J. below which the two antibodies will not react at all. The allowed reactions between different antibodies and between antibodies and antigens are found by searching the complementary matches between strings. Thus.H. where p represents paratope and e represents the epitope string.D. The strings are allowed to match in any possible match in order to model the two molecules in more than one way. the matching threshold is ). So. the antibodies are viewed as to be composed of two amino acids .6. represents the length of ( ) denote represents the length of paratope string. So. In this way twenty amino acids can be represented.

i. G( ) = x for x > 0 and G( ) = 0 otherwise.1 Procedure Used for Computing Partial Matches: Figure (7) Epitope and Paratope string matching [5] In this example. G is 0 if less than s bits are complimentary and G = 1 + α 22 .Now. G( ) = 1. G determines the strength of a possible reaction between the epiopte and the paratope. the sum over k allows the epitope to be shifted with respect to the paratope . For the above example. 6. for k = -1 and G( ) = 0 for = 1. that ( ) is = = 8 and s = 6. The sum over n ranges over all possible positions on the epitope and paratope. For goven alignment.. Here k = -1 so ( ).e. the matching specificities is given by: ∑ (∑ ( ) ( ) ) . Alignments with -2 ≤ k ≤ 2 are possible. represents the exclusive-or operation for complementary matching. hence So. value of k.. (7) In above equation (7). comparable to all other values of k.

when s or more bits are complimentary. If matches occur at more than one alignment, we sum their strength to consider that the molecules might be able to interact in more than one way, and thus react more strongly because they spend more time together than molecules that can interact in only one alignment [5].

In this model, free antibodies with antibodies attached to cells are lumped together and only of the total number of antibodies of a given type i in terms of the concentration variable xi are kept track of.

What happens when two different antibodies interact? In this interaction Farmer and Packard assume the paratope on one antibody recognizes the epitopes on the other antibody. They agin aasume that the result of such interaction is that the antibody with the paratope reproduces some fixed numbers of times, while some fixed probability , the antibody with the epitope is eliminated. The degree to which one antibody reproduces and the other dies is controlled by the degree of complementarity between the paratope and the epitope. So, the model is symmetric with regard to antibody interaction.

Suppose N be the number of antibodies with concentrations { , with concentrations { , ,

,

,…

} and n antigens

….. }. It is possible to avoid simulating the microscopic

dynamics in differential equations for the concentrations. This is only possible only when the system is well mixed and sufficiently large such that the number of interactions needed to produce a significant change in the concentration of any particular type of antibody is huge.

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On the basis of assumptions:

̇

[∑

]

…(8)

In above equation (8), the first term represents the stimulation of the paratope of an i-th anitibody by the epitope of j-th antibody. The second term represents the suppression of i-th antibody by jth antibody. The probabaility of collision of antibody of type i with antibody of typr j is shown by term and parameter c indicates the number of collisions per unit time and rate of

amtibody production simulated by collision.

The match specificities term indicates what reactions occur and how strongly. probable inequality between stimulation and suppression. When =

represents , there are

symmetrical interactions between paratopes and epitopes and the model is similar to one proposed by Hoffman.

In order to model entire immune response, the concentrations of antigens should also be introduced that may change depending upon the number of antigens increase or decrease. The last term shows the death rate. The best way to change of the system at a fixed value[5]. in such a way the total concentration

The list of antibody and antigen types is dynamic. The changing occurs due to new types are added or removed. The value N and n changes with time but on time scale it is slow as compared to changes in . In eqn. (8), we do integration over a period of time. The composition of system

is examined and updated as it is needed. To update we put minimum threshold an all concentrations so that a variable and all of its reactions is eliminated when the concentration goes below threshold.
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The generation of new antibody types is done through genetic operators that is applied to paratope and epitope strings such as Crossover, inversion and point mutation. In crossover, two antibody types are randomly selected and randomly positions within the two strings are chosen and then the pieces on one side of the chosen position are interchanged in order to produce two new types. Epitopes and paratopes are crossed over separately. By randomly changing one of the bits in a given string point mutation is implemented and the implementation of inversion is performed by inverting a randomly chosen segment of the string.

Antigens can be generated by a variety of mechanisms either randomly or by design. The same antigen type can be given to the system so that we can see whether it can eliminate it or not. Once the system learns to eliminate it, the number of antigens can be presented to see whether system forget to eliminate or remember to eliminate the antigen. The number of antigen provided to the system can be varied [5].

The antibodies whose paratopes match epitopes are amplified at the expense of other antibodies. If = 1 (equal suppression and stimulation) and > 0 then every antibody type eventually

dies due to the damping term. Letting

< 1 favors the formation of loops of reaction, since all

the numbers of reaction loop gain concentration and can neutralize the damping term. When N increases, the number of loops and respective lengths also increases.

Even when the system is disturbed by introduction of new types, it can remember certain states due to robust properties of the reaction loops. The antibodies that can recognize the internal and external other molecules are retained in the system and their concentration is increased. Antibodies that do not recognize the other molecules are eliminated. Hence, together with immunological memory, the system posses the immunological forgetting [5].

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But as antigens are potentially dangerous. Another theory is that the B-cells that have reacted to antigens undergo the dormant state and surface up when similar or kind of antigen occurs again. Another hypothesis is proposed by Farmer and Packard by means of idiotypic network. Such dormant state can last for periods of weeks or may be months [1]. let ab‟n be the concentation of antibody that recognize the paratope of ab „(n-1) antibodies. then it is like a loop because ab1 is going to recognize ab‟n [3].2 Hypothesis: Let the concentration of antibodies that recognize the antigen be ab1.”[5] 26 . Figure (8) The formation of a cycle allows the antigen with epitope e0 to be “remembered. this theory is highly risky. Now the concentration of antibodies that recognize the epitopes of ab1 antibodies be ab2.In the bio-logical immune system. 6. One theory states that the antigen remain in degraded form in lymph nodes and their periodic exposure to immune system retain memory. antigens are sometimes restored in the system for long time which is comparable to lifespan of organism. The exact reason for this is not now known. Continuing this way. If ab‟n is like original antigen.

the operation within bracket shows the x-or operation [7]. If you are dealing with categorical data. the existence of the cycle can maintain the concentration of ab1. 7. and represents the i-th bit of the respective strings.” and the distance measure that the former is based on are the cornerstones in any detection.2 …n. then for sure the values of n resemble the antigen [5]. To form a cycle. we assume that by chance p(i) recognizes en in addition to e0. or recognition algorithms. If the antigen is eliminated. classification.Arrows denote recognition through string matching algorithmn. Paratope p(i) recognizes epitope e (i-1) for i= 1. If the paratopes are assumed to functions as epiotpes.1 Hamming Distance: It is defined as the number of different characters between two strings. en must resemble the antigen e0. Thus. String Matching Rules A matching rule defines “matching” or “recognition. Several string-matching rules are described below: 7. then a string representation may be more suitable and a matching rule like rcb is useful [7]. The hamming distance between x and y strings is expressed as: ( ) ∑ ( ) … (9) N = length of the string. 27 . an antibody that specifically recognizes the antigen [5].

28 . ∑ { …(11) ∑ { … (12) ∑ { … (13) a counts the number of 1s that match at the same position of both the strings. and c counts the number of 0s in string x that do not match string y [7]. d enumerates the number of 0s that match at the same position of both the strings.7. the extensions of hamming distance have proposed.2 Binary Distance: ∑ { … (10) Based on the number of bits that match or differ. b counts the number of 1s in string x that do not match string y.

Jacard and Needham (14) 3. Sokal and Michener ( 6) 5. Russel and Rao … (13) 2. Rogers and Tanimoto ( ) ( 7) 29 .Different similarity measures are developed which are as follows: 1. Kulzinski ( 5) 4.

Value Difference Metric: ( Where ) ∑ ( ) ( ) … (19) ( ) ∑ ( ( ) ( )) And ( ) √∑ ( ) ( ) denotes the probability that xi equals to the character c in the alphabet C [7].6. it is a generalization of the hamming distance [7]. 30 .3 Edit Distance: It is defined as the minimum number of string transformations between two strings s1 and s2 required to change string s1 into s2 where the possible string transformations include (i) changing a character. It is also termed as „Levenshtein‟ distance. Yule ( 8) 7. (ii) inserting a character and (iii) deleting a character.

two strings are compared [7]. Three different similarity measures are defined as: Difference Matching Rule: ∑ | | …(20) Slope-Matching Rule: ∑ |( ) ( )|… (21) Physical matching: ∑ |( ) ( ( )|…(22) 7. Input string and antibody string are converted to bytes and then into positive integers to create landscape. Using sliding window.y) is true. 31 .5 R-Contiguous Bits Matching: The rcb matching rule is defined as follows: If x and y are equal length strings.7. then they are said to be matched if x and y match at atleast r contiguous locations and we say match(x.4 Landscape –Affinity Matching: This type of matching is used to capture the notion of matching biochemical and physical structures and approximate matching to immune system.

matching rule used is rcb where a detector d is specified by a binary string c and the threshold value r. 7. According to r-chunk. d1 d2. 32 . In other words. E. are classes. An r-chunk detector d is said to match a string x if all the bits of c are equal to the r bits of x in the window defined by c.. then we can say that match (x. a network of B cell objects and antigen population.6 R-chunk Matching Rule: The generalization of rcb matching rule is r-chunk matching rule..) with r<=m. antigens.Example: If x=ABADCBAB and y=CAGDCBBA.p+r-1. detector d is specified by a binary string c and parameter r. x and d match if ei = di for i=p…. Such an AIS has been implemented in CLOS (common lisp object system) and so b-cells. E. Hunt and D.y) is true for r<=3. In binary strings. Example: x= e1 e2…em (an element in shape space) d=(p. Cooke have developed an artificial immune system which composed of a bone marrow objects. detector of any size can be used and hence the detector covers more self-space.d. Learning Using Artificial Immune Systems J. In rcb matching rule. and d matches a string x if rcb of c matches the corresponding bits at the same positions of x [7]. 8. The matching window is specified for detectors. In r-chunk. etc. A cluster of r-chunk detectors that cover all possible windows has the same effect as an rcb detector. element x matches detector d if at position p there is sequence of length r where all characters are equal [7]. p<=m-r+1 .

If this score is more than or equal to threshold. The algorithm is as below: Randomly initialize B-cell population Load antigen population Till end is reach DO Select antigen randomly from antigen population And insert such selected antigen in random point in B-cell network. an immune response is elicited and a match score is recorded. Arrange these B-cells by the level of their avidity Delete 5% bad cells out of B-cell population Create n new B-cells (n = 25% of B-cell population) Out of this n. For every B-cell selected Do interaction between antigen and each B-cell selected for immune response. Select the approximate percentage of B-cells around insertion point. select m cells to join the immune network (m = 5% of population) [9] B-cell Object The B-cell object possesses a pattern matching element. Antibodies When an antigen meets antibody. The B-cell object records the affinity level of the B-cell and looks after the links to any other B-cell object it is in connection within network of B-cells. The bone marrow object possesses main algorithm which starts immune response by inserting antigen in b-cell network. which B-cell is dying and causing increase in concentration of cells beneficial to the network.1 The Bone-Marrow Object It decides where in network the antigen has to be inserted. 33 .8. the binding between antibody and antigen occurs.

The bit string is copied by AIS in complementary manner. B-cell Stimulation [∑ ( ) ∑ ( ) ∑ ( )] - Above equation represents the stimulation of B-cell. Antibodies Bit String representation is used for pattern recognition problem. B-cell Objects The antibody‟s paratope is created from mRNA list. The antigens are defined in external ASCII files and are inserted into AIS by the antigen population object. So. 2. 3. the antibody representation is of 0s and 1s.2 Applying AIS to Pattern Recognition Problem 1. 8. The antigen population used to immunize the AIS is of three pattern type forming 33% of the population of antigen.Antigens Each antigen which is potential is represented by antigen object possessing one epiotpe. 34 . The population consists of originals as well as the modified bit strings introducing noise into the data. Antigens AIS is tested by two diverse antigen‟s population possessing the antigens‟ binary list of 20 elements. The object realizes the a series of lists from files and instantiates those series of list as objects of antigens.

Antigen Population Representation: 11111111110000000000 00000000001111111111 00000111111111100000 33% 33% 33% 4. Hence. Bit Shifted Antibody: Antibody Antigen Bit Shifted Antibody 0010101110 1000111010 0111000101 8.3 The match algorithm: Repeat ∑ For each region consisting of 2 or more 1s note their length ∑ if ≥ then = Shift Ab right 1 bit Until Ab shift complete 35 . Antigen/Antibody In order to determine the match between Ag-Ab. a circular approach is followed. if the pattern described by the antibody starts halfway along the antigen. then the antibody is shifted half way along its length and hence a entire match is noted. instead of following match to start at any point on the antigen.

each bit selected was flipped and in sub-string regeneration. all the elements between the two desired points are flipped. 8. 36 . The learning part was turned off while testing phase and hence the system is capable of showing the secondary immune response. Then comes the turn for secondary response by presenting antigens as shown below. 50 Iterations were performed for the immunization process in which the antibody population increased from 10 to 28.4 Running the System 99 binary antigens were used to immunize the system. In other words. The test population was then presented to AIS.Calculating Match Value: Antigen: 011000011110110 Antibody: XOR: 100111000101101 1 1 1 1 1 1 0 1 1 0 1 1 0 1 1 → 12 Length: 6 2 2 2 → 88 MatchValue: 12 + + + + Hypermutation: In milti-point mutation. the system can determine whether the antibody determine the antigen or not.

9. TEST 2. 37 .1111111110000000000 0000111000110010001 1110010010010010010 0000000001111111111 1010101000101001110 1111001010100110100 0000011111111110000 TEST 1 * TEST 2 TEST 3 TEST 4* TEST 5 TEST 6 TEST 7* TEST 1.4 and 7 are original antigens used in primary response. They try to evolve affinities among antibodies using genetic operators. The arbitration among competence modules arises difficulties in behavior-based arbitration.3 are modified versions of TEST1.6 without any difficulty [9]. Dynamic Behavior Arbitration using AIS Akio Ishiguro et.5. TEST 5. al proposed a inference making system inspired from immune system in living organism and applied it to behavior arbitration of autonomous mobile robot as conventional AI systems have brittleness under dynamic changing environment. Much attention has been focused on the behavioral decomposition approaches as there are limitations on the functional decomposition for conventional AI. On the same lines. AIS should be able to identify TEST 2.6 are noised version of TEST 4.3.

Maes proposed behavior network system under which an action suitable for the current situation and the given goals emerges on account of interaction between different competence modules.To overcome such difficulties. Figure (9) Architecture of Algorithm [9] As shown in figure. respectively. like. current situation. 38 . Akio Ishiguro et. direction to the detected obstacle perform action like antigen and competence modules and interactions between modules perform action as antibody and stimulation/suppression between antibodies. distance. 6. al approached this problem from immunological point of view as shown in fig. The baseline for such approach is that the best possible antibody is selected for antigen.

If the immunobot is captured by predators. the immunobot consumes energy say Em.Figure (10) Immune Networks [8. it gets Ef energy. The figure below shows the structure of immunobot used in the simulations. If the immunobot get the food. 5. For quantitative evaluation. 4. 2. Eo energy is vanished. For movement. The predators attack immuno-bot only if they are in predefined limit or range. the obtain-food behavior is not emerged after sufficient of food is already obtained. If immunobot collides. External detectors are sensors in eight directions detecting 39 . It is armed with external and internal detectors. So. 3. following assumptions are made: 1. There are three kinds of objects in this simulated environment: a] predators. they simulated it. the best possible antibody is desired. Ep amount of energy is consumed. For avoiding over-charging. 9] In order to verify the ability of their proposed. b] obstacles and c] foods. to survive.

The internal detector detects energy level. The typical inference/consensus system adopt a condition-action description just like in fuzzy inference and 40 . direction and distance. mid and far. The paratope and idiotope are divided into three positions: obstacles. The distance is also detected by each detector in terms like near. Figure (11) Structure of Robot [8] 9. The important thing for immunobot is to select the best antibody for antigen and such is dependent on the how the antibodies are described.1 Description of Antibodies The prepared competence module is antibody. The selection should be made in bottom-up manner with proper communication between the modules.predators. Paratope is desirable condition and the epitope is disallowed condition. obstacle and food. The structure of paratope and epitope is crucial for specificity or we can say for identity of any specific antibody.

and makes the immunobot move forward to pick it up. Figure (12) Antibody Description [9] The prepared antibody for antigen can be like below: The antibody is activated if the immunobot detects the food in the front direction and mid-range. Figure (13) Prepared Antibody [9] 41 .the proposed system uses condition-action-condition manner. Such manner provides decentralized dynamic inference in a bottom-up manner.

the prepared antibody can hesitate to be activated. One state variable is introduced in terms of concentration of each antibody. antibody 1 means that the food is detected by immunobot in far range in front direction and so it is allowed to move forward. or if a food is in near range. Other situations involve immunobot identifies food in near range/predator in front/high energy level. the authors allow only one antibody to get activated when it surpasses the prespecified threshold. For instance. 42 .2 Dynamics In this model. if a predator exists in front and near/mid range. =matching ratio between antibody i and j. the other antibodies are designed. 9. 9. {∑ ∑ } … (23) = concentration of antibody that varies with time.3 Basic mechanism of the proposed inference making network Four antigens are listed in the figure shown and the listed five antibodies mainly participate in the inference/consensus making. On similar lines. this antibody would stimulate other antibodies whose paratopes displays such conditions.However.

Aickelin and Cayzer include the following aspects in their AIS from danger theory: 1. Danger signal is either positive or negative. The concentrations of these very antibodies are incremented in accordance to its antigen. Appropriate number of APC to display danger signals needs to be modeled.1 Danger Theory based algorithms In 2002. 2. representing the presence or absence of the signal. 3. Latest Immune Models and Hybrid Approaches 10. antibody 3 is selected [9]. the antibodies 1.Figure (14) Antibody Selection [7. 10. 43 . antibody 5 is selected in figure 9. and 5 are stimulated by the antigen. In the end.9] Consider current energy level high. The interaction within immune network‟s antibodies is importan. In the case of current energy level low. 2.

So far as biology is concerned.3. Sometimes the killer cells causes self cell death.These aspects are used to build better AIS for anomaly detection in which the non-self do not trigger immune response without danger signal [7]. DT depends on the concentration so different immune cells. Figure 15 (a) One Signal Model [7] Figure 15 (b) Two Signal Model [7] 44 Figure 15 (c) APC controlling IR [7] . the danger zone is spatial but in computation model the other notions such as temporal proximity is used. 5. this should not generate other danger signals. Antibody migration rule should specify the concentration of antibodies receiving signal 1 and signal 2 from a given APC. 4. Priming killer cells should be considered via APCs in AIS models 6.

Figure 15 (d) INS with third signal [7] Figure 15 (e) danger in control through zoning[7] Figure 15 (f) Control through INS and zoning [7] 45 .

Present antigen to the system 5.In 2010. Introduce antibody population and memory 2. For i=0 to antigen population do 4. Antibodies that receives both 0 and 1 signals are selected 9. General antibody population receives signal 0 from antigen presented 7. Now the calculate the interaction between antibody and antigen 12. The proposed method is described below: The algorithm regarding the proposed method are as follows: Algorithm 1 Danger theory based immune algorithm. 1. End for 46 . For all antibodies belonging to stimulated antibodies 10. Now the danger is created by antigen presented 6. General antibody population receives signal 1 from danger zone 8. the online supervised two-class classification problem was attempted to solve by using danger theory. While stopping conditions are not met do 3. Change the status of antibodies 11.

Check the stopping criteria 22. For all antibodies belonging to stimulated antibodies 16. End for 20. Initialization: The above algorithm mentioned starts with the antibody random population and they are assigned labels. Apply clonal selection algorithm 18. If the antibodies stimulation reaches certain threshold value then 17. Their status are set to zero and memory are set to empty set. Decrease the danger from the antigen which has been already considered 15. End if 19. A simple process in which an unknown antigen will be classified as the same class as the antibody with which it has the very low affinity. the output antibodies are used to classify for unknown antigens. 2. End while 23. Suppress antibody population 14. Two kinds of signals: The detection of danger signals are co stimulation signal which are termed as 1 while other are termed as 0. Output is the memory of antibodies selected via clonal selection and met threshold value When the learning algorithm is ended.13. Learning Algorithm explained: 1. The antibodies populations are divide in to 47 . End for 21.

So. The memory antibodies are not interested in reaction with antigens. The general antibodies get signal 0 when presented with antigen. Var = stimulated antibody population 11. Antibody-Antigen reaction =1 4.two parts. End if 7. Calculate the antibody stimulation = antibody +antibody . Antibody stimulated = antibody stimulated +1. a] general and b] memory. Variable danger zone (var) = affinity between antigen and antibody 9. Antibody – relevance = antibody-relevance + antibody antigen reaction 8. Algorithm 2 1. Else 5. the antibody can detect the stimuli of current antigen and when signal 0 is perceived only when danger zone is created. Antigen danger = Var *var*antibody stimulation 48 .antigen reaction * var 10. If antibody label == antigen label then 3. They are changed only when they are suppressed. 2. Antibody-Antigen reaction = -1 6. They are the fixed memory of antigens. The antibodies receiving both signals are stimulated and can change their status.

as =0 7. If random < p1 then 49 . For all pairs do 3. Randomly pair the stimulated antibodies 2. now convert the antibody to memory antibody 11.Algorithm 3 1. If antibody stimulation (as) < threshold value (t) then 2. Antibody label = -1 * antibody label 5. end if Algorithm 4 1. Calculate probability p1 4. else 8. clone antibody that has high affinity 9. Antibody stimulation = 0 6. Delete antibody population that are less than threshold 3. then perform mutation process for cloned antibody 10. Else if as <= t then 4.

5. End if 7. If random< p2 then 12. The presence of danger signal may or may not show change but the probability of change is higher than the normal situations. Yeom used a approach of mixing DT and DC to form model for signal precategorization. The sudden and bizarre or chaotic death of internal components of cell causes danger signal to surface up. 50 . For all pairs do 10. End if 14. Pathogens associated molecular proteins (PAMPs) are expressed by bacteria that can be identified by DCs for change in behavior. 2. Delete the antibody with high interactivity 6. DCs are sensitive to concentration of danger signals. Calculate probability p2 11. The following are principles: 1.2 Combining Dendritic Cells and Danger Theory In 2007. End for 8. End for 10. Group the memory antibodies in to pairs 9. Danger signals are generated by unplanned death of necrotic cells. Remove the memory antibody with high affinity 13.

Such safe signals give rise to suppression signals. DCs can stimulate naïve T cells and have number/ of functional properties (Yeom. It is inspired by the communication and processes of T-cell dependent humoral immune response. then DC gets matured differently [7]. According to Yeom (2007). DCs collect antigen and experience danger signals from necrosing cells and safe signals from apoptotic cells.3 Multilevel Immune Learning Algorithm (MILA) Both T and B level recognition mechanism is used in this algorithm. apoptotic signal and inflammatory signal.3. Maturation of DCs occurs in response to the receipt of these signals. In biological immune system. 51 . if there is concentration of danger signals in the tissue at the time of pick of antigen. although the process of inflammation is not enough to stimulate DCs alone. namely. if there is safe signal. the DC is fully matures. In tissue. Modulation between these state is facilitated by identification of signal between tissues. DCs perform different functions depending upon their state of maturation.cells recognize antigen through immnoglobin receptors on their surfaces but they are not proliferate and differentiate until the green signal is given from Th cells. Conversely. 4. B. Inflammatory cytokines can be released as a result of injury. 2007) DCs first function is to inform immune system to respond when there is attack. 10. danger signal. Safe signals are due to normal death of any cell for regulations reasons and the tightly controlled process results in the release of various signals into the tissue.

Th cells should get stimulated and that happens only when Th cells recognize antigens in the context of major histocompatibilty complex (MHC). similar to populations of Th. The concept of prematuration and crossover operators can be used. Ts. the intermediate one. an abstraction of above events is incorporated to develop detection algorithm. The algorithm consists of initialization. In initialization phase. 3.cell level. An evolutionary phase in MILA is a process of refining the detector set if the earlier detection rates can be evaluated. however cloning in MILA is targeted one only those detectors that are activated in the recognition phase can cloned [7]. Th. In MILA. B-cell level. mutate. APCs level. This phase involves cloning. bit level for local patterns. select. Suppression of B cells also occurs due to suppressor T cells. evolutionary and response. The activated B and T cells move to lymph nodes where they proliferate. MILA use rcb-matching rule for real valued representations. B cells uses randomly chosen w elements. and selection. The another feature of MILA is positive selection by Ts cells that are based on self samples. and death of B cell takes place in germinal centres (GCs). Bcells which participate in immune response (humoral). mutation. differentiate. There are three level : 1. However.For Th cells to allow B cells to proliferate and differentiate. The result of initialization is used to produce detectors. the detection system is trained to recognize the self. recognition. 52 . A Th cell uses the slide window to get the w elements. 2. that corresponds to highest one.

only positive samples are available (self-sample) at the training stage. Then samples from the both classes are used for neural network for self organizing map (SOM). a hybrid algorithm is proposed by Gonzalez (2002) which is used to create synthetic samples from a set of self-samples. Figure (16) NS-SOM in generation classifier dataset [7] . negative samples are generated from positive samples.4 Combining Negative Selection and Classification technique In anomaly detection technique. The algo develop the detector set that covers the non-self space using NS and then points are used to generate the samples for non-self class allowing the use of conventional algorithm useful. is a type of AIN that is trained to produce 53 .10. In order to allow conventional algorithm to be used. most conventional classification algorithms need noth self as wells as non-self algorithms. Particularly. An SOM. composed of nodes or neurons (that are able to identify input type) . However. when only self samples are there.

8]. a hybrid algorithm is proposed by Gonzalez (2002) which is used to create synthetic samples from a set of self-samples. when only self samples are there. The three phases of NS-SOM are shown in figure below: Figure (17) NS-SOM Model Structure [7.a low-dimensional representation of the input space or self/non-self feature space of the training samples called “map. The algo develop the detector set that covers the non-self space using NS and then points are used to generate the samples for non-self class allowing the use of conventional algorithm useful.8] 54 . In order to allow conventional algorithm to be used.” [7.

The first two sensors are not ON in their Khepera II robot 2. The subset of 20 antibodies is chosen randomly. Immune Networks and Negative Selection Based algorithm The mixture of Negative selection and Ab-Ab communications algorithm was developed for navigation control and path mapping of autonomous mobile robot by Prashant Rao (2008) for Khepera II robot. Each antigen stimulates many antibodies but only one is perfectly matched and so selected for process. The following is the step by step formulation of the algorithm: 1. Population Loop: i) Antigenic Recognition: The information from the sensors is collected and an antigen is formed based on that information. iii) Network Communications: The interactions between different selected randomly antibodies is calculated. Initialization: First initialize a network of immune cells (there is superset of 64 antibodies from 0 to 63). iv) Dynamics: The stimulation minus suppression added to affinity between antibodies subtracted from the natural death co-efficient gives over all stimulation 55 . The initial concentrations of antibodies are initialized and the robot is reset.11. The matching is determined between antigen and randomly selected antibodies and affinities are allotted. ii) Self-Nonself Determination: The antigen is seen for matching to self set in case innate memory takes over and system is allotted standard solution and the loop executes again OR the system moves on to next step. The stimulation and suppression between antibodies using basic matching function is defined.

Feedback: The penalty allotted T-cell helper is activated and its calculation is determined at each step. The antibody with high concentration is sent to critic that rewards or penalize and in respect to this affinity are modified. Step 2 and 3 are repeated until convergence criteria is met. The product from the stimulation and concentration of antibodie provides us with the rate of change of concentration with time. Adaption function is determined by interaction between T-cell and other cells in network by modifying the affinities between antibodies employing a suitable learning rate. 4. Figure (18) Algorithm based on Negative selection and Ab-Ab interaction [6] 56 . 3.of the system.

Figure (19) Algorithm based on Negative selection and Ab-Ab interaction [6] 11. APCs stimulate T-helper cells and which finally gives rise to adaptive immune response. mature and semimature. The danger signals are detected by dendritic cells which acts in three modes namely immature.1 Latest Dendritic Cell Algorithm Inspired from Danger Theory Danger theory states that the dangers signals are generated to activate APCs. If the signal detected is safe then the dendritic cell become immature upon presenting 57 .

stop stop forall data items in S do count the number of times data item is presented by a mature and semi-mature DC Label item to be safe if if presented by more than semi-mature DCs than mature DCs. [11] ALGORITHM: input : S = set of data items to be labeled safe or dangerous output :D = set of data items labeled as safe ordangerous. P forall DCs in set P do Add data item to DCs collected list Update safe. If the dangerous signal is found then the dendritic cell is matured and T-cell become antigen reactive. The dendritic cell algorithm takes into consideration safe. D Create a set to include the migrated DCs. danger and PAMPs signals. Start Generate initial population of dendritic cells (DCs). M forall items in set S do Select a set of DCs by randomly selecting from D.antigen to T-cell. danger and PAMPs concentrations Update cytokines‟s concentration Move DC from D to M and generate a new DC in set D if the concentration is above threshold. Add data item to labeled set M Stop [11] 58 .

11. Collect set of system calls that are made in training data 2. Collect signal values correspondingly 3. Figure (20) Systematic Overview of TLR algorithm [7] 59 .2 Latest TLR (toll-like receptor) Algorithm Algorithmic steps of TLR algo as described by Aickelin and Greensmith (2007) which is simply designed for anomaly detection in computer networks are as below: 1. Determine the complement set of sets in step 1 and step 2.

Migrated smDCs and mDCs and killed nTCs are replaced by new cells as per steps 4 and 5. 6. it matures (mDCs) and migrates. 7. If smDC expressing antigen matches nTC . then nTCs are activated and it is said that we have anomaly. 10. 12. Similarly. Generate immature DCs (iDCs) set with signal receptors selected randomly from the complement signal set and with antigen receptors randomly selected from the complement system call set. respectively. If an iDC do not migrate in its lifetime. Immature DCs are exposed to sample signals and antigens. 8. If mDC presenting antigen matches to naïve T cell. it is semi mature DC (smDCs) and then it migrates. 9. If iDCs matches the signal. then it kills nTC to lower false positives. 5. 11. generate naïve T-cells (nTCs) with antigen receptors randomly drawn from complement system call set. [7] 60 . Migrated smDCs and mDCs present their antigen and try and match nTCs.4.

Figure (21) Problem Solving Using AIS [7] 61 . Next step is to decide which AIS is beneficial to create a set of suitable entities that can provide a good solution to the problem in the context [7]. To encode such entities. The first step is to identify the elements involved into the problem and how they can be represented in terms of particular AIS.12. one must first select the immune algorithm depending on the type of problem. bit-string. Then the affinity determination measure is selected related to matching rules employed. Recent Developments and Real world Applications Solving problems using Immunological Computation In order to apply the knowledge of biological immune system to real world problems. etc. real valued. representation approaches can be chosen.

The virus detection software continuously scans the system to detect the changes. In this.12. known viruses are identified by their computer coded sequences and unknown viruses are detected by their unusual behavior in the system. Figure (22) Flow Diagram for Khephart approach for virus detection [7] 62 . These changes triggers the release of decoy programs whose sole intention is to become infected by virus [7].1 Virus Detection Kephart(1994) proposed immunologically inspired approach to detect viruses in computer system.

Once the best possible signature is found from virus infected programs. The signature extractor also must select the virus signature so that it can avoid false-positives and false-negatives.” for high level characteristics of self / non-self space. 12. The repair information is checked by testing on samples of the virus and again by human expert [7]. then an alarm is raised [7].3 Danger theory in Network Security Aickelin (2002) first proposed danger theory application to network security. The infected decoy programs are processed by signature extractor to generate the recognizer for the respective virus. If one or more decoy programs are modifies. AIS approach was able to produce detectors that gave a good estimation of the amount of deviation from the normal [7]. Their system behaves like DCs looking for danger signals just like impulse increase in network traffic or abnormally high flow of error messages.2 Immunogenetic Approaches in Intrusion detection Gonzalez (2002) proposed negative selection with detector rules to detect attacks by monitoring network traffic. it id compared with half-gigabyte corpus of legitimate programs to make sure that there is no false-positive. then it is sure that the virus has entered the system and each decoy program contains the sample of virus. The signature extractor also extracts the attachment pattern of virus to the host in order to repair the host in case. A real valued representation is used for evolving hyper-rectangular shaped detectors.A diverse suit of decoy programs are kept at different locations in the system‟s memory to detect virus. If such signals goes above threshold. 63 . 12. The experiments were performed using data from 1999 Defense Advanced Research Project Agency intrusion detection evaluation dataset. The signature must be found in each sample of virus and it is very likely not to be found in uninfected programs in computer system. interpreted as “if-then rules.

data mining. wall. The metaphor of antibodies.5 Conserved Self Pattern Recognition Algorithm (CSPRA) This very algorithm is recent algorithm in AIS area with an inspiration from Pattern Recognition Receptors Model (PRR). For the immunoid to take decide to the best. 1999) and Lee et. etc.12. fault detection. Vertebrate immune systems are inspiration for computer scientist and engineers to create new algorithms in order to solve real world problems. (1996. Artificial immune networks 3. According to PRR Model. Danger theory and dendritic cell algorithm The recent development include AIS application in computer security. (1999) focused on the development of dynamic decentralized consensus-making mechanism based on the immune network theory. Hart and Timmins (2010) discussed application of AIS and proposed a set of problems features for the heavy applications of AIS. Wantanabe et. which were potential behaviors of immunoid . Clonal selection algorithm 4. home base. the immunoid is able to collect the garbage. (1998. Many authors have explained the recent developments in AIS just like Garret (2005) who tried to deal with the development before 2005 and attempt to make evaluation of AIS in criteria of distinctiveness and effectiveness. al. four main AIS algorithms are: 1.4 Robotics and Control Robot controlled by Ishiguro et. al. 1998) . In dynamic environment. optimization. Some of the recent developed models and Hybrid approaches are explained below: 12. antigens were related to environmental inputs just like garbage. the self/nonself discrimination requires 64 . Negative selection algorithms 2. it matches antigen to antibody [7]. al.

Self pattern recognition by APCs is not done till antigen is not detected by T-cell negative selection algorithm. MHC layer. On the other hand if one sees.…. By evaluating the maximum. 13] 12.. The generation of APC detector includes two major steps: 1. competitive layer and stimulation layer. we define the conserved self pattern that can be pre-defined from the data. 4.. then the molecular complex pattern formed is given to MHC layer for processing. min. the PRR model added additional layers of molecular patterns. (loc2. [3. CSPRA (2010) naturally include negative selection algorithm and the anomaly detection in CSPRA is performed by combining the results from APCs self pattern recognition and T-cell negative selection..6 Recent Complex Artificial Immune Systems (CAIS) CAIS consisted of five encountered layers namely encounter layer. In this Th layer.. max. The input is given to APC layer. APCs are not stimulated until and unless they are activated via PRR that identify molecular patterns on bacteria. mean). mean)…. loc2……. the cells receive different responses from MHC layer and develop a set that consists of Th cells that provide better response to input antigens. As compared to classical negative selection algorithm. minimum and mean of all the values in the features space of loc1. max. preprocessing layer. So.generate APC detector R = {(loc1. Depending on the function between antigen and its feature space.stimulation from APC.} within the conserved self pattern of features located in loc1. The information coming from APC is transformed and translated into MHC and feed to Th layer. miin. Antigen and Antibody are termed as the input and output. One is in which B cell direct recognition and the other way is through the APC layers. B-cells 65 . loc2. This very data includes the empirical one from the laboratory or it can be calculated mechanically by using Pearson‟s co-efficient values between the coloum of each attribute and their respective label. 2. Suppose an antigen is encountered by the system then there are two ways in which we can recognize it. for sure. the proposed and tested CSPRA Algorithm shows more better and promising results reducing the number of false errors without increase the complexity.

Now put randomly generated antibodies in the selected ones to maintain diversity [13]. It can be applied to hand writing pattern recognition problem [11. BAIS is capable of capturing the most relevant interactions between the problem variables. Sample the antibodies d. The very algorithm adopts the population based strategy for search and Bayesian network for implementing the probabilistic model. c. It has the ability to handle the building block in optimization of Trap-5 and such building blocks are non-overlapping and overlapping. Remove the antibodies with lower fitness and so the similar ones in the criteria e. Once the population is initiated. the CAIS has invariant feature to recognize translation. b. BAIS can be applied for feature selection using wrapper approach. It is capable of identifying 66 . develop the Bayesian networks that best fits to the selected best solutions. An antibody is the difference between an input and weights associated with b cells. select the best population from the given set. the algorithm starts the loop with stopping condition and the following steps are evaluated for loops: a. rotation and scale patterns.become activated due to stimulation from Th layer and also by input pattern. As compared to binary immune systems. Ts cells modulate the weights associated with immune cells located in neighborhood set. Such a approach is termed as the Multiobjective Bayesian Artificial Immune Systems (MOBAIS) that can be applied for classification problems. 12. 13]. For the best solutions. Using proper selection technique. The multi objective Knapsack optimization can also be solved very efficiently by BAIS algorithm.7 Hybrid Approaches BAIS (Bayesian Artificial Immune Systems) is developed by removing the mutation and cloning operators from the probabilistic model for solving the optimization problems and multiobjective optimization.

Radial Basis Function (RBF) artificial neural network and AIS are combined for compression of the data in the set. In the immune RBF neural network model. Such a tool is called as aiNET. A multiple valued immune network classifier (MVINC) based on immune netwotk theory was applied for remote sensing images and performing immune memory using logic theory and immune theory for classification. AIS with SVM can be used for fault diagnosis of induction motors. this algorithm for the evolution for memory cells. each agent recognizer is an immune RBF neural network model. 67 . In this algorithm. Furthermore the Bayesian networks were enhanced by learning to avoid the synthesis of the network at each iteration and only update those two parameters that are crucial for example the conditional and marginal probabilities at each iteration [13]. The algorithm with an unstructured damage classification based on the data clustering and AIS pattern recognition can be performed. EaiNET combined the AIS and Particle Swarm optimization which uses the learning technique of PSO which is nothing but the each individual is able to learn the best from the social population on account of which the convergence rate increases.IS pattern recognition algorithms. Such a technique uses the data clustering training data to a specified number of clusters and generate the initial memory cell set. The practical application shows that it has parsimonious results and thus shows accurate results. local optimal. antigen is input and the antigens are the compression cluster mapping that is the hidden layers. This can also be used for determining the number of RBF in ANNs and thus termed as RBFNN. In immune multiagent recognizer. each level of recognition systems contain recognizer that can recognize a sort of antigen. By combining Afor example.and preserving the building blocks effectively while it can search and find diverse high leve. The output weight can be determined by using least square algorithm. AIS is used for tuning the parameters of kernel and penalty for classification accuracy.

The performance of the proposed method shows promising result in terms of pattern recognition. The gene immune detection algorithm with complement operator decreases effectively false position surfaced up in the previous gene immune detection. Also the vaccine and the complement are introduced. 68 . The design part includes the diversity evaluation that is very complex and fault detection is hard. Particularly. the computational properties of degenerate recognition systems are investigated. The complement operator overcome the defect of the gene immune algorithm and the detection time can be increased drastically. the Network Affinity Threshold (NAT) does not calculate the network evolution process because the network granularity is determined by NAT and the initial value is calculated by distance between the antigens. The convergence of the public and the stability can be impaired by pure clonal selection and random change operation. recognition appears quickly. In this. It is possible to determine the degenerate receptors and that when compared to a non degenerate system. fault calculation technique integrated the induction and static was designed [13]. The number of detector are reduced and the efficiency of detection is increased. ICAIS for incremental clustering based on the principles of AIS was introduced and it implements incremental clustering and uses the basic immunity response to determine the data regarding to novel clusters and it also uses the secondary immune response to identify the data to old patterns [13]. by combining the agent based modeling and UML.Immune Network method based om Multi Epitope approach.A fault diagnosis model was proposed based on the immune evolution algorithm. Based on Learning Vector Quantization (LVQ) and immune network [13] model that is an extension to the basic Jerns‟s Model was proposed that can be used for pattern recognition. The new classification Hybrid Fuzzy Neuro. In the resource limited AIS.

-> weight matrix (Ab population) -> winner for each Ag (v) -> amount of winning of each individual (tau) -> hamming distance of each Ag with relation to its mapped class -> antigen population to be recognized (n2xs2) -> ball of stimulation -> comparison: 1 for comparing complementary chains 0 for comparing identical chains (Hamm. end. Hamming Distance.alfa.APPENDIX A Pattern Recognition in the Immune System using a Growing SOM [ The following project is taken from Ph.eps.. [C. if maxno > np.6.eps.')).win.cwin. D Thesis of Leonardo De Castro ] function [w.win. [np.1.no)).D] = abnet(ag.pm). vno = [1:1:no].s2] = size(ag).C)). MATCH. disp(sprintf('Possible number of classes: %d'. SPLIT. disp(sprintf('Initial number of classes: %d'.pc.maxno] = cover(ni. alfa = 3. vep = [0]. no = 1. beta = 3.pc.pm).maxno)). TESTGSOM The columns of w must be similar to each Ag if nargin == 2.comp. dist. alfa0 = alfa.np)). % disp(sprintf('Affinity threshold: %d'. disp(sprintf('Maximum number of classes (N): %d'. disp(sprintf('Press any key to continue.beta. 69 . UPDATE. TD = 1.. % % % % % % % % % % % % % % % % % % % % % Pattern Recognition in the Immune System using a Growing SOM Bipolar Splitting/Pruning Self-Organizing Feature Map (GSOM) with Evolutionary Phase Main features: bipolar weights. PRUNE.comp.beta. maxno = np. pm = 0.eps)). CADEIA. disp(sprintf('Coverage of each Ab: %d'.) -> amount of bits to be changed -> number of iterations for reducing the learning rate Auxiliar functions: COVER. end.cwin. comp = 0. [n2.eps).alfa.D] = hybrid(ag. % Network parameters ep = 0. Winner takes all PHASE I: Growing followed by Pruning PHASE II: Supervised Evolution function w win cwin D ag eps comp alfa beta [w.ni] = size(ag). pc = 0.

if alfa > 1.no. s2 = s1. n2 = n1.0d no: %d LR: %d TD: %d'. disp(cwin). vet = randperm(np). alfa = alfa . bip = 1.cwin.'or').perc] = testgsom(w.alfa0).alfa] = prune(w.ind. disp(sprintf('Final Architecture: [%d.alfa.ag. disp('Concentration Level: '). plot(vep.no). hold on. k = 0. bip = 1.alfa.indmin.05*max_ep & rem(ep.% % INTERNAL SUBFUNCTIONS % % --------------------------. [v(k). disp('Minimal Antigenic Affinity (HD)'). end. % Growing Phase if (rem(ep. 70 . D = [].no. i = vet(k).2f%%'. vep = [vep ep]. % Learning rate decreasing if (ep > 0.'. TD = sum(v). end.win. end.vno).1).alfa0).ep. w = update(w. [v.TD)).s1. if aux == 0.alfa. k = k+1.perc)). figure(1). hold off.n2.pause. % Pruning Phase [aux. % Network Definition while (ep < max_ep & TD > 0)% & no < maxno).ag] = cadeia(n1.comp).indmin] = min(cwin).s2. end. elseif nargin == 4.alfa] = split(cwin. [w. disp(v).ag.0. [w.bip) if nargin == 2. axis([0 ep+1 0 no+1]). win(i) = ind. end. ep = ep + 1.vno.no. end.05*max_ep)==0). disp(sprintf('Percentage of misclassified Ag: %3.%d].win.ind] = min(D). cwin = zeros(1. vno = [vno no]. % --------------------------. max_ep = (beta + 1) * maxno. vno = [vno no].eps).% % Function CADEIA function [ab.:)').no)).beta)==0). end. % Assincronous while k < np.mXOR] = match(w'.mXOR(ind.:). [D.ni. cwin(ind) = cwin(ind) + 1.0.ag(i.1.w.eps.no.0. [w] = cadeia(ni. disp(sprintf('IT: %4. title('Growing Evolution'). plot(vep.xlabel('Iteration').

end.1. [val.ind] = min(D). w = [w. k = 100 * (sum(v > eps) / np). end.1. for i=1:np. [ind] = find(cwin > 1). [v(i).% Antibody (Ab) chains ab = 2 . end.:). [aux.out+1:end)].no. v = find(win==out). alfa = alfa0. Mag = ag(v.alfa] = split(cwin. [np. if bip == 1.* rand(n1. k = 0. w = [Mag(new. % matrix of ag mapped in the same output D = match(Mag.eps).:)'. else. % out = ind(1). if out == 1.eps.0).cwin.Mag(new.no] = size(w).out)'. end. end.out] = max(cwin). cwin = zeros(1.:)'.* rand(n2. % End Function CADEIA % Function SPLIT function [w.win.ag. % End Function SPLIT % Function TESTGSOM function [v.new] = max(D). disp('** Growing **').w(:.alfa. ag = hardlims(ag). % End Function TESTGSOM 71 . ag = hardlim(ag). else.alfa0) [ni.Mag(new.w. elseif out == no.2)). else. end.:)']. no = no + 1.s2) .1:out).win.0).size(w.k] = testgsom(w. % Antigen (Ag) chains ag = 2 .ag. ab = hardlim(ab).:). if aux > eps. ab = hardlims(ab).ni] = size(ag).s1) . cwin(ind) = cwin(ind) + 1. [D] = match(w'.w]. if bip == 1.ag(i. % disp('** Running the trained network **'). win(i) = ind.w(:. w = [w(:. % which outputs map more than one Ag if ~isempty(ind).

ind) = -1 * w(pto.vXOR). disp('** Pruning **').no] = size(w). [ni.1:ind-1) w(:. C = 0. disp(sprintf('Ball of stimulation bigger than chain length %d'.no] = size(w).alfa.ind. else. fat = prod(1:1:m). fat = 1. eps = input('Enter a new ball of stimulation: '). end. 72 .no. disp('Negative value'). else. w = w(:.% Function PRUNE function [w. while eps > len.ind). break. fat = fatorial(len). [val.pto] = max(vXOR). alfa = alfa0. end. [ni. w(pto. elseif ind == no. vXOR(pto) = 0.2:no).1.ind. C = C + (fat/(fatorial(i) * fatorial(len-i))). end. for j = 1:alfa.eps). if m == 0. elseif m < 0. no = no . w = w(:. % exit loop if vectors are equal end. no = ceil((2^len)/C).alfa] = prune(w.len)). % End Function PRUNE % Function COVER function [C. end. % End Function FATORIAL % Function UPDATE function [w] = update(w.no.eps] = cover(len. for i=0:eps.1:no-1). if val == 0. w = [w(:.ind+1:no)].alfa0). % End Function COVER % Function FATORIAL function fat = fatorial(m). if ind == 1.

ag.mXOR] = match(ab. % End Function MATCH clear all alfa = 3. OUTPUT: Coverage of each Ab: 2069256 Initial number of classes: 1 Possible number of classes: 2 Maximum number of classes (N): 1 Press any key to continue. pc = 0. pm = 0. w = abnet (ag. beta = 3. end. % Using the XOR operator for calculating the match score [n1. if comp == 1.ag). comp = 0.1) * ag. comp = 0. msc = 1 . msc = [].+1) strings to binary ones (0.comp.6.s1] = size(ab).end. eps = 15.1. % Hamming distance end. ag = hardlim(ag). % End Function UPDATE % Function MATCH function [ms. ag = ones(n1.beta.. ms = sum(mXOR').. IT: 1 no: 1 LR: 2 TD: 13 IT: 2 no: 1 LR: 1 TD: 10 IT: 3 no: 1 LR: 1 TD: 8 IT: 4 no: 1 LR: 1 TD: 7 73 .pm). ms = msc.comp) if nargin == 2. % ms complement % Converting bipolar (-1.ms. ag=[1 2 3 9 8 7 6 5 3 4 5 6 7 8 9 9 5 3 2 1 4].eps. % Multiply the Antigen mXOR = xor(ab.alfa.pc.+1) ab = hardlim(ab).

8 0.4 1.00% Minimal Antigenic Affinity (HD) 6 Concentration Level: 1 Final Architecture: [21.5 2 2.5 5 74 .4 0.6 0.1].6 1.5 1 1. w = 1 1 1 1 1 1 1 1 1 1 1 1 1 -1 1 1 -1 -1 -1 -1 -1 Growing Evolution 2 1.8 1.Percentage of misclassified Ag: 0.5 Iteration 3 3.5 4 4.2 1 0.2 0 0 0.

However. Clonal selection algorithm 4. the success of these applications is till limited by the lack of any exemplars that really stand out as killers AIS application 75 . Danger theory and dendritic cell algorithms. Though an extensive amount of AIS applications has been developed. The field of AIS has obtained a significant degree of success as a branch of Computational Intelligence since it emerged in 1990s. Artificial immune networks 3. the other aspects of the biological immune systems are motivating computer scientists and engineers to develop new models and problem solving methos. It has been revealed that research is centered on four majors AIS algorithms: 1. Negative selection 2.Conclusion: The immune system is a remarkable information processing and self learning system that offers inspiration to build artificial immune systems (AIS).

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