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Transgenetic NeuroEvolutionRatings:

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Published by Dr. Florian Neukart

Transgenetic algorithms can be used for performing a stochastic search by simulating endosymbiotic interactions between a host and a population of endosymbionts as well as information exchange between the host and endosymbionts by agents. The already introduced, computationally intelligent Data Mining system "System applying High Order Computational Intelligence in Data Mining” (SHOCID) applies such for Artificial Neural Network (ANN) learning by the combination of one of its learning approaches with a host organism, serving as genetic pool, and transgenetic vectors.

The application of an algorithm combining horizontal gene transfer between a host and a symbiont is a completely new ANN learning approach, which increases both learning performance and accuracy to a considerable degree. A further advantage is that the application of transgenetic vectors massively increases the chance of reaching the desired stopping criteria (like a minimum Root Mean Squared Error [RMSE]) instead of abort criteria (like the evolutionary stop after 5,000 generations without improvement although the desired have not been fulfilled), as even learning algorithms like back propagation cannot oscillate or get stuck in local minima due to the inescapable transfer of host genetic material.

The application of an algorithm combining horizontal gene transfer between a host and a symbiont is a completely new ANN learning approach, which increases both learning performance and accuracy to a considerable degree. A further advantage is that the application of transgenetic vectors massively increases the chance of reaching the desired stopping criteria (like a minimum Root Mean Squared Error [RMSE]) instead of abort criteria (like the evolutionary stop after 5,000 generations without improvement although the desired have not been fulfilled), as even learning algorithms like back propagation cannot oscillate or get stuck in local minima due to the inescapable transfer of host genetic material.

Transgenetic algorithms can be used for performing a stochastic search by simulating endosymbiotic interactions between a host and a population of endosymbionts as well as information exchange between the host and endosymbionts by agents. The already introduced, computationally intelligent Data Mining system "System applying High Order Computational Intelligence in Data Mining” (SHOCID) applies such for Artificial Neural Network (ANN) learning by the combination of one of its learning approaches with a host organism, serving as genetic pool, and transgenetic vectors.

The application of an algorithm combining horizontal gene transfer between a host and a symbiont is a completely new ANN learning approach, which increases both learning performance and accuracy to a considerable degree. A further advantage is that the application of transgenetic vectors massively increases the chance of reaching the desired stopping criteria (like a minimum Root Mean Squared Error [RMSE]) instead of abort criteria (like the evolutionary stop after 5,000 generations without improvement although the desired have not been fulfilled), as even learning algorithms like back propagation cannot oscillate or get stuck in local minima due to the inescapable transfer of host genetic material.

The application of an algorithm combining horizontal gene transfer between a host and a symbiont is a completely new ANN learning approach, which increases both learning performance and accuracy to a considerable degree. A further advantage is that the application of transgenetic vectors massively increases the chance of reaching the desired stopping criteria (like a minimum Root Mean Squared Error [RMSE]) instead of abort criteria (like the evolutionary stop after 5,000 generations without improvement although the desired have not been fulfilled), as even learning algorithms like back propagation cannot oscillate or get stuck in local minima due to the inescapable transfer of host genetic material.

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https://www.scribd.com/doc/107134332/Transgenetic-NeuroEvolution

11/29/2012

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© 2012 IEEE. Personal use of this material is permitted. Permission from IEEEmust be obtained for all other uses, in any current or future media, includingreprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuseof any copyrighted component of this work in other works.

This paper appears in:

Date of Conference:

24-26 May 2012

Author(s):

Neukart, F.Dept. of Electr. Eng. & Comput. Sci., Transilvania Univ. of Brasov, Brasov, RomaniaMoraru, S.-A.; Grigorescu, C.-M.; Szakacs-Simon, P.

Page(s):

1120 - 1125

Product Type:

Conference Publications

Transgenetic NeuroEvolution

Florian Neukart Sorin-Aurel Moraru Costin-Marius Grigorescu Peter Szakacs-SimonDepartment of Electrical Engineering and Computer ScienceTransilvania University of BrasovBrasov, Romania 500036florian.neukart@campus02.at smoraru@unitbv.ro costin.grigorescu@unitbv.ro peter.szakacs@unitbv.ro

Abstract-

Transgenetic algorithms can be used for performing astochastic search by simulating endosymbiotic interactionsbetween a host and a population of endosymbionts as well asinformation exchange between the host and endosymbionts byagents. The already introduced, computationally intelligent DataMining system "System applying High Order ComputationalIntelligence in Data Mining

”

(SHOCID) applies such forArtificial Neural Network (ANN) learning by the combination of one of its learning approaches with a host organism, serving asgenetic pool, and transgenetic vectors.The application of an algorithm combining horizontal genetransfer between a host and a symbiont is a completely newANN learning approach, which increases both learningperformance and accuracy to a considerable degree. A furtheradvantage is that the application of transgenetic vectorsmassively increases the chance of reaching the desired stoppingcriteria (like a minimum Root Mean Squared Error [RMSE])instead of abort criteria (like the evolutionary stop after 5,000generations without improvement although the desired have notbeen fulfilled), as even learning algorithms like back propagation cannot oscillate or get stuck in local minima due tothe inescapable transfer of host genetic material.

I.

I

NTRODUCTION

The biological fundamentals of transgenetic algorithms,which have been introduced by Gouvêa [1], for solving NP-hard combinatorial problems have already been elucidated indetail by Goldbarg & Goldbarg [2], but have to be adapted for ANN evolution. According to Gouvêa ComputationalTransgenetics (CT) [3] brings the following ideas to theevolutionary context:

Usage exogenous and endogenous information tointerfere on the processes of formation andmodification of individuals of a given population.

Usage of the intracellular flow as an operational wayto carry the required manipulations on theindividuals.

Exploration new processes of populationimprovement using transgenetic agents andcompetition between agents and individuals.

Guidance of the evolutionary process allows theoccurrence of evolutionary jumps [4].As in nature, the relationship between a host organism anda symbiont may be an advantage for both organisms, and thedescendants share genetic material of both the host and thesymbiont. The host organism in SHOCID [5] mostly servesas genetic database and contributes to the final solution withgene sequences. The endosymbiont is the real solution, whichis being evolved until predefined stopping criteria have beenmet. However, the manipulation of the endosymbiont'sgenetic material does not only happen through horizontalgene (sequence) transfer of the host's genetic material to theformer one, but also by some special types of mutation in itschromosomes, or in case of population-based learning,genomes.Both changes in the endosymbiotic DNA are carried out byagents, the so-called transgenetic vectors. SHOCIDtransgenetic NeuroEvolution makes use of the followingtypes of vectors:

Plasmids

o

Weight Plasmid

o

Structure Plasmid

Transposons

o

Jump and Swap Transposon

o

Erase and Jump TransposonPlasmids are used for the transportation of geneticinformation from the host to the endosymbiont, andtransposons mutate the genetic material of the endosymbiont.Figure 1 provides a brief overview of how transgenetic NeuroEvolution works:

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R e - i n t e g r a t i o n

Host genetic materialEndosymbiont

Fig. 1 - Transgenetic NeuroEvolution

The picture shows on the left side the host, which serves asgenetic database for the horizontal gene transfer, carried out by plasmid vector agents. One weight plasmid on the left side below transports a sequence of weights to the endosymbiont,as well as a structural plasmid above the host transfers theweights, biases and activation functions. On the right side a jump and swap transposon vector mutates the chromosome of the endosymbiont.

A.

Host genetic material

The host within SHOCID consists "rough" solutions to the problem statement, meaning several populations eachconsisting of thousands individuals each of them subject of continuous evolution. Therefore, the host is not only oneorganism, but thousands of organisms in different populations.

B.

Endosymbiont

The endosymiont within SHOCID is a simulated annealingANN solution, which simulates the cooling of metal.Simulated annealing belongs to the group of metaheuristicalgorithms, suitable for solving optimization or search problems. In physics, the term 'annealing' refers to the veryslow cooling of gas or metal into a crystalline solid of minimum energy configuration [6]. The atoms of suchmaterials have very high energy values at very hightemperatures, which gives the atoms a great deal of freedomin their ability to restructure themselves [7]. The energyvalues of such materials decreases during cooling down. If the ideal speed (continuous temperature reduction) has beenfound, the material will be stable in its structure and moreconsistent then if cooling it down too quick. Simulatedannealing (SA) [8] algorithms therefore simulate this behaviour, which can also be applied within ANN training.The simulated annealing algorithm always works with twosolutions, the first being the best one having been achieveduntil the point in time , represented by , and thesecond being the one currently being created and comparedwith the first one, represented by(2)If the second one performs better than the first one, thus theoutcome of the above equation is positive, it is used to replacethe latter as the current best one. In some cases, simulatedannealing also makes use of a probability of when to replacea solution with a better one, meaning that in someimplementations a better new solution might not alwaysreplace the actual one:(3), where

T

represents the current temperature, meaning thevalue that influences the change of weights within a weightmatrix of an ANN:(4)The ratio for changing the weights within anANN is calculated by multiplying the temperature by arandom number . The higher the temperature is, the higher isthe probability of a high weight change. Changes with aspecific temperature are carried out as long as a predefinednumber of iterations (cycles) has not been reached. After having fulfilled the last iteration of a temperature, thealgorithm verifies if the lowest, predefined temperature has been reached. If not, the temperature will be lowered byeither a constant or by logarithmically decreasing it by a ratio between a beginning and an ending temperature, as thefollowing equation shows [4]:(1)The variable s represents the starting temperature, e theending temperature. c represents the cycle count. The aboveequation calculates a ratio that should be multiplied by thecurrent temperature T, which produces a change that willcause the temperature to reach the ending temperature in thespecified number of cycles.The transgenetic vectors are being applied during thesimulated cooling process. Each iteration creates a new possible solution, and each new solution must endure theattacks of both plasmid and transposon vector agents to see if a better solution can be found.II.

A

LGORITHM

The algorithm for applying transgenetic NeuroEvolution isas follows:

TABLE IT

RANSGENETIC

N

EURO

E

VOLUTION

Start

1.

Creation of initial host populations.

2.

Repeat

a)

Randomization of weights and threshold values of each chromosome.

i.

Repeat

1.

Calculate the network output for the value2.

Evaluate the fitness of each chromosome:a.

Calculate the error for each outputneuron

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