A DNA Codification for Genetic Algorithms Simulation

In this paper we propose a model of encoding data into DNA strands so that this data can be used in the simulation of a genetic algorithm based on molecular operations. DNA computing is an impressive computational model that needs algorithms to work properly and efficiently. The first problem when trying to apply an algorithm in DNA computing must be how to codify the data that the algorithm will use. In a genetic algorithm the first objective must be to codify the genes, which are the main data. A concrete encoding of the genes in a single DNA strand is presented and we discuss what this codification is suitable for. Previous work on DNA coding defined bond-free languages which several properties assuring the stability of any DNA word of such a language. We prove that a bond-free language is necessary but not sufficient to codify a gene giving the correct codification.

On Solving the Maximum Betweenness Problem Using Genetic Algorithms

In this paper a genetic algorithm (GA) is applied on Maximum Betweennes Problem (MBP). The maximum of the objective function is obtained by finding a permutation which satisfies a maximal number of betweenness constraints. Every permutation considered is genetically coded with an integer representation. Standard operators are used in the GA. Instances in the experimental results are randomly generated. For smaller dimensions, optimal solutions of MBP are obtained by total enumeration. For those instances, the GA reached all optimal solutions except one. The GA also obtained results for larger instances of up to 50 elements and 1000 triples. The running time of execution and finding optimal results is quite short.

Parameter Identification of a Fed-Batch Cultivation of S. Cerevisiae using Genetic Algorithms

Fermentation processes as objects of modelling and high-quality control are characterized with interdependence and time-varying of process variables that lead to non-linear models with a very complex structure. This is why the conventional optimization methods cannot lead to a satisfied solution. As an alternative, genetic algorithms, like the stochastic global optimization method, can be applied to overcome these limitations. The application of genetic algorithms is a precondition for robustness and reaching of a global minimum that makes them eligible and more workable for parameter identification of fermentation models. Different types of genetic algorithms, namely simple, modified and multi-population ones, have been applied and compared for estimation of nonlinear dynamic model parameters of fed-batch cultivation of S. cerevisiae.

Solving Travelling Salesman Problem in a Simulation of Genetic Algorithms with DNA

In this paper it is explained how to solve a fully connected N-City travelling salesman problem (TSP) using a genetic algorithm. A crossover operator to use in the simulation of a genetic algorithm (GA) with DNA is presented. The aim of the paper is to follow the path of creating a new computational model based on DNA molecules and genetic operations. This paper solves the problem of exponentially size algorithms in DNA computing by using biological methods and techniques. After individual encoding and fitness evaluation, a protocol of the next step in a GA, crossover, is needed. This paper also shows how to make the GA faster via different populations of possible solutions.

DNA Simulation of Genetic Algorithms: Fitness Computation

* This work has been partially supported by Spanish Project TIC2003-9319-c03-03 “Neural Networks and Networks of Evolutionary Processors”.

Online Genetic Algorithms

This paper present a technique based on genetic algorithms for generating online adaptive services. Online adaptive systems provide flexible services to a mass of clients/users for maximising some system goals, they dynamically adapt the form and the content of the issued services while the population of clients evolve over time. The idea of online genetic algorithms (online GAs) is to use the online clients response behaviour as a fitness function in order to produce the next generation of services. The principle implemented in online GAs, “the application environment is the fitness”, allow modelling highly evolutionary domains where both services providers and clients change and evolve over time. The flexibility and the adaptive behaviour of this approach seems to be very relevant and promising for applications characterised by highly dynamical features such as in the web domain (online newspapers, e- markets, websites and advertising engines). Nevertheless the proposed technique has a more general aim for application environments characterised by a massive number of anonymous clients/users which require personalised services, such as in the case of many new IT applications.

Implementation of Genetic Algorithms for Transit Points Arrangement

The problem of transit points arrangement is presented in the paper. This issue is connected with accuracy of tariff distance calculation and it is the urgent problem at present. Was showed that standard method of tariff distance discovering is not optimal. The Genetic Algorithms are used in optimization problem resolution. The UML application class diagram and class content are showed. In the end the example of transit points arrangement is represented.

Genetic Algorithm for Finding the Key’s Length and Cryptanalysis of the Permutation Cipher

In this article we discuss a possibility to use genetic algorithms in cryptanalysis. We developed and described the genetic algorithm for finding the secret key of a block permutation cipher. In this case key is a permutation of some first natural numbers. Our algorithm finds the exact key’s length and the key with controlled accuracy. Evaluation of conducted experiment’s results shows that the almost automatic cryptanalysis is possible.

Genetic Algorithm Approach for Solving the Task Assignment Problem

This research was partially supported by the Serbian Ministry of Science and Ecology under project 144007. The authors are grateful to Ivana Ljubić for help in testing and to Vladimir Filipović for useful suggestions and comments.

Distributed Genetic Algorithm Implementation by Means of Remote Methods Invocation Technique – Java RMI

The aim of this work is distributed genetic algorithm implementation (so called island algorithm) to accelerate the optimum searching process in space of solutions. Distributed genetic algorithm has also smaller chances to fall in local optimum. This conception depends on mutual cooperation of the clients which realize separate working of genetic algorithms on local machines. As a tool for implementation of distributed genetic algorithm, created to produce net's applications Java technology was chosen. In Java technology, there is a technique of remote methods invocation - Java RMI. By means of invoking remote methods it can send objects between clients and server RMI.

An Adaptive Genetic Algorithm with Dynamic Population Size for Optimizing Join Queries

The problem of finding the optimal join ordering executing a query to a relational database management system is a combinatorial optimization problem, which makes deterministic exhaustive solution search unacceptable for queries with a great number of joined relations. In this work an adaptive genetic algorithm with dynamic population size is proposed for optimizing large join queries. The performance of the algorithm is compared with that of several classical non-deterministic optimization algorithms. Experiments have been performed optimizing several random queries against a randomly generated data dictionary. The proposed adaptive genetic algorithm with probabilistic selection operator outperforms in a number of test runs the canonical genetic algorithm with Elitist selection as well as two common random search strategies and proves to be a viable alternative to existing non-deterministic optimization approaches.