An analysis of the XOR dynamic problem generator based on the dynamical system

This is the post-print version of the article - Copyright @ 2010 Springer-VerlagIn this paper, we use the exact model (or dynamical system approach) to describe the standard evolutionary algorithm (EA) as a discrete dynamical system for dynamic optimization problems (DOPs). Based on this dynamical system model, we analyse the properties of the XOR DOP Generator, which has been widely used by researchers to create DOPs from any binary encoded problem. DOPs generated by this generator are described as DOPs with permutation, where the fitness vector is changed according to a permutation matrix. Some properties of DOPs with permutation are analyzed, which allows explaining some behaviors observed in experimental results. The analysis of the properties of problems created by the XOR DOP Generator is important to understand the results obtained in experiments with this generator and to analyze the similarity of such problems to real world DOPs.This work was supported by Brazil FAPESP under Grant 04/04289-6 and by UK EPSRC under Grant EP/E060722/2

Using the clustering coefficient to guide a genetic-based communities finding algorithm

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-23878-9_20Proceedings of 12th International Conference IDEAL, Norwich, UK, September 7-9, 2011.We describe an approach taken for automatically associating entries from an on-line encyclopedia with concepts in an ontology or a lexical semantic network. It has been tested with the Simple English Wikipedia and WordNet, although it can be used with other resources. The accuracy in disambiguating the sense of the encyclopedia entries reaches 91.11% (83.89% for polysemous words). It will be applied to enriching ontologies with encyclopedic knowledge

Level-Based Analysis of Genetic Algorithms and Other Search Processes

The fitness-level technique is a simple and old way to derive upper bounds for the expected runtime of simple elitist evolutionary algorithms (EAs). Recently, the technique has been adapted to deduce the runtime of algorithms with non-elitist populations and unary variation operators [2,8]. In this paper, we show that the restriction to unary variation operators can be removed. This gives rise to a much more general analytical tool which is applicable to a wide range of search processes. As introductory examples, we provide simple runtime analyses of many variants of the Genetic Algorithm on well-known benchmark functions, such as OneMax, LeadingOnes, and the sorting problem

Genetic algorithm in ab initio protein structure prediction using low resolution model : a review

Proteins are sequences of amino acids bound into a linear chain that adopt a specific folded three-dimensional (3D) shape. This specific folded shape enables proteins to perform specific tasks. The protein structure prediction (PSP) by ab initio or de novo approach is promising amongst various available computational methods and can help to unravel the important relationship between sequence and its corresponding structure. This article presents the ab initio protein structure prediction as a conformational search problem in low resolution model using genetic algorithm. As a review, the essence of twin removal, intelligence in coding, the development and application of domain specific heuristics garnered from the properties of the resulting model and the protein core formation concept discussed are all highly relevant in attempting to secure the best solution

Coarse graining selection and mutation

Abstract. Coarse graining is defined in terms of a commutative diagram. Necessary and sufficient conditions are given in the continuously differentiable case. The theory is applied to linear coarse grainings arising from partitioning the population space of a simple Genetic Algorithm (GA). Cases considered include proportional selection, binary tournament selection, and mutation. A nonlinear coarse graining for ranking selection is also presented. Within the context of GAs, the primary contribution made is the introduction and illustration of a technique by which the possibility for coarse grainings may be analyzed. A secondary contribution is that a number of new coarse graining results are obtained.