This thesis studies a class of optimisation algorithms, namely Memetic Computing Structures, and proposes a novel set of promising algorithms that move the first step towards an implementation for the automatic generation of optimisation algorithms for continuous domains. This thesis after a thorough review of local search algorithms and popular meta-heuristics, focuses on Memetic Computing in terms of algorithm structures and design philosophy. In particular, most of the design carried out during my doctoral studies is inspired by the lex parsimoniae, aka Ockham’s Razor. It has been shown how simple algorithms, when well implemented can outperform complex implementations. In order to achieve this aim, the design is always carried out by attempting to identify the role of each algorithmic component/operator. In this thesis, on the basis of this logic, a set of variants of a recently proposed algorithms are presented. Subsequently a novel memetic structure, namely Parallel Memetic Structure is proposed and tested against modern algorithms representing the state of the art in optimisation. Furthermore, an initial prototype of an automatic design platform is also included. This prototype performs an analysis on separability of the optimisation problem and, on the basis of the analysis results, designs some parts of the parallel structure. Promising results are included. Finally, an investigation of the correlation among the variables and problem dimensionality has been performed. An extremely interesting finding of this thesis work is that the degree of correlation among the variables decreases when the dimensionality increases. As a direct consequence of this fact, large scale problems are to some extent easier to handle than problems in low dimensionality since, due to the lack of correlation among the variables, they can effectively be tackled by an algorithm that performs moves along the axes.

Many real-world decision processes require solving optimization problems which may involve different types of constraints such as inequality and equality constraints. The hurdles in solving these Constrained Optimization Problems (COPs) arise from the challenge of searching a huge variable space in order to locate feasible points with acceptable solution quality. Over the last decades Evolutionary Algorithms (EAs) have brought a tremendous advancement in the area of computer science and optimization with their ability to solve various problems. However, EAs have inherent difficulty in dealing with constraints when solving COPs. This thesis presents a new Agent-based Memetic Algorithm (AMA) for solving COPs, where the agents have the ability to independently select a suitable Life Span Learning Process (LSLP) from a set of LSLPs. Each agent represents a candidate solution of the optimization problem and tries to improve its solution through cooperation with other agents. Evolutionary operators consist of only crossover and one of the self-adaptively selected LSLPs. The performance of the proposed algorithm is tested on benchmark problems, and the experimental results show convincing performance. The quality of individuals in the initial population influences the performance of evolutionary algorithms, especially when the feasible region of the constrained optimization problems is very tiny in comparison to the entire search space. This thesis proposes a method that improves the quality of randomly generated initial solutions by sacrificing very little in diversity of the population. The proposed Search Space Reduction Technique (SSRT) is tested using five different existing EAs, including AMA, by solving a number of state-of-the-art test problems and a real world case problem. The experimental results show SSRT improves the solution quality, and speeds up the performance of the algorithms. The handling of equality constraints has long been a difficult issue for evolutionary optimization methods, although several methods are available in the literature for handling functional constraints. In any optimization problems with equality constraints, to satisfy the condition of feasibility and optimality the solution points must lie on each and every equality constraint. This reduces the size of the feasible space and makes it difficult for EAs to locate feasible and optimal solutions. A new Equality Constraint Handling Technique (ECHT) is presented in this thesis, to enhance the performance of AMA in solving constrained optimization problems with equality constraints. The basic concept is to reach a point on the equality constraint from its current position by the selected individual solution and then explore on the constraint landscape. The technique is used as an agent learning process in AMA. The experimental results confirm the improved performance of the proposed algorithm. This thesis also proposes a Modified Genetic Algorithm (MGA) for solving COPs with equality constraints. After achieving inspiring performance in AMA when dealing with equality constraints, the new technique is used in the design of MGA. The experimental results show that the proposed algorithm overcomes the limitations of GA in solving COPs with equality constraints, and provides good quality solutions.

Many important applications in the real world that can be modelled as combinatorial optimization problems are actually dynamic in nature. However, research on dynamic optimization focuses on continuous optimization problems, and rarely targets combinatorial problems. Moreover, dynamic combinatorial problems, when addressed, are typically tackled within an application context. <br /><br /> In this thesis, dynamic combinatorial problems are addressed collectively by adopting an evolutionary based algorithmic approach. On the plus side, their ability to manipulate several solutions at a time, their robustness and their potential for adaptability make evolutionary algorithms a good choice for solving dynamic problems. However, their tendency to converge prematurely, the difficulty in fine-tuning their search and their lack of diversity in tracking optima that shift in dynamic environments are drawbacks in this regard. <br /><br /> Developing general methodologies to tackle these conflicting issues constitutes the main theme of this thesis. First, definitions and measures of algorithm performance are reviewed. Second, methods of benchmark generation are developed under a generalized framework. Finally, methods to improve the ability of evolutionary algorithms to efficiently track optima shifting due to environmental changes are investigated. These methods include adapting genetic parameters to population diversity and environmental changes, the use of multi-populations as an additional means to control diversity, and the incorporation of local search heuristics to fine-tune the search process efficiently. <br /><br /> The methodologies developed for algorithm enhancement and benchmark generation are used to build and test evolutionary models for dynamic versions of the travelling salesman problem and the flexible manufacturing system. Results of experimentation demonstrate that the methods are effective on both problems and hence have a great potential for other dynamic combinatorial problems as well.

Algoritmos meméticos são meta-heurísticas evolutivas voltadas intrinsecamente à exploração e incorporação de conhecimentos relacionados ao problema em estudo. Nesta dissertação, foi proposto um algoritmo memético multi populacional baseado em conhecimento para lidar com o problema de predição de estruturas tridimensionais de proteínas voltado à modelagem de estruturas livres de similaridades conformacionais com estruturas de proteínas determinadas experimentalmente. O algoritmo em questão, foi estruturado em duas etapas principais de processamento: (i) amostragem e inicialização de soluções; e (ii) otimização dos modelos estruturais provenientes da etapa anterior. A etapa I objetiva a geração e classificação de diversas soluções, a partir da estratégia Lista de Probabilidades Angulares, buscando a definição de diferentes grupos estruturais e a criação de melhores estruturas a serem incorporadas à meta-heurística como soluções iniciais das multi populações. A segunda etapa consiste no processo de otimização das estruturas oriundas da etapa I, realizado por meio da aplicação do algoritmo memético de otimização, o qual é fundamentado na organização da população de indivíduos em uma estrutura em árvore, onde cada nodo pode ser interpretado como uma subpopulação independente, que ao longo do processo interage com outros nodos por meio de operações de busca global voltadas a características do problema, visando o compartilhamento de informações, a diversificação da população de indivíduos, e a exploração mais eficaz do espaço de busca multimodal do problema O algoritmo engloba ainda uma implementação do algoritmo colônia artificial de abelhas, com o propósito de ser utilizado como uma técnica de busca local a ser aplicada em cada nodo da árvore. O algoritmo proposto foi testado em um conjunto de 24 sequências de aminoácidos, assim como comparado a dois métodos de referência na área de predição de estruturas tridimensionais de proteínas, Rosetta e QUARK. Os resultados obtidos mostraram a capacidade do método em predizer estruturas tridimensionais de proteínas com conformações similares a estruturas determinadas experimentalmente, em termos das métricas de avaliação estrutural Root-Mean-Square Deviation e Global Distance Total Score Test. Verificou-se que o algoritmo desenvolvido também foi capaz de atingir resultados comparáveis ao Rosetta e ao QUARK, sendo que em alguns casos, os superou. Corroborando assim, a eficácia do método. / Memetic algorithms are evolutionary metaheuristics intrinsically concerned with the exploiting and incorporation of all available knowledge about the problem under study. In this dissertation, we present a knowledge-based memetic algorithm to tackle the threedimensional protein structure prediction problem without the explicit use of template experimentally determined structures. The algorithm was divided into two main steps of processing: (i) sampling and initialization of the algorithm solutions; and (ii) optimization of the structural models from the previous stage. The first step aims to generate and classify several structural models for a determined target protein, by the use of the strategy Angle Probability List, aiming the definition of different structural groups and the creation of better structures to initialize the initial individuals of the memetic algorithm. The Angle Probability List takes advantage of structural knowledge stored in the Protein Data Bank in order to reduce the complexity of the conformational search space. The second step of the method consists in the optimization process of the structures generated in the first stage, through the applying of the proposed memetic algorithm, which uses a tree-structured population, where each node can be seen as an independent subpopulation that interacts with others, over global search operations, aiming at information sharing, population diversity, and better exploration of the multimodal search space of the problem The method also encompasses ad-hoc global search operators, whose objective is to increase the exploration capacity of the method turning to the characteristics of the protein structure prediction problem, combined with the Artificial Bee Colony algorithm to be used as a local search technique applied to each node of the tree. The proposed algorithm was tested on a set of 24 amino acid sequences, as well as compared with two reference methods in the protein structure prediction area, Rosetta and QUARK. The results show the ability of the method to predict three-dimensional protein structures with similar foldings to the experimentally determined protein structures, regarding the structural metrics Root-Mean-Square Deviation and Global Distance Total Score Test. We also show that our method was able to reach comparable results to Rosetta and QUARK, and in some cases, it outperformed them, corroborating the effectiveness of our proposal.

The design of facility layout takes into account a number of issues including the formation of departments, the layout of these, the determination of the material handling methods to be used, etc. To achieve an efficient layout, these issues should be examined simultaneously. However, in practice, these problems are generally formulated and solved sequentially due to the complicated nature of the integrated problem. Specifically, there is close interaction between the formation of departments and layout of these departments. These problems are treated as separate problems that are solved sequentially. This procedure is mainly due to the complexity of each problem and the interrelationships between them. In this research, we take a first step toward integrating the flow-based department formation and departmental layout into comprehensive mathematical models and develop appropriate solution procedures. It is expected that these mathematical models and the solution procedures developed will generate more efficient manufacturing system designs, insights into the nature of the concurrent facility layout problem, and new research directions.

Many important applications in the real world that can be modelled as combinatorial optimization problems are actually dynamic in nature. However, research on dynamic optimization focuses on continuous optimization problems, and rarely targets combinatorial problems. Moreover, dynamic combinatorial problems, when addressed, are typically tackled within an application context. <br /><br /> In this thesis, dynamic combinatorial problems are addressed collectively by adopting an evolutionary based algorithmic approach. On the plus side, their ability to manipulate several solutions at a time, their robustness and their potential for adaptability make evolutionary algorithms a good choice for solving dynamic problems. However, their tendency to converge prematurely, the difficulty in fine-tuning their search and their lack of diversity in tracking optima that shift in dynamic environments are drawbacks in this regard. <br /><br /> Developing general methodologies to tackle these conflicting issues constitutes the main theme of this thesis. First, definitions and measures of algorithm performance are reviewed. Second, methods of benchmark generation are developed under a generalized framework. Finally, methods to improve the ability of evolutionary algorithms to efficiently track optima shifting due to environmental changes are investigated. These methods include adapting genetic parameters to population diversity and environmental changes, the use of multi-populations as an additional means to control diversity, and the incorporation of local search heuristics to fine-tune the search process efficiently. <br /><br /> The methodologies developed for algorithm enhancement and benchmark generation are used to build and test evolutionary models for dynamic versions of the travelling salesman problem and the flexible manufacturing system. Results of experimentation demonstrate that the methods are effective on both problems and hence have a great potential for other dynamic combinatorial problems as well.

The design of facility layout takes into account a number of issues including the formation of departments, the layout of these, the determination of the material handling methods to be used, etc. To achieve an e&#64259;cient layout, these issues should be examined simultaneously. However, in practice, these problems are generally formulated and solved sequentially due to the complicated nature of the integrated problem. Speci&#64257;cally, there is close interaction between the formation of departments and layout of these departments. These problems are treated as separate problems that are solved sequentially. This procedure is mainly due to the complexity of each problem and the interrelationships between them. In this research, we take a &#64257;rst step toward integrating the &#64258;ow-based department formation and departmental layout into comprehensive mathematical models and develop appropriate solution procedures. It is expected that these mathematical models and the solution procedures developed will generate more e&#64259;cient manufacturing system designs, insights into the nature of the concurrent facility layout problem, and new research directions.

The aim of this study is to introduce a real-world timetabling problem that exists in some private schools in Turkey and to solve such problem instances utilizing memetic algorithms. Being a new type of problem and for privacy reasons, there is no real data available. Hence for benchmarking purposes, a random data generator has been implemented. Memetic algorithms (MAs) combining genetic algorithms and hill-climbing are applied to solve synthetic problem instances produced by this generator. Different types of recombination and mutation operators based on the hierarchical structure of the timetabling problem are proposed. A modified version of the violation directed hierarchical hill-climbing method (VDHC), introduced by A. Alkan and E. Ozcan, coordinates the process of 12 different low-level hill-climbing operators grouped in two distinct arrangements that attempt to resolve corresponding constraint violations. VDHC is an adaptive method advocating cooperation of hill-climbing operators. In addition, MAs with VDHC are compared with different versions of multimeme algorithms and pure genetic algorithms. Experimental results on synthetic benchmark data set indicate the success of the proposed MA.

Algoritmos meméticos são meta-heurísticas evolutivas voltadas intrinsecamente à exploração e incorporação de conhecimentos relacionados ao problema em estudo. Nesta dissertação, foi proposto um algoritmo memético multi populacional baseado em conhecimento para lidar com o problema de predição de estruturas tridimensionais de proteínas voltado à modelagem de estruturas livres de similaridades conformacionais com estruturas de proteínas determinadas experimentalmente. O algoritmo em questão, foi estruturado em duas etapas principais de processamento: (i) amostragem e inicialização de soluções; e (ii) otimização dos modelos estruturais provenientes da etapa anterior. A etapa I objetiva a geração e classificação de diversas soluções, a partir da estratégia Lista de Probabilidades Angulares, buscando a definição de diferentes grupos estruturais e a criação de melhores estruturas a serem incorporadas à meta-heurística como soluções iniciais das multi populações. A segunda etapa consiste no processo de otimização das estruturas oriundas da etapa I, realizado por meio da aplicação do algoritmo memético de otimização, o qual é fundamentado na organização da população de indivíduos em uma estrutura em árvore, onde cada nodo pode ser interpretado como uma subpopulação independente, que ao longo do processo interage com outros nodos por meio de operações de busca global voltadas a características do problema, visando o compartilhamento de informações, a diversificação da população de indivíduos, e a exploração mais eficaz do espaço de busca multimodal do problema O algoritmo engloba ainda uma implementação do algoritmo colônia artificial de abelhas, com o propósito de ser utilizado como uma técnica de busca local a ser aplicada em cada nodo da árvore. O algoritmo proposto foi testado em um conjunto de 24 sequências de aminoácidos, assim como comparado a dois métodos de referência na área de predição de estruturas tridimensionais de proteínas, Rosetta e QUARK. Os resultados obtidos mostraram a capacidade do método em predizer estruturas tridimensionais de proteínas com conformações similares a estruturas determinadas experimentalmente, em termos das métricas de avaliação estrutural Root-Mean-Square Deviation e Global Distance Total Score Test. Verificou-se que o algoritmo desenvolvido também foi capaz de atingir resultados comparáveis ao Rosetta e ao QUARK, sendo que em alguns casos, os superou. Corroborando assim, a eficácia do método. / Memetic algorithms are evolutionary metaheuristics intrinsically concerned with the exploiting and incorporation of all available knowledge about the problem under study. In this dissertation, we present a knowledge-based memetic algorithm to tackle the threedimensional protein structure prediction problem without the explicit use of template experimentally determined structures. The algorithm was divided into two main steps of processing: (i) sampling and initialization of the algorithm solutions; and (ii) optimization of the structural models from the previous stage. The first step aims to generate and classify several structural models for a determined target protein, by the use of the strategy Angle Probability List, aiming the definition of different structural groups and the creation of better structures to initialize the initial individuals of the memetic algorithm. The Angle Probability List takes advantage of structural knowledge stored in the Protein Data Bank in order to reduce the complexity of the conformational search space. The second step of the method consists in the optimization process of the structures generated in the first stage, through the applying of the proposed memetic algorithm, which uses a tree-structured population, where each node can be seen as an independent subpopulation that interacts with others, over global search operations, aiming at information sharing, population diversity, and better exploration of the multimodal search space of the problem The method also encompasses ad-hoc global search operators, whose objective is to increase the exploration capacity of the method turning to the characteristics of the protein structure prediction problem, combined with the Artificial Bee Colony algorithm to be used as a local search technique applied to each node of the tree. The proposed algorithm was tested on a set of 24 amino acid sequences, as well as compared with two reference methods in the protein structure prediction area, Rosetta and QUARK. The results show the ability of the method to predict three-dimensional protein structures with similar foldings to the experimentally determined protein structures, regarding the structural metrics Root-Mean-Square Deviation and Global Distance Total Score Test. We also show that our method was able to reach comparable results to Rosetta and QUARK, and in some cases, it outperformed them, corroborating the effectiveness of our proposal.

Algoritmos meméticos são meta-heurísticas evolutivas voltadas intrinsecamente à exploração e incorporação de conhecimentos relacionados ao problema em estudo. Nesta dissertação, foi proposto um algoritmo memético multi populacional baseado em conhecimento para lidar com o problema de predição de estruturas tridimensionais de proteínas voltado à modelagem de estruturas livres de similaridades conformacionais com estruturas de proteínas determinadas experimentalmente. O algoritmo em questão, foi estruturado em duas etapas principais de processamento: (i) amostragem e inicialização de soluções; e (ii) otimização dos modelos estruturais provenientes da etapa anterior. A etapa I objetiva a geração e classificação de diversas soluções, a partir da estratégia Lista de Probabilidades Angulares, buscando a definição de diferentes grupos estruturais e a criação de melhores estruturas a serem incorporadas à meta-heurística como soluções iniciais das multi populações. A segunda etapa consiste no processo de otimização das estruturas oriundas da etapa I, realizado por meio da aplicação do algoritmo memético de otimização, o qual é fundamentado na organização da população de indivíduos em uma estrutura em árvore, onde cada nodo pode ser interpretado como uma subpopulação independente, que ao longo do processo interage com outros nodos por meio de operações de busca global voltadas a características do problema, visando o compartilhamento de informações, a diversificação da população de indivíduos, e a exploração mais eficaz do espaço de busca multimodal do problema O algoritmo engloba ainda uma implementação do algoritmo colônia artificial de abelhas, com o propósito de ser utilizado como uma técnica de busca local a ser aplicada em cada nodo da árvore. O algoritmo proposto foi testado em um conjunto de 24 sequências de aminoácidos, assim como comparado a dois métodos de referência na área de predição de estruturas tridimensionais de proteínas, Rosetta e QUARK. Os resultados obtidos mostraram a capacidade do método em predizer estruturas tridimensionais de proteínas com conformações similares a estruturas determinadas experimentalmente, em termos das métricas de avaliação estrutural Root-Mean-Square Deviation e Global Distance Total Score Test. Verificou-se que o algoritmo desenvolvido também foi capaz de atingir resultados comparáveis ao Rosetta e ao QUARK, sendo que em alguns casos, os superou. Corroborando assim, a eficácia do método. / Memetic algorithms are evolutionary metaheuristics intrinsically concerned with the exploiting and incorporation of all available knowledge about the problem under study. In this dissertation, we present a knowledge-based memetic algorithm to tackle the threedimensional protein structure prediction problem without the explicit use of template experimentally determined structures. The algorithm was divided into two main steps of processing: (i) sampling and initialization of the algorithm solutions; and (ii) optimization of the structural models from the previous stage. The first step aims to generate and classify several structural models for a determined target protein, by the use of the strategy Angle Probability List, aiming the definition of different structural groups and the creation of better structures to initialize the initial individuals of the memetic algorithm. The Angle Probability List takes advantage of structural knowledge stored in the Protein Data Bank in order to reduce the complexity of the conformational search space. The second step of the method consists in the optimization process of the structures generated in the first stage, through the applying of the proposed memetic algorithm, which uses a tree-structured population, where each node can be seen as an independent subpopulation that interacts with others, over global search operations, aiming at information sharing, population diversity, and better exploration of the multimodal search space of the problem The method also encompasses ad-hoc global search operators, whose objective is to increase the exploration capacity of the method turning to the characteristics of the protein structure prediction problem, combined with the Artificial Bee Colony algorithm to be used as a local search technique applied to each node of the tree. The proposed algorithm was tested on a set of 24 amino acid sequences, as well as compared with two reference methods in the protein structure prediction area, Rosetta and QUARK. The results show the ability of the method to predict three-dimensional protein structures with similar foldings to the experimentally determined protein structures, regarding the structural metrics Root-Mean-Square Deviation and Global Distance Total Score Test. We also show that our method was able to reach comparable results to Rosetta and QUARK, and in some cases, it outperformed them, corroborating the effectiveness of our proposal.