O alinhamento de seqüências biológicas é uma operação básica em Bioinformática, já que serve como base para outros processos como, por exemplo, a determinação da estrutura tridimensional das proteínas. Dada a grande quantidade de dados presentes nas seqüencias, são usadas técnicas matemáticas e de computação para realizar esta tarefa. Tradicionalmente, o Problema de Alinhamento de Seqüências Biológicas é formulado como um problema de otimização de objetivo simples, onde alinhamento de maior semelhança, conforme um esquema de pontuação, é procurado. A Otimização Multi-Objetivo aborda os problemas de otimização que possuem vários critérios a serem atingidos. Para este tipo de problema, existe um conjunto de soluções que representam um "compromiso" entre os objetivos. Uma técnica que se aplica com sucesso neste contexto são os Algoritmos Evolutivos, inspirados na Teoria da Evolução de Darwin, que trabalham com uma população de soluções que vão evoluindo até atingirem um critério de convergência ou de parada. Este trabalho formula o Problema de Alinhamento de Seqüências Biológicas como um Problema de Otimização Multi-Objetivo, para encontrar um conjunto de soluções que representem um compromisso entre a extensão e a qualidade das soluções. Aplicou-se vários modelos de Algoritmos Evolutivos para Otimização Multi-Objetivo. O desempenho de cada modelo foi avaliado por métricas de performance encontradas na literatura. / The Biological Sequence Alignment is a basic operation in Bioinformatics since it serves as a basis for other processes, i.e. determination of the protein's three-dimensional structure. Due to the large amount of data involved, mathematical and computational methods have been used to solve this problem. Traditionally, the Biological Alignment Sequence Problem is formulated as a single optimization problem. Each solution has a score that reflects the similarity between sequences. Then, the optimization process looks for the best score solution. The Multi-Objective Optimization solves problems with multiple objectives that must be reached. Frequently, there is a solution set that represents a trade-off between the objectives. Evolutionary Algorithms, which are inspired by Darwin's Evolution Theory, have been applied with success in solving this kind of problems. This work formulates the Biological Sequence Alignment as a Multi-Objective Optimization Problem in order to find a set of solutions that represent a trade-off between the extension and the quality of the solutions. Several models of Evolutionary Algorithms for Multi-Objetive Optimization have been applied and were evaluated using several performance metrics found in the literature.

"Gas carburizing is an important heat treatment process used for steel surface hardening of automotive and aerospace components. The quality of the carburized parts is determined by the hardness and the case depth required for a particular application. Despite its worldwide application, the current carburizing process performance faces some challenges in process control and variability. Case depth variability if often encountered in the carburized parts and may present problems with i) manufacturing quality rejections when tight tolerances are imposed or ii) insufficient mechanical properties and increased failure rate in service. The industrial approach to these problems often involves trial and error methods and empirical analysis, both of which are expensive, time consuming and, most importantly, rarely yield optimal solutions. The objective for this work was to develop a fundamental understanding of the mass transfer during gas carburizing process and to develop a strategy for the process control and optimization. The research methodology was based on both experimental work and theoretical developments, and included modeling the thermodynamics of the carburizing atmosphere with various enriching gasses, kinetics of mass transfer at the gas-steel interface and carbon diffusion in steel. The models accurately predict: 1) the atmosphere gas composition during the enriching stage of carburizing, 2) the kinetics of carbon transfer at the gas-steel surfaces, and 3) the carbon diffusion coefficient in steel for various process conditions and steel alloying. The above models and investigations were further combined to accurately predict the surface carbon concentration and the carbon concentration profile in the steel during the heat treatment process. Finally, these models were used to develop a methodology for the process optimization to minimize case depth variation, carburizing cycle time and total cycle cost. Application of this optimization technique provides a tradeoff between minimizing the case depth variation and total cycle cost and results in significant energy reduction by shortening cycle time and thereby enhancing carburizing furnace capacity."

Este trabalho apresenta um modelo de otimização multiobjetivo aplicado ao projeto de concepção de submarinos convencionais (i.e. de propulsão dieselelétrica). Um modelo de síntese que permite a estimativa de pesos, volume, velocidade, carga elétrica e outras características de interesse para a o projeto de concepção é formulado. O modelo de síntese é integrado a um modelo de otimização multiobjetivo baseado em algoritmos genéticos (especificamente, o algoritmo NSGA II). A otimização multiobjetivo consiste na maximização da efetividade militar do submarino e na minimização de seu custo. A efetividade militar do submarino é representada por uma Medida Geral de Efetividade (OMOE) estabelecida por meio do Processo Analítico Hierárquico (AHP). O Custo Básico de Construção (BCC) do submarino é estimado a partir dos seus grupos de peso. Ao fim do processo de otimização, é estabelecida uma Fronteira de Pareto composta por soluções não dominadas. Uma dessas soluções é selecionada para refinamento preliminar e os resultados são discutidos. Subsidiariamente, esta dissertação apresenta discussão sucinta sobre aspectos históricos e operativos relacionados a submarinos, bem como sobre sua metodologia de projeto. Alguns conceitos de Arquitetura Naval, aplicada ao projeto dessas embarcações, são também abordados. / This thesis presents a multi-objective optimization model applied to concept design of conventional submarines (i.e. diesel-electric powered boats). A synthesis model that allows the estimation of weights, volume, speed, electrical load and other design features of interest is formulated. The synthesis model is integrated with a multi-objective optimization model based on genetic algorithms (specifically, the NSGA II algorithm). The multi-objective optimization consists of maximizing the submarine\'s military effectiveness and minimizing its cost. The military effectiveness is represented by an Overall Measure of Effectiveness (OMOE) established via the Analytic Hierarchy Process (AHP). The submarine\'s Basic Construction Cost (BCC) is estimated from its weight groups. At the end of the optimization process, a Pareto Front composed of non-dominated solutions is established. One of these solutions is selected for preliminary refinement and the results are discussed. This work also presents succinct discussion about submarine historical and operational aspects and design methodology. Some Naval Architectural concepts, applied to submarine design, are also discussed.

O problema reconstrução filogenética têm como objetivo determinar as relações evolutivas das espécies, usualmente representadas em estruturas de árvores. No entanto, esse problema tem se mostrado muito difícil uma vez que o espaço de busca das possíveis árvores é muito grande. Diversos métodos de reconstrução filogenética têm sido propostos. Vários desses métodos definem um critério de otimalidade para avaliar as possíveis soluções do problema. Porém, a aplicação de diferentes critérios resulta em árvores diferentes, inconsistentes entre sim. Nesse contexto, uma abordagem multi-objetivo para a reconstrução filogenética pode ser útil produzindo um conjunto de árvores consideradas adequadas por mais de um critério. Nesta tese é proposto um algoritmo evolutivo multi-objetivo, denominado PhyloMOEA, para o problema de reconstrução filogenética. O PhyloMOEA emprega os critérios de parcimônia e verossimilhança que são dois dos métodos de reconstru ção filogenética mais empregados. Nos experimentos, o PhyloMOEA foi testado utilizando quatro bancos de seqüências freqüentemente empregados na literatura. Para cada banco de teste, o PhyloMOEA encontrou as soluções da fronteira de Pareto que representam um compromisso entre os critérios considerados. As árvores da fronteira de Pareto foram validadas estatisticamente utilizando o teste SH. Os resultados mostraram que o PhyloMOEA encontrou um número de soluções intermediárias que são consistentes com as soluções obtidas por análises de máxima parcimônia e máxima verossimilhança realizados separadamente. Além disso, os graus de suporte dos clados pertencentes às árvores encontradas pelo PhyloMOEA foram comparadas com a probabilidade posterior dos clados calculados pelo programa Mr.Bayes aplicados aos quatro bancos de teste. Os resultados indicaram que há uma relação entre ambos os valores para vários grupos de clados. Em resumo, o PhyloMOEA é capaz de encontrar uma diversidade de soluções intermediárias que são estatisticamente tão boas quanto as melhores soluções de máxima parcimônia e máxima verossimilhança. Tais soluções apresentam um compromisso entre os dois objetivos / The phylogeny reconstruction problem consists of determining the evolutionary relationships (usually represented as a tree) among species. This is a very complex problem since the tree search space is huge. Several phylogenetic reconstruction methods have been proposed. Many of them defines an optimality criterion for evaluation of possible solutions. However, different criteria may lead to distinct phylogenies, which often conflict with each other. In this context, a multi-objective approach for phylogeny reconstruction can be useful since it could produce a set of optimal trees according to mdifficultultiple criteria. In this thesis, a multi-objective evolutionary algorithm for phylogenetic reconstruction, called PhyloMOEA, is proposed. PhyloMOEA uses the parsimony and likelihood criteria, which are two of the most used phylogenetic reconstruction methods. PhyloMOEA was tested using four datasets of nucleotide sequences found in the literature. For each dataset, the proposed algorithm found a Pareto front representing a trade-off between the used criteria. Trees in the Pareto front were statistically validated using the SH-test, which has shown that a number of intermediate solutions from PhyloMOEA are consistent with solutions found by phylogenetic methods using one criterion. Moreover, clade support values from trees found by PhyloMOEA was compared to clade posterior probabilities obtained by Mr.Bayes. Results indicate a correlation between these probabilities for several clades. In summary, PhyloMOEA is able to find diverse intermediate solutions, which are not statistically worse than the best solutions for the maximum parsimony and maximum likelihood criteria. Moreover, intermediate solutions represent a trade-off between these criteria

Em sentido geral, a quimiotaxia é o movimento dirigido que desenvolvem alguns seres vivos em resposta aos gradientes químicos presentes no seu ambiente. Uma bactéria é um organismo unicelular que usa a quimiotaxia como mecanismo de mobilização para encontrar os nutrientes de que precisa para sobreviver e para escapar de ambientes nocivos. Evoluída durante milhões de anos pela natureza, a quimiotaxia de bactérias é um processo altamente otimizado de busca e exploração em espaços desconhecidos. Graças aos avanços no campo da computação, as estratégias quimiotácticas das bactérias e sua excelente capacidade de busca podem ser modeladas, simuladas e emuladas para desenvolver métodos de otimização inspirados na natureza que sejam uma alternativa aos métodos já existentes. Neste trabalho, desenvolvem-se dois algoritmos baseados em estratégias quimiotácticas de bactérias: o BCBTOA (Bacterial Chemotaxis Based Topology Optimization Algorithm) e o BCMOA (Bacterial Chemotaxis Multiobjective Optimization Algorithm) os quais são um algoritmo de otimização topológica e um algoritmo de otimização multi-objetivo, respectivamente. O desempenho dos algoritmos é avaliado mediante a sua aplicação à solução de diversos problemas de prova e os resultados são comparados com os de outros algoritmos atualmente relevantes. O algoritmo de otimização multi-objetivo desenvolvido, também foi aplicado na solução de três problemas de otimização de projeto mecânico de eixos. Os resultados obtidos e os analise comparativos feitos, permitem concluir que os algoritmos desenvolvidos são altamente competitivos e demonstram o potencial do processo de quimiotaxia de bactérias como fonte de inspiração de algoritmos de otimização distribuída, contribuindo assim, a dar resposta à constante demanda por técnicas de otimização mais eficazes e robustas. / In general, chemotaxis is the biased movement developed by certain living organisms as a response to chemical gradients present in their environment. A bacterium is a unicellular organism that uses chemotaxis as a mechanism for mobilization that allows it to find nutrients needed to survive and to escape from harmful environments. Millions of years of natural evolution became bacterial chemotaxis a highly optimized process in searching and exploration of unknown spaces. Thanks to advances in the computing field, bacterial chemotactical strategies and its excellent ability in searching can be modeled, simulated and emulated developing bio-inspired optimization methods as alternatives to classical methods. Two algorithms based on bacterial chemotactical strategies were designed, developed and implemented in this work: i) the topology optimization algorithm, BCBTOA (Bacterial Chemotaxis Based Topology Optimization Algorithm) and ii) the multi-objective optimization algorithm, BCMOA (Bacterial Chemotaxis Multiobjective Optimization Algorithm). Algorithms performances were evaluated by their applications in the solution of benchmark problems and the results obtained were compared with other algorithms also relevant today. The BCMOA developed here was also applied in the solution of three mechanical design problems. The results obtained as well as the comparative analysis conducted lead to conclude that the algorithms developed were competitive. This also demonstrates the potential of bacterial chemotaxis as a process in which distributed optimization techniques can be inspired.

Vibrations of a wind turbine have a negative impact on its performance and therefore approaches to effectively control turbine vibrations are sought by wind industry. The body of previous research on wind turbine vibrations has focused on physics-based models. Such models come with limitations as some ideal assumptions do not reflect reality. In this Thesis a data-driven approach to analyze the wind turbine vibrations is introduced. Improvements in the data collection of information system allow collection of large volumes of industrial process data. Although the sufficient information is contained in collected data, they cannot be fully utilized to solve the challenging industrial modeling issues. Data-mining is a novel science offers platform to identify models or recognize patterns from large data set. Various successful applications of data mining proved its capability in extracting models accurately describing the processes of interest. The vibrations of a wind turbine originate at various sources. This Thesis focuses on mitigating vibrations with wind turbine control. Data mining algorithms are utilized to construct vibration models of a wind turbine that are represented by two parameters, drive train acceleration and tower acceleration. An evolutionary strategy algorithm is employed to optimize the wind turbine performance expressed with three objectives, power generation, vibration of wind turbine drive train, and vibration of wind turbine tower. The methodology presented in this Thesis is applicable to industrial processes other than wind industry.

Heating, ventilating and air-conditioning (HVAC) system is complex non-linear system with multi-variables simultaneously contributing to the system process. It poses challenges for both system modeling and performance optimization. Traditional modeling methods based on statistical or mathematical functions limit the characteristics of system operation and management. Data-driven models have shown powerful strength in non-linear system modeling and complex pattern recognition. Sufficient successful applications of data mining have proved its capability in extracting models accurately describing the relation of inner system. The heuristic techniques such as neural networks, support vector machine, and boosting tree have largely expanded to the modeling process of HVAC system. Evolutionary computation has rapidly merged to the center stage of solving the multi-objective optimization problem. Inspired from the biology behavior, it has shown the tremendous power in finding the optimal solution of complex problem. Different applications of evolutionary computation can be found in business, marketing, medical and manufacturing domains. The focus of this thesis is to apply the evolutionary computation approach in optimizing the performance of HVAC system. The energy saving can be achieved by implementing the optimal control setpoints with IAQ maintained at an acceptable level. A trade-off between energy saving and indoor air quality maintenance is also investigated by assigning different weights to the corresponding objective function. The major contribution of this research is to provide the optimal settings for the existing system to improve its efficiency and different preference-based operation methods to optimally utilize the resources.

In traditional optimization approaches the interaction of parameters associated with a problem is not a significant issue, but in the domain of Evolutionary Multi-Objective Optimization (EMOO) traditional genetic algorithm approaches have difficulties in optimizing problems with parameter interactions. Parameter interactions can be introduced when the search space is rotated. Genetic algorithms are referred to as being not rotationally invariant because their behavior changes depending on the orientation of the search space. Many empirical studies in single and multi-objective evolutionary optimization are done with respect to test problems which do not have parameter interactions. Such studies provide a favorably biased indication of genetic algorithm performance. This motivates the first aspect of our work; the improvement of the testing of EMOO algorithms with respect to the aforementioned difficulties that genetic algorithms experience in the presence of para meter interactions. To this end, we examine how EMOO algorithms can be assessed when problems are subject to an arbitrarily uniform degree of parameter interactions. We establish a theoretical basis for parameter interactions and how they can be measured. Furthermore, we ask the question of what difficulties a multi-objective genetic algorithm experiences on optimization problems exhibiting parameter interactions. We also ask how these difficulties can be overcome in order to efficiently find the Pareto-optimal front on such problems. Existing multi-objective test problems in the literature typically introduce parameter interactions by altering the fitness landscape, which is undesirable. We propose a new suite of test problems that exhibit parameter interactions through a rotation of the decision space, without altering the fitness landscape. In addition, we compare the performance of a number of recombination operators on these test problems. The second aspect of this work is concerned with developing an efficient multi-objective optimization algorithm which works well on problems with parameter interactions. We investigate how an evolutionary algorithm can be made more efficient on multi-objective problems with parameter interactions by developing four novel rotationally invariant differential evolution approaches. We also ask whether the proposed approaches are competitive in comparison with a state-of-the-art EMOO algorithm. We propose several differential evolution approaches incorporating directional information from the multi-objective search space in order to accelerate and direct the search. Experimental results indicate that dramatic improvements in efficiency can be achieved by directing the search towards points which are more dominant and more diverse. We also address the important issue of diversity loss in rotationally invariant vector-wise differential evolution. Being able to generate diverse solutions is critically important in order to avoid stagnation. In order to address this issue, one of the directed approaches that we examine incorporates a novel sampling scheme around better individuals in the search space. This variant is able to perform exceptionally well on the test problems with much less computational cost and scales to very high decision space dimensions even in the presence of parameter interactions.

Sustainability concerns are increasingly shaping customers' behavior as well as companies' strategy. In this context, optimizing the supply chain with sustainability considerations is becoming a critical issue. However, work with quantitative models is still scarce. Our research contributes by revisiting classical inventory models taking sustainability concerns into account. We believe that reducing all aspects of sustainable development to a single objective is not desirable. We thus reformulate single and multi-echelon economic order quantity models as multi-objective problems. These models are then used to study several options such as buyer-supplier coordination or green technology investment. We also consider that firms are becoming increasingly proactive with respect to sustainability. We thus propose to apply multiple criteria decision aid techniques instead of considering sustainability as a constraint. In this sense, the firm may provide preference information about economic, environmental and social tradeoffs and quickly identify a satisfactory solution.

No description available.