120 research outputs found

    A Multi-objective Genetic Algorithm for Peptide Optimization

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    The peptide-based drug design process requires the identification of a wide range of candidate molecules with specific biological, chemical and physical properties. The laboratory analysis in terms of in vitro methods for the discovery of several physiochemical properties of theoretical candidate molecules is time- and cost-intensive. Hence, in silico methods are required for this purpose. Metaheuristics like evolutionary algorithms are considered to be adequate in silico methods providing good approximate solutions to the underlying multiobjective optimization problems. The general issue in this area is the design of a multi-objective evolutionary algorithm to achieve a maximum number of high-quality candidate peptides that differ in their genetic material, in a minimum number of generations. A multi-objective evolutionary algorithm as an in silico method of discovering a large number of high-quality peptides within a low number of generations for a broad class of molecular optimization problems of different dimensions is challenging, and the development of such a promising multi-objective evolutionary algorithm based on theoretical considerations is the major contribution of this thesis. The design of this algorithm is based on a qualitative landscape analysis applied on a three- and four-dimensional biochemical optimization problem. The conclusions drawn from the empirical landscape analysis of the three- and four-dimensional optimization problem result in the formulation of hypotheses regarding the types of evolutionary algorithm components which lead to an optimized search performance for the purpose of peptide optimization. Starting from the established types of variation operators and selection strategies, different variation operators and selection strategies are proposed and empirically verified on the three- and four-dimensional molecular optimization problem with regard to an optimized interaction and the identification of potential interdependences as well as a fine-tuning of the parameters. Moreover, traditional issues in the field of evolutionary algorithms such as selection pressure and the influence of multi-parent recombination are investigated

    Evolutionary Algorithms

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    Evolutionary algorithms (EAs) are population-based metaheuristics, originally inspired by aspects of natural evolution. Modern varieties incorporate a broad mixture of search mechanisms, and tend to blend inspiration from nature with pragmatic engineering concerns; however, all EAs essentially operate by maintaining a population of potential solutions and in some way artificially 'evolving' that population over time. Particularly well-known categories of EAs include genetic algorithms (GAs), Genetic Programming (GP), and Evolution Strategies (ES). EAs have proven very successful in practical applications, particularly those requiring solutions to combinatorial problems. EAs are highly flexible and can be configured to address any optimization task, without the requirements for reformulation and/or simplification that would be needed for other techniques. However, this flexibility goes hand in hand with a cost: the tailoring of an EA's configuration and parameters, so as to provide robust performance for a given class of tasks, is often a complex and time-consuming process. This tailoring process is one of the many ongoing research areas associated with EAs.Comment: To appear in R. Marti, P. Pardalos, and M. Resende, eds., Handbook of Heuristics, Springe

    An Artificial Immune System-Inspired Multiobjective Evolutionary Algorithm with Application to the Detection of Distributed Computer Network Intrusions

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    Today\u27s predominantly-employed signature-based intrusion detection systems are reactive in nature and storage-limited. Their operation depends upon catching an instance of an intrusion or virus after a potentially successful attack, performing post-mortem analysis on that instance and encoding it into a signature that is stored in its anomaly database. The time required to perform these tasks provides a window of vulnerability to DoD computer systems. Further, because of the current maximum size of an Internet Protocol-based message, the database would have to be able to maintain 25665535 possible signature combinations. In order to tighten this response cycle within storage constraints, this thesis presents an Artificial Immune System-inspired Multiobjective Evolutionary Algorithm intended to measure the vector of trade-off solutions among detectors with regard to two independent objectives: best classification fitness and optimal hypervolume size. Modeled in the spirit of the human biological immune system and intended to augment DoD network defense systems, our algorithm generates network traffic detectors that are dispersed throughout the network. These detectors promiscuously monitor network traffic for exact and variant abnormal system events, based on only the detector\u27s own data structure and the ID domain truth set, and respond heuristically. The application domain employed for testing was the MIT-DARPA 1999 intrusion detection data set, composed of 7.2 million packets of notional Air Force Base network traffic. Results show our proof-of-concept algorithm correctly classifies at best 86.48% of the normal and 99.9% of the abnormal events, attributed to a detector affinity threshold typically between 39-44%. Further, four of the 16 intrusion sequences were classified with a 0% false positive rate

    Strategies for multiobjective genetic algorithm development: Application to optimal batch plant design in process systems engineering

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    This work deals with multiobjective optimization problems using Genetic Algorithms (GA). A MultiObjective GA (MOGA) is proposed to solve multiobjective problems combining both continuous and discrete variables. This kind of problem is commonly found in chemical engineering since process design and operability involve structural and decisional choices as well as the determination of operating conditions. In this paper, a design of a basic MOGA which copes successfully with a range of typical chemical engineering optimization problems is considered and the key points of its architecture described in detail. Several performance tests are presented, based on the influence of bit ranging encoding in a chromosome. Four mathematical functions were used as a test bench. The MOGA was able to find the optimal solution for each objective function, as well as an important number of Pareto optimal solutions. Then, the results of two multiobjective case studies in batch plant design and retrofit were presented, showing the flexibility and adaptability of the MOGA to deal with various engineering problems

    From evolutionary computation to the evolution of things

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    Evolution has provided a source of inspiration for algorithm designers since the birth of computers. The resulting field, evolutionary computation, has been successful in solving engineering tasks ranging in outlook from the molecular to the astronomical. Today, the field is entering a new phase as evolutionary algorithms that take place in hardware are developed, opening up new avenues towards autonomous machines that can adapt to their environment. We discuss how evolutionary computation compares with natural evolution and what its benefits are relative to other computing approaches, and we introduce the emerging area of artificial evolution in physical systems

    Evolutionary multiobjective optimization : review, algorithms, and applications

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    Programa Doutoral em Engenharia Industrial e SistemasMany mathematical problems arising from diverse elds of human activity can be formulated as optimization problems. The majority of real-world optimization problems involve several and con icting objectives. Such problems are called multiobjective optimization problems (MOPs). The presence of multiple con icting objectives that have to be simultaneously optimized gives rise to a set of trade-o solutions, known as the Pareto optimal set. Since this set of solutions is crucial for e ective decision-making, which generally aims to improve the human condition, the availability of e cient optimization methods becomes indispensable. Recently, evolutionary algorithms (EAs) have become popular and successful in approximating the Pareto set. The population-based nature is the main feature that makes them especially attractive for dealing with MOPs. Due to the presence of two search spaces, operators able to e ciently perform the search in both the decision and objective spaces are required. Despite the wide variety of existing methods, a lot of open research issues in the design of multiobjective evolutionary algorithms (MOEAs) remains. This thesis investigates the use of evolutionary algorithms for solving multiobjective optimization problems. Innovative algorithms are developed studying new techniques for performing the search either in the decision or the objective space. Concerning the search in the decision space, the focus is on the combinations of traditional and evolutionary optimization methods. An issue related to the search in the objective space is studied in the context of many-objective optimization. Application of evolutionary algorithms is addressed solving two di erent real-world problems, which are modeled using multiobjective approaches. The problems arise from the mathematical modelling of the dengue disease transmission and a wastewater treatment plant design. The obtained results clearly show that multiobjective modelling is an e ective approach. The success in solving these challenging optimization problems highlights the practical relevance and robustness of the developed algorithms.Muitos problemas matemáticos que surgem nas diversas áreas da atividade humana podem ser formulados como problemas de otimização. A maioria dos problemas do mundo real envolve vários objetivos conflituosos. Tais problemas chamam-se problemas de otimização multiobjetivo. A presença de vários objetivos conflituosos, que têm de ser otimizados em simultâneo, dá origem a um conjunto de soluções de compromisso, conhecido como conjunto de soluções ótimas de Pareto. Uma vez que este conjunto de soluções é fundamental para uma tomada de decisão eficaz, cujo objetivo em geral é melhorar a condição humana, o desenvolvimento de métodos de otimização eficientes torna-se indispensável. Recentemente, os algoritmos evolucionários tornaram-se populares e bem-sucedidos na aproximação do conjunto de Pareto. A natureza populacional é a principal característica que os torna especialmente atraentes para lidar com problemas de otimização multiobjetivo. Devido à presença de dois espaços de procura, operadores capazes de realizar a procura de forma eficiente, tanto no espaço de decisão como no espaço dos objetivos, são necessários. Apesar da grande variedade de métodos existentes, várias questões de investigação permanecem em aberto na área do desenvolvimento de algoritmos evolucionários multiobjetivo. Esta tese investiga o uso de algoritmos evolucionários para a resolução de problemas de otimização multiobjetivo. São desenvolvidos algoritmos inovadores que estudam novas técnicas de procura, quer no espaço de decisão, quer no espaço dos objetivos. No que diz respeito à procura no espaço de decisão, o foco está na combinação de métodos de otimização tradicionais com algoritmos evolucionários. A questão relacionada com a procura no espaço dos objetivos é desenvolvida no contexto da otimização com muitos objetivos. A aplicação dos algoritmos evolucionários é abordada resolvendo dois problemas reais, que são modelados utilizando abordagens multiobjectivo. Os problemas resultam da modelação matemática da transmissão da doença do dengue e do desenho ótimo de estações de tratamento de águas residuais. O sucesso na resolução destes problemas de otimização constitui um desafio e destaca a relevância prática e robustez dos algoritmos desenvolvidos

    Optimización multi-objetivo en las ciencias de la vida.

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    Para conseguir este objetivo, en lugar de intentar incorporar nuevos algoritmos directamente en el código fuente de AutoDock, se utilizó un framework orientado a la resolución de problemas de optimización con metaheurísticas. Concretamente, se usó jMetal, que es una librería de código libre basada en Java. Ya que AutoDock está implementado en C++, se desarrolló una versión en C++ de jMetal (posteriormente distribuida públicamente). De esta manera, se consiguió integrar ambas herramientas (AutoDock 4.2 y jMetal) para optimizar la energía libre de unión entre compuesto químico y receptor. Después de disponer de una amplia colección de metaheurísticas implementadas en jMetalCpp, se realizó un detallado estudio en el cual se aplicaron un conjunto de metaheurísticas para optimizar un único objetivo minimizando la energía libre de unión, el cual es el resultado de la suma de todos los términos de energía de la función objetivo de energía de AutoDock 4.2. Por lo tanto, cuatro metaheurísticas tales como dos variantes de algoritmo genético gGA (Algoritmo Genético generacional) y ssGA (Algoritmo Genético de estado estacionario), DE (Evolución Diferencial) y PSO (Optimización de Enjambres de Partículas) fueron aplicadas para resolver el problema del acoplamiento molecular. Esta fase se dividió en dos subfases en las que se usaron dos conjuntos de instancias diferentes, utilizando como receptores HIV-proteasas con cadenas laterales de aminoacidos flexibles y como ligandos inhibidores HIV-proteasas flexibles. El primer conjunto de instancias se usó para un estudio de configuración de parámetros de los algoritmos y el segundo para comparar la precisión de las conformaciones ligando-receptor obtenidas por AutoDock y AutoDock+jMetalCpp. La siguiente fase implicó aplicar una formulación multi-objetivo para resolver problemas de acoplamiento molecular dados los resultados interesantes obtenidos en estudios previos existentes en los que dos objetivos como la energía intermolecular y la energía intramolecular fueron minimizados. Por lo tanto, se comparó y analizó el rendimiento de un conjunto de metaheurísticas multi-objetivo mediante la resolución de complejos flexibles de acoplamiento molecular minimizando la energía inter- e intra-molecular. Estos algoritmos fueron: NSGA-II (Algoritmo Genético de Ordenación No dominada) y su versión de estado estacionario (ssNSGA-II), SMPSO (Optimización Multi-objetivo de Enjambres de Partículas con Modulación de Velocidad), GDE3 (Tercera versión de la Evolución Diferencial Generalizada), MOEA/D (Algoritmo Evolutivo Multi-Objetivo basado en la Decomposición) y SMS-EMOA (Optimización Multi-objetivo Evolutiva con Métrica S). Después de probar enfoques multi-objetivo ya existentes, se probó uno nuevo. En concreto, el uso del RMSD como un objetivo para encontrar soluciones similares a la de la solución de referencia. Se replicó el estudio previo usando este conjunto diferente de objetivos. Por último, se analizó de forma detallada el algoritmo que obtuvo mejores resultados en los estudios previos. En concreto, se realizó un estudio de variantes del SMPSO minimizando la energía intermolecular y el RMSD. Este estudio proporcionó algunas pistas sobre cómo nuevos algoritmos basados en SMPSO pueden ser adaptados para mejorar los resultados de acoplamiento molecular para aquellas simulaciones que involucren ligandos y receptores flexibles. Esta tesis demuestra que la inclusión de técnicas metaheurísticas de jMetalCpp en la herramienta de acoplamiento molecular AutoDock incrementa las posibilidades a los usuarios de ámbito biológico cuando resuelven el problema del acoplamiento molecular. El uso de técnicas de optimización mono-objetivo diferentes aparte de aquéllas ampliamente usadas en las comunidades de acoplamiento molecular podría dar lugar a soluciones de mayor calidad. En nuestro caso de estudio mono-objetivo, el algoritmo de evolución diferencial obtuvo mejores resultados que aquellos obtenidos por AutoDock. También se propone diferentes enfoques multi-objetivo para resolver el problema del acoplamiento molecular, tales como la decomposición de los términos de la energía de unión o el uso del RMSD como un objetivo. Finalmente, se demuestra que el SMPSO, una metaheurística de optimización multi-objetivo de enjambres de partículas, es una técnica remarcable para resolver problemas de acoplamiento molecular cuando se usa un enfoque multi-objetivo, obteniendo incluso mejores soluciones que las técnicas mono-objetivo.Las herramientas de acoplamiento molecular han llegado a ser bastante eficientes en el descubrimiento de fármacos y en el desarrollo de la investigación de la industria farmacéutica. Estas herramientas se utilizan para elucidar la interacción de una pequeña molécula (ligando) y una macro-molécula (diana) a un nivel atómico para determinar cómo el ligando interactúa con el sitio de unión de la proteína diana y las implicaciones que estas interacciones tienen en un proceso bioquímico dado. En el desarrollo computacional de las herramientas de acoplamiento molecular los investigadores de este área se han centrado en mejorar los componentes que determinan la calidad del software de acoplamiento molecular: 1) la función objetivo y 2) los algoritmos de optimización. La función objetivo de energía se encarga de proporcionar una evaluación de las conformaciones entre el ligando y la proteína calculando la energía de unión, que se mide en kcal/mol. En esta tesis, se ha usado AutoDock, ya que es una de las herramientas de acoplamiento molecular más citada y usada, y cuyos resultados son muy precisos en términos de energía y valor de RMSD (desviación de la media cuadrática). Además, se ha seleccionado la función de energía de AutoDock versión 4.2, ya que permite realizar una mayor cantidad de simulaciones realistas incluyendo flexibilidad en el ligando y en las cadenas laterales de los aminoácidos del receptor que están en el sitio de unión. Se han utilizado algoritmos de optimización para mejorar los resultados de acoplamiento molecular de AutoDock 4.2, el cual minimiza la energía libre de unión final que es la suma de todos los términos de energía de la función objetivo de energía. Dado que encontrar la solución óptima en el acoplamiento molecular es un problema de gran complejidad y la mayoría de las veces imposible, se suelen utilizar algoritmos no exactos como las metaheurísticas, para así obtener soluciones lo suficientemente buenas en un tiempo razonable

    A study of evolutionary multiobjective algorithms and their application to knapsack and nurse scheduling problems

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    Evolutionary algorithms (EAs) based on the concept of Pareto dominance seem the most suitable technique for multiobjective optimisation. In multiobjective optimisation, several criteria (usually conflicting) need to be taken into consideration simultaneously to assess a quality of a solution. Instead of finding a single solution, a set of trade-off or compromise solutions that represents a good approximation to the Pareto optimal set is often required. This thesis presents an investigation on evolutionary algorithms within the framework of multiobjective optimisation. This addresses a number of key issues in evolutionary multiobjective optimisation. Also, a new evolutionary multiobjective (EMO) algorithm is proposed. Firstly, this new EMO algorithm is applied to solve the multiple 0/1 knapsack problem (a wellknown benchmark multiobjective combinatorial optimisation problem) producing competitive results when compared to other state-of-the-art MOEAs. Secondly, this thesis also investigates the application of general EMO algorithms to solve real-world nurse scheduling problems. One of the challenges in solving real-world nurse scheduling problems is that these problems are highly constrained and specific-problem heuristics are normally required to handle these constraints. These heuristics have considerable influence on the search which could override the effect that general EMO algorithms could have in the solution process when applied to this type of problems. This thesis outlines a proposal for a general approach to model the nurse scheduling problems without the requirement of problem-specific heuristics so that general EMO algorithms could be applied. This would also help to assess the problems and the performance of general EMO algorithms more fairly

    Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis

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    Insect-bacterial symbioses are ubiquitous, but there is still much to uncover about how these relationships establish, persist and evolve. The tsetse endosymbiont Sodalis glossinidius displays intriguing metabolic adaptations to its microenvironment, but the process by which this relationship evolved remains to be elucidated. The recent chance discovery of the free-living species of the genus Sodalis, Sodalis praecaptivus, provides a serendipitous starting point from which to investigate the evolution of this symbiosis. Here, we present a flux balance model for S. praecaptivus and empirically verify its predictions. Metabolic modelling is used in combination with a multi-objective evolutionary algorithm to explore the trajectories that S. glossinidius may have undertaken from this starting point after becoming internalized. The order in which key genes are lost is shown to influence the evolved populations, providing possible targets for future in vitro genetic manipulation. This method provides a detailed perspective on possible evolutionary trajectories for S. glossinidius in this fundamental process of evolutionary and ecological change
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