A Study of Memetic Search with Multi-parent Combination for UBQP

We present a multi-parent hybrid genetic–tabu algorithm (denoted by GTA) for the Unconstrained Binary Quadratic Programming (UBQP) problem, by incorporating tabu search into the framework of genetic algorithm. In this paper, we propose a new multi-parent combination operator for generating offspring solutions. A pool updating strategy based on a quality-and-distance criterion is used to manage the population. Experimental comparisons with leading methods for the UBQP problem on 25 large public instances demonstrate the efficacy of our proposed algorithm in terms of both solution quality and computational efficiency

DISCOVERING DRIVER MUTATIONS IN BIOLOGICAL DATA

Background Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accumulate in the DNA of cancer cells. An ongoing problem is to figure out which mutations are drivers - play a role in oncogenesis, and which are passengers - do not play a role. One way of addressing this question is through inspection of somatic mutations in DNA of cancer samples from a cohort of patients and detection of patterns that differentiate driver from passenger mutations. Results We propose QuaDMutEx an QuadMutNetEx, a method that incorporates three novel elements: a new gene set penalty that includes non-linear penalization of multiple mutations in putative sets of driver genes, an ability to adjust the method to handle slow- and fast-evolving tumors, and a computationally efficient method for finding gene sets that minimize the penalty, through a combination of heuristic Monte Carlo optimization and exact binary quadratic programming. QuaDMutNetEx is our proposed method that combines protein-protein interaction networks to the method elements of QuaDMutEx. In particular, QuaDMutEx incorporates three novel elements: a non-linear penalization of multiple mutations in putative sets of driver genes, an ability to adjust the method to handle slow- and fast-evolving tumors, and a computationally efficient method for finding gene sets that minimize the penalty. In the new method, we incorporated a new quadratic rewarding term that prefers gene solution set that is connected with respect to protein-protein interaction networks. Compared to existing methods, the proposed algorithm finds sets of putative driver genes that show higher coverage and lower excess coverage in eight sets of cancer samples coming from brain, ovarian, lung, and breast tumors. Conclusions Superior ability to improve on both coverage and excess coverage on different types of cancer shows that QuaDMutEx and QuaDMutNetEx are tools that should be part of a state-of-the-art toolbox in the driver gene discovery pipeline. It can detect genes harboring rare driver mutations that may be missed by existing methods

Innovative hybrid MOEA/AD variants for solving multi-objective combinatorial optimization problems

Orientador : Aurora Trinidad Ramirez PozoCoorientador : Roberto SantanaTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 16/12/2016Inclui referências : f. 103-116Resumo: Muitos problemas do mundo real podem ser representados como um problema de otimização combinatória. Muitas vezes, estes problemas são caracterizados pelo grande número de variáveis e pela presença de múltiplos objetivos a serem otimizados ao mesmo tempo. Muitas vezes estes problemas são difíceis de serem resolvidos de forma ótima. Suas resoluções tem sido considerada um desafio nas últimas décadas. Os algoritimos metaheurísticos visam encontrar uma aproximação aceitável do ótimo em um tempo computacional razoável. Os algoritmos metaheurísticos continuam sendo um foco de pesquisa científica, recebendo uma atenção crescente pela comunidade. Uma das têndencias neste cenário é a arbordagem híbrida, na qual diferentes métodos e conceitos são combinados objetivando propor metaheurísticas mais eficientes. Nesta tese, nós propomos algoritmos metaheurísticos híbridos para a solução de problemas combinatoriais multiobjetivo. Os principais ingredientes das nossas propostas são: (i) o algoritmo evolutivo multiobjetivo baseado em decomposição (MOEA/D framework), (ii) a otimização por colônias de formigas e (iii) e os algoritmos de estimação de distribuição. Em nossos frameworks, além dos operadores genéticos tradicionais, podemos instanciar diferentes modelos como mecanismo de reprodução dos algoritmos. Além disso, nós introduzimos alguns componentes nos frameworks objetivando balancear a convergência e a diversidade durante a busca. Nossos esforços foram direcionados para a resolução de problemas considerados difíceis na literatura. São eles: a programação quadrática binária sem restrições multiobjetivo, o problema de programação flow-shop permutacional multiobjetivo, e também os problemas caracterizados como deceptivos. Por meio de estudos experimentais, mostramos que as abordagens propostas são capazes de superar os resultados do estado-da-arte em grande parte dos casos considerados. Mostramos que as diretrizes do MOEA/D hibridizadas com outras metaheurísticas é uma estratégia promissora para a solução de problemas combinatoriais multiobjetivo. Palavras-chave: metaheuristicas, otimização multiobjetivo, problemas combinatoriais, MOEA/D, otimização por colônia de formigas, algoritmos de estimação de distribuição, programação quadrática binária sem restrições multiobjetivo, problema de programação flow-shop permutacional multiobjetivo, abordagens híbridas.Abstract: Several real-world problems can be stated as a combinatorial optimization problem. Very often, they are characterized by the large number of variables and the presence of multiple conflicting objectives to be optimized at the same time. These kind of problems are, usually, hard to be solved optimally, and their solutions have been considered a challenge for a long time. Metaheuristic algorithms aim at finding an acceptable approximation to the optimal solution in a reasonable computational time. The research on metaheuristics remains an attractive area and receives growing attention. One of the trends in this scenario are the hybrid approaches, in which different methods and concepts are combined aiming to propose more efficient approaches. In this thesis, we have proposed hybrid metaheuristic algorithms for solving multi-objective combinatorial optimization problems. Our proposals are based on (i) the multi-objective evolutionary algorithm based on decomposition (MOEA/D framework), (ii) the bio-inspired metaheuristic ant colony optimization, and (iii) the probabilistic models from the estimation of distribution algorithms. Our algorithms are considered MOEA/D variants. In our MOEA/D variants, besides the traditional genetic operators, we can instantiate different models as the variation step (reproduction). Moreover, we include some design modifications into the frameworks to control the convergence and the diversity during their search (evolution). We have addressed some important problems from the literature, e.g., the multi-objective unconstrained binary quadratic programming, the multiobjective permutation flowshop scheduling problem, and the problems characterized by deception. As a result, we show that our proposed frameworks are able to solve these problems efficiently by outperforming the state-of-the-art approaches in most of the cases considered. We show that the MOEA/D guidelines hybridized to other metaheuristic components and concepts is a powerful strategy for solving multi-objective combinatorial optimization problems. Keywords: meta-heuristics, multi-objective optimization, combinatorial problems, MOEA/D, ant colony optimization, estimation of distribution algorithms, unconstrained binary quadratic programming, permutation flowshop scheduling problem, hybrid approaches

Effectiveness of Selection Mechanisms on the efficiency of Multi Parent Crossover Operator

Multi-parent crossover has been proven its ability to address many of combinatorial optimization problems such as the traveling salesman problem and the vehicle routing problem with time windows. The successful use of multi-parent crossover arises from its abilities to enhance the search performance via utilizing information exchanged by more than two parents and inheriting by offspring. These parents are selected according to one of the selection mechanisms. Selecting the most appropriate parents for a crossover process might leads to improving the effectiveness of genetic algorithm. Therefore, this work investigates the effect of selection mechanism on the efficiency of multi-parent crossover. To test this, seven selection mechanisms have been used; random selection mechanism, roulette wheel mechanism, stochastic universal sampling mechanism, tournament selection mechanism, best selection mechanism, single best-couple random selection mechanism and couple best- single random selection mechanism. The performance of the proposed algorithm is tested using Solomon VRPTW benchmark. The experimental results show the superiority of multi-parent crossover that employs the selection mechanism which selects the outstanding individuals to form most of parents over multi-parent crossover that employ other selection mechanisms. This demonstrates the efficiency of employing best parents in a crossover process that can assist the search process to attain a better solution

Preventing premature convergence and proving the optimality in evolutionary algorithms

http://ea2013.inria.fr//proceedings.pdfInternational audienceEvolutionary Algorithms (EA) usually carry out an efficient exploration of the search-space, but get often trapped in local minima and do not prove the optimality of the solution. Interval-based techniques, on the other hand, yield a numerical proof of optimality of the solution. However, they may fail to converge within a reasonable time due to their inability to quickly compute a good approximation of the global minimum and their exponential complexity. The contribution of this paper is a hybrid algorithm called Charibde in which a particular EA, Differential Evolution, cooperates with a Branch and Bound algorithm endowed with interval propagation techniques. It prevents premature convergence toward local optima and outperforms both deterministic and stochastic existing approaches. We demonstrate its efficiency on a benchmark of highly multimodal problems, for which we provide previously unknown global minima and certification of optimality

Ant Colony Algorithms for the Resolution of Semantic Searches in P2P Networks

Tesis por compendio[EN] The long-lasting trend in the field of computation of stress and resource distribution has found its way into computer networks via the concept of peer-to-peer (P2P) connectivity. P2P is a symmetrical model, where each network node is enabled a comparable range of capacities and resources. It stands in a stark contrast to the classical, strongly asymmetrical client-server approach. P2P, originally considered only a complimentary, server-side structure to the straightforward client-server model, has been shown to have the substantial potential on its own, with multiple, widely known benefits: good fault tolerance and recovery, satisfactory scalability and intrinsic load distribution. However, contrary to client-server, P2P networks require sophisticated solutions on all levels, ranging from network organization, to resource location and managing. In this thesis we address one of the key issues of P2P networks: performing efficient resource searches of semantic nature under realistic, dynamic conditions. There have been numerous solutions to this matter, with evolutionary, stigmergy-based, and simple computational foci, but few attempt to resolve the full range of challenges this problem entails. To name a few: real-life P2P networks are rarely static, nodes disconnect, reconnect and change their content. In addition, a trivial incorporation of semantic searches into well-known algorithms causes significant decrease in search efficiency. In our research we build a solution incrementally, starting with the classic Ant Colony System (ACS) within the Ant Colony Optimization metaheuristic (ACO). ACO is an algorithmic framework used for solving combinatorial optimization problems that fits contractually the problem very well, albeit not providing an immediate solution to any of the aforementioned problems. First, we propose an efficient ACS variant in structured (hypercube structured) P2P networks, by enabling a path-post processing algorithm, which called Tabu Route Optimization (TRO). Next, we proceed to resolve the issue of network dynamism with an ACO-compatible information diffusion approach. Consequently, we attempt to incorporate the semantic component of the searches. This initial approximation to the problem was achieved by allowing ACS to differentiate between search types with the pheromone-per-concept idea. We called the outcome of this merger Routing Concept ACS (RC-ACS). RC-ACS is a robust, static multipheromone implementation of ACS. However, we were able to conclude from it that the pheromone-per-concept approach offers only limited scalability and cannot be considered a global solution. Thus, further progress was made in this respect when we introduced to RC-ACS our novel idea: dynamic pheromone creation, which replaces the static one-to-one assignment. We called the resulting algorithm Angry Ant Framework (AAF). In AAF new pheromone levels are created as needed and during the search, rather than prior to it. The final step was to enable AAF, not only to create pheromone levels, but to reassign them to optimize the pheromone usage. The resulting algorithm is called EntropicAAF and it has been evaluated as one of the top-performing algorithms for P2P semantic searches under all conditions.[ES] La popular tendencia de distribución de carga y recursos en el ámbito de la computación se ha transmitido a las redes computacionales a través del concepto de la conectividad peer-to-peer (P2P). P2P es un modelo simétrico, en el cual a cada nodo de la red se le otorga un rango comparable de capacidades y recursos. Se trata de un fuerte contraste con el clásico y fuertemente asimétrico enfoque cliente-servidor. P2P, originalmente considerado solo como una estructura del lado del servidor complementaria al sencillo modelo cliente-servidor, ha demostrado tener un potencial considerable por sí mismo, con múltiples beneficios ampliamente conocidos: buena tolerancia a fallos y recuperación, escalabilidad satisfactoria y distribución de carga intrínseca. Sin embargo, al contrario que el modelo cliente-servidor, las redes P2P requieren de soluciones sofisticadas a todos los niveles, desde la organización de la red hasta la gestión y localización de recursos. Esta tesis aborda uno de los problemas principales de las redes P2P: la búsqueda eficiente de recursos de naturaleza semántica bajo condiciones dinámicas y realistas. Ha habido numerosas soluciones a este problema basadas en enfoques evolucionarios, estigmérgicos y simples, pero pocas han tratado de resolver el abanico completo de desafíos. En primer lugar, las redes P2P reales son raramente estáticas: los nodos se desconectan, reconectan y cambian de contenido. Además, la incorporación trivial de búsquedas semánticas en algoritmos conocidos causa un decremento significativo de la eficiencia de la búsqueda. En esta investigación se ha construido una solución de manera incremental, comenzando por el clásico Ant Colony System (ACS) basado en la metaheurística de Ant Colony Optimization (ACO). ACO es un framework algorítmico usado para búsquedas en grafos que encaja perfectamente con las condiciones del problema, aunque no provee una solución inmediata a las cuestiones mencionadas anteriormente. En primer lugar, se propone una variante eficiente de ACS para redes P2P estructuradas (con estructura de hipercubo) permitiendo el postprocesamiento de las rutas, al que hemos denominado Tabu Route Optimization (TRO). A continuación, se ha tratado de resolver el problema del dinamismo de la red mediante la difusión de la información a través de una estrategia compatible con ACO. En consecuencia, se ha tratado de incorporar el componente semántico de las búsquedas. Esta aproximación inicial al problema ha sido lograda permitiendo al ACS diferenciar entre tipos de búsquedas através de la idea de pheromone-per-concept. El resultado de esta fusión se ha denominado Routing Concept ACS (RC-ACS). RC-ACS es una implementación multiferomona estática y robusta de ACS. Sin embargo, a partir de esta implementación se ha podido concluir que el enfoque pheromone-per-concept ofrece solo escalabilidad limitada y que no puede ser considerado una solución global. Por lo tanto, para lograr una mejora a este respecto, se ha introducido al RC-ACS una novedosa idea: la creación dinámica de feromonas, que reemplaza la asignación estática uno a uno. En el algoritmo resultante, al que hemos denominado Angry Ant Framework (AAF), los nuevos niveles de feromona se crean conforme se necesitan y durante la búsqueda, en lugar de crearse antes de la misma. La mejora final se ha obtenido al permitir al AAF no solo crear niveles de feromona, sino también reasignarlos para optimizar el uso de la misma. El algoritmo resultante se denomina EntropicAAF y ha sido evaluado como uno de los algoritmos más exitosos para las búsquedas semánticas P2P bajo todas las condiciones.[CA] La popular tendència de distribuir càrrega i recursos en el camp de la computació s'ha estès cap a les xarxes d'ordinadors a través del concepte de connexions d'igual a igual (de l'anglès, peer to peer o P2P). P2P és un model simètric on cada node de la xarxa disposa del mateix nombre de capacitats i recursos. P2P, considerat originàriament només una estructura situada al servidor complementària al model client-servidor simple, ha provat tindre el suficient potencial per ella mateixa, amb múltiples beneficis ben coneguts: una bona tolerància a errades i recuperació, una satisfactòria escalabilitat i una intrínseca distribució de càrrega. No obstant, contràriament al client-servidor, les xarxes P2P requereixen solucions sofisticades a tots els nivells, que varien des de l'organització de la xarxa a la localització de recursos i la seua gestió. En aquesta tesi s'adreça un dels problemes clau de les xarxes P2P: ser capaç de realitzar eficientment cerques de recursos de naturalesa semàntica sota condicions realistes i dinàmiques. Existeixen nombroses solucions a aquest tema basades en la computació simple, evolutiva i també basades en l'estimèrgia (de l'anglès, stigmergy), però pocs esforços s'han realitzat per intentar resoldre l'ampli conjunt de reptes existent. En primer lloc, les xarxes P2P reals són rarament estàtiques: els nodes es connecten, desconnecten i canvien els seus continguts. A més a més, la incorporació trivial de cerques semàntiques als algorismes existents causa una disminució significant de l'eficiència de la cerca. En aquesta recerca s'ha construït una solució incremental, començant pel sistema clàssic de colònia de formigues (de l'anglés, Ant Colony System o ACS) dins de la metaheurística d'optimització de colònies de formigues (de l'anglès, Ant Colony Optimization o ACO). ACO és un entorn algorísmic utilitzat per cercar en grafs i que aborda el problema de forma satisfactòria, tot i que no proveeix d'una solució immediata a cap dels problemes anteriorment mencionats. Primer, s'ha proposat una variant eficient d'ACS en xarxes P2P estructurades (en forma d'hipercub) a través d'un algorisme de processament post-camí el qual s'ha anomenat en anglès Tabu Route Optimization (TRO). A continuació, s'ha procedit a resoldre el problema del dinamisme de les xarxes amb un enfocament de difusió d'informació compatible amb ACO. Com a conseqüència, s'ha intentat incorporar la component semàntica de les cerques. Aquest enfocament inicial al problema s'ha realitzat permetent a ACS diferenciar entre tipus de cerques amb la idea de ''feromona per concepte'', i s'ha anomenat a aquest producte Routing Concept ACS o RC-ACS. RC-ACS és una implementació multi-feromona robusta i estàtica d'ACS. No obstant, s'ha pogut concloure que l'enfocament de feromona per concepte ofereix només una escalabilitat limitada i no pot ser considerada una solució global. En aquest respecte s'ha realitzat progrés posteriorment introduint una nova idea a RC-ACS: la creació dinàmica de feromones, la qual reemplaça a l'assignació un a un de les mateixes. A l'algorisme resultant se l'ha anomenat en anglès Angry Ant Framework (AAF). En AAF es creen nous nivells de feromones a mesura que es necessiten durant la cerca, i no abans d'aquesta. El progrés final s'ha aconseguit quan s'ha permès a AAF, no sols crear nivells de feromones, sinó reassignar-los per optimitzar la utilització de feromones. L'algorisme resultant s'ha anomenat EntropicAAF i ha sigut avaluat com un dels algorismes per a cerques semàntiques P2P amb millors prestacions.Krynicki, KK. (2016). Ant Colony Algorithms for the Resolution of Semantic Searches in P2P Networks [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/61293TESISPremios Extraordinarios de tesis doctoralesCompendi

Advances and Novel Approaches in Discrete Optimization

Discrete optimization is an important area of Applied Mathematics with a broad spectrum of applications in many fields. This book results from a Special Issue in the journal Mathematics entitled ‘Advances and Novel Approaches in Discrete Optimization’. It contains 17 articles covering a broad spectrum of subjects which have been selected from 43 submitted papers after a thorough refereeing process. Among other topics, it includes seven articles dealing with scheduling problems, e.g., online scheduling, batching, dual and inverse scheduling problems, or uncertain scheduling problems. Other subjects are graphs and applications, evacuation planning, the max-cut problem, capacitated lot-sizing, and packing algorithms