Currently, one of the main research problems in Structural Bioinformatics is associated to the study and prediction of the 3-D structure of proteins. The 1990’s GENOME projects resulted in a large increase in the number of protein sequences. However, the number of identified 3-D protein structures have not followed the same growth trend. The number of protein sequences is much higher than the number of known 3-D structures. Many computational methodologies, systems and algorithms have been proposed to address the protein structure prediction problem. However, the problem still remains challenging because of the complexity and high dimensionality of a protein conformational search space. This work presents a new computational strategy for the 3-D protein structure prediction problem. A first principle strategy which uses database information for the prediction of the 3-D structure of polypeptides was developed. The proposed technique manipulates structural information from the PDB in order to generate torsion angles intervals. Torsion angles intervals are used as input to a genetic algorithm with a local-search operator in order to search the protein conformational space and predict its 3-D structure. Results show that the 3-D structures obtained by the proposed method were topologically comparable to their correspondent experimental structure.

O trabalho a seguir apresenta o desenvolvimento e resultados da pesquisa acerca de modelos de estoques para múltiplos fornecedores, baseado na distribuição de peças de manutenção de empresas de tecnologia no Brasil. Em função de características de demandas erráticas, altos custos das peças e demanda por tempos de entrega reduzidos, costuma-se adotar uma estratégia de distribuir peças em diversos centros de estoques por todo território nacional. Entretanto, manter altos estoques em cada uma das localidades do sistema pode trazer custos elevados. Devido às características da demanda, muitas vezes ocorrem faltas de estoques de itens críticos, que são enviados aos locais de demanda por meio de transportes emergenciais de alto custo e prazos de entregas reduzidos. Entretanto, os modelos convencionais de estoques adotados, não consideram as possibilidades de envios emergenciais em suas formulações, fazendo desta solução uma situação não prevista na modelagem e potencialmente não ótima. A presente pesquisa tem por objetivo desenvolver e avaliar os modelos convencionais de estoques para a situação de múltiplos fornecedores considerando custos e prazos de entregas diferentes, como alternativa para os modelos adotados na distribuição de peças de manutenção. Sua aplicação a outros problemas, inclusive ambientes de múltiplos fornecedores independentemente de diferenças de transportes é imediata. A pesquisa abrange sete modelos, sendo três modelos reativos (reposição da base, reposição do máximo e lote fixo) em regimes de revisão periódica e contínua, e um modelo ativo considerando previsão de demanda. Foi utilizada busca local com simulação de eventos discretos para resolver os modelos propostos. / The present work presents research and development of multiple supplier inventory models, based on the service parts logistics in the technology industry. Because of the lumpy demand characteristics, high costs of parts and low delivery time expectations, a strategy to spread parts inventories all over the country was adopted. However, maintaining high inventory in every location of the system can lead to high costs. Because of the demand characteristics critical items can get unavailable in certain location, which are supplied by emergency shipment from supplying locations with high transportation costs and reduced delivery times. However, the conventional inventory models that are used do not consider the possibility of emergency shipments, leading to potential non optimal distribution of parts. The present research aims to develop and evaluate the inventory models considering multiple transportation modals with different lead times and costs, to serve as an alternative to the current inventory models used. The application to other problems, including different suppliers independent of transportation mode, is immediate. The research covers seven different models: three reactive, (s, S), (S-1, S) and (R, Q) in continuous and periodic review, and one demand prediction based model. Local search and discrete events simulation was used to resolve the models.

Cette thèse présente des algorithmes de résolution de quatre problèmes de clique : clique de poids maximum (MVWCP), s-plex maximum (MsPlex), clique maximum équilibrée dans un graphe biparti (MBBP) et clique partition (CPP). Les trois premiers problèmes sont des généralisations ou relaxations du problème de la clique maximum, tandis que le dernier est un problème de couverture. Ces problèmes, ayant de nombreuses applications pratiques, sont NP-difficiles, rendant leur résolution ardue dans le cas général. Nous présentons ici des algorithmes de recherche locale, principalement basés sur la recherche tabou, permettant de traiter efficacement ces problèmes ; chacun de ces algorithmes emploie des composants originaux et spécifiquement adaptés aux problèmes traités, comme de nouveaux opérateurs ou mécanismes perturbatifs. Nous y intégrons également des stratégies telles que la réduction de graphe ou la propagation afin de traiter des réseaux de plus grande taille. Des expérimentations basées sur des jeux d’instances nombreux et variés permettent de montrer la compétitivité de nos algorithmes en comparaison avec les autres stratégies existantes. / This thesis considers four clique problems: the maximum vertex weight clique problem (MVWCP), the maximum s-plex problem (MsPlex), the maximum balanced biclique problem (MBBP) and the clique partitioning problem (CPP). The first three are generalization and relaxation of the classic maximum clique problem (MCP), while the last problem belongs to a clique grouping problem. These combinatorial problems have numerous practical applications. Given that they all belong to the NP-Hard family, it is computationally difficult to solve them in the general case. For this reason, this thesis is devoted to develop effective algorithms to tackle these challenging problems. Specifically, we propose two restart tabu search algorithms based on a generalized PUSH operator for MVWCP, a frequency driven local search algorithms for MsPlex, a graph reduction based tabu search as well as effective exact branch and bound algorithms for MBBP and lastly, a three phase local search algorithm for CPP. In addition to the design of efficient move operators for local search algorithms, we also integrate components like graph reduction or upper bound propagation in order to deal deal with very large real-life networks. The experimental tests on a wide range of instances show that our algorithms compete favorably with the main state-of-the-art algorithms.

The thesis work intends to provide architecture for mobile local information search service using Wireless LAN and cellular integration. Search technology has been popular and driving business bodies with increasing e-commerce opportunities. The search technology has been recently brought to portable devices such as mobile phones and PDA devices by extending the research scope. Mobile search revenues are expected to surpass Internet search revenues in near future. Mobile local search on the other hand is getting much popular with growing number of mobile subscribers. Mobile phones have been chosen to provide mobile local search services because of its high possessivity and portable nature. In this thesis work, the author would like to propose a generalized architecture for mobile local information search in a new perspective by involving cellular service provider directly with a minimum co-operation from consumers and retailers. When providing mobile local search services, cellular operator has to maintain a replica of databases of all the existing retailers. Updating the replica at cellular operator at regular intervals has been leading to synchronization problems that produce out-dated results to mobile users. The aspects that have driven the author towards proposing the architecture are solving database synchronization problems and thriving for effective search results. The existing architecture of web search, mobile search and mobile local search are analyzed to identify the domain specific challenges and research gaps. Proposed architecture is designed and evaluated by using an approach called Architecture Tradeoff Analysis Method (ATAM). The architecture is evaluated against its quality attributes and the results are presented. / Sridher Rao Sidduri Lindblomsvagen, 97, Rum no 555, 372 33 Ronneby, Sweden E-mail: srsi05@student.bth.se

In this paper we view learning as an unconstrained non-linear minimization problem in which the objective function is defined by the negative log-likelihood function and the search space by the parameter space of an origin constrained product unit neural spatial interaction model. We consider Alopex based global search, as opposed to local search based upon backpropagation of gradient descents, each in combination with the bootstrapping pairs approach to solve the maximum likelihood learning problem. Interregional telecommunication traffic flow data from Austria are used as test bed for comparing the performance of the two learning procedures. The study illustrates the superiority of Alopex based global search, measured in terms of Kullback and Leibler's information criterion.

In this thesis we focus on Stochastic combinatorial Optimization Problems (SCOPs), a wide class of combinatorial optimization problems under uncertainty, where part of the information about the problem data is unknown at the planning stage, but some knowledge about its probability distribution is assumed.<p><p>Optimization problems under uncertainty are complex and difficult, and often classical algorithmic approaches based on mathematical and dynamic programming are able to solve only very small problem instances. For this reason, in recent years metaheuristic algorithms such as Ant Colony Optimization, Evolutionary Computation, Simulated Annealing, Tabu Search and others, are emerging as successful alternatives to classical approaches.<p><p>In this thesis, metaheuristics that have been applied so far to SCOPs are introduced and the related literature is thoroughly reviewed. In particular, two properties of metaheuristics emerge from the survey: they are a valid alternative to exact classical methods for addressing real-sized SCOPs, and they are flexible, since they can be quite easily adapted to solve different SCOPs formulations, both static and dynamic. On the base of the current literature, we identify the following as the key open issues in solving SCOPs via metaheuristics: <p>(1) the design and integration of ad hoc, fast and effective objective function approximations inside the optimization algorithm;<p>(2) the estimation of the objective function by sampling when no closed-form expression for the objective function is available, and the study of methods to reduce the time complexity and noise inherent to this type of estimation;<p>(3) the characterization of the efficiency of metaheuristic variants with respect to different levels of stochasticity in the problem instances. <p><p>We investigate the above issues by focusing in particular on a SCOP belonging to the class of vehicle routing problems: the Probabilistic Traveling Salesman Problem (PTSP). For the PTSP, we consider the Ant Colony Optimization metaheuristic and we design efficient local search algorithms that can enhance its performance. We obtain state-of-the-art algorithms, but we show that they are effective only for instances above a certain level of stochasticity, otherwise it is more convenient to solve the problem as if it were deterministic.<p>The algorithmic variants based on an estimation of the objective function by sampling obtain worse results, but qualitatively have the same behavior of the algorithms based on the exact objective function, with respect to the level of stochasticity. Moreover, we show that the performance of algorithmic variants based on ad hoc approximations is strongly correlated with the absolute error of the approximation, and that the effect on local search of ad hoc approximations can be very degrading.<p><p>Finally, we briefly address another SCOP belonging to the class of vehicle routing problems: the Vehicle Routing Problem with Stochastic Demands (VRPSD). For this problem, we have implemented and tested several metaheuristics, and we have studied the impact of integrating in them different ad hoc approximations.<p> / Doctorat en sciences appliquées / info:eu-repo/semantics/nonPublished

Plusieurs problèmes d'optimisation combinatoire sont dits NP-difficiles et ne peuvent être résolus de façon optimale par des algorithmes exacts. Les métaheuristiques ont prouvé qu'elles pouvaient être efficaces pour résoudre un grand nombre de ces problèmes en leur trouvant des solutions approchées en un temps raisonnable. Cependant, face à des instances de grande taille, elles ont besoin d'un temps de calcul et d'une quantité d'espace mémoire considérables pour être performantes dans l'exploration de l'espace de recherche. Par conséquent, l'intérêt voué à leur déploiement sur des architectures de calcul haute performance a augmenté durant ces dernières années. Les approches de parallélisation existantes suivent généralement les paradigmes de passage de messages ou de mémoire partagée qui conviennent aux architectures traditionnelles à base de microprocesseurs, aussi appelés CPU (Central Processing Unit).Cependant, la recherche évolue très rapidement dans le domaine du parallélisme et de nouvelles architectures émergent, notamment les accélérateurs matériels qui permettent de décharger le CPU de certaines de ses tâches. Parmi ceux-ci, les processeurs graphiques ou GPU (Graphics Processing Units) présentent une architecture massivement parallèle possédant un grand potentiel mais aussi de nouvelles difficultés d'algorithmique et de programmation. En effet, les modèles de parallélisation de métaheuristiques existants sont généralement inadaptés aux environnements de calcul de type GPU. Certains travaux ont d'ailleurs abordé ce sujet sans toutefois y apporter une vision globale et fondamentale.L'objectif général de cette thèse est de proposer un cadre de référence permettant l'implémentation efficace des métaheuristiques sur des architectures parallèles basées sur les GPU. Elle débute par un état de l'art décrivant les travaux existants sur la parallélisation GPU des métaheuristiques et les classifications générales des métaheuristiques parallèles. Une taxonomie originale est ensuite proposée afin de classifier les implémentations recensées et de formaliser les stratégies de parallélisation sur GPU dans un cadre méthodologique cohérent. Cette thèse vise également à valider cette taxonomie en exploitant ses principales composantes pour proposer des stratégies de parallélisation originales spécifiquement adaptées aux architectures GPU. Plusieurs implémentations performantes basées sur les métaheuristiques d'Optimisation par Colonie de Fourmis et de Recherche Locale Itérée sont ainsi proposées pour la résolution du problème du Voyageur de Commerce. Une étude expérimentale structurée et minutieuse est réalisée afin d'évaluer et de comparer la performance des approches autant au niveau de la qualité des solutions trouvées que de la réduction du temps de calcul. / Several combinatorial optimization problems are NP-hard and can only be solved optimally by exact algorithms for small instances. Metaheuristics have proved to be effective in solving many of these problems by finding approximate solutions in a reasonable time. However, dealing with large instances, they may require considerable computation time and amount of memory space to be efficient in the exploration of the search space. Therefore, the interest devoted to their deployment on high performance computing architectures has increased over the past years. Existing parallelization approaches generally follow the message-passing and shared-memory computing paradigms which are suitable for traditional architectures based on microprocessors, also called CPU (Central Processing Unit). However, research in the field of parallel computing is rapidly evolving and new architectures emerge, including hardware accelerators which offloads the CPU of some of its tasks. Among them, graphics processors or GPUs (Graphics Processing Units) have a massively parallel architecture with great potential but also imply new algorithmic and programming challenges. In fact, existing parallelization models of metaheuristics are generally unsuited to computing environments like GPUs. Few works have tackled this subject without providing a comprehensive and fundamental view of it.The general purpose of this thesis is to propose a framework for the effective implementation of metaheuristics on parallel architectures based on GPUs. It begins with a state of the art describing existing works on GPU parallelization of metaheuristics and general classifications of parallel metaheuristics. An original taxonomy is then designed to classify identified implementations and to formalize GPU parallelization strategies in a coherent methodological framework. This thesis also aims to validate this taxonomy by exploiting its main components to propose original parallelization strategies specifically tailored to GPU architectures. Several effective implementations based on Ant Colony Optimization and Iterated Local Search metaheuristics are thus proposed for solving the Travelling Salesman Problem. A structured and thorough experimental study is conducted to evaluate and compare the performance of approaches on criteria related to solution quality and computing time reduction.

Local search algorithms have been proved to be effective in refining solutions that have been found by other algorithms. Evolutionary algorithms, in particular global search algorithms, have shown to be successful in producing approximate solutions for optimisation and classification problems in acceptable computation times. A relatively new method, memetic algorithms, uses local search to refine the approximate solutions produced by global search algorithms. This thesis develops such a memetic algorithm. The global search algorithm used as part of the new memetic algorithm is a genetic program that implements the building block hypothesis by building simplistic decision trees representing valid solutions, and gradually increases the complexity of the trees. The specific building block hypothesis implementation is known as the building block approach to genetic programming, BGP. The effectiveness and efficiency of the new memetic algorithm, which combines the BGP algorithm with a local search algorithm, is demonstrated. / Dissertation (MSc)--University of Pretoria, 2006. / Computer Science / unrestricted

Cette thèse porte sur la résolution du problème d'optimisation Maximum Satisfiability (Max-SAT). Nous y étudions en particulier les mécanismes liés à la détection et à la transformation des sous-ensembles inconsistants par la règle de la max-résolution. Dans le contexte des solveurs de type séparation et évaluation, nous présentons plusieurs contributions liées au calcul de la borne inférieure. Cela va du schéma d'application de la propagation unitaire utilisé pour détecter les sous-ensembles inconsistants à l'extension des critères d'apprentissage et à l'évaluation de l'impact des transformations par max-résolution sur l'efficacité des solveurs. Nos contributions ont permis l'élaboration d'un nouvel outil de résolution compétitif avec les meilleurs solveurs de l'état de l'art. Elles permettent également de mieux comprendre le fonctionnement des méthodes de type séparation et évaluation et apportent des éléments théoriques pouvant expliquer l'efficacité et les limites des solveurs existants. Cela ouvre de nouvelles perspectives d'amélioration, en particulier sur l'augmentation de l'apprentissage et la prise en compte de la structure interne des instances. Nous présentons également un exemple d'utilisation de la règle de la max-résolution dans un algorithme de recherche local. / This PhD thesis is about solving the Maximum Satisfiability (Max-SAT) problem. We study the mechanisms related to the detection and transformations of the inconsistent subsets by the max-resolution rule. In the context of the branch and bound (BnB) algorithms, we present several contributions related to the lower bound computation. They range from the study of the unit propagation scheme used to detect inconsistent subsets to the extension of the learning criteria and to the evaluation of the impact of the max-resolution transformations on the BnB solvers efficiency. Thanks to our contributions, we have implemented a new solver which is competitive with the state of art ones. We give insights allowing a better understanding of the behavior of BnB solvers as well as theoretical elements which contribute to explain the efficiency of these solvers and their limits. It opens new development perspectives on the learning mechanisms used by BnB solvers which may lead to a better consideration of the instances structural properties. We also present an example of integration of the max-resolution inference rule in a local search algorithm.

Afin d’améliorer la qualité de prédiction des techniques de classification automatique et de fouilles de données, plusieurs modèles ont été proposés dans la littérature en vue d’extraire des connaissances à partir des données. Toutefois, avec l’expansion des systèmes d’information et des technologies associées, ces techniques d’apprentissage s’avèrent de moins en moins adaptées aux nouvelles tailles et dimensions des données. On s’intéresse dans cette étude aux problèmes de grande dimensionnalité et à l’amélioration du processus d’apprentissage des méthodes de classification à travers les techniques de filtrage et de sélection d’attributs. Le problème « d’identification d’attributs pertinents » (Feature Selection Problem), tel qu’il est défini dans la littérature, relève d’une nature combinatoire. Dans le cadre de cette thèse, on s’est intéressé au développement de nouvelles techniques d’optimisation approchées et spécifiques au problème traité ainsi qu’à l’amélioration d’algorithmes existants. La conception, l’implémentation et l’étude empirique ont montré l’efficacité et la pertinence des métaheuristiques proposées. / Although the expansion of storage technologies, networking systems, and information system methodologies, the capabilities of conventional data processing techniques remain limited. The need to knowledge extraction, compact representation and data analysis are highly motivated by data expansion. Nevertheless, learning from data might be a complex task, particularly when it includes noisy, redundant and information-less attributes. Feature Selection (FS) tries to select the most relevant attributes from raw data, and hence guides the construction of final classification models or decision support systems. Selected features should be representative of the underlying data and provide effective usefulness to the targeted learning paradigm (i.e. classification). In this thesis, we investigate different optimization paradigms as well as its adaptation to the requirements of the feature selection challenges, namely the problem combinatorial nature. Both theoritical and empirical aspects were studied, and confirm the effectiveness of the adopted methodology as well as the proposed metaheuristic based approaches.