The Experts below are selected from a list of 6165 Experts worldwide ranked by ideXlab platform
Olivier Gascuel - One of the best experts on this subject based on the ideXlab platform.
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Topological Rearrangements and Local Search Method for Tandem Duplication Trees
IEEE ACM Transactions on Computational Biology and Bioinformatics, 2005Co-Authors: Denis Bertrand, Olivier GascuelAbstract:Topological Rearrangements and Local Search Method for Tandem Duplication Trees
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Topological Rearrangements and Local Search Method for Tandem Duplication Trees
IEEE ACM transactions on computational biology and bioinformatics, 2005Co-Authors: Denis Bertrand, Olivier GascuelAbstract:The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch (1977). Many recent studies deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees. In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on duplication trees. We show that restricting the neighborhood defined by the SPR (Subtree Pruning and Regrafting) rearrangement to valid duplication trees, allows exploring the whole duplication tree space. We use these restricted rearrangements in a Local Search Method which improves an initial tree via successive rearrangements. This Method is applied to the optimization of parsimony and minimum evolution criteria. We show through simulations that this Method improves all existing programs for both reconstructing the topology of the true tree and recovering its duplication events. We apply this approach to tandemly repeated human Zinc finger genes and observe that a much better duplication tree is obtained by our Method than using any other program.
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topological rearrangements and Local Search Method for tandem duplication trees
Workshop on Algorithms in Bioinformatics, 2004Co-Authors: Denis Bertrand, Olivier GascuelAbstract:The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch (1977). Many recent works deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees (DT). In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on DT. We demonstrate that restricting the neighborhood defined by the SPR (Subtree Pruning and Re-grafting) rearrangement to valid duplication trees, allows exploring the whole space of DT. We use these restricted rearrangements in a Local Search Method which improves an initial tree via successive rearrangements and optimizes the parsimony criterion. We show through simulations that this Method improves all existing programs for both reconstructing the initial tree and recovering its duplication events.
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WABI - Topological Rearrangements and Local Search Method for Tandem Duplication Trees
Lecture Notes in Computer Science, 2004Co-Authors: Denis Bertrand, Olivier GascuelAbstract:The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch (1977). Many recent works deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees (DT). In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on DT. We demonstrate that restricting the neighborhood defined by the SPR (Subtree Pruning and Re-grafting) rearrangement to valid duplication trees, allows exploring the whole space of DT. We use these restricted rearrangements in a Local Search Method which improves an initial tree via successive rearrangements and optimizes the parsimony criterion. We show through simulations that this Method improves all existing programs for both reconstructing the initial tree and recovering its duplication events.
Denis Bertrand - One of the best experts on this subject based on the ideXlab platform.
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Topological Rearrangements and Local Search Method for Tandem Duplication Trees
IEEE ACM Transactions on Computational Biology and Bioinformatics, 2005Co-Authors: Denis Bertrand, Olivier GascuelAbstract:Topological Rearrangements and Local Search Method for Tandem Duplication Trees
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Topological Rearrangements and Local Search Method for Tandem Duplication Trees
IEEE ACM transactions on computational biology and bioinformatics, 2005Co-Authors: Denis Bertrand, Olivier GascuelAbstract:The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch (1977). Many recent studies deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees. In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on duplication trees. We show that restricting the neighborhood defined by the SPR (Subtree Pruning and Regrafting) rearrangement to valid duplication trees, allows exploring the whole duplication tree space. We use these restricted rearrangements in a Local Search Method which improves an initial tree via successive rearrangements. This Method is applied to the optimization of parsimony and minimum evolution criteria. We show through simulations that this Method improves all existing programs for both reconstructing the topology of the true tree and recovering its duplication events. We apply this approach to tandemly repeated human Zinc finger genes and observe that a much better duplication tree is obtained by our Method than using any other program.
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topological rearrangements and Local Search Method for tandem duplication trees
Workshop on Algorithms in Bioinformatics, 2004Co-Authors: Denis Bertrand, Olivier GascuelAbstract:The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch (1977). Many recent works deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees (DT). In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on DT. We demonstrate that restricting the neighborhood defined by the SPR (Subtree Pruning and Re-grafting) rearrangement to valid duplication trees, allows exploring the whole space of DT. We use these restricted rearrangements in a Local Search Method which improves an initial tree via successive rearrangements and optimizes the parsimony criterion. We show through simulations that this Method improves all existing programs for both reconstructing the initial tree and recovering its duplication events.
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WABI - Topological Rearrangements and Local Search Method for Tandem Duplication Trees
Lecture Notes in Computer Science, 2004Co-Authors: Denis Bertrand, Olivier GascuelAbstract:The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch (1977). Many recent works deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees (DT). In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on DT. We demonstrate that restricting the neighborhood defined by the SPR (Subtree Pruning and Re-grafting) rearrangement to valid duplication trees, allows exploring the whole space of DT. We use these restricted rearrangements in a Local Search Method which improves an initial tree via successive rearrangements and optimizes the parsimony criterion. We show through simulations that this Method improves all existing programs for both reconstructing the initial tree and recovering its duplication events.
Chris T. Kiranoudis - One of the best experts on this subject based on the ideXlab platform.
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An integrated Local Search Method for inventory and routing decisions
Expert Systems with Applications, 2009Co-Authors: Emmanouil E. Zachariadis, Christos D. Tarantilis, Chris T. KiranoudisAbstract:The present article studies an inventory routing model which integrates two important components of the supply chain: transportation logistics and inventory control. The distribution system examined consists of customers that face product demand at a deterministic and constant rate. Customer demand is satisfied by a fixed vehicle fleet located at the central depot. The aim of the problem is to determine the timing and size of the replenishment services together with the vehicle routes, so that the total transportation and inventory holding cost of the system is minimized. In Methodological terms, we propose a solution approach applying two innovative Local Search operators for jointly dealing with the inventory and routing aspects of the examined problem, and Tabu Search for further reducing the transportation costs. The proposed algorithmic framework was tested on a set of new benchmark instances of various scales. It produced satisfactory results both in terms of effectiveness and robustness.
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A modern Local Search Method for operations scheduling of dehydration plants
Journal of Food Engineering, 2002Co-Authors: Christos D. Tarantilis, Chris T. KiranoudisAbstract:Drying operations constitute an important field of food engineering, which is still governed by empiricism. The utilisation of different raw materials to be processed sequentially so that demand constraints are met, broadly characterise dehydration plants as multi-product. Processing of raw materials is implemented through a series of pre-processing operations that together with drying constitute the production procedure of a pre-specified campaign. The basic component of the manufacturing system that a typical dehydration plant involves, is scheduling of operations so that demand is fulfilled within a pre-described time horizon imposed by production planning. The typical scheduling operation that dehydration plants involve, can be formulated as a general job shop scheduling problem. The aim of this study is to describe a new metaheuristic Method for solving the job shop scheduling problem of dehydration plants, termed as backtracking adaptive threshold accepting (BATA) Method. Our effort focuses on developing an innovative Method, which produces reliable and good solutions, requiring reasonable computing effort. The main innovation of the Method, towards a typical threshold accepting algorithm, is that the value of the threshold is not only lowered, but also raised or backtracked according to how effective a Local Search is. BATA is described in detail while its performance and characteristic job shop scheduling case studies for dehydration plant operations are presented.
Marco Franchini - One of the best experts on this subject based on the ideXlab platform.
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Use of a genetic algorithm combined with a Local Search Method for the automatic calibration of conceptual rainfall-runoff models
Hydrological Sciences Journal, 1996Co-Authors: Marco FranchiniAbstract:Abstract Wang (1991) reported that a genetic algorithm (GA), combined with a Local Search Method, is an efficient and robust means for the calibration of conceptual rainfall-runoff models. In this article Wang's genetic algorithm has been slightly modified in order to improve its efficiency. The “optimal parameter set” produced by the GA has then been used as the starting point for a Local optimization procedure based on Sequential Quadratic Programming (SQP). The purpose of this paper is to investigate the ability of the resulting algorithm, GA-SQP, to find the optimal parameter values during calibration of a conceptual rainfallrunoff (CRR) model. Two types of analysis were performed. The first refers to a theoretical case free of model and data errors, while the second refers to a real case in which the rainfall and runoff data were affected by evaluation errors. Specifically, in the synthetic data study, where the real set of parameters was known a priori, a 100% success rate was observed, and in all c...
Christophe Wilbaut - One of the best experts on this subject based on the ideXlab platform.
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a hybrid quantum particle swarm optimization for the multidimensional knapsack problem
Engineering Applications of Artificial Intelligence, 2016Co-Authors: Boukthir Haddar, Mahdi Khemakhem, Said Hanafi, Christophe WilbautAbstract:In this paper we propose a new hybrid heuristic approach that combines the Quantum Particle Swarm Optimization technique with a Local Search Method to solve the Multidimensional Knapsack Problem. The approach also incorporates a heuristic repair operator that uses problem-specific knowledge instead of the penalty function technique commonly used for constrained problems. Experimental results obtained on a wide set of benchmark problems clearly demonstrate the competitiveness of the proposed Method compared to the state-of-the-art heuristic Methods.
