O Problema de Minimização do Número Máximo de Pilhas Abertas (MOSP, do inglês minimization of open stacks problem) é um problema de otimização combinatória da família NP-Difícil que vem recebendo grande atenção na literatura especializada. Este trabalho apresenta novas contribuições em termos de modelos e técnicas de resolução para o problema. A primeira parte deste trabalho lidou com modelos matemáticos, sendo analisados os modelos existentes que se baseiam em programação inteira mista. Variações de um modelo da literatura foram propostas, com o objetivo de tentar diminuir o tempo de execução necessário para se obter uma solução exata com a utilização de pacotes comerciais. Os resultados mostraram que as propostas são capazes de acelerar a solução de algumas classes de instâncias mas, que de maneira geral, métodos baseados em relaxação linear encontram dificuldade em provar a otimalidade devido à baixa qualidade dos limitantes inferiores. Uma outra contribuição deste trabalho foi o desenvolvimento de um modelo conjunto para o problema MOSP e para o problema de minimização da duração de pedidos (MORP, do inglês minimization of order spread problem). Este modelo propõe um framework unificado em que os dois problemas podem ser resolvidos ao mesmo tempo, tendo suas funções objetivo individuais ponderadas através de pesos definidos pelo usuário. A segunda parte do trabalho voltou-se para o desenvolvimento de métodos heurísticos para o MOSP. Duas estratégias de solução foram desenvolvidas. O primeiro método propõe uma transformação heurística entre o problema MOSP e o clássico problema do caixeiro viajente (TSP, do inglês traveling salesman problem). A partir de uma representação em grafo do MOSP, o TSP é definido por meio de uma regra de atribuição de distâncias baseadas nos graus dos nós. Nos testes computacionais, a estratégia proposta mostrou-se eficiente em relação às heurísticas específicas para o MOSP, obtendo a solução ótima do MOSP em 80,42% das instâncias testadas e sendo competitiva em termos de tempo computacional com algumas das melhores heurísticas da literatura. O segundo método heurístico proposto utilizou a ideia de decomposição. De fato, neste método, um corte no grafo associado ao problema original divide-o em problemas menores, que são resolvidos. A solução global é obtida através da junção das soluções dos subproblemas e, em alguns casos, é possível demonstrar a otimalidade da solução obtida. Testes computacionais indicam a validade da proposta e apontam caminhos para pesquisas futuras / The minimization of open stacks problem (MOSP) is a well known NP-hard combinatorial optimization problem that has been extensively discussed in the specialized literature. This study presents some new contributions in terms of models and solution methods for this problem. The first part of this thesis dealt with mathematical models. The existing mixedinteger models have been analyzed and variants of a well known model have been proposed, with the goal of reducing the time needed by commercial packages to obtain proved-optimal solutions. The results of computational tests on a widely used set of instances have indicated that the modifications proposed are able to reduce the time needed to obtain optimal solutions for some classes of instances. Nevertheless, a conclusion has been the fact that mixed-integer programming models have difficulty in obtaining convergence due to the low quality linear relaxation bounds. Another contribution of this thesis is the proposal of a single model that is able to deal with both the MOSP and with the Minimization of Order Spread Problem (MORP). This unified framework allows both problems to be jointly solved, by using a weighted objective function that included both original objectives. The second part of this thesis dealt with the development of heuristic strategies. Two solution strategies have been proposed. The first method proposes a heuristic conversion between MOSP and Traveling Salesman Problem (TSP) instances. This conversion relies the assignment distances to the TSP instance based on the degree of the vertices of the associated MOSP graph. Computational tests have shown that the proposed methodology is efficient, both in terms of solution quality (optimal solutions were obtained for 80.42% of the tested instances) and computational effort. The second method uses a decomposition idea. A cut is made in the graph associated with the original MOSP problem, yielding two smaller problems, which are solved. In some cases, the obtained combined solution can be prover optimal. Computational tests have shown the validity of the proposal and indicate new research opportunities

In this doctoral thesis, four questions related to computational geometry are considered. The first is an extremal combinatorics question regarding triangles with vertices taken from a set of n points in convex position. More precisely, two such triangles can exhibit eight distinct configurations and, for each subset of these configurations, we are interested in the asymptotics of how many triangles one can have while avoiding configurations in the subset (as a function of n). For most of these subsets, we answer this question optimally up to a logarithmic factor in the form of several Turán-type theorems. The answers for the remaining few were in turn tied to that of a long-standing open problem which appeared in the literature in the contexts of monotone matrices, tripod packing and 2-comparable sets. The second problem, called Line Segment Covering (LSC), is about covering the cells of an arrangement of line segments with these line segments, where a segment covers the cells it is incident to. Recently, a PTAS, an APX -hardness proof and a FPT algorithm for variants of this problem have been shown. This paper and a new slight generalization of one of its results is included as a chapter. The third problem has been posed in the Sixth Annual Workshop on Geometry and Graphs and concerns the design of road networks to minimize the maximum travel time between two point sets in the plane. Traveling outside the roads costs more time per unit of distance than traveling on the roads and the total length of the roads can not exceed a budget. When the point sets are the opposing sides of a unit square and the budget is at most √2, we were able to come up with a few network designs that cover all possible cases and are provably optimal. Furthermore, when both point sets are the boundary of a unit circle, we managed to disprove the natural conjecture that a concentric circle is an optimal design. Finally, we consider collision-avoiding schedules of unit-velocity axis-aligned trains departing and arriving from points in the integer lattice. We prove a few surprising results on the existence of constant upper bounds on the maximum delay that are independent of the train network. In particular, these upper bounds are shown to always exist in two dimensions and to exist in three dimensions for unit-length trains. We also showed computationally that, for several scenarios, these upper bounds are tight.

In this dissertation, we consider extensions of dynamic programming for combinatorial optimization. We introduce two exact multi-objective optimization algorithms: the multi-stage optimization algorithm that optimizes the problem relative to the ordered sequence of objectives (lexicographic optimization) and the bi-criteria optimization algorithm that simultaneously optimizes the problem relative to two objectives (Pareto optimization). We also introduce a counting algorithm to count optimal solution before and after every optimization stage of multi-stage optimization. We propose a fairly universal approach based on so-called circuits without repetitions in which each element is generated exactly one time. Such circuits represent the sets of elements under consideration (the sets of feasible solutions) and are used by counting, multi-stage, and bi-criteria optimization algorithms. For a given optimization problem, we should describe an appropriate circuit and cost functions. Then, we can use the designed algorithms for which we already have proofs of their correctness and ways to evaluate the required number of operations and the time. We construct conventional (which work directly with elements) circuits without repetitions for matrix chain multiplication, global sequence alignment, optimal paths in directed graphs, binary search trees, convex polygon triangulation, line breaking (text justification), one-dimensional clustering, optimal bitonic tour, and segmented least squares. For these problems, we evaluate the number of operations and the time required by the optimization and counting algorithms, and consider the results of computational experiments. If we cannot find a conventional circuit without repetitions for a problem, we can either create custom algorithms for optimization and counting from scratch or can transform a circuit with repetitions into a so-called syntactical circuit, which is a circuit without repetitions that works not with elements but with formulas representing these elements. We apply both approaches to the optimization of matchings in trees and apply the second approach to the 0/1 knapsack problem. We also briefly introduce our work in operation research with applications to health care. This work extends our interest in the optimization field from developing new methods included in this dissertation towards the practical application.

Given a graph, a matching is a set of vertex-disjoint edges. Graph matchings have been well studied, since they play a fundamental role in algorithmic theory as well as motivate many practical applications. Of particular interest is the problem of finding a maximum cardinality matching of a graph. Also of interest is the weighted variant: the problem of computing a minimum-cost maximum cardinality matching. For an arbitrary graph with m edges and n vertices, there are known, long-standing combinatorial algorithms that compute a maximum cardinality matching in O(m\sqrt{n}) time. For graphs with non-negative integer edge costs at most C, it is known how to compute a minimum-cost maximum cardinality matching in roughly O(m\sqrt{n} log(nC)) time using combinatorial methods. While non-combinatorial methods exist, they are generally impractical and not well understood due to their complexity. As a result, there is great interest in obtaining faster matching algorithms that are purely combinatorial in nature. Improving existing combinatorial algorithms for arbitrary graphs is considered to be a very difficult problem. To make the problem more approachable, it is desirable to make some additional assumptions about the graph. For our work, we make two such assumptions. First, we assume the graph is bipartite. Second, we assume that the graph has a small balanced separator, meaning it is possible to split the graph into two roughly equal-size components by removing a relatively small portion of the graph. Several well-studied classes of graphs have separator-like properties, including planar graphs, minor-free graphs, and geometric graphs. For such graphs, we describe a framework, a general set of techniques for designing efficient algorithms. We demonstrate this framework by applying it to yield polynomial-factor improvements for several open-problems in bipartite matching. / Doctor of Philosophy / Assume we are given a list of objects, and a list of compatible pairs of these objects. A matching consists of a chosen subset of these compatible pairs, where each object participates in at most one chosen pair. For any chosen pair of objects, we say the these two objects are matched. Generally, we seek to maximize the number of compatible matches. A maximum cardinality matching is a matching with the largest possible size. In many cases, there are multiple options for maximizing the number of compatible pairings. While maximizing the size of the matching is often the primary concern, one may also seek to minimize the cost of the matching. This is known as the minimum-cost maximum-cardinality matching problem. These two matching problems have been well studied, since they play a fundamental role in algorithmic theory as well as motivate many practical applications. Our interest is in the design of algorithms for both of these problems that are efficiently scalable, even as the number of objects involved grows very large. To aid in the design of scalable algorithms, we observe that some inputs have good separators, meaning that by removing some subset S of objects, one can divide the remaining objects into two sets V and V', where all pairs of objects between V and V' are incompatible. We design several new algorithms that exploit good separators, and prove that these algorithms scale better than previously existing approaches.

The initial question addressed in this thesis is how to take into account the multi-objective aspect of decision problems in inverse optimization. The most straightforward extension consists of finding a minimal adjustment of the objective functions coefficients such that a given feasible solution becomes efficient. However, there is not only a single question raised by inverse multi-objective optimization, because there is usually not a single efficient solution. The way we define inverse multi-objective<p>optimization takes into account this important aspect. This gives rise to many questions which are identified by a precise notation that highlights a large collection of inverse problems that could be investigated. In this thesis, a selection of inverse problems are presented and solved. This selection is motivated by their possible applications and the interesting theoretical questions they can rise in practice. / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished

International Telemetering Conference Proceedings / October 18-21, 2004 / Town & Country Resort, San Diego, California / The Broadcast Scheduling Problem (BSP) is a well known NP-complete problem that arises in the study of wireless networks. In the BSP, a finite set of stations are to be scheduled in a time division multiple access (TDMA) frame. The objective is a collision free transmission schedule with the minimum number of TDMA slots and maximal slot utilization. Such a schedule will minimize the total system delay. We present variations of a Greedy Randomized Adaptive Search Procedure (GRASP) for the BSP. Path-relinking, a post-optimization strategy is applied. Also, a reactivity method is used to balance GRASP parameters. Numerical results of our research are reported and compared with other heuristics from the literature.

Combinatorial optimization problems are of high academical as well as practical importance. Many instances of relevant combinatorial optimization problems are, due to their dimensions, intractable for complete methods such as branch and bound. Therefore, approximate algorithms such as metaheuristics received much attention in the past 20 years. Examples of metaheuristics are simulated annealing, tabu search, and evolutionary computation. One of the most recent metaheuristics is ant colony optimization (ACO), which was developed by Prof. M. Dorigo (who is the supervisor of this thesis) and colleagues. This thesis deals with theoretical as well as practical aspects of ant colony optimization. * A survey of metaheuristics. Chapter 1 gives an extensive overview on the nowadays most important metaheuristics. This overview points out the importance of two important concepts in metaheuristics: intensification and diversification. * The hyper-cube framework. Chapter 2 introduces a new framework for implementing ACO algorithms. This framework brings two main benefits to ACO researchers. First, from the point of view of the theoretician: we prove that Ant System (the first ACO algorithm to be proposed in the literature) in the hyper-cube framework generates solutions whose expected quality monotonically increases with the number of algorithm iterations when applied to unconstrained problems. Second, from the point of view of the experimental researcher, we show through examples that the implementation of ACO algorithms in the hyper-cube framework increases their robustness and makes the handling of the pheromone values easier. * Deception. In the first part of Chapter 3 we formally define the notions of first and second order deception in ant colony optimization. Hereby, first order deception corresponds to deception as defined in the field of evolutionary computation and is therefore a bias introduced by the problem (instance) to be solved. Second order deception is an ACO-specific phenomenon. It describes the observation that the quality of the solutions generated by ACO algorithms may decrease over time in certain settings. In the second part of Chapter 3 we propose different ways of avoiding second order deception. * ACO for the KCT problem. In Chapter 4 we outline an ACO algorithm for the edge-weighted k-cardinality tree (KCT) problem. This algorithm is implemented in the hyper-cube framework and uses a pheromone model that was determined to be well-working in Chapter 3. Together with the evolutionary computation and the tabu search approaches that we develop in Chapter 4, this ACO algorithm belongs to the current state-of-the-art algorithms for the KCT problem. * ACO for the GSS problem. Chapter 5 describes a new ACO algorithm for the group shop scheduling (GSS) problem, which is a general shop scheduling problem that includes among others the well-known job shop scheduling (JSS) and the open shop scheduling (OSS) problems. This ACO algorithm, which is implemented in the hyper-cube framework and which uses a new pheromone model that was experimentally tested in Chapter 3, is currently the best ACO algorithm for the JSS as well as the OSS problem. In particular when applied to OSS problem instances, this algorithm obtains excellent results, improving the best known solution for several OSS benchmark instances. A final contribution of this thesis is the development of a general method for the solution of combinatorial optimization problems which we refer to as Beam-ACO. This method is a hybrid between ACO and a tree search technique known as beam search. We show that Beam-ACO is currently a state-of-the-art method for the application to the existing open shop scheduling (OSS) problem instances.

The <i>mixed postman problem</i> consists of finding a minimum cost tour of a mixed graph <i>M</i> = (<i>V</i>,<i>E</i>,<i>A</i>) traversing all its edges and arcs at least once. We prove that two well-known linear programming relaxations of this problem are equivalent. The <i>extra cost</i> of a mixed postman tour <i>T</i> is the cost of <i>T</i> minus the cost of the edges and arcs of <i>M</i>. We prove that it is <i>NP</i>-hard to approximate the minimum extra cost of a mixed postman tour. A related problem, known as the <i>windy postman problem</i>, consists of finding a minimum cost tour of an undirected graph <i>G</i>=(<i>V</i>,<i>E</i>) traversing all its edges at least once, where the cost of an edge depends on the direction of traversal. We say that <i>G</i> is <i>windy postman perfect</i> if a certain <i>windy postman polyhedron O</i> (<i>G</i>) is integral. We prove that series-parallel undirected graphs are windy postman perfect, therefore solving a conjecture of Win. Given a mixed graph <i>M</i> = (<i>V</i>,<i>E</i>,<i>A</i>) and a subset <i>R</i> &#8838; <i>E</i> &#8746; <i>A</i>, we say that a mixed postman tour of <i>M</i> is <i>restricted</i> if it traverses the elements of <i>R</i> exactly once. The <i>restricted mixed postman problem</i> consists of finding a minimum cost restricted tour. We prove that this problem is <i>NP</i>-hard even if <i>R</i>=<i>A</i> and we restrict <i>M</i> to be planar, hence solving a conjecture of Veerasamy. We also prove that it is <i>NP</i>-complete to decide whether there exists a restricted tour even if <i>R</i>=<i>E</i> and we restrict <i>M</i> to be planar. The <i>edges postman problem</i> is the special case of the restricted mixed postman problem when <i>R</i>=<i>A</i>. We give a new class of valid inequalities for this problem. We introduce a relaxation of this problem, called the <i>b-join problem</i>, that can be solved in polynomial time. We give an algorithm which is simultaneously a 4/3-approximation algorithm for the edges postman problem, and a 2-approximation algorithm for the extra cost of a tour. The <i>arcs postman problem</i> is the special case of the restricted mixed postman problem when <i>R</i>=<i>E</i>. We introduce a class of necessary conditions for <i>M</i> to have an arcs postman tour, and we give a polynomial-time algorithm to decide whether one of these conditions holds. We give linear programming formulations of this problem for mixed graphs arising from windy postman perfect graphs, and mixed graphs whose arcs form a forest.

Abstract not available

Un des buts principaux de la biologie évolutive et de la médecine moléculaire consiste à reconstruire les relations phylogénétiques entre organismes à partir de leurs séquences moléculaires. En littérature, cette question est connue sous le nom d’inférence phylogénétique et a d'importantes applications dans la recherche médicale et pharmaceutique, ainsi que dans l’immunologie, l’épidémiologie, et la dynamique des populations. L’accumulation récente de données de séquences d’ADN dans les bases de données publiques, ainsi que la facilité relative avec laquelle des données nouvelles peuvent être obtenues, rend l’inférence phylogénétique particulièrement difficile (l'inférence phylogénétique est un problème NP-Hard sous tous les critères d’optimalité connus), de telle manière que des nouveaux critères et des algorithmes efficaces doivent être développés. Cette thèse a pour but: (i) d’analyser les limites mathématiques et biologiques des critères utilisés en inférence phylogénétique, (ii) de développer de nouveaux algorithmes efficaces permettant d’analyser de plus grands jeux de données.