Based on the recent successes in stochastic linear programming and mixed integer programming, in this thesis we combine these two important areas of mathematical programming; specifically we study stochastic integer programming. We first study a simple and important stochastic integer programming problem, called stochastic uncapacitated lot-sizing (SLS), which is motivated by production planning under uncertainty. We describe a multi-stage stochastic integer programming formulation of the problem and develop a family of valid inequalities, called the (Q, S) inequalities. We establish facet-defining conditions and show that these inequalities are sufficient to describe the convex hull of integral solutions for two-period instances. A separation heuristic for (Q, S) inequalities is developed and incorporated into a branch-and-cut algorithm. A computational study verifies the usefulness of the inequalities as cuts. Then, motivated by the polyhedral study of (Q, S) inequalities for SLS, we analyze the underlying integer programming scheme for general stochastic integer programming problems. We present a scheme for generating new valid inequalities for mixed integer programs by taking pair-wise combinations of existing valid inequalities. The scheme is in general sequence-dependent and therefore leads to an exponential number of inequalities. For some special cases, we identify combination sequences that lead to a manageable set of all non-dominated inequalities. For the general scenario tree case, we identify combination sequences that lead to non-dominated inequalities. We also analyze the conditions such that the inequalities generated by our approach are facet-defining and describe the convex hull of integral solutions. We illustrate the framework for some deterministic and stochastic integer programs and we present computational results which show the efficiency of adding the new generated inequalities as cuts.

This dissertation studies in depth the structure of the Discrete Ordered Median Problem (DOMP), to define new formulations and resolution algorithms. Furthermore we analyze an interesting extension for DOMP, namely MDOMP (Monotone Discrete Ordered Median Problem). This thesis is structured in three main parts.First, a widely theoretical and computational study is reported. It presents several new formulations for the Discrete Ordered Median Problem (DOMP) based on its similarity with some scheduling problems. Some of the new formulations present a considerably smaller number of constraints to define the problem with respect to some previously known formulations. Furthermore, the lower bounds provided by their linear relaxations improve the ones obtained with previous formulations in the literature even when strengthening is not applied. We also present a polyhedral study of the assignment polytope of our tightest formulation showing its proximity to the convex hull of the integer solutions of the problem. Several resolution approaches, among which we mention a branch and cut algorithm, are compared. Extensive computational results on two families of instances, namely randomly generated and from Beasley's OR-library, show the power of our methods for solving DOMP. One of the achievements of the new formulation consists in its tighter LP-bound. Secondly, DOMP is addressed with a new set partitioning formulation using an exponential number of variables. This chapter develops a new formulation in which each variable corresponds to a set of demand points allocated to the same facility with the information of the sorting position of their corresponding distances. We use a column generation approach to solve the continuous relaxation of this model. Then, we apply a branch-cut-and-price algorithm to solve to optimality small to moderate size of DOMP in competitive computational time.To finish, the third contribution of this dissertation is to analyze and compare formulations for the monotone discrete ordered median problem. These formulations combine different ways to represent ordered weighted averages of elements by using linear programs together with the p-median polytope. This approach gives rise to two efficient formulations for DOMP under a hypothesis of monotonicity in the lambda vectors. These formulations are theoretically compared and also compared with some other formulations valid for the case of general lambda vector. In addition, it is also developed another new formulation, for the general case, that exploits the efficiency of the rationale of monotonicity. This representation allows to solve very efficiently some DOMP instances where the monotonicity is only slightly lost. Detailed computational tests on all these formulations is reported in the dissertation. They show that specialized formulations allow to solve to optimality instances with sizes that are far beyond the limits of those that can solve in the general case. / Cette dissertation étudie en profondeur la structure du "Discrete Ordered Median Problem" (DOMP), afin de proposer de nouvelles formulations et de nouveaux algorithmes de résolution. De plus, une extension intéressante du DOMP nommée MDOMP ("Monotone Discrete Ordered Median Problem") a été étudiée.Cette thèse a été structurée en trois grandes parties.La première partie présente une étude riche aux niveaux théorique et expérimentale. Elle développe plusieurs formulations pour le DOMP qui sont basées sur des problèmes d'ordonnancement largement étudiés dans la littérature. Plusieurs d'entres elles nécessitent un nombre réduit de contraintes pour définir le problème en ce qui concerne certaines formulations connues antérieurement. Les bornes inférieures, qui sont obtenues par la résolution de la relaxation linéaire, donnent de meilleurs résultats que les formulations précédentes et ceci même avec tout processus de renforcement désactivé. S'ensuit une étude du polyhèdre de notre formulation la plus forte qui montre sa proximité entre l'enveloppe convexe des solutions entières de notre problème. Un algorithme de branch and cut et d'autres méthodes de résolution sont ensuite comparés. Les expérimentations qui montrent la puissance de nos méthodes s'appuient sur deux grandes familles d'instances. Les premières sont générées aléatoirement et les secondes proviennent de Beasley's OR-library. Ces expérimentations mettent en valeur la qualité de la borne obtenue par notre formulation.La seconde partie propose une formulation "set partitioning" avec un nombre exponentiel de variables. Dans ce chapitre, la formulation comporte des variables associées à un ensemble de demandes affectées à la même facilité selon l'ordre établi sur leurs distances correspondantes. Nous avons alors développé un algorithme de génération de colonnes pour la résolution de la relaxation continue de notre modèle mathématique. Cet algorithme est ensuite déployé au sein d'un Branch-and-Cut-and-Price afin de résoudre des instances de petites et moyennes tailles avec des temps compétitifs.La troisième partie présente l'analyse et la comparaison des différentes formulations du problème DOMP Monotone. Ces formulations combinent plusieurs manières de formuler l'ordre des éléments selon les moyennes pondérées en utilisant plusieurs programmes linéaires du polytope du p-median. Cette approche donne lieu à deux formulations performantes du DOMP sous l'hypothèse de monotonie des vecteurs lambda. Ces formulations sont comparées de manière théorique puis comparées à d'autres formulations valides pour le cas général du vecteur lambda. Une autre formulation est également proposée, elle exploite l'efficacité du caractère rationnel de la monotonie. Cette dernière permet de résoudre efficacement quelques instances où la monotonie a légèrement disparue. Ces formulations ont fait l'objet de plusieurs expérimentations dècrites dans ce manuscrit de thèse. Elles montrent que les formulations spécifiques permettent de résoudre des instances plus importantes que pour le cas général. / Este trabajo estudia en profundidad la estructura del problema disctreto de la mediana ordenada (DOMP, por su acrónimo en inglés) con el objetivo de definir nuevas formulaciones y algoritmos de resolución. Además, analizamos una interesante extensión del DOMP conocida como el problema monótono discreto de la mediana ordenada (MDOMP, de su acrónimo en inglés).Esta tesis se compone de tres grandes bloques.En primer lugar, se desarrolla un detallado estudio teórico y computacional. Se presentan varias formulaciones nuevas para el problema discreto de la mediana ordenada (DOMP) basadas en su similaridad con algunos problemas de secuenciación. Algunas de estas formulaciones requieren de un cosiderable menor número de restricciones para definir el problema respecto a algunas de las formulaciones previamente conocidas. Además, las cotas inferiores proporcionadas por las relajaciones lineales mejoran a las obtenidas con formulaciones previas de la literatura incluso sin reforzar la nueva formulación. También presentamos un estudio poliédrico del politopo de asignación de nuestra formulación más compacta mostrando su proximidad con la envolvente convexa de las soluciones enteras del problema. Se comparan algunos procedimientos de resolución, entre los que destacamos un algoritmo de ramificación y corte. Amplios resultados computacionales sobre dos familias de instancias -aleatoriamente generadas y utilizando la Beasley's OR-library- muestran la potencia de nuestros métodos para resolver el DOMP.En el segundo bloque, el problema discreto de la mediana ordenada es abordado con una formulación de particiones de conjuntos empleando un número exponencial de variables. Este capítulo desarrolla una nueva formulación en la que cada variable corresponde a un conjunto de puntos de demanda asignados al mismo servidor con la información de la posición obtenida de ordenar las distancias correspondientes. Utilizamos generación de columnas para resolver la relajación continua del modelo. Después, empleamos un algoritmo de ramificación, acotación y "pricing" para resolver a optimalidad tamaños moderados del DOMP en un tiempo computacional competitivo.Por último, el tercer bloque de este trabajo se dedica a analizar y comparar formulaciones para el problema monótono discreto de la mediana ordenada. Estas formulaciones combinan diferentes maneras de representar medidas de pesos ordenados de elementos utilizando programación lineal junto con el politopo de la $p$-mediana. Este enfoque da lugar a dos formulaciones eficientes para el DOMP bajo la hipótesis de monotonía en su vector $lambda$. Se comparan teóricamente las formulaciones entre sí y frente a algunas de las formulaciones válidas para el caso general. Adicionalmente, se desarrolla otra formulación válida para el caso general que explota la eficiencia de las ideas de la monotonicidad. Esta representación permite resolver eficientemente algunos ejemplos donde la monotonía se pierde ligeramente. Finalmente, llevamos a cabo un detallado estudio computacional, en el que se aprecia que las formulaciones ad hoc permiten resolver a optimalidad ejemplos cuyo tamaño supera los límites marcados en al caso general. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Cette thèse porte sur la résolution exacte et heuristique de plusieurs problèmes ayant des applications dans le domaine de l'Informatique dématérialisé (cloud computing). L'Informatique dématérialisée est un domaine en plein extension qui consiste à mutualiser les machines/serveurs en définissant des machines virtuelles représentant des fractions des machines/serveurs. Il est nécessaire d'apporter des solutions algorithmiques performantes en termes de temps de calcul et de qualité des solutions. Dans cette thèse, nous nous sommes intéressés dans un premier temps au problème d'ordonnancement sur plusieurs machines (les machines virtuelles) avec contraintes de précédence, c.-à-d., que certaines tâches ne peuvent s'exécuter que si d'autres sont déjà finies. Ces contraintes représentent une subdivision des tâches en sous tâches pouvant s'exécuter sur plusieurs machines virtuelles. Nous avons proposé plusieurs algorithmes génétiques permettant de trouver rapidement une bonne solution réalisable. Nous les avons comparés avec les meilleurs algorithmes génétiques de la littérature et avons défini les types d'instances où les solutions trouvées sont meilleures avec notre algorithme. Dans un deuxième temps, nous avons modélisé ce problème à l'aide de la programmation linéaire en nombres entiers permettant de résoudre à l'optimum les plus petites instances. Nous avons proposé de nouvelles inégalités valides permettant d'améliorer les performances de notre modèle. Nous avons aussi comparé cette modélisation avec plusieurs formulations trouvées dans la littérature. Dans un troisième temps, nous avons analysé de manière approfondie la sous-structure du sous-graphe d'intervalle ne possédant pas de clique de taille donnée. Nous avons étudié le polytope associé à cette sous-structure et nous avons montré que les facettes que nous avons trouvées sont valides pour le problème d'ordonnancement sur plusieurs machines avec contraintes de précédence mais elles le sont aussi pour tout problème d'ordonnancement sur plusieurs machines. Nous avons étendu la modélisation permettant de résoudre le précédent problème afin de résoudre le problème d'ordonnancement sur plusieurs machines avec des contraintes disjonctives entre les tâches, c.-à-d., que certaines tâches ne peuvent s'exécuter en même temps que d'autres. Ces contraintes représentent le partage de ressources critiques ne pouvant pas être utilisées par plusieurs tâches. Nous avons proposé des algorithmes de séparation afin d'insérer de manière dynamique nos facettes dans la résolution du problème puis avons développé un algorithme de type Branch-and-Cut. Nous avons analysé les résultats obtenus afin de déterminer les inégalités les plus intéressantes afin de résoudre ce problème. Enfin dans le dernier chapitre, nous nous sommes intéressés au problème d'ordonnancement d'atelier généralisé ainsi que la version plus classique d'ordonnancement d'atelier (open shop). En effet, le problème d'ordonnancement d'atelier généralisé est aussi un cas particulier du problème d'ordonnancement sur plusieurs machines avec des contraintes disjonctives entre les tâches. Nous avons proposé une formulation à l'aide de la programmation mathématique pour résoudre ces deux problèmes et nous avons proposé plusieurs familles d'inégalités valides permettant d'améliorer les performances de notre algorithme. Nous avons aussi pu utiliser les contraintes définies précédemment afin d'améliorer les performances pour le problème d'ordonnancement d'atelier généralisé. Nous avons fini par tester notre modèle amélioré sur les instances classiques de la littérature pour le problème d'ordonnancement d'atelier. Nous obtenons de bons résultats permettant d'être plus rapide sur certaines instances / The Cloud Computing appears as a strong concept to share costs and resources related to the use of end-users. As a consequence, several related models exist and are widely used (IaaS, PaaS, SaaS. . .). In this context, our research focused on the design of new methodologies and algorithms to optimize performances using the scheduling and combinatorial theories. We were interested in the performance optimization of a Cloud Computing environment where the resources are heterogeneous (operators, machines, processors...) but limited. Several scheduling problems have been addressed in this thesis. Our objective was to build advanced algorithms by taking into account all these additional specificities of such an environment and by ensuring the performance of solutions. Generally, the scheduling function consists in organizing activities in a specific system imposing some rules to respect. The scheduling problems are essential in the management of projects, but also for a wide set of real systems (telecommunication, computer science, transportation, production...). More generally, solving a scheduling problem can be reduced to the organization and the synchronization of a set of activities (jobs or tasks) by exploiting the available capacities (resources). This execution has to respect different technical rules (constraints) and to provide the maximum of effectiveness (according to a set of criteria). Most of these problems belong to the NP-Hard problems class for which the majority of computer scientists do not expect the existence of a polynomial exact algorithm unless P=NP. Thus, the study of these problems is particularly interesting at the scientific level in addition to their high practical relevance. In particular, we aimed to build new efficient combinatorial methods for solving parallel-machine scheduling problems where resources have different speeds and tasks are linked by precedence constraints. In our work we studied two methodological approaches to solve the problem under the consideration : exact and meta-heuristic methods. We studied three scheduling problems, where the problem of task scheduling in cloud environment can be generalized as unrelated parallel machines, and open shop scheduling problem with different constraints. For solving the problem of unrelated parallel machines with precedence constraints, we proposed a novel genetic-based task scheduling algorithms in order to minimize maximum completion time (makespan). These algorithms combined the genetic algorithm approach with different techniques and batching rules such as list scheduling (LS) and earliest completion time (ECT). We reviewed, evaluated and compared the proposed algorithms against one of the well-known genetic algorithms available in the literature, which has been proposed for the task scheduling problem on heterogeneous computing systems. Moreover, this comparison has been extended to an existing greedy search method, and to an exact formulation based on basic integer linear programming. The proposed genetic algorithms show a good performance dominating the evaluated methods in terms of problems' sizes and time complexity for large benchmark sets of instances. We also extended three existing mathematical formulations to derive an exact solution for this problem. These mathematical formulations were validated and compared to each other by extensive computational experiments. Moreover, we proposed an integer linear programming formulations for solving unrelated parallel machine scheduling with precedence/disjunctive constraints, this model based on the intervaland m-clique free graphs with an exponential number of constraints. We developed a Branch-and-Cut algorithm, where the separation problems are based on graph algorithms. [...]

Étant donnés un graphe simple non orienté G = (V, E) et un sommet particulier r dans V appelé racine, un arbre enraciné, ou r-arbre, de G est soit le graphe nul soit un arbre contenant r. Si un vecteur de capacités sur les sommets est donné, un sous-graphe de G est dit borné si le degré de chaque sommet dans le sous-graphe est inférieur ou égal à sa capacité. Soit w un vecteur de poids sur les arêtes et p un vecteur de profits sur les sommets. Le problème du r-arbre borné maximum (MBrT, de l’anglais Maximum Bounded r-Tree) consiste à trouver un r-arbre borné T = (U, F) de G tel que son poids soit maximisé. Si la contrainte de capacité du problème MBrT est relâchée, nous obtenons le problème du r-arbre maximum (MrT, de l’anglais Maximum r-Tree). Cette thèse contribue à l’étude des problèmes MBrT et MrT.Tout d’abord, ces deux problèmes sont formellement définis et leur complexité est étudiée. Nous présentons ensuite des polytopes associés ainsi qu’une formulation pour chacun d’entre eux. Par la suite, nous proposons plusieurs algorithmes combinatoires pour résoudre le problème MBrT (et donc le problème MrT) en temps polynomial sur les arbres, les cycles et les cactus. En particulier, un algorithme de programmation dynamique est utilisé pour résoudre le problème MBrT sur les arbres. Pour les cycles, nous sommes amenés a considérer trois cas différents pour lesquels le problem MBrT se réduit à certains problèmes polynomiaux. Pour les cactus, nous montrons tout d’abord que le problème MBrT peut être résolu en temps polynomial sur un type de graphes appelé cactus basis. En utilisant une série de décompositions en sous-problèmes sur les arbres et les cactus basis, nous obtenons un algorithme pour les graphes de type cactus.La deuxième partie de ce travail étudie la structure polyédrale de trois polytopes associés aux problèmes MBrT et MrT. Les deux premiers polytopes, Bxy(G,r,c) et Bx(G,r,c) sont associés au problème MBrT. Tous deux considèrent des variables sur les arêtes de G, mais seuls Bxy(G,r,c) possède également des variables sur les sommets de G. Le troisième polytope, Rx(G,r), est associé au problème MrT et repose uniquement sur les variables sur les arêtes. Pour chacun de ces trois polytopes, nous étudions sa dimension, caractérisons certaines inégalités définissant des facettes, et présentons les moyens possibles de décomposition. Nous introduisons également de nouvelles familles de contraintes. L’ajout de ces contraintes nous permettent de caractériser ces trois polytopes dans plusieurs classes de graphes.Pour finir, nous étudions les problèmes de séparation pour toutes les inégalités que nous avons trouvées jusqu’ici. Des algorithmes polynomiaux de séparation sont présentés, et lorsqu’un problème de séparation est NP-difficile, nous donnons des heuristiques de séparation. Tous les résultats théoriques développés dans ce travail sont implémentés dans plusieurs algorithmes de coupes et branchements auxquels une matheuristique est également jointe pour générer rapidement des solutions réalisables. Des expérimentations intensives ont été menées via le logiciel CPLEX afin de comparer les formulations renforcées et originales. Les résultats obtenus montrent de manière convaincante la force des formulations renforcées. / Given a simple undirected graph G = (V, E) with a so-called root node r in V, a rooted tree, or an r-tree, of G is either the empty graph, or a tree containing r. If a node-capacity vector c is given, then a subgraph of G is said to be bounded if the degree of each node in the subgraph does not exceed its capacity. Let w be an edge-weight vector and p a node-price vector. The Maximum Bounded r-Tree (MBrT) problem consists of finding a bounded r-tree T = (U, F) of G such that its weight is maximized. If the capacity constraint from the MBrT problem is relaxed, we then obtain the Maximum r-Tree (MrT) problem. This dissertation contributes to the study of the MBrT problem and the MrT problem.First we introduce the problems with their definitions and complexities. We define the associated polytopes along with a formulation for each of them. We present several polynomial-time combinatorial algorithms for both the MBrT problem (and thus the MrT problem) on trees, cycles and cactus graphs. Particularly, a dynamic-programming-based algorithm is used to solve the MBrT problem on trees, whereas on cycles we reduce it to some polynomially solvable problems in three different cases. For cactus graphs, we first show that the MBrT problem can be solved in polynomial time on a so-called cactus basis, then break down the problem on any cactus graph into a series of subproblems on trees and on cactus basis.The second part of this work investigates the polyhedral structure of three polytopes associated with the MBrT problem and the MrT problem, namely Bxy(G, r, c), Bx(G, r, c) and Rx(G, r). Bxy(G, r, c) and Bx(G, r, c) are polytopes associated with the MBrT problem, where Bxy(G, r, c) considers both edge- and node-indexed variables and Bx(G, r, c) considers only edge-indexed variables. Rx(G, r) is the polytope associated with the MrT problem that only considers edge-indexed variables. For each of the three polytopes, we study their dimensions, facets as well as possible ways of decomposition. We introduce some newly discovered constraints for each polytope, and show that these new constraints allow us to characterize them on several graph classes. Specifically, we provide characterization for Bxy (G, r, c) on cactus graphs with the help of a decomposition through 1-sum. On the other hand, a TDI-system that characterizes Bx(G,r,c) is given in each case of trees and cycles. The characterization of Rx(G,r) on trees and cycles then follows as an immediate result.Finally, we discuss the separation problems for all the inequalities we have found so far, and present algorithms or cut-generation heuristics accordingly. A couple of branch-and-cut frameworks are implemented to solve the MBrT problem together with a greedy-based matheuristic. We compare the performances of the enhanced formulations with the original formulations through intensive computational test, where the results demonstrate convincingly the strength of the enhanced formulations.

Neste trabalho, estudamos o problema a recoloração convexa de grafos, denotado por RC. Dizemos que uma coloração dos vértices de um grafo G é convexa se, para cada cor tribuída d, os vértices de G com a cor d induzem um subgrafo conexo. No problema RC, é dado um grafo G e uma coloração de seus vértices, e o objetivo é recolorir o menor número possível de vértices de G tal que a coloração resultante seja convexa. A motivação para o estudo deste problema surgiu em contexto de árvores filogenéticas. Sabe-se que este problema é NP-difícil mesmo quando G é um caminho. Mostramos que o problema RC parametrizado pelo número de mudanças de cor é W[2]-difícil mesmo se a coloração inicial usa apenas duas cores. Além disso, provamos alguns resultados sobre a inaproximabilidade deste problema. Apresentamos uma formulação inteira para a versão com pesos do problema RC em grafos arbitrários, e então a especializamos para o caso de árvores. Estudamos a estrutura facial do politopo definido como a envoltória convexa dos pontos inteiros que satisfazem as restrições da formulação proposta, apresentamos várias classes de desigualdades que definem facetas e descrevemos os correspondentes algoritmos de separação. Implementamos um algoritmo branch-and-cut para o problema RC em árvores e mostramos os resultados computacionais obtidos com uma grande quantidade de instâncias que representam árvores filogenéticas reais. Os experimentos mostram que essa abordagem pode ser usada para resolver instâncias da ordem de 1500 vértices em 40 minutos, um desempenho muito superior ao alcançado por outros algoritmos propostos na literatura. / In this work we study the convex recoloring problem of graphs, denoted by CR. We say that a vertex coloring of a graph G is convex if, for each assigned color d, the vertices of G with color d induce a connected subgraph. In the CR problem, given a graph G and a coloring of its vertices, we want to find a recoloring that is convex and minimizes the number of recolored vertices. The motivation for investigating this problem has its roots in the study of phylogenetic trees. It is known that this problem is NP-hard even when G is a path. We show that the problem CR parameterized by the number of color changes is W[2]-hard even if the initial coloring uses only two colors. Moreover, we prove some inapproximation results for this problem. We also show an integer programming formulation for the weighted version of this problem on arbitrary graphs, and then specialize it for trees. We study the facial structure of the polytope defined as the convex hull of the integer points satisfying the restrictions of the proposed ILP formulation, present several classes of facet-defining inequalities and the corresponding separation algorithms. We also present a branch-and-cut algorithm that we have implemented for the special case of trees, and show the computational results obtained with a large number of instances. We considered instances which are real phylogenetic trees. The experiments show that this approach can be used to solve instances up to 1500 vertices in 40 minutes, comparing favorably to other approaches that have been proposed in the literature.

Neste trabalho, estudamos o problema a recoloração convexa de grafos, denotado por RC. Dizemos que uma coloração dos vértices de um grafo G é convexa se, para cada cor tribuída d, os vértices de G com a cor d induzem um subgrafo conexo. No problema RC, é dado um grafo G e uma coloração de seus vértices, e o objetivo é recolorir o menor número possível de vértices de G tal que a coloração resultante seja convexa. A motivação para o estudo deste problema surgiu em contexto de árvores filogenéticas. Sabe-se que este problema é NP-difícil mesmo quando G é um caminho. Mostramos que o problema RC parametrizado pelo número de mudanças de cor é W[2]-difícil mesmo se a coloração inicial usa apenas duas cores. Além disso, provamos alguns resultados sobre a inaproximabilidade deste problema. Apresentamos uma formulação inteira para a versão com pesos do problema RC em grafos arbitrários, e então a especializamos para o caso de árvores. Estudamos a estrutura facial do politopo definido como a envoltória convexa dos pontos inteiros que satisfazem as restrições da formulação proposta, apresentamos várias classes de desigualdades que definem facetas e descrevemos os correspondentes algoritmos de separação. Implementamos um algoritmo branch-and-cut para o problema RC em árvores e mostramos os resultados computacionais obtidos com uma grande quantidade de instâncias que representam árvores filogenéticas reais. Os experimentos mostram que essa abordagem pode ser usada para resolver instâncias da ordem de 1500 vértices em 40 minutos, um desempenho muito superior ao alcançado por outros algoritmos propostos na literatura. / In this work we study the convex recoloring problem of graphs, denoted by CR. We say that a vertex coloring of a graph G is convex if, for each assigned color d, the vertices of G with color d induce a connected subgraph. In the CR problem, given a graph G and a coloring of its vertices, we want to find a recoloring that is convex and minimizes the number of recolored vertices. The motivation for investigating this problem has its roots in the study of phylogenetic trees. It is known that this problem is NP-hard even when G is a path. We show that the problem CR parameterized by the number of color changes is W[2]-hard even if the initial coloring uses only two colors. Moreover, we prove some inapproximation results for this problem. We also show an integer programming formulation for the weighted version of this problem on arbitrary graphs, and then specialize it for trees. We study the facial structure of the polytope defined as the convex hull of the integer points satisfying the restrictions of the proposed ILP formulation, present several classes of facet-defining inequalities and the corresponding separation algorithms. We also present a branch-and-cut algorithm that we have implemented for the special case of trees, and show the computational results obtained with a large number of instances. We considered instances which are real phylogenetic trees. The experiments show that this approach can be used to solve instances up to 1500 vertices in 40 minutes, comparing favorably to other approaches that have been proposed in the literature.

The vertex coloring problem is a classic problem in graph theory that asks for a partition of the vertex set into a minimum number of stable sets. This thesis presents our studies on three vertex (re)coloring problems on graphs and on a problem related to a long-standing conjecture on subdivision of digraphs. Firstly, we address the convex recoloring problem in which an arbitrarily colored graph G is given and one wishes to find a minimum weight recoloring such that each color class induces a connected subgraph of G. We show inapproximability results, introduce an integer linear programming (ILP) formulation that models the problem and present some computational experiments using a column generation approach. The k-fold coloring problem is a generalization of the classic vertex coloring problem and consists in covering the vertex set of a graph by a minimum number of stable sets in such a way that every vertex is covered by at least k (possibly identical) stable sets. We present an ILP formulation for this problem and show a detailed polyhedral study of the polytope associated with this formulation. The last coloring problem studied in this thesis is the proper orientation problem. It consists in orienting the edge set of a given graph so that adjacent vertices have different in-degrees and the maximum in-degree is minimized. Clearly, the in-degrees induce a partition of the vertex set into stable sets, that is, a coloring (in the conventional sense) of the vertices. Our contributions in this problem are on hardness and upper bounds for bipartite graphs. Finally, we study a problem related to a conjecture of Mader from the eighties on subdivision of digraphs. This conjecture states that, for every acyclic digraph H, there exists an integer f(H) such that every digraph with minimum out-degree at least f(H) contains a subdivision of H as a subdigraph. We show evidences for this conjecture by proving that it holds for some particular classes of acyclic digraphs. / O problema de coloração de grafos é um problema clássico em teoria dos grafos cujo objetivo é particionar o conjunto de vértices em um número mínimo de conjuntos estáveis. Nesta tese apresentamos nossas contribuições sobre três problemas de coloração de grafos e um problema relacionado a uma antiga conjectura sobre subdivisão de digrafos. Primeiramente, abordamos o problema de recoloração convexa no qual é dado um grafo arbitrariamente colorido G e deseja-se encontrar uma recoloração de peso mínimo tal que cada classe de cor induza um subgrafo conexo de G. Mostramos resultados sobre inaproximabilidade, introduzimos uma formulação linear inteira que modela esse problema, e apresentamos alguns resultados computacionais usando uma abordagem de geração de colunas. O problema de k-upla coloração é uma generalização do problema clássico de coloração de vértices e consiste em cobrir o conjunto de vértices de um grafo com uma quantidade mínima de conjuntos estáveis de tal forma que cada vértice seja coberto por pelo menos k conjuntos estáveis (possivelmente idênticos). Apresentamos uma formulação linear inteira para esse problema e fazemos um estudo detalhado do politopo associado a essa formulação. O último problema de coloração estudado nesta tese é o problema de orientação própria. Ele consiste em orientar o conjunto de arestas de um dado grafo de tal forma que vértices adjacentes possuam graus de entrada distintos e o maior grau de entrada seja minimizado. Claramente, os graus de entrada induzem uma partição do conjunto de vértices em conjuntos estáveis, ou seja, induzem uma coloração (no sentido convencional) dos vértices. Nossas contribuições nesse problema são em complexidade computacional e limitantes superiores para grafos bipartidos. Finalmente, estudamos um problema relacionado a uma conjectura de Mader, dos anos oitenta, sobre subdivisão de digrafos. Esta conjectura afirma que, para cada digrafo acíclico H, existe um inteiro f(H) tal que todo digrafo com grau mínimo de saída pelo menos f(H) contém uma subdivisão de H como subdigrafo. Damos evidências para essa conjectura mostrando que ela é válida para classes particulares de digrafos acíclicos.

The vertex coloring problem is a classic problem in graph theory that asks for a partition of the vertex set into a minimum number of stable sets. This thesis presents our studies on three vertex (re)coloring problems on graphs and on a problem related to a long-standing conjecture on subdivision of digraphs. Firstly, we address the convex recoloring problem in which an arbitrarily colored graph G is given and one wishes to find a minimum weight recoloring such that each color class induces a connected subgraph of G. We show inapproximability results, introduce an integer linear programming (ILP) formulation that models the problem and present some computational experiments using a column generation approach. The k-fold coloring problem is a generalization of the classic vertex coloring problem and consists in covering the vertex set of a graph by a minimum number of stable sets in such a way that every vertex is covered by at least k (possibly identical) stable sets. We present an ILP formulation for this problem and show a detailed polyhedral study of the polytope associated with this formulation. The last coloring problem studied in this thesis is the proper orientation problem. It consists in orienting the edge set of a given graph so that adjacent vertices have different in-degrees and the maximum in-degree is minimized. Clearly, the in-degrees induce a partition of the vertex set into stable sets, that is, a coloring (in the conventional sense) of the vertices. Our contributions in this problem are on hardness and upper bounds for bipartite graphs. Finally, we study a problem related to a conjecture of Mader from the eighties on subdivision of digraphs. This conjecture states that, for every acyclic digraph H, there exists an integer f(H) such that every digraph with minimum out-degree at least f(H) contains a subdivision of H as a subdigraph. We show evidences for this conjecture by proving that it holds for some particular classes of acyclic digraphs. / O problema de coloração de grafos é um problema clássico em teoria dos grafos cujo objetivo é particionar o conjunto de vértices em um número mínimo de conjuntos estáveis. Nesta tese apresentamos nossas contribuições sobre três problemas de coloração de grafos e um problema relacionado a uma antiga conjectura sobre subdivisão de digrafos. Primeiramente, abordamos o problema de recoloração convexa no qual é dado um grafo arbitrariamente colorido G e deseja-se encontrar uma recoloração de peso mínimo tal que cada classe de cor induza um subgrafo conexo de G. Mostramos resultados sobre inaproximabilidade, introduzimos uma formulação linear inteira que modela esse problema, e apresentamos alguns resultados computacionais usando uma abordagem de geração de colunas. O problema de k-upla coloração é uma generalização do problema clássico de coloração de vértices e consiste em cobrir o conjunto de vértices de um grafo com uma quantidade mínima de conjuntos estáveis de tal forma que cada vértice seja coberto por pelo menos k conjuntos estáveis (possivelmente idênticos). Apresentamos uma formulação linear inteira para esse problema e fazemos um estudo detalhado do politopo associado a essa formulação. O último problema de coloração estudado nesta tese é o problema de orientação própria. Ele consiste em orientar o conjunto de arestas de um dado grafo de tal forma que vértices adjacentes possuam graus de entrada distintos e o maior grau de entrada seja minimizado. Claramente, os graus de entrada induzem uma partição do conjunto de vértices em conjuntos estáveis, ou seja, induzem uma coloração (no sentido convencional) dos vértices. Nossas contribuições nesse problema são em complexidade computacional e limitantes superiores para grafos bipartidos. Finalmente, estudamos um problema relacionado a uma conjectura de Mader, dos anos oitenta, sobre subdivisão de digrafos. Esta conjectura afirma que, para cada digrafo acíclico H, existe um inteiro f(H) tal que todo digrafo com grau mínimo de saída pelo menos f(H) contém uma subdivisão de H como subdigrafo. Damos evidências para essa conjectura mostrando que ela é válida para classes particulares de digrafos acíclicos.