本研究開發一個以區域最佳解為基礎的群體式 (population-based) 啟發式演算法(簡稱HLBS)，來求解流程式排程（flow shop）之最大流程時間的最小化問題。其中，HLBS會先建置一個跟隨模型來導引搜尋機制，然後，運用過濾策略來預防重複搜尋相同解空間而陷入區域最佳解的困境；但搜尋仍有可能會陷入區域最佳解，這時，HLBS則會啟動跳脫策略來協助跳出區域最佳解，以進入新的區域之搜尋；為驗證HLBS演算法的績效，本研究利用著名的Taillard 測試題庫來進行評估，除證明跟隨模型、過濾策略和跳脫策略的效用外，也提出實驗結果證明HLBS較其他知名群體式啟發式演算法(如基因演算法、蟻群演算法以及粒子群最佳化演算法)之效能為優。 / This research proposes population-based metaheuristic based on the local best solution (HLBS) for the permutation flow shop scheduling problem (PFSP-makespan). The proposed metaheuristic operates through three mechanisms: (i) it introduces a new method to produce a trace-model for guiding the search, (ii) it applies a new filter strategy to filter the solution regions that have been reviewed and guides the search to new solution regions in order to keep the search from trapping into local optima, and (iii) it initiates a new jump strategy to help the search escape if the search does become trapped at a local optimum. Computational experiments on the well-known Taillard's benchmark data sets will be performed to evaluate the effects of the trace-model generating rule, the filter strategy, and the jump strategy on the performance of HLBS, and to compare the performance of HLBS with all the promising population-based metaheuristics related to Genetic Algorithms (GA), Ant Colony Optimization (ACO) and Particle Swarm Optimization (PSO).

Philosophiae Doctor - PhD (Mathematics) / The main theme of this thesis is the construction of linear codes from adjacency matrices or sub-matrices of adjacency matrices of regular graphs. We first examine the binary codes from the row span of biadjacency matrices and their transposes for some classes of bipartite graphs. In this case we consider a sub-matrix of an adjacency matrix of a graph as the generator of the code. We then shift our attention to uniform subset graphs by exploring the automorphism groups of graph covers and some classes of uniform subset graphs. In the sequel, we explore equal codes from adjacency matrices of non-isomorphic uniform subset graphs and finally consider codes generated by an adjacency matrix formed by adding adjacency matrices of two classes of uniform subset graphs.

Neste trabalho abordamos o problema de programação de tarefas em um ambiente flow shop permutacional com mais de duas máquinas. Restringimos o estudo para o caso em que todas as tarefas têm uma data de entrega comum e restritiva, e onde o objetivo é minimizar a soma total dos adiantamentos e atrasos das tarefas em relação a tal data de entrega. É assumido também um ambiente estático e determinístico. Havendo soluções com o mesmo custo, preferimos aquelas que envolvem menos tempo de espera no buffer entre cada máquina. Devido à dificuldade de resolver o problema, mesmo para instâncias pequenas (o problema pertence à classe NP-difícil), apresentamos uma abordagem heurística para lidar com ele, a qual está baseada em busca local e faz uso de um algoritmo linear para atribuir datas de conclusão às tarefas na última máquina. Este algoritmo baseia-se em algumas propriedades analíticas inerentes às soluções ótimas. Além disso, foi desenvolvida uma formulação matemática do problema em programação linear inteira mista (PLIM) que vai permitir validar a eficácia da abordagem. Examinamos também o desempenho das heurísticas com testes padrões (benchmarks) e comparamos nossos resultados com outros obtidos na literatura. / In this work we approach the permutational flow shop scheduling problem with more than two machines. We restrict the study to the case where all the jobs have a common and restrictive due date, and where the objective is to minimize the total sum of the earliness and tardiness of jobs relative to the due date. A static and deterministic environment is also assumed. If there are solutions with the same cost, we prefer those that involve less buffer time between each machine. Due to the difficulty of solving the problem, even for small instances (the problem belongs to the NP-hard class), we present a heuristic approach to dealing with it, which is based on local search and makes use of a linear algorithm to assign conclusion times to the jobs on the last machine. This algorithm is based on some analytical properties inherent to optimal solutions. In addition, a mathematical formulation of the problem in mixed integer linear programming (MILP) was developed that will validate the effectiveness of the approach. We also examined the performance of our heuristics with benchmarks and compared our results with those obtained in the literature.

Submitted by Geandra Rodrigues (geandrar@gmail.com) on 2018-10-30T13:59:20Z No. of bitstreams: 1 ednailtonsantossilva.pdf: 606910 bytes, checksum: 393b9af5bb01a2b06e9ebb6ee0eee4cb (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2018-11-23T12:29:01Z (GMT) No. of bitstreams: 1 ednailtonsantossilva.pdf: 606910 bytes, checksum: 393b9af5bb01a2b06e9ebb6ee0eee4cb (MD5) / Made available in DSpace on 2018-11-23T12:29:01Z (GMT). No. of bitstreams: 1 ednailtonsantossilva.pdf: 606910 bytes, checksum: 393b9af5bb01a2b06e9ebb6ee0eee4cb (MD5) Previous issue date: 2018-09-13 / O objetivo desse trabalho é apresentar algumas classes clássicas e outras mais recentes de polinômios de permutação sobre corpos finitos. A fim de atingir esse objetivo, apresentamos a construção e uma lista de propriedades de corpos finitos, bem como uma introdução à teoria dos polinômios sobre corpos finitos. / The main goal of this text is to present some known classes of permutation polynomials over finite fields. With this goal, we begin by presenting the construction and some properties of finite fields, as well as an introduction to the theory of polynomials over finite fields.

Orientador: João Meidanis / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Computação / Made available in DSpace on 2018-08-21T17:01:05Z (GMT). No. of bitstreams: 1 Feijao_PedroCipriano_D.pdf: 1943126 bytes, checksum: 4c547e8c568bbd0f2eb8235dfde05524 (MD5) Previous issue date: 2012 / Resumo: Rearranjo de genomas é o nome dado a eventos onde grandes blocos de DNA trocam de posição durante o processo evolutivo. Com a crescente disponibilidade de sequências completas de DNA, a análise desse tipo de eventos pode ser uma importante ferramenta para o entendimento da genômica evolutiva. Vários modelos matemáticos de rearranjo de genomas foram propostos ao longo dos últimos vinte anos. Nesta tese, desenvolvemos dois novos modelos. O primeiro foi proposto como uma definição alternativa ao conceito de distância de breakpoint. Essa distância é uma das mais simples medidas de rearranjo, mas ainda não há um consenso quanto à sua definição para o caso de genomas multi-cromossomais. Pevzner e Tesler deram uma definição em 2003 e Tannier et al. a definiram de forma diferente em 2008. Nesta tese, nós desenvolvemos uma outra alternativa, chamada de single-cut-or-join (SCJ). Nós mostramos que, no modelo SCJ, além da distância, vários problemas clássicos de rearranjo, como a mediana de rearranjo, genome halving e pequena parcimônia são fáceis, e apresentamos algoritmos polinomiais para eles. O segundo modelo que apresentamos é o formalismo algébrico por adjacências, uma extensão do formalismo algébrico proposto por Meidanis e Dias, que permite a modelagem de cromossomos lineares. Esta era a principal limitação do formalismo original, que só tratava de cromossomos circulares. Apresentamos algoritmos polinomiais para o cálculo da distância algébrica e também para encontrar cenários de rearranjo entre dois genomas. Também mostramos como calcular a distância algébrica através do grafo de adjacências, para facilitar a comparação com outras distâncias de rearranjo. Por fim, mostramos como modelar todas as operações clássicas de rearranjo de genomas utilizando o formalismo algébrico / Abstract: Genome rearrangements are events where large blocks of DNA exchange places during evolution. With the growing availability of whole genome data, the analysis of these events can be a very important and promising tool for understanding evolutionary genomics. Several mathematical models of genome rearrangement have been proposed in the last 20 years. In this thesis, we propose two new rearrangement models. The first was introduced as an alternative definition of the breakpoint distance. The breakpoint distance is one of the most straightforward genome comparison measures, but when it comes to defining it precisely for multichromosomal genomes, there is more than one way to go about it. Pevzner and Tesler gave a definition in a 2003 paper, and Tannier et al. defined it differently in 2008. In this thesis we provide yet another alternative, calling it single-cut-or-join (SCJ). We show that several genome rearrangement problems, such as genome median, genome halving and small parsimony, become easy for SCJ, and provide polynomial time algorithms for them. The second model we introduce is the Adjacency Algebraic Theory, an extension of the Algebraic Formalism proposed by Meidanis and Dias that allows the modeling of linear chromosomes, the main limitation of the original formalism, which could deal with circular chromosomes only. We believe that the algebraic formalism is an interesting alternative for solving rearrangement problems, with a different perspective that could complement the more commonly used combinatorial graph-theoretic approach. We present polynomial time algorithms to compute the algebraic distance and find rearrangement scenarios between two genomes. We show how to compute the rearrangement distance from the adjacency graph, for an easier comparison with other rearrangement distances. Finally, we show how all classic rearrangement operations can be modeled using the algebraic theory / Doutorado / Ciência da Computação / Doutor em Ciência da Computação

The dissertation covers two problems motivated by computational biology: genome rearrangements, and haplotype networks.<p><p>Genome rearrangement problems are a particular case of edit distance problems, where one seeks to transform two given objects into one another using as few operations as possible, with the additional constraint that the set of allowed operations is fixed beforehand; we are also interested in computing the corresponding distances between those objects, i.e. merely computing the minimum number of operations rather than an optimal sequence. Genome rearrangement problems can often be formulated as sorting problems on permutations (viewed as linear orderings of {1,2,n}) using as few (allowed) operations as possible. In this thesis, we focus among other operations on ``transpositions', which displace intervals of a permutation. Many questions related to sorting by transpositions are open, related in particular to its computational complexity. We use the disjoint cycle decomposition of permutations, rather than the ``standard tools' used in genome rearrangements, to prove new upper bounds on the transposition distance, as well as formulae for computing the exact distance in polynomial time in many cases. This decomposition also allows us to solve a counting problem related to the ``cycle graph' of Bafna and Pevzner, and to construct a general framework for obtaining lower bounds on any edit distance between permutations by recasting their computation as factorisation problems on related even permutations.<p><p>Haplotype networks are graphs in which a subset of vertices is labelled, used in comparative genomics as an alternative to trees. We formalise a new method due to Cassens, Mardulyn and Milinkovitch, which consists in building a graph containing a given set of partially labelled trees and with as few edges as possible. We give exact algorithms for solving the problem on two graphs, with an exponential running time in the general case but with a polynomial running time if at least one of the graphs belong to a particular class.<p>/<p>La thèse couvre deux problèmes motivés par la biologie: l'étude des réarrangements génomiques, et celle des réseaux d'haplotypes.<p><p>Les problèmes de réarrangements génomiques sont un cas particulier des problèmes de distances d'édition, où l'on cherche à transformer un objet en un autre en utilisant le plus petit nombre possible d'opérations, les opérations autorisées étant fixées au préalable; on s'intéresse également à la distance entre les deux objets, c'est-à-dire au calcul du nombre d'opérations dans une séquence optimale plutôt qu'à la recherche d'une telle séquence. Les problèmes de réarrangements génomiques peuvent souvent s'exprimer comme des problèmes de tri de permutations (vues comme des arrangements linéaires de {1,2,n}) en utilisant le plus petit nombre d'opérations (autorisées) possible. Nous examinons en particulier les ``transpositions', qui déplacent un intervalle de la permutation. Beaucoup de problèmes liés au tri par transpositions sont ouverts, en particulier sa complexité algorithmique. Nous nous écartons des ``outils standards' utilisés dans le domaine des réarrangements génomiques, et utilisons la décomposition en cycles disjoints des permutations pour prouver de nouvelles majorations sur la distance des transpositions ainsi que des formules permettant de calculer cette distance en temps polynomial dans de nombreux cas. Cette décomposition nous sert également à résoudre un problème d'énumération concernant le ``graphe des cycles' de Bafna et Pevzner, et à construire une technique générale permettant d'obtenir de nouvelles minorations en reformulant tous les problèmes de distances d'édition sur les permutations en termes de factorisations de permutations paires associées.<p><p>Les réseaux d'haplotypes sont des graphes dont une partie des sommets porte des étiquettes, utilisés en génomique comparative quand les arbres sont trop restrictifs, ou quand l'on ne peut choisir une ``meilleure' topologie parmi un ensemble donné d'arbres. Nous formalisons une nouvelle méthode due à Cassens, Mardulyn et Milinkovitch, qui consiste à construire un graphe contenant tous les arbres partiellement étiquetés donnés et possédant le moins d'arêtes possible, et donnons des algorithmes résolvant le problème de manière optimale sur deux graphes, dont le temps d'exécution est exponentiel en général mais polynomial dans quelques cas que nous caractérisons.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Philosophiae Doctor - PhD / In this thesis, we describe linear codes over prime fields obtained from incidence designs of iterated line graphs of complete graphs Li(Kn) where i = 1, 2. In the binary case, results are extended to codes from neighbourhood designs of the line graphs Li+1(Kn) using certain elementary relations. Codes from incidence designs of complete graphs, Kn, and neighbourhood designs of their line graphs, L1(Kn) (the so-called triangular graphs), have been considered elsewhere by others. We consider codes from incidence designs of L1(Kn) and L2(Kn), and neighbourhood designs of L2(Kn) and L3(Kn). In each case, basic parameters of the codes are determined. Further, we introduce a family of vertex-transitive graphs Γn that are embeddable into the strong product L1(Kn)⊠  K2, of triangular graphs and K2, a class which at first sight may seem unnatural but, on closer look, is a repository of graphs rich with combinatorial structures. For instance, unlike most regular graphs considered here and elsewhere that only come with incidence and neighbourhood designs, Γn also has what we have termed as 6-cycle designs. These are designs in which the point set contains vertices of the graph and every block contains vertices of a 6-cycle in the graph. Also, binary codes from incidence matrices of these graphs have other minimum words in addition to incidence vectors of the blocks. In addition, these graphs have induced subgraphs isomorphic to the family Hn of complete porcupines (see Definition 4.11). We describe codes from incidence matrices of Γn and Hn and determine their parameters. / South Africa

In 1972, professor Grigore Moisil, the most famous Romanian academician for Mathematics, said about Combinatorics, that it is “an opportunity of a renewed gladness”, because “each problem in the domain asks for its solving, an expenditure without any economy of the human intelligence”. More, the research methods, used in Combinatorics, are different from a problem to the other! This is the explanation for the existence of my actual paper, in which I propose to teach Combinatorics, using selected problems. MS classification: 05A05, 97D50.

Philosophiae Doctor - PhD / In this thesis, we describe linear codes over prime fields obtained from incidence designs of iterated line graphs of complete graphs Li(Kn) where i = 1,2. In the binary case, results are extended to codes from neighbourhood designs of the line graphs Li+l(Kn) using certain elementary relations. Codes from incidence designs of complete graphs, Kn' and neighbourhood designs of their line graphs, £1(Kn) (the so-called triangular graphs), have been considered elsewhere by others. We consider codes from incidence designs of Ll(Kn) and L2(Kn), and neighbourhood designs of L2(Kn) and L3(Kn). In each case, the basic parameters of the codes are determined. Further, we introduce a family of vertex-transitive graphs Rn that are embeddable into the strong product Ll(Kn) ~ K2' of triangular graphs and K2' a class that at first sight may seem unnatural but, on closer look, is a repository of graphs rich with combinatorial structures. For instance, unlike most regular graphs considered here and elsewhere that only come with incidence and neighbourhood designs, Rn also has what we have termed as 6-cycle designs. These are designs in which the point set contains vertices of the graph and every block contains vertices of a 6-cycle in the graph. Also, binary codes from incidence matrices of these graphs have other minimum words in addition to incidence vectors of the blocks. In addition, these graphs have induced subgraphs isomorphic to the family Hn of complete porcupines (see Definition 4.11). We describe codes from incidence matrices of Rn and Hn and determine their parameters. The discussion is concluded with a look at complements of Rn and Hn, respectively denoted by Rn and Hn. Among others, the complements rn are contained in the union of the categorical product Ll(Kn) x Kn' and the categorical product £1(Kn) x Kn (where £1(Kn) is the complement of the iii triangular graph £1(Kn)). As with the other graphs, we have also considered codes from the span of incidence matrices of Rn and Hn and determined some of their properties. In each case, automorphisms of the graphs, designs and codes have been determined. For the codes from incidence designs of triangular graphs, embeddings of Ll(Kn) x K2 and complements of complete porcupines, we have exhibited permutation decoding sets (PD-sets) for correcting up to terrors where t is the full error-correcting capacity of the codes. For the remaining codes, we have only been able to determine PD-sets for which it is possible to correct a fraction of t-errors (partial permutation decoding). For these codes, we have also determined the number of errors that can be corrected by permutation decoding in the worst-case.

Masters of Science / The multivariate two-sample tests provide a means to test the match between two multivariate distributions. Although many tests exist in the literature, relatively little is known about the relative power of these procedures. The studies reported in the thesis contrasts the effectiveness, in terms of power, of seven such tests with a Monte Carlo study. The relative power of the tests was investigated against location, scale, and correlation alternatives. Samples were drawn from bivariate exponential, normal and uniform populations. Results from the power studies show that there is no single test which is the most powerful in all situations. The use of particular test statistics is recommended for specific alternatives. A possible supplementary non-parametric graphical procedure, such as the Depth-Depth plot, can be recommended for diagnosing possible differences between the multivariate samples, if the null hypothesis is rejected. As an example of the utility of the procedures for real data, the multivariate two-sample tests were applied to photometric data of twenty galactic globular clusters. The results from the analyses support the recommendations associated with specific test statistics.