Let Ω be the Fraïssé limit of a class of relational structures. We seek to answer the following semigroup theoretic question about Ω. What are the group H-classes, i.e. the maximal subgroups, of End(Ω)? Fraïssé limits for which we answer this question include the random graph R, the random directed graph D, the random tournament T, the random bipartite graph B, Henson's graphs G[subscript n] (for n greater or equal to 3) and the total order Q. The maximal subgroups of End(Ω) are closely connected to the automorphism groups of the relational structures induced by the images of idempotents from End(Ω). It has been shown that the relational structure induced by the image of an idempotent from End(Ω) is algebraically closed. Accordingly, we investigate which groups can be realised as the automorphism group of an algebraically closed relational structure in order to determine the maximal subgroups of End(Ω) in each case. In particular, we show that if Γ is a countable graph and Ω = R,D,B, then there exist 2[superscript aleph-naught] maximal subgroups of End(Ω) which are isomorphic to Aut(Γ). Additionally, we provide a complete description of the subsets of Q which are the image of an idempotent from End(Q). We call these subsets retracts of Q and show that if Ω is a total order and f is an embedding of Ω into Q such that im f is a retract of Q, then there exist 2[superscript aleph-naught] maximal subgroups of End(Q) isomorphic to Aut(Ω). We also show that any countable maximal subgroup of End(Q) must be isomorphic to Zⁿ for some natural number n. As a consequence of the methods developed, we are also able to show that when Ω = R,D,B,Q there exist 2[superscript aleph-naught] regular D-classes of End(Ω) and when Ω = R,D,B there exist 2[superscript aleph-naught] J-classes of End(Ω). Additionally we show that if Ω = R,D then all regular D-classes contain 2[superscript aleph-naught] group H-classes. On the other hand, we show that when Ω = B,Q there exist regular D-classes which contain countably many group H-classes.

Devido a restrições de aplicabilidade presentes nos algoritmos para a solução de problemas de otimização combinatória, os sistemas baseados em redes neurais artificiais e algoritmos genéticos oferecem um método alternativo para solucionar tais problemas eficientemente. Os algoritmos genéticos devem a sua popularidade à possibilidade de percorrer espaços de busca não-lineares e extensos. Já as redes neurais artificiais possuem altas taxas de processamento por utilizarem um número elevado de elementos processadores simples com alta conectividade entre si. Complementarmente, redes neurais com conexões realimentadas fornecem um modelo computacional capaz de resolver vários tipos de problemas de otimização, os quais consistem, geralmente, da otimização de uma função objetivo que pode estar sujeita ou não a um conjunto de restrições. Esta tese apresenta uma abordagem inovadora para resolver problemas de conexão em otimização combinatória utilizando uma arquitetura neuro-genética. Mais especificamente, uma rede neural de Hopfield modificada é associada a um algoritmo genético visando garantir a convergência da rede em direção aos pontos de equilíbrio factíveis que representam as soluções para os problemas de otimização combinatória. / Due to applicability constraints involved with the algorithms for solving combinatorial optimization problems, systems based on artificial neural networks and genetic algorithms are alternative methods for solving these problems in an efficient way. The genetic algorithms must its popularity to make possible cover nonlinear and extensive search spaces. On the other hand, artificial neural networks have high processing rates due to the use of a massive number of simple processing elements and the high degree of connectivity between these elements. Additionally, neural networks with feedback connections provide a computing model capable of solving a large class of optimization problems, which refer to optimization of an objective function that can be subject to constraints. This thesis presents a novel approach for solving connection problems in combinatorial optimization using a neurogenetic approach. More specifically, a modified Hopfield neural network is associated with a genetic algorithm in order to guarantee the convergence of the network to the equilibrium points, which represent feasible solutions for the combinatorial optimization problems.

Devido a restrições de aplicabilidade presentes nos algoritmos para a solução de problemas de otimização combinatória, os sistemas baseados em redes neurais artificiais e algoritmos genéticos oferecem um método alternativo para solucionar tais problemas eficientemente. Os algoritmos genéticos devem a sua popularidade à possibilidade de percorrer espaços de busca não-lineares e extensos. Já as redes neurais artificiais possuem altas taxas de processamento por utilizarem um número elevado de elementos processadores simples com alta conectividade entre si. Complementarmente, redes neurais com conexões realimentadas fornecem um modelo computacional capaz de resolver vários tipos de problemas de otimização, os quais consistem, geralmente, da otimização de uma função objetivo que pode estar sujeita ou não a um conjunto de restrições. Esta tese apresenta uma abordagem inovadora para resolver problemas de conexão em otimização combinatória utilizando uma arquitetura neuro-genética. Mais especificamente, uma rede neural de Hopfield modificada é associada a um algoritmo genético visando garantir a convergência da rede em direção aos pontos de equilíbrio factíveis que representam as soluções para os problemas de otimização combinatória. / Due to applicability constraints involved with the algorithms for solving combinatorial optimization problems, systems based on artificial neural networks and genetic algorithms are alternative methods for solving these problems in an efficient way. The genetic algorithms must its popularity to make possible cover nonlinear and extensive search spaces. On the other hand, artificial neural networks have high processing rates due to the use of a massive number of simple processing elements and the high degree of connectivity between these elements. Additionally, neural networks with feedback connections provide a computing model capable of solving a large class of optimization problems, which refer to optimization of an objective function that can be subject to constraints. This thesis presents a novel approach for solving connection problems in combinatorial optimization using a neurogenetic approach. More specifically, a modified Hopfield neural network is associated with a genetic algorithm in order to guarantee the convergence of the network to the equilibrium points, which represent feasible solutions for the combinatorial optimization problems.

Gene prioritization involves ranking genes by possible relevance to a disease of interest. This is important in order to narrow down the set of genes to be investigated biologically, and over the years, several computational approaches have been proposed for automat-ically prioritizing genes using some form of gene-related data, mostly using statistical or machine learning methods. Recently, Agarwal and Sengupta (2009) proposed the use of learning-to-rank methods, which have been used extensively in information retrieval and related fields, to learn a ranking of genes from a given data source, and used this approach to successfully identify novel genes related to leukemia and colon cancer using only gene expression data. In this work, we explore the possibility of combining such learning-to-rank methods with rank aggregation techniques to learn a ranking of genes from multiple heterogeneous data sources, such as gene expression data, gene ontology data, protein-protein interaction data, etc. Rank aggregation methods have their origins in voting theory, and have been used successfully in meta-search applications to aggregate webpage rankings from different search engines. Here we use graph-based learning-to-rank methods to learn a ranking of genes from each individual data source represented as a graph, and then apply rank aggregation methods to aggregate these rankings into a single ranking over the genes. The thesis describes our approach, reports experiments with various data sets, and presents our findings and initial conclusions.

中文摘要 有限離散條件分配相容性問題可依相容性檢驗、唯一性檢驗以及找出所有的聯合機率分配三層次來討論。目前的文獻資料有幾種研究方法，本文僅分析、比較其中的比值矩陣法和圖形法。 二維中，我們發現簡化二分圖的分支與IBD矩陣中的對角塊狀矩陣有密切的對應關係。在檢驗相容性時，圖形法只需檢驗簡化二分圖中的每個分支，正如同比值矩陣法只需檢驗IBD矩陣中的每一個對角塊狀矩陣即可。在檢驗唯一性時，圖形法只需檢驗簡化二分圖中的分支數是否唯一，正如同比值矩陣法只需檢驗IBD矩陣中的對角塊狀數是否唯一即可。在求所有的聯合機率分配時，運用比值矩陣法可推算出所有的聯合機率分配，但是圖形法則無法求出。 三維中，本文提出了修正比值矩陣法，將比值數組按照某種索引方式在平面上有規則地呈現，可降低所需處理矩陣的大小。此外，我們也發現修正比值矩陣中的橫直縱迴路和簡化二分圖中的迴路有對應的關係，因此可觀察出兩種方法所獲致某些結論的關聯性。在檢驗唯一性時，圖形法是檢驗簡化二分圖中的分支數是否唯一，而修正比值矩陣法是檢驗兩個修正比值矩陣是否分別有唯一的GROPE矩陣。修正比值矩陣法可推算出所有的聯合機率分配。 圖形法可用於任何維度中，修正比值矩陣法也可推廣到任何維度中，但在應用上，修正比值矩陣法比圖形法較為可行。 / The issue of the compatibility of finite discrete conditional distributions could be discussed hierarchically according to the compatibility, the uniqueness, and finding all possible joint probability distributions. There are several published methods, but only the Ratio Matrix Method and the Graphical Method are analyzed and compared in this thesis. In bivariate case, a close correspondence between the components of the reduced bipartite graph and the diagonal block matrices of the IBD matrix can be found. When we examine the compatibility, just as simply each diagonal block matrix of the IBD matrix needs to be examined using the Ratio Matrix Method, so does each component of the reduced bipartite graph using the Graphical Method. When we examine the uniqueness, just as whether the number of the diagonal blocks of the IBD matrix is unique needs to be examined, so does the number of the components of the reduced bipartite graph. The Ratio Matrix Method can provide all possible joint probability distributions, but the Graphical Method cannot. In trivariate case, this thesis proposes a Revised Ratio Matrix Method, in which we can present the ratio array regularly in the plane according to the index and reduce the corresponding matrix size. It is also found that each circuit in the revised ratio matrix corresponds to a circuit in the reduced bipartite graph. Therefore, the relation between the results of the two methods can be observed. When we examine the uniqueness with the Graphical Method, we examine whether the number of the components in the reduced bipartite graph is unique. But with the Revised Ratio Matrix Method, we examine whether each revised ratio matrix has a unique GROPE matrix. All possible joint probability distributions can be derived through the Revised Ratio Matrix Method. The Graphical Method can be applied to the higher dimensional cases, so can the Revised Ratio Matrix Method. But the Revised Ratio Matrix Method is more feasible than the Graphical Method in application.