Copy-number variation (CNV) has been implicated in many complex diseases. It is of great interest to detect and locate such regions through genetic association testings. However, the association testings are complicated by the fact that CNVs usually span multiple markers and thus such markers are correlated to each other. To overcome the difficulty, it is desirable to pool information across the markers. In this thesis, we propose a kernel-based method for aggregation of marker-level tests, in which first we obtain a bunch of p-values through association tests for every marker and then the association test involving CNV is based on the statistic of p-values combinations. In addition, we explore several aspects of its implementation. Since p-values among markers are correlated, it is complicated to obtain the null distribution of test statistics for kernel-base aggregation of marker-level tests. To solve the problem, we develop two proper methods that are both demonstrated to preserve the family-wise error rate of the test procedure. They are permutation based and correlation base approaches. Many implementation aspects of kernel-based method are compared through the empirical power studies in a number of simulations constructed from real data involving a pharmacogenomic study of gemcitabine. In addition, more performance comparisons are shown between permutation-based and correlation-based approach. We also apply those two approaches to the real data. The main contribution of the dissertation is the development of marker-level association testing, a comparable and powerful approach to detect phenotype-associated CNVs. Furthermore, the approach is extended to high dimension setting with high efficiency.

The work of mathematical giants, such as Lobachevsky, Gauss, Riemann, Klein and Poincaré, to name a few, lies at the foundation of the study of the highly structured Riemann surfaces, which allow definition of holomorphic maps, corresponding to analytic maps in the theory of complex analysis. A topological result of Poincaré states that every path-connected Riemann surface can be realised by a construction of identifying congruent points in the complex plane, the Riemann sphere or the hyperbolic plane; just three simply connected surfaces that cover the underlying Riemann surface. This requires the discontinuous action of a discrete subgroup of the automorphisms of the corresponding space. In the hyperbolic plane, which is the richest source for Riemann surfaces, these groups are called Fuchsian, and there are several ways to study the action of such groups geometrically by computing fundamental domains. What is accomplished in this thesis is a combination of the methods found by Reidemeister & Schreier, Singerman and Voight, and thus provides a unified way of finding Dirichlet domains for subgroups of cofinite groups with a given index. Several examples are considered in-depth.

In 2010 Chung-Graham-Knuth proved an interesting symmetric identity for the Eulerian numbers and asked for a q-analog version. Using the q-Eulerian polynomials introduced by Shareshian-Wachs we find such a q-identity. Moreover, we provide a bijective proof that we further generalize to prove other symmetric qidentities using a combinatorial model due to Foata-Han. Meanwhile, Hyatt has introduced the colored Eulerian quasisymmetric functions to study the joint distribution of the excedance number and major index on colored permutations. Using the Decrease Value Theorem of Foata-Han we give a new proof of his main generating function formula for the colored Eulerian quasisymmetric functions. Furthermore, certain symmetric q-Eulerian identities are generalized and expressed as identities involving the colored Eulerian quasisymmetric functions. Next, generalizing the recent works of Savage-Visontai and Beck-Braun we investigate some q-descent polynomials of general signed multipermutations. The factorial and multivariate generating functions for these q-descent polynomials are obtained and the real rootedness results of some of these polynomials are given. Finally, we study the diagonal generating function of the Jacobi-Stirling numbers of the second kind by generalizing the analogous results for the Stirling and Legendre-Stirling numbers of the second kind. It turns out that the generating function is a rational function, whose numerator is a polynomial with nonnegative integral coefficients. By applying Stanley's theory of P-partitions we find combinatorial interpretations of those coefficients

A distinguishing colouring of a graph G is a labelling of the vertices of G with colours such that no non-trivial automorphism of G preserves all colours. The distinguishing number of G is the minimum number of colours in a distinguishing colouring. This thesis presents a survey of the history of distinguishing colouring problems and proves new bounds and computational results about distinguishability. An algorithm to generate all labellings of a graph up to isomorphism is presented and compared to a previously published algorithm. The new algorithm is shown to have performance competitive with the existing algorithm, as well as being able to process automorphism groups far larger than the previous limit. A specialization of the algorithm is used to generate all minimal distinguishing colourings of a set of graphs with large automorphism groups and compute their distinguishing numbers. / Graduate / 0984 / 0405 / bbird@uvic.ca

Many graphs arising in practice can be represented in a concise and intuitive way that conveys their structure. For example: A planar graph can be represented in the plane with points for vertices and non-crossing curves for edges. An interval graph can be represented on the real line with intervals for vertices and intersection of intervals representing edges. The concept of ``simultaneity'' applies for several types of graphs: the idea is to find representations for two graphs that share some common vertices and edges, and ensure that the common vertices and edges are represented the same way. Simultaneous representation problems arise in any situation where two related graphs should be represented consistently. A main instance is for temporal relationships, where an old graph and a new graph share some common parts. Pairs of related graphs arise in many other situations. For example, two social networks that share some members; two schedules that share some events, overlap graphs of DNA fragments of two similar organisms, circuit graphs of two adjacent layers on a computer chip etc. In this thesis, we study the simultaneous representation problem for several graph classes. For planar graphs the problem is defined as follows. Let G1 and G2 be two graphs sharing some vertices and edges. The simultaneous planar embedding problem asks whether there exist planar embeddings (or drawings) for G1 and G2 such that every vertex shared by the two graphs is mapped to the same point and every shared edge is mapped to the same curve in both embeddings. Over the last few years there has been a lot of work on simultaneous planar embeddings, which have been called `simultaneous embeddings with fixed edges'. A major open question is whether simultaneous planarity for two graphs can be tested in polynomial time. We give a linear-time algorithm for testing the simultaneous planarity of any two graphs that share a 2-connected subgraph. Our algorithm also extends to the case of k planar graphs, where each vertex [edge] is either common to all graphs or belongs to exactly one of them. Next we introduce a new notion of simultaneity for intersection graph classes (interval graphs, chordal graphs etc.) and for comparability graphs. For interval graphs, the problem is defined as follows. Let G1 and G2 be two interval graphs sharing some vertices I and the edges induced by I. G1 and G2 are said to be `simultaneous interval graphs' if there exist interval representations of G1 and G2 such that any vertex of I is assigned to the same interval in both the representations. The `simultaneous representation problem' for interval graphs asks whether G1 and G2 are simultaneous interval graphs. The problem is defined in a similar way for other intersection graph classes. For comparability graphs and any intersection graph class, we show that the simultaneous representation problem for the graph class is equivalent to a graph augmentation problem: given graphs G1 and G2, sharing vertices I and the corresponding induced edges, do there exist edges E' between G1-I and G2-I such that the graph G1 U G_2 U E' belongs to the graph class. This equivalence implies that the simultaneous representation problem is closely related to other well-studied classes in the literature, namely, sandwich graphs and probe graphs. We give efficient algorithms for solving the simultaneous representation problem for interval graphs, chordal graphs, comparability graphs and permutation graphs. Further, our algorithms for comparability and permutation graphs solve a more general version of the problem when there are multiple graphs, any two of which share the same common graph. This version of the problem also generalizes probe graphs.

Transmitting quantum information across quantum channels is an important task. However quantum information is delicate, and is easily corrupted. We address the task of protecting quantum information from an information theoretic perspective -- we encode some message qudits into a quantum code, send the encoded quantum information across the noisy quantum channel, then recover the message qudits by decoding. In this dissertation, we discuss the coding problem from several perspectives.} The noisy quantum channel is one of the central aspects of the quantum coding problem, and hence quantifying the noisy quantum channel from the physical model is an important problem. We work with an explicit physical model -- a pair of initially decoupled quantum harmonic oscillators interacting with a spring-like coupling, where the bath oscillator is initially in a thermal-like state. In particular, we treat the completely positive and trace preserving map on the system as a quantum channel, and study the truncation of the channel by truncating its Kraus set. We thereby derive the matrix elements of the Choi-Jamiolkowski operator of the corresponding truncated channel, which are truncated transition amplitudes. Finally, we give a computable approximation for these truncated transition amplitudes with explicit error bounds, and perform a case study of the oscillators in the off-resonant and weakly-coupled regime numerically. In the context of truncated noisy channels, we revisit the notion of approximate error correction of finite dimension codes. We derive a computationally simple lower bound on the worst case entanglement fidelity of a quantum code, when the truncated recovery map of Leung et. al. is rescaled. As an application, we apply our bound to construct a family of multi-error correcting amplitude damping codes that are permutation-invariant. This demonstrates an explicit example where the specific structure of the noisy channel allows code design out of the stabilizer formalism via purely algebraic means. We study lower bounds on the quantum capacity of adversarial channels, where we restrict the selection of quantum codes to the set of concatenated quantum codes. The adversarial channel is a quantum channel where an adversary corrupts a fixed fraction of qudits sent across a quantum channel in the most malicious way possible. The best known rates of communicating over adversarial channels are given by the quantum Gilbert-Varshamov (GV) bound, that is known to be attainable with random quantum codes. We generalize the classical result of Thommesen to the quantum case, thereby demonstrating the existence of concatenated quantum codes that can asymptotically attain the quantum GV bound. The outer codes are quantum generalized Reed-Solomon codes, and the inner codes are random independently chosen stabilizer codes, where the rates of the inner and outer codes lie in a specified feasible region. We next study upper bounds on the quantum capacity of some low dimension quantum channels. The quantum capacity of a quantum channel is the maximum rate at which quantum information can be transmitted reliably across it, given arbitrarily many uses of it. While it is known that random quantum codes can be used to attain the quantum capacity, the quantum capacity of many classes of channels is undetermined, even for channels of low input and output dimension. For example, depolarizing channels are important quantum channels, but do not have tight numerical bounds. We obtain upper bounds on the quantum capacity of some unital and non-unital channels -- two-qubit Pauli channels, two-qubit depolarizing channels, two-qubit locally symmetric channels, shifted qubit depolarizing channels, and shifted two-qubit Pauli channels -- using the coherent information of some degradable channels. We use the notion of twirling quantum channels, and Smith and Smolin's method of constructing degradable extensions of quantum channels extensively. The degradable channels we introduce, study and use are two-qubit amplitude damping channels. Exploiting the notion of covariant quantum channels, we give sufficient conditions for the quantum capacity of a degradable channel to be the optimal value of a concave program with linear constraints, and show that our two-qubit degradable amplitude damping channels have this property.

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.

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.