Moderní výzkum v environmentální mikrobiologii využívá k popisu mikrobiálních komunit genomická data, především sekvenaci DNA. Oblast, která zkoumá veškerý genetický materiál přítomný v environmentálním vzorku, se nazývá metagenomika. Tato doktorská práce se zabývá metagenomikou z pohledu bioinformatiky, která je nenahraditelná při výpočetním zpracování dat. V teoretické části práce jsou popsány dva základní přístupy metagenomiky, včetně jejich základních principů a slabin. První přístup, založený na cíleném sekvenování, je dobře rozpracovanou oblastí s velkou řadou bioinformatických technik. Přesto mohou být metody pro porovnávání vzorků z několika prostředí podstatně vylepšeny. Přístup představený v této práci používá unikátní transformaci dat do podoby bipartitního grafu, kde je jedna partita tvořena taxony a druhá vzorky, případně různými prostředími. Takový graf plně reflektuje kvalitativní i kvantitativní složení analyzované mikrobiální sítě. Umožňuje masivní redukci dat pro jednoduché vizualizace bez negativních vlivů na automatickou detekci komunit, která dokáže odhalit shluky podobných vzorků a jejich typických mikrobů. Druhý přístup využívá sekvenace celého metagenomu. Tato strategie je novější a příslušející bioinformatické nástroje jsou méně propracované. Hlavní výzvou přitom zůstává rychlá klasifikace sekvencí, v metagenomice označovaná jako „binning“. Metoda představená v této práci využívá přístupu zpracování genomických signálů. Tato unikátní metodologie byla navržena na základě podrobné analýzy redundance genetické informace uložené v genomických signálech. Využívá transformace znakových sekvencí do několika variant fázových signálů. Navíc umožňuje přímé zpracování dat ze sekvenace nanopórem v podobě nativních proudových signálů.

This diploma thesis deals with optimization models with design of a new waste management infrastructure in the Czech Republic, such that combustible waste, which is not utilized by the material recovering, can be used by energy recovering. This task is handled by optimization models, including trac and mixing problems. First of all, the concepts of graph theory and optimization are presented in this paper. Subsequently, some of the GAMS functions are discussed, and later the VBA programming language used to handle the larger data quickly is presented. In the main part, three gradually expanding models are developed. At the end the data from the waste management information system are implemented into them.

<p>Turniri su najvi&scaron;e istraživana klasa orijentisanih grafova. U tezi su prezentovana dva tipa rezultata. Prvi se odnosi na tzv. neizbežne podgrafove. Obuhvata Hamiltonove bajpase, podgrafove C(<em>n, i</em>) i alternativne Hamiltonove konture. Drugi se bavi problemima frekvencija skorova u običnim, bipartitnim i 3-partitnim turnirima.</p> / <p>Tournaments are the most investigated class of oriented graphs. Two type of results are presented in the thesis. First one is related to so called unavoidable subgraphs. It discusses Hamiltonian bypasses, subgraphs C(n, i) and antidirected Hamiltonian cycles. The second deals with problems of score frequencies in ordinary, bipartite and 3-partite tournaments.</p>

Dans cette thèse, nous étudions trois catégories de problèmes : les d-extensibles, les d-bloqueurs et les d-transversaux.Les d-extensibles de stables optimaux sont des ensembles de sommets d'un graphe G tels que tout stable de cardinal d du sous-graphe induit par un d-extensible peut être étendu à un stable optimal de G à l'aide de sommets qui n'appartiennent pas au d-extensible. Nous étudions les d-extensibles de cardinal maximal de stables dans les graphes bipartis. Nous démontrons quelques propriétés structurelles puis nous déterminons une borne inférieure du cardinal maximal d'un d-extensible. Nous étudions quelques classes de graphes dans lesquelles déterminer un d-extensible optimal de stables est un problème polynomial. Nous nous intéressons ensuite aux d-extensibles de stables dans les arbres. Nous prouvons plusieurs propriétés structurelles, déterminons une autre borne inférieure du cardinal maximal d'un d-extensible et étudions quelques classes d'arbres dans lesquelles déterminer un d-extensible optimal de stables est un problème polynomial.Les d-bloqueurs de stables sont des ensembles de sommets d'un graphe G tels que, si on retire les sommets d'un d-bloqueur, le cardinal maximal d'un stable du graphe induit par les sommets restants est inférieur d'au moins d au cardinal maximal d'un stable du graphe initial. Nous nous intéressons ici aux d-bloqueurs de coût minimal de stables dans les arbres. Après avoir prouvé une caractérisation des d-bloqueurs de stables dans les arbres, nous démontrons que déterminer un d-bloqueur de coût minimal de stable est un problème polynomial dans une classe d'arbres particulière.Soit Pi un problème d'optimisation sur un ensemble d'éléments fini. Un d-transversal de Pi est un ensembles d'éléments tel que l'intersection entre le d-transversal et toute solution optimale au problème Pi est de cardinal supérieur égal à d. Nous proposons ici une approche de génération de contraintes pour déterminer des d-transversaux de cardinal maximal de problèmes modélisés par des programmes mathématiques en variables binaires. Nous étudions deux variantes de cette approche que nous testons sur des instances de graphes générés aléatoirement pour déterminer des d-transversaux de stables optimaux et des d-transversaux de couplages optimaux / In this thesis, we study three types of problems : the d-extensibles sets, the d-blockers and the d-transversals.In a graph G, a d-extensible set of maximum independent sets is a subset of vertices of G such that every stable set of cardinality d in the subgraph restricted to the d-extensible set can be extented to a maximum stable set of G using only vertices that do not belong to the d-extensible set. We study d-extensible sets of mxaimum cardinality of stable sets in bipartite graphs. We show some structural properties and we determine a lower bound of the maximum cardinality of a d-extensible set. We consider some classes of graph where finding an optimum d-extensible set can be done in polynomial time. Then, we study the d-extensibles sets of stable sets in trees. We prove some properties on the structures of the d-extensibles sets and we determine another lower bound of the maximum cardinality of a d-extensible set. Finaly, we study somme classes of tree where a d-extensible sets of maximum cardinality can be done in polynomial time.In a graph G, a d-blocker is a subset of vertices such that, if removed, a maximum stable set of the resulting subgraph is of cardinality at most the cardinality of a maximum stable set of G minus d. We study d-blocker of minimal cost of stable sets in tree.We prove a caracterisation of d-blockers in tree and we study a particular classe of trees where computing a d-blocker of minimal cost of stable sets can be done in polynomial time.Let Pi be an optimisation problem on a finite set of elements. A d-transversal of Pi is a subset of elements such that the intersection between the d-transversal and every optimal solution of Pi contains at lest d elements. We propose an approach to compute d-transversal of any optimisation problem modelised by mathematical program with binary variables. We use a contraints generation approach. We compare two variations of this approach on randomly generated graph by computing d-transversals of stables sets and d-transversals of matching

No description available.

We give a strongly polynomial time combinatorial algorithm to minimise the largest eigenvalue of the weighted Laplacian of a bipartite graph. This is accomplished by solving the dual graph embedding problem which arises from a semidefinite programming formulation. In particular, the problem for trees can be solved in time cubic in the number of vertices.

Structural algorithms incorporate the interdependence of outputs into the prediction, the loss, or both. Frank-Wolfe optimizations of pairwise losses and Gaussian conditional random fields for multivariate output regression are two such structural algorithms. Pairwise losses are standard 0-1 classification surrogate losses applied to pairs of features and outputs, resulting in improved ranking performance (area under the ROC curve, average precision, and F-1 score) at the cost of increased learning complexity. In this dissertation, it is proven that the balanced loss 0-1 SVM and the pairwise SVM have the same dual loss and the pairwise dual coefficient domain is a subdomain of the balanced loss 0-1 SVM with bias dual coefficient domain. This provides a theoretical advancement in the understanding of pairwise loss, which we exploit for the development of a novel ranking algorithm that is fast and memory efficient method with state the art ranking metric performance across eight benchmark data sets. Various practical advancements are also made in multivariate output regression. The learning time for Gaussian conditional random fields is greatly reduced and the parameter domain is expanded to enable repulsion between outputs. Last, a novel multivariate regression is presented that keeps the desirable elements of GCRF and infuses them into a local regression model that improves mean squared error and reduces learning complexity. / Computer and Information Science

Recommendation systems are information filtering systems that help users effectively and efficiently explore large amount of information and identify items of interest. Accurate predictions of users' interests improve user satisfaction and are beneficial to business or service providers. Researchers have been making tremendous efforts to improve the accuracy of recommendations. Emerging trends of technologies and application scenarios, however, lead to challenges other than accuracy for recommendation systems. Three new challenges include: (1) opinion spam results in untrustworthy content and makes recommendations deceptive; (2) users prefer diversified content; (3) in some applications user behavior data may not be available to infer users' preference. This thesis tackles the above challenges. We identify features of untrustworthy commercial campaigns on a question and answer website, and adopt machine learning-based techniques to implement an adaptive detection system which automatically detects commercial campaigns. We incorporate diversity requirements into a classic theoretical model and develop efficient algorithms with performance guarantees. We propose a novel and robust approach to infer user preference profile from recommendations using copula models. The proposed approach can offer in-depth business intelligence for physical stores that depend on Wi-Fi hotspots for mobile advertisement. / Graduate / 0984 / cchenv@uvic.ca

Made available in DSpace on 2016-03-15T19:34:23Z (GMT). No. of bitstreams: 1 Rodrigo Guedes Casali.pdf: 50227586 bytes, checksum: 737e1069d703888bd9e4cc046ac94f81 (MD5) Previous issue date: 2015-02-13 / The work aims to study the collective bargaining labour institute, with the presenting of his concept for both the homeland doctrine as to the ILO, its specific principles, its relation to the principle of freedom of association, the regulatory instruments (agreement and collective bargaining agreement), scope, finally, its main aspects. Study will be, even if it is possible federal civil servants carry out collective bargaining work, as they are submitted to a constitutional pay system requiring budgetary provision for the creation of job or change in salary is preceded by legal provision, and as that that law should be a private initiative of the Chief Executive (Article 167, item II, Article 61, paragraph 1, item II, point a, Article 169, paragraph 1, Article 37, item X, all of the Constitution) . Presents other arguments that prevent collective bargaining in the federal public service, for example, the absence of item XXVI of Article 7 of the Constitution in the list of social rights of civil servants contained in paragraph 3 of Article 39 also of the Constitution; the decision of the Supreme Court handed down in the records of direct action of unconstitutionality No. 492-1 / 1990, which was the origin of the subtraction of paragraph d of Article 240 of Law No. 8,112 / 1990, which provided for collective bargaining as a right of server, but it was revoked. It also presents some arguments conducive to the realization of collective bargaining in the federal public service, as the entry into force of the Convention in our legal system No. 151 of the ILO, 1978 and the forecast of the right to free union association and union strike to the servers, so, how can design the right to strike without providing for the right to collective bargaining? Finally, it is practical aspects of the implementation of the negotiation that takes place today between federal public servants and the Union (Direct and Indirect Administration). / O trabalho tem por objetivo estudar o instituto da negociação coletiva de trabalho com a apresentação de seu conceito tanto para a doutrina pátria quanto para a OIT, seus princípios específicos, sua relação com o princípio da liberdade sindical, os instrumentos normativos (acordo e convenção coletiva de trabalho), abrangência, enfim, seus principais aspectos. Estudar-se-á, ainda, se é possível os servidores públicos federais realizarem negociação coletiva de trabalho, pois estão submetidos a um sistema constitucional de remuneração que exige previsão orçamentária para a criação de cargo ou alteração no vencimento que seja precedida de previsão legal, bem como que referida lei deve ser de iniciativa privativa do Chefe do Poder Executivo (artigo 167, inciso II; artigo 61, §1&#351;, inciso II, alínea a; artigo 169, §1&#351;; artigo 37, inciso X, todos da Constituição). Apresentam-se outros argumentos que impedem a negociação coletiva de trabalho no serviço público federal, como, por exemplo, a ausência do inciso XXVI, do artigo 7&#351;, da Constituição no rol de direitos sociais dos servidores públicos contido no §3&#351;, do artigo 39, também da Constituição; a decisão do Supremo Tribunal Federal proferida nos autos da Ação Direta de Inconstitucionalidade nº 492-1/1990, que foi a origem da subtração da alínea d, do artigo 240, da Lei nº 8.112/1990, que previa a negociação coletiva como direito do servidor, mas foi revogada. Também se apresentam alguns argumentos favoráveis à realização da negociação coletiva no serviço público federal, como a entrada em vigor em nosso ordenamento jurídico da Convenção nº 151 da OIT, de 1978 e a previsão dos direitos à livre associação sindical e realização de greve aos servidores, assim, como é possível conceber o direito de greve sem prever o direito à negociação coletiva? Por fim, trata-se de aspectos práticos da realização da negociação que acontece hoje entre servidores públicos federais e a União (Administração Direta e Indireta).

Thèse en cotutelle avec l'Université de Strasbourg. / Le vieillissement de la population nous amène à imaginer de nouvelles approches pour promouvoir la santé et le bien-être à un âge avancé. Les liens sociaux et la mobilité quotidienne jouent potentiellement un rôle important, mais ces dynamiques sont actuellement mal comprises. Cette thèse vise à explorer comment les réseaux sociaux des aînés s'intègrent dans leurs espaces d'activité, et comment les relations sociales, inscrites dans l'environnement spatial, sont associées au bien-être. La thèse explore les données de l’étude CURHA collectées au Québec au sein de la cohorte NuAge. La population d’étude comprend 183 aînés âgés de 79 ans et plus enquêtés en 2014 et 2015, habitant dans les régions de Montréal et Sherbrooke. Le premier volet de cette thèse est de nature méthodologique, et concerne le développement d’un module de questionnaire cartographique interactif permettant de recueillir à la fois des lieux d’activité réguliers et des relations sociales, ces deux niveaux d'information connectés en fonction des “personnes vues dans les lieux d’activités”. Ces données ont été représentées en réseaux bipartites, ce qui a permis de distinguer des structures en étoile formées d’un nœud central connecté à un ensemble de nœuds périphériques. Ces structures identifient d’une part un lieu où l’aîné voit plusieurs personnes, qui pour la plupart, ne sont rencontrées qu’en ce lieu, et d’autre part une personne centrale avec qui plusieurs activités sont réalisées, de manière relativement exclusive.  Le deuxième volet de la thèse porte sur les liens entre les relations sociales et le bien-être émotionnel. Les relations sociales peuvent être catégorisées en relations proches, personnelles, ou de camaraderie. Le nombre de camarades et la présence d’une relation proche sont positivement associés au niveau de bien-être émotionnel, tandis que le nombre de relations personnelles est associé négativement au bien-être émotionnel.  Le dernier volet décrit de manière plus détaillée la distribution des catégories de relations sociales au sein des structures en étoiles identifiées dans les réseaux bipartites. Les relations proches représentent la majorité des personnes qui sont rencontrées ou qui accompagnent les personnes âgées dans un grand nombre de lieux d’activités. La résidence primaire est un lieu de socialisation importante, tandis que les lieux non résidentiels semblent servir de cadre privilégié aux relations de groupes. Les relations personnelles sont plus fréquentes au domicile des participants que dans les autres lieux d'activités. Cette thèse montre que l'analyse de réseau offre un cadre utile pour étudier les relations sociales en rapport avec l'environnement géospatial. Elle met en lumière la concentration de la vie sociale des aînés dans un nombre restreint de lieux d’activités, ainsi que la distribution spatiale différentielle de catégories de relations sociales spécifiquement associée au bien-être émotionnel. Ces approches peuvent soutenir la compréhension des influences socio-environnementales et favoriser la santé et le bien-être des aînés. / The aging of the population leads us to imagine new approaches to promote health and well-being in old age. Social connections and daily mobility potentially play an important role, but these dynamics are currently poorly understood. This thesis aims to explore how older adults' social networks fit into their activity spaces, and how social relationships, embedded in the spatial environment, are associated with well-being. The thesis explores data from the Contrasted Urban settings for Healthy Aging (CURHA) study collected in Quebec within the NuAge cohort. The study population includes 183 older adults aged 79 years and older surveyed in 2014 and 2015, living in the Montréal and Sherbrooke regions. The first part of this thesis is methodological, and concerns the development of an interactive cartographic questionnaire module allowing to collect both regular activity locations and social relationships, those two layers of information connected by “people seen at activity locations”. These data were represented as bipartite networks, which allowed us to identify star-like structures formed by a central node connected to a set of peripheral nodes. These structures identify, on the one hand, a location where the older adult sees several people, most of whom he or she meets only in that place, and on the other hand, a central person with whom several activities are carried out, while being the only person seen in most of these locations. The second part of the thesis focuses on the links between social relationships and emotional well-being. Social relationships can be categorized into close relationships, personal relationships, or companionship. The number of companions and the presence of a close relationship are positively associated with emotional well-being, while the number of personal relationships is negatively associated with emotional well-being.  The final section describes in more detail the distribution of social relationship categories within the star-like structures identified within the bipartite networks. Close relations represent the majority of people who are met or accompany the elderly in a large number of activity locations. The primary residence is an important place of socialization, while non-residential places seem to serve as a privileged setting for group relations. Personal relationships are most common in participants' homes. This thesis shows that network analysis provides a useful framework for studying social relationships within the geospatial environment. It highlights the concentration of older adults' social lives in a limited number of activity locations, as well as the differential spatial distribution of social relationship categories specifically associated with emotional well-being. These approaches can help to understand the socio-environmental influences on older adults' health and well-being.