The performances of high-speed network communications frequently rest with the distribution of data-stream. In this paper, a dynamic data-stream balancing architecture based on link information is introduced and discussed firstly. Then the algorithms for simultaneously acquiring the passing nodes and links of a path between any two source-destination nodes rapidly, as well as a dynamic data-stream distribution planning are proposed. Some related topics such as data fragment disposal, fair service, etc. are further studied and discussed. Besides, the performance and efficiency of proposed algorithms, especially for fair service and convergence, are evaluated through a demonstration with regard to the rate of bandwidth utilization. Hoping the discussion presented here can be helpful to application developers in selecting an effective strategy for planning the distribution of data-stream. / Singapore-MIT Alliance (SMA)

We describe the structure of those graphs that have largest spectral radius in the class of all connected graphs with a given degree sequence. We show that in such a graph the degree sequence is non-increasing with respect to an ordering of the vertices induced by breadth-first search. For trees the resulting structure is uniquely determined up to isomorphism. We also show that the largest spectral radius in such classes of trees is strictly monotone with respect to majorization. This paper is the revised final version of the preprint no. 35 of this research report series. (author´s abstract) / Series: Research Report Series / Department of Statistics and Mathematics

Spatial analysis methods used for detecting, interpolating or predicting local patterns require a delineation of a neighbourhood defining the extent of spatial interaction in geographic data. The most common neighbourhood delineation techniques include fixed distance bands, k-nearest neighbours, or spatial adjacency (contiguity) matrices optimized to represent spatial dependency in data. However, these standard approaches do not take into consideration the geographic or environmental constraints such as impassable mountain ranges, road networks or coastline barriers. Specifically, complex marine landscapes and coastlines present common problematic neighbourhood definitions for standard neighbourhood matrices used in the spatial analysis of marine environments. Therefore, the goal of our research is to present a new approach to constraining spatial neighbourhoods when conducting geographical analysis in marine environments. To meet this goal, we developed methods and software (COnstraining SpatIal NEighbourhoods - COSINE) for modifying spatial neighbourhoods, and demonstrate their utility in two case studies. Our method enables delineation of neighbourhoods that are constrained by coastlines and the direction of marine currents. Our software calculates and evaluates whether neighbouring features are separated by land, or are within a user defined angle that excludes interaction based on directional processes. Using decision rules a modified spatial weight matrix is created, either in binary or row-standardized format. Within open source software (R), a graphical user interface enables users to modify the standard spatial neighbourhood definition distance, inverse distance and k-nearest neighbour. Two case studies are presented to demonstrate the usefulness of the new approach for detecting spatial patterns: the first case study observes marine mammals’ abundance and the second, oil spill observation. Our results indicate that constraining spatial neighbourhoods in marine environments is particularly important at larger spatial scales. The COSINE tool has many applications for modelling both environmental and human processes. / Graduate / 0463 / 0366 / suarezc@uvic.ca

In network design, a communication network is optimized for a given set of parameters like cost, reliability and delay. This study analyzes network design problem using Genetic Algorithms in detail and makes comparison of different approaches and representations. Encoding of a problem is one of the most crucial design choices in Genetic Algorithms. For network design problem, this study compares adjacency matrix representation with list of edges representation. Also, another problem is defining a fair fitness function that will not favor one optimization parameter to the other. Multi-objective optimization is a recommended solution for such problems. This study describes and compares some of those approaches for different combinations in network design problem.

A semiregular tree is a tree where all non-pendant vertices have the same degree. Among all semiregular trees with fixed order and degree, a graph with minimal (adjacency / Laplacian) spectral radius is a caterpillar. Counter examples show that the result cannot be generalized to the class of trees with a given (non-constant) degree sequence. / Series: Research Report Series / Department of Statistics and Mathematics

L'évolution moléculaire, basée sur l'étude des données de séquençage, s'est imposée comme une approche majeure pour l'étude de l'Histoire des organismes vivants (notamment à travers les arbres phylogénétiques). Ses méthodes classiques reposent sur un découpage des génomes en entités supposées indépendantes : les gènes. Or, les gènes n'évoluent pas indépendamment : au sein de l'histoire des espèces qui le portent, l'histoire d'un gène s'inscrit. En outre, leur position le long des chromosomes fait qu'ils partagent des événements de mutations structurales (duplications, pertes de fragments chromosomiques) avec les gènes proches. Enfin, leur potentielle fonction biologique les amène à être influencés par (et à influencer en retour) l'évolution d'autres gènes. Je montre que ne pas prendre en compte ces relations d'inter-dépendances évolutives (de coévolution) lors de l'inférence d'arbres de gènes résulte en une suresti mation des différences entre les arbres des différents gènes ainsi qu'entre les arbres des gènes et l'arbre des espèces. Des modèles permettent déjà d'intégrer la coévolution des gènes avec les espèces à la reconstruction des arbres de gènes. Par ailleurs, on connaît des modèles décrivant l'évolution des relations entre gènes, néanmoins sans intégrer ces informations à la reconstruction des arbres de gènes. Je reprends ces avancées et les combine au sein d'une méthode qui modifie les arbres de gènes selon un critère qui prend en compte les séquences ainsi que des relations de coévolution avec les espèces et d'autres gènes. Cette méthode, appliquée à des mammifères et des champignons, permet de produire des histoires de gènes cohérentes entre elles / Molecular evolution, based on the study of sequencing data, established itself as a fundamental approach in the study of the history of living organisms (noticeably through the inference of phylogenetic trees). Classical molecular evolution methods rely on the decomposition of genomes into entities that are supposed independent: genes. However we know that genes do not evolve independently: their potential biological function lead them to be influenced by (and influence) the evolution of other genes. Moreover, their position along chromosomes imply that they share events of structural mutations (duplication, loss of a chromosome fragment) with neighbouring genes. Similarly, a gene individual history inscribes itself in the history of the species that bears it. I show that not taking into account this inter-dependency relationships (co- evolutionary relationships) during the inference of gene trees results in an overesti- mation of the differences between gene trees as well as between gene tree and species tree. Modelling efforts these last year have allowed the integration of gene and species co-evolution information to the reconstruction of gene trees. Besides, researchers have proposed models describing the evolution of the relationships linking genes, but without integration of this information in the tree building process. My works aim to combine these advances in a method that modify gene trees according to a criterion that integrates sequence information and information coming from co-evolution relationships. This method, applied to mammals and fungi, leads to gene histories that are more congruent (simpler adjacency histories, longer events of loss or transfer, ...)

A semiregular tree is a tree where all non-pendant vertices have the same degree. Belardo et al. (MATCH Commun. Math. Chem. 61(2), pp. 503-515, 2009) have shown that among all semiregular trees with a fixed order and degree, a graph with index is caterpillar. In this technical report we provide a different proof for this theorem. Furthermore, we give counter examples that show that this result cannot be generalized to the class of trees with a given (non-constant) degree sequence. / Series: Research Report Series / Department of Statistics and Mathematics

L'évolution des génomes peut être observée à plusieurs échelles, chaque échelle révélant des processus évolutifs différents. A l'échelle de séquences ADN, il s'agit d'insertions, délétions et substitutions de nucléotides. Si l'on s'intéresse aux gènes composant les génomes, il s'agit de duplications, pertes et transferts horizontaux de gènes. Et à plus large échelle, on observe des réarrangements chromosomiques modifiant l'agencement des gènes sur les chromosomes. Reconstruire l'histoire évolutive des génomes implique donc de comprendre et de modéliser tous les processus à l'œuvre, ce qui reste hors de notre portée. A la place, les efforts de modélisation ont exploré deux directions principales. D'un côté, les méthodes de reconstruction phylogénétique se sont concentrées sur l'évolution des séquences, certaines intégrant l'évolution des familles de gènes. D'un autre côté, les réarrangements chromosomiques ont été très largement étudiés, donnant naissance à de nombreux modèles d'évolution de l'architecture des génomes. Ces deux voies de modélisation se sont rarement rencontrées jusqu'à récemment. Au cours de ma thèse, j'ai développé un modèle d'évolution de l'architecture des génomes prenant en compte l'évolution des gènes et des séquences. Ce modèle rend possible une reconstruction probabiliste de l'histoire évolutive d'adjacences et de l'ordre des gènes de génomes ancestraux en tenant compte à la fois d'évènements modifiant le contenu en gènes des génomes (duplications et pertes de gènes), et d'évènements modifiant l'architecture des génomes (les réarrangements chromosomiques). Intégrer l'information phylogénétique à la reconstruction d'ordres des gènes permet de reconstruire des histoires évolutives plus complètes. Inversement, la reconstruction d'ordres des gènes ancestraux peut aussi apporter une information complémentaire à la phylogénie et peut être utilisée comme un critère pour évaluer la qualité d'arbres de gènes, ouvrant la voie à un modèle et une reconstruction intégrative / Genomes evolve through processes that modify their content and organization at different scales, ranging from the substitution, insertion or deletion of a single nucleotide to the duplication, loss or transfer of a gene and to large scale chromosomal rearrangements. Extant genomes are the result of a combination of many such processes, which makes it difficult to reconstruct the overall picture of genome evolution. As a result, most models and methods focus on one scale and use only one kind of data, such as gene orders or sequence alignments. Most phylogenetic reconstruction methods focus on the evolution of sequences. Recently, some of these methods have been extended to integrate gene family evolution. Chromosomal rearrangements have also been extensively studied, leading to the development of many models for the evolution of the architecture of genomes. These two ways to model genome evolution have not exchanged much so far, mainly because of computational issues. In this thesis, I present a new model of evolution for the architecture of genomes that accounts for the evolution of gene families. With this model, one can reconstruct the evolutionary history of gene adjacencies and gene order accounting for events that modify the gene content of genomes (duplications and losses of genes) and for events that modify the architecture of genomes (chromosomal rearrangements). Integrating these two types of information in a single model yields more accurate evolutionary histories. Moreover, we show that reconstructing ancestral gene orders can provide feedback on the quality of gene trees thus paving the way for an integrative model and reconstruction method

<p>Det är viktigt med ett effektivt samarbete och en välfungerande kommunikation i dynamiska miljöer, till exempel vid släckningsarbetet av en brand. Bristande kommunikation i en sådan miljö skulle kunna få förödande konsekvenser.</p><p>Denna uppsats bygger på material från studien ”Bridging Cultural Barriers to Collaborative Decision Making in On-Site Operations Coordination Centers”, där 32 svenskar samarbetade i olika lagkonstellationer med att släcka simulerade eldar i mikrovärlden C3Fire.</p><p>Kommunikationsteorier visar på att personer samtalar med varandra efter en viss struktur; deras yttranden tenderar att komma i par, så kallade närhetspar. Denna studie syftade till att undersöka närhetspar i beställningssekvenser, i form av en beställning av vatten och/eller bränsle följd av en bekräftelse. Till sin hjälp hade försöksdeltagarna en datorskärm med en karta samt tillgång till ett e-postverktyg för att kommunicera inom laget. Varje person genomgick åtta spelomgångar, vilket resulterade i totalt 64 spelomgångar. De lag som lyckades släcka elden antogs ha större andel närhetspar i beställningssekvenserna, vilket innebar att de skulle bekräfta varandras beställningar mer kontinuerligt än de lag som inte lyckades släcka elden. För studiet av närhetsparen kategoriserades e-postmeddelandena från samtliga spelomgångar, för att se hur strukturen i kommunikationen såg ut.</p><p>Resultatet visade på att något annat måste ha påverkat de medverkandes prestation, eftersom det inte fanns någon påtaglig skillnad i andelen närhetspar i beställningssekvenserna mellan de olika lagen. Det uppmärksammades att de inte bekräftade varandras beställningar endast genom e-postmeddelanden utan även genom direkta manipulationer. Anledningen till detta antas vara att alla lagmedlemmar blev presenterade samma information på sina datorskärmar, vilket frambringade en mer implicit kommunikation.</p> / <p>Efficient communication and cooperation is important in dynamic environments, for instance in fire-fighting teamwork. A lack of communication in this environment could cause devastating consequences.</p><p>This Master’s thesis is based on material from ”Bridging Cultural Barriers to Collaborative Decision Making in On-Site Operations Coordination Centers”, a study where 32 Swedes collaborated in teams conducting fire-fighting exercises in the micro-world C3Fire.</p><p>Communication theories propose that people talk with each other after a certain structure; their utterances tend to come in pairs, so-called adjacency pairs. The purpose of this study was to examine adjacency pairs in request sequences, in form of a request for water and/or fuel followed by a confirmation. The participants had access to a computer screen with a map together with an e-mail tool, to communicate within the team. Every person participated in eight rounds of the game, which resulted in 64 rounds of the game altogether. The teams who managed to extinguish the fire were assumed to have a larger amount of adjacency pairs in their request sequences than the teams who did not extinguish the fire. For the study of the adjacency pairs, the e-mails were categorized, to see what the structure of the communication looked like.</p><p>The result showed that some other factor must have influenced the participants’ performance, since there was no obvious difference in the amount of the adjacency pairs in the request sequence between the teams. It was observed that the team members did not confirm each other’s requests just by sending e-mail, but also by direct manipulations. The reason for this is assumed to be that every member of the team was shown the same information on his computer screen, which gave rise to a more implicit communication.</p>

We show that amongst all trees with a given degree sequence it is a ball where the vertex degrees decrease with increasing distance from its center that maximizes the spectral radius of the graph (i.e., its adjacency matrix). The resulting Perron vector is decreasing on every path starting from the center of this ball. This result it also connected to Faber-Krahn like theorems for Dirichlet matrices on trees. The above result is extended to connected graphs with given degree sequence. Here we give a necessary condition for a graph that has greatest maximum eigenvalue. Moreover, we show that the greatest maximum eigenvalue is monotone on degree sequences with respect to majorization. (author's abstract). Note: There is a more recent version of this paper available: "Graphs with Given Degree Sequence and Maximal Spectral Radius", Research Report Series / Department of Statistics and Mathematics, no. 72. / Series: Research Report Series / Department of Statistics and Mathematics