<p>Query composition is an often complicated and cumbersome task for persons performing a literature search. This thesis is part of a project which aims to present possible queries to the user in form of natural language expressions. The thesis presents methods of ontology slice generation. Slices are parts of ontologies connecting two concepts along all possible paths between them. Those slices hence represent all relevant queries connecting the concepts and the paths can in a later step be translated into natural language expressions. Methods of slice alignment, connecting slices that originate from different ontologies, are also presented. The thesis concludes with some example scenarios and comparisons to related work.</p>

Query composition is an often complicated and cumbersome task for persons performing a literature search. This thesis is part of a project which aims to present possible queries to the user in form of natural language expressions. The thesis presents methods of ontology slice generation. Slices are parts of ontologies connecting two concepts along all possible paths between them. Those slices hence represent all relevant queries connecting the concepts and the paths can in a later step be translated into natural language expressions. Methods of slice alignment, connecting slices that originate from different ontologies, are also presented. The thesis concludes with some example scenarios and comparisons to related work.

Network theory is finding applications in the life and social sciences for ecology, epidemiology, finance and social-ecological systems. While there are methods to generate specific types of networks, the broad literature is focused on generating unweighted networks. In this paper, we present a framework for generating weighted networks that satisfy user- defined criteria. Each criterion hierarchically defines a feature of the network and, in doing so, complements existing algorithms in the literature. We use a general example of ecological species dispersal to illustrate the method and provide open- source code for academic purposes.

Code clones are identical or similar code fragments in a single software system or across multiple systems. Frequent copy-paste-modify activities and reuse of existing systems result in maintenance difficulties and security issues. Addressing these problems requires analysts to undertake code clone analysis, which is an intensive process to discover problematic clones in existing software. To improve the efficiency of this process, tools for code clone detection and analysis, such as Kam1n0 and CCFinder, were created. Kam1n0 is an efficient code clone search engine that facilitates assembly code analysis. However, Kam1n0 search results can contain millions of function-clone pairs, and efficiently exploring and comprehensively understanding the resulting data can be challenging. This thesis presents a design study whereby we collaborated with analyst stakeholders to identify requirements for a tool that visualizes and scales to millions of function-clone pairs. These requirements led to the design of an interactive visual tool, CloneCompass, consisting of novel TreeMap Matrix and Adjacency Matrix visualizations to aid in the exploration of assembly code clones extracted from Kam1n0. We conducted a preliminary evaluation with the analyst stakeholders, and we show how CloneCompass enables these users to visually and interactively explore assembly code clones detected by Kam1n0 with suspected vulnerabilities. To further validate our tool and extend its usability to source code clones, we carried out a Linux case study, where we explored the clones in the Linux kernel detected by CCFinder and gained a number of insights about the cloning activities that may have occurred in the development of the Linux kernel. / Graduate

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

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

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

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

[pt] Estudaremos dinâmicas simbólicas associadas a alfabetos finitos. Consideraremos seqüências bi-infinitas e espaços com memória finita. Estudaremos propriedades invariantes por conjugação. Analisaremos a relação entre os espaços de seqüências e propriedades de matrizes não negativas. O principal exemplo desta correlação é o Teorema de Perron- Frobenius que relaciona a entropia de um espaço de seqüências e os autovalores de uma matriz não negativa associada ao espaço. Neste contexto, certos grafos e suas propriedades aparecem de forma natural. / [en] We study symbolic dynamics associated to finite alphabets. We consider bi-infinite sequences and spaces with finite memory. We pay attention to properties which are invariant by conjugations. We analyze the relation between spaces of sequences and properties of non-negative matrices. The main example is given by the Perron-Frobenius theorem relating the entropy of a space of sequences and the eigerrvalues of a non-negative matrix associated to the space. In this setting, certain graphs and their properties appear in a natural way.