Self-Evaluation Applied Mathematics 2003-2008 University of Twente

This report contains the self-study for the research assessment of the Department of Applied Mathematics (AM) of the Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) at the University of Twente (UT). The report provides the information for the Research Assessment Committee for Applied Mathematics, dealing with mathematical sciences at the three universities of technology in the Netherlands. It describes the state of affairs pertaining to the period 1 January 2003 to 31 December 2008

Multipartite Graph Algorithms for the Analysis of Heterogeneous Data

The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of biomolecules within an organism. This dissertation describes the design, implementation and application of graph algorithms, with the goal of seeking dense structure in data derived from omics experiments in order to detect latent associations between often heterogeneous entities, such as genes, diseases and phenotypes. Exact combinatorial solutions are developed and implemented, rather than relying on approximations or heuristics, even when problems are exceedingly large and/or difficult. Datasets on which the algorithms are applied include time series transcriptomic data from an experiment on the developing mouse cerebellum, gene expression data measuring acute ethanol response in the prefrontal cortex, and the analysis of a predicted protein-protein interaction network. A bipartite graph model is used to integrate heterogeneous data types, such as genes with phenotypes and microbes with mouse strains. The techniques are then extended to a multipartite algorithm to enumerate dense substructure in multipartite graphs, constructed using data from three or more heterogeneous sources, with applications to functional genomics. Several new theoretical results are given regarding multipartite graphs and the multipartite enumeration algorithm. In all cases, practical implementations are demonstrated to expand the frontier of computational feasibility

Desenvolvimentos da Conjetura de Fulkerson

Orientador: Christiane Neme CamposDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Em 1971, Fulkerson propôs a seguinte conjetura: todo grafo cúbico sem arestas de corte admite seis emparelhamentos perfeitos tais que cada aresta do grafo pertence a exatamente dois destes emparelhamentos. A Conjetura de Fulkerson tem desafiado pesquisadores desde sua publicação. Esta conjetura é facilmente verificada para grafos cúbicos 3-aresta-coloráveis. Portanto, a dificuldade do problema reside em estabelecer a conjetura para grafos cúbicos sem arestas de corte que não possuem 3-coloração de arestas. Estes grafos são chamados snarks. Nesta dissertação, a Conjetura de Fulkerson e os snarks são introduzidos com ¿ênfase em sua história e resultados mais relevantes. Alguns resultados relacionados à Conjetura de Fulkerson são apresentados, enfatizando suas conexões com outras conjeturas. Um breve histórico do Problema das Quatro Cores e suas relações com snarks também são apresentados. Na segunda parte deste trabalho, a Conjetura de Fulkerson é verificada para algumas famílias infinitas de snarks construídas com o método de Loupekine, utilizando subgrafos do Grafo de Petersen. Primeiramente, mostramos que a família dos LP0-snarks satisfaz a Conjetura de Fulkerson. Em seguida, generalizamos este resultado para a família mais abrangente dos LP1-snarks. Além disto, estendemos estes resultados para Snarks de Loupekine construídos com subgrafos de snarks diferentes do Grafo de PetersenAbstract: In 1971, Fulkerson proposed a conjecture that states that every bridgeless cubic graph has six perfect matchings such that each edge of the graph belongs to precisely two of these matchings. Fulkerson's Conjecture has been challenging researchers since its publication. It is easily verified for 3-edge-colourable cubic graphs. Therefore, the difficult task is to settle the conjecture for non-3-edge-colourable bridgeless cubic graphs, called snarks. In this dissertation, Fulkerson's Conjecture and snarks are presented with emphasis in their history and remarkable results. We selected some results related to Fulkerson's Conjecture, emphasizing their reach and connections with other conjectures. It is also presented a brief history of the Four-Colour Problem and its connections with snarks. In the second part of this work, we verify Fulkerson's Conjecture for some infinite families of snarks constructed with Loupekine's method using subgraphs of the Petersen Graph. More specifically, we first show that the family of LP0-snarks satisfies Fulkerson's Conjecture. Then, we generalise this result by proving that Fulkerson's Conjecture holds for the broader family of LP1-snarks. We also extend these results to even more general Loupekine Snarks constructed with subgraphs of snarks other than the Petersen GraphMestradoCiência da ComputaçãoMestre em Ciência da Computaçã