A simple linear-time algorithm for finding path-decompositions of small width

We described a simple algorithm running in linear time for each fixed constant $k$, that either establishes that the pathwidth of a graph $G$ is greater than $k$, or finds a path-decomposition of $G$ of width at most $O(2^{k})$. This provides a simple proof of the result by Bodlaender that many families of graphs of bounded pathwidth can be recognized in linear time.Comment: 9 page

The structure of graphs not admitting a fixed immersion

We present an easy structure theorem for graphs which do not admit an immersion of the complete graph. The theorem motivates the definition of a variation of tree decompositions based on edge cuts instead of vertex cuts which we call tree-cut decompositions. We give a definition for the width of tree-cut decompositions, and using this definition along with the structure theorem for excluded clique immersions, we prove that every graph either has bounded tree-cut width or admits an immersion of a large wall

The structure of graphs not admitting a fixed immersion

We present an easy structure theorem for graphs which do not admit an immersion of the complete graph. The theorem motivates the definition of a variation of tree decompositions based on edge cuts instead of vertex cuts which we call tree-cut decompositions. We give a definition for the width of tree-cut decompositions, and using this definition along with the structure theorem for excluded clique immersions, we prove that every graph either has bounded tree-cut width or admits an immersion of a large wall

Improved self-reduction algorithms for graphs with bounded treewidth

AbstractRecent results of Robertson and Seymour show that every class that is closed under taking of minors can be recognized in O(n3) time. If there is a fixed upper bound on the treewidth of the graphs in the class, i.e., if there is a planar graph not in the class, then the class can be recognized in O(n2) time. However, this result is nonconstructive in two ways: the algorithm only decides on membership, but does not construct “a solution”, e.g., a linear ordering, decomposition or embedding; and no method is given to find the algorithms. In many cases, both nonconstructive elements can be avoided, using techniques of Brown (1989) and Fellows and Langston (1989), based on self-reduction. In this paper we introduce two techniques that help to reduce the running time of self-reduction algorithms. With the help of these techniques we show that there exist O(n2) algorithms that decide on membership and construct solutions for treewidth, pathwidth, search number, vertex search number, node search number, cutwidth, modified cutwidth, vertex separation number, gate matrix layout, and progressive black–white pebbling, where in each case the parameter k is a fixed constant

A Reconfigurable Computing Solution to the Parameterized Vertex Cover Problem

Active research has been done in the past two decades in the field of computational intractability. This thesis explores parallel implementations on a RC (reconfigurable computing) platform for FPT (fixed-parameter tractable) algorithms. Reconfigurable hardware implementations of algorithms for solving NP-Complete problems have been of great interest for research in the past few years. However, most of the research that has been done target exact algorithms for solving problems of this nature. Although such implementations have generated good results, it should be kept in mind that the input sizes were small. Moreover, most of these implementations are instance-specific in nature making it mandatory to generate a different circuit for every new problem instance. In this work, we present an efficient and scalable algorithm that breaks out of the conventional instance-specific approach towards a more general parameterized approach to solve such problems. We present approaches based on the theory of fixed-parameter tractability. The prototype problem used as a case study here is the classic vertex cover problem. The hardware implementation has demonstrated speedups of the order of 100x over the software version of the vertex cover problem

Graph-Theoretical Tools for the Analysis of Complex Networks

We are currently experiencing an explosive growth in data collection technology that threatens to dwarf the commensurate gains in computational power predicted by Moore’s Law. At the same time, researchers across numerous domain sciences are finding success using network models to represent their data. Graph algorithms are then applied to study the topological structure and tease out latent relationships between variables. Unfortunately, the problems of interest, such as finding dense subgraphs, are often the most difficult to solve from a computational point of view. Together, these issues motivate the need for novel algorithmic techniques in the study of graphs derived from large, complex, data sources. This dissertation describes the development and application of graph theoretic tools for the study of complex networks. Algorithms are presented that leverage efficient, exact solutions to difficult combinatorial problems for epigenetic biomarker detection and disease subtyping based on gene expression signatures. Extensive testing on publicly available data is presented supporting the efficacy of these approaches. To address efficient algorithm design, a study of the two core tenets of fixed parameter tractability (branching and kernelization) is considered in the context of a parallel implementation of vertex cover. Results of testing on a wide variety of graphs derived from both real and synthetic data are presented. It is shown that the relative success of kernelization versus branching is found to be largely dependent on the degree distribution of the graph. Throughout, an emphasis is placed upon the practicality of resulting implementations to advance the limits of effective computation

Performance Improvements of Common Sparse Numerical Linear Algebra Computations

Manufacturers of computer hardware are able to continuously sustain an unprecedented pace of progress in computing speed of their products, partially due to increased clock rates but also because of ever more complicated chip designs. With new processor families appearing every few years, it is increasingly harder to achieve high performance rates in sparse matrix computations. This research proposes new methods for sparse matrix factorizations and applies in an iterative code generalizations of known concepts from related disciplines. The proposed solutions and extensions are implemented in ways that tend to deliver efficiency while retaining ease of use of existing solutions. The implementations are thoroughly timed and analyzed using a commonly accepted set of test matrices. The tests were conducted on modern processors that seem to have gained an appreciable level of popularity and are fairly representative for a wider range of processor types that are available on the market now or in the near future. The new factorization technique formally introduced in the early chapters is later on proven to be quite competitive with state of the art software currently available. Although not totally superior in all cases (as probably no single approach could possibly be), the new factorization algorithm exhibits a few promising features. In addition, an all-embracing optimization effort is applied to an iterative algorithm that stands out for its robustness. This also gives satisfactory results on the tested computing platforms in terms of performance improvement. The same set of test matrices is used to enable an easy comparison between both investigated techniques, even though they are customarily treated separately in the literature. Possible extensions of the presented work are discussed. They range from easily conceivable merging with existing solutions to rather more evolved schemes dependent on hard to predict progress in theoretical and algorithmic research

A list of parameterized problems in bioinformatics

In this report we present a list of problems that originated in bionformatics. Our aim is to collect information on such problems that have been analyzed from the point of view of Parameterized Complexity. For every problem we give its definition and biological motivation together with known complexity results.Postprint (published version

Topics in Graph Algorithms: Structural Results and Algorithmic Techniques, with Applications

Coping with computational intractability has inspired the development of a variety of algorithmic techniques. The main challenge has usually been the design of polynomial time algorithms for NP-complete problems in a way that guarantees some, often worst-case, satisfactory performance when compared to exact (optimal) solutions. We mainly study some emergent techniques that help to bridge the gap between computational intractability and practicality. We present results that lead to better exact and approximation algorithms and better implementations. The problems considered in this dissertation share much in common structurally, and have applications in several scientific domains, including circuit design, network reliability, and bioinformatics. We begin by considering the relationship between graph coloring and the immersion order, a well-quasi-order defined on the set of finite graphs. We establish several (structural) results and discuss their potential algorithmic consequences. We discuss graph metrics such as treewidth and pathwidth. Treewidth is well studied, mainly because many problems that are NP-hard in general have polynomial time algorithms when restricted to graphs of bounded treewidth. Pathwidth has many applications ranging from circuit layout to natural language processing. We present a linear time algorithm to approximate the pathwidth of planar graphs that have a fixed disk dimension. We consider the face cover problem, which has potential applications in facilities location and logistics. Being fixed-parameter tractable, we develop an algorithm that solves it in time O(5k + n2) where k is the input parameter. This is a notable improvement over the previous best known algorithm, which runs in O(8kn). In addition to the structural and algorithmic results, this text tries to illustrate the practicality of fixed-parameter algorithms. This is achieved by implementing some algorithms for the vertex cover problem, and conducting experiments on real data sets. Our experiments advocate the viewpoint that, for many practical purposes, exact solutions of some NP-complete problems are affordable