Efficient Algorithms for Graph-Theoretic and Geometric Problems

This thesis studies several different algorithmic problems in graph theory and in geometry. The applications of the problems studied range from circuit design optimization to fast matrix multiplication. First, we study a graph-theoretical model of the so called ''firefighter problem''. The objective is to save as much as possible of an area by appropriately placing firefighters. We provide both new exact algorithms for the case of general graphs as well as approximation algorithms for the case of planar graphs. Next, we study drawing graphs within a given polygon in the plane. We present asymptotically tight upper and lower bounds for this problem Further, we study the problem of Subgraph Isormorphism, which amounts to decide if an input graph (pattern) is isomorphic to a subgraph of another input graph (host graph). We show several new bounds on the time complexity of detecting small pattern graphs. Among other things, we provide a new framework for detection by testing polynomials for non-identity with zero. Finally, we study the problem of partitioning a 3D histogram into a minimum number of 3D boxes and it's applications to efficient computation of matrix products for positive integer matrices. We provide an efficient approximation algorithm for the partitioning problem and several algorithms for integer matrix multiplication. The multiplication algorithms are explicitly or implicitly based on an interpretation of positive integer matrices as 3D histograms and their partitions

Scheduling algorithms for throughput maximization in data networks

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.Includes bibliographical references (p. 215-226).This thesis considers the performance implications of throughput optimal scheduling in physically and computationally constrained data networks. We study optical networks, packet switches, and wireless networks, each of which has an assortment of features and constraints that challenge the design decisions of network architects. In this work, each of these network settings are subsumed under a canonical model and scheduling framework. Tools of queueing analysis are used to evaluate network throughput properties, and demonstrate throughput optimality of scheduling and routing algorithms under stochastic traffic. Techniques of graph theory are used to study network topologies having desirable throughput properties. Combinatorial algorithms are proposed for efficient resource allocation. In the optical network setting, the key enabling technology is wavelength division multiplexing (WDM), which allows each optical fiber link to simultaneously carry a large number of independent data streams at high rate. To take advantage of this high data processing potential, engineers and physicists have developed numerous technologies, including wavelength converters, optical switches, and tunable transceivers.(cont.) While the functionality provided by these devices is of great importance in capitalizing upon the WDM resources, a major challenge exists in determining how to configure these devices to operate efficiently under time-varying data traffic. In the WDM setting, we make two main contributions. First, we develop throughput optimal joint WDM reconfiguration and electronic-layer routing algorithms, based on maxweight scheduling. To mitigate the service disruption associated with WDM reconfiguration, our algorithms make decisions at frame intervals. Second, we develop analytic tools to quantify the maximum throughput achievable in general network settings. Our approach is to characterize several geometric features of the maximum region of arrival rates that can be supported in the network. In the packet switch setting, we observe through numerical simulation the attractive throughput properties of a simple maximal weight scheduler. Subsequently, we consider small switches, and analytically demonstrate the attractive throughput properties achievable using maximal weight scheduling. We demonstrate that such throughput properties may not be sustained in larger switches.(cont.) In the wireless network setting, mesh networking is a promising technology for achieving connectivity in local and metropolitan area networks. Wireless access points and base stations adhering to the IEEE 802.11 wireless networking standard can be bought off the shelf at little cost, and can be configured to access the Internet in minutes. With ubiquitous low-cost Internet access perceived to be of tremendous societal value, such technology is naturally garnering strong interest. Enabling such wireless technology is thus of great importance. An important challenge in enabling mesh networks, and many other wireless network applications, results from the fact that wireless transmission is achieved by broadcasting signals through the air, which has the potential for interfering with other parts of the network. Furthermore, the scarcity of wireless transmission resources implies that link activation and packet routing should be effected using simple distributed algorithms. We make three main contributions in the wireless setting. First, we determine graph classes under which simple, distributed, maximal weight schedulers achieve throughput optimality.(cont.) Second, we use this acquired knowledge of graph classes to develop combinatorial algorithms, based on matroids, for allocating channels to wireless links, such that each channel can achieve maximum throughput using simple distributed schedulers. Third, we determine new conditions under which distributed algorithms for joint link activation and routing achieve throughput optimality.by Andrew Brzezinski.Ph.D

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

Decomposing and packing polygons / Dania el-Khechen.

In this thesis, we study three different problems in the field of computational geometry: the partitioning of a simple polygon into two congruent components, the partitioning of squares and rectangles into equal area components while minimizing the perimeter of the cuts, and the packing of the maximum number of squares in an orthogonal polygon. To solve the first problem, we present three polynomial time algorithms which given a simple polygon P partitions it, if possible, into two congruent and possibly nonsimple components P 1 and P 2 : an O ( n 2 log n ) time algorithm for properly congruent components and an O ( n 3 ) time algorithm for mirror congruent components. In our analysis of the second problem, we experimentally find new bounds on the optimal partitions of squares and rectangles into equal area components. The visualization of the best determined solutions allows us to conjecture some characteristics of a class of optimal solutions. Finally, for the third problem, we present three linear time algorithms for packing the maximum number of unit squares in three subclasses of orthogonal polygons: the staircase polygons, the pyramids and Manhattan skyline polygons. We also study a special case of the problem where the given orthogonal polygon has vertices with integer coordinates and the squares to pack are (2 {604} 2) squares. We model the latter problem with a binary integer program and we develop a system that produces and visualizes optimal solutions. The observation of such solutions aided us in proving some characteristics of a class of optimal solutions

Optimization in Geometric Graphs: Complexity and Approximation

We consider several related problems arising in geometric graphs. In particular, we investigate the computational complexity and approximability properties of several optimization problems in unit ball graphs and develop algorithms to find exact and approximate solutions. In addition, we establish complexity-based theoretical justifications for several greedy heuristics. Unit ball graphs, which are defined in the three dimensional Euclidian space, have several application areas such as computational geometry, facility location and, particularly, wireless communication networks. Efficient operation of wireless networks involves several decision problems that can be reduced to well known optimization problems in graph theory. For instance, the notion of a \virtual backbone" in a wire- less network is strongly related to a minimum connected dominating set in its graph theoretic representation. Motivated by the vastness of application areas, we study several problems including maximum independent set, minimum vertex coloring, minimum clique partition, max-cut and min-bisection. Although these problems have been widely studied in the context of unit disk graphs, which are the two dimensional version of unit ball graphs, there is no established result on the complexity and approximation status for some of them in unit ball graphs. Furthermore, unit ball graphs can provide a better representation of real networks since the nodes are deployed in the three dimensional space. We prove complexity results and propose solution procedures for several problems using geometrical properties of these graphs. We outline a matching-based branch and bound solution procedure for the maximum k-clique problem in unit disk graphs and demonstrate its effectiveness through computational tests. We propose using minimum bottleneck connected dominating set problem in order to determine the optimal transmission range of a wireless network that will ensure a certain size of "virtual backbone". We prove that this problem is NP-hard in general graphs but solvable in polynomial time in unit disk and unit ball graphs. We also demonstrate work on theoretical foundations for simple greedy heuristics. Particularly, similar to the notion of "best" approximation algorithms with respect to their approximation ratios, we prove that several simple greedy heuristics are "best" in the sense that it is NP-hard to recognize the gap between the greedy solution and the optimal solution. We show results for several well known problems such as maximum clique, maximum independent set, minimum vertex coloring and discuss extensions of these results to a more general class of problems. In addition, we propose a "worst-out" heuristic based on edge contractions for the max-cut problem and provide analytical and experimental comparisons with a well known "best-in" approach and its modified versions

The Traveling Salesman Problem

This paper presents a self-contained introduction into algorithmic and computational aspects of the traveling salesman problem and of related problems, along with their theoretical prerequisites as seen from the point of view of an operations researcher who wants to solve practical problem instances. Extensive computational results are reported on most of the algorithms described. Optimal solutions are reported for instances with sizes up to several thousand nodes as well as heuristic solutions with provably very high quality for larger instances