On Hamiltonian Line-Graphsq
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Tutorial 13 Travelling Salesman Problem1
MTAT.03.286: Design and Analysis of Algorithms University of Tartu Tutorial 13 Instructor: Vitaly Skachek; Assistants: Behzad Abdolmaleki, Oliver-Matis Lill, Eldho Thomas. Travelling Salesman Problem1 Basic algorithm Definition 1 A Hamiltonian cycle in a graph is a simple circuit that passes through each vertex exactly once. + Problem. Let G(V; E) be a complete undirected graph, and c : E 7! R be a cost function defined on the edges. Find a minimum cost Hamiltonian cycle in G. This problem is called a travelling salesman problem. To illustrate the motivation, imagine that a salesman has a list of towns it should visit (and at the end to return to his home city), and a map, where there is a certain distance between any two towns. The salesman wants to minimize the total distance traveled. Definition 2 We say that the cost function defined on the edges satisfies a triangle inequality if for any three edges fu; vg, fu; wg and fv; wg in E it holds: c (fu; vg) + c (fv; wg) ≥ c (fu; wg) : In what follows we assume that the cost function c satisfies the triangle inequality. The main idea of the algorithm: Observe that removing an edge from the optimal travelling salesman tour leaves a path through all vertices, which contains a spanning tree. We have the following relations: cost(TSP) ≥ cost(Hamiltonian path without an edge) ≥ cost(MST) : 1Additional reading: Section 3 in the book of V.V. Vazirani \Approximation Algorithms". 1 Next, we describe how to build a travelling salesman path. Find a minimum spanning tree in the graph. -
Matroid Theory
MATROID THEORY HAYLEY HILLMAN 1 2 HAYLEY HILLMAN Contents 1. Introduction to Matroids 3 1.1. Basic Graph Theory 3 1.2. Basic Linear Algebra 4 2. Bases 5 2.1. An Example in Linear Algebra 6 2.2. An Example in Graph Theory 6 3. Rank Function 8 3.1. The Rank Function in Graph Theory 9 3.2. The Rank Function in Linear Algebra 11 4. Independent Sets 14 4.1. Independent Sets in Graph Theory 14 4.2. Independent Sets in Linear Algebra 17 5. Cycles 21 5.1. Cycles in Graph Theory 22 5.2. Cycles in Linear Algebra 24 6. Vertex-Edge Incidence Matrix 25 References 27 MATROID THEORY 3 1. Introduction to Matroids A matroid is a structure that generalizes the properties of indepen- dence. Relevant applications are found in graph theory and linear algebra. There are several ways to define a matroid, each relate to the concept of independence. This paper will focus on the the definitions of a matroid in terms of bases, the rank function, independent sets and cycles. Throughout this paper, we observe how both graphs and matrices can be viewed as matroids. Then we translate graph theory to linear algebra, and vice versa, using the language of matroids to facilitate our discussion. Many proofs for the properties of each definition of a matroid have been omitted from this paper, but you may find complete proofs in Oxley[2], Whitney[3], and Wilson[4]. The four definitions of a matroid introduced in this paper are equiv- alent to each other. -
Matroids You Have Known
26 MATHEMATICS MAGAZINE Matroids You Have Known DAVID L. NEEL Seattle University Seattle, Washington 98122 [email protected] NANCY ANN NEUDAUER Pacific University Forest Grove, Oregon 97116 nancy@pacificu.edu Anyone who has worked with matroids has come away with the conviction that matroids are one of the richest and most useful ideas of our day. —Gian Carlo Rota [10] Why matroids? Have you noticed hidden connections between seemingly unrelated mathematical ideas? Strange that finding roots of polynomials can tell us important things about how to solve certain ordinary differential equations, or that computing a determinant would have anything to do with finding solutions to a linear system of equations. But this is one of the charming features of mathematics—that disparate objects share similar traits. Properties like independence appear in many contexts. Do you find independence everywhere you look? In 1933, three Harvard Junior Fellows unified this recurring theme in mathematics by defining a new mathematical object that they dubbed matroid [4]. Matroids are everywhere, if only we knew how to look. What led those junior-fellows to matroids? The same thing that will lead us: Ma- troids arise from shared behaviors of vector spaces and graphs. We explore this natural motivation for the matroid through two examples and consider how properties of in- dependence surface. We first consider the two matroids arising from these examples, and later introduce three more that are probably less familiar. Delving deeper, we can find matroids in arrangements of hyperplanes, configurations of points, and geometric lattices, if your tastes run in that direction. -
Incremental Dynamic Construction of Layered Polytree Networks )
440 Incremental Dynamic Construction of Layered Polytree Networks Keung-Chi N g Tod S. Levitt lET Inc., lET Inc., 14 Research Way, Suite 3 14 Research Way, Suite 3 E. Setauket, NY 11733 E. Setauket , NY 11733 [email protected] [email protected] Abstract Many exact probabilistic inference algorithms1 have been developed and refined. Among the earlier meth ods, the polytree algorithm (Kim and Pearl 1983, Certain classes of problems, including per Pearl 1986) can efficiently update singly connected ceptual data understanding, robotics, discov belief networks (or polytrees) , however, it does not ery, and learning, can be represented as incre work ( without modification) on multiply connected mental, dynamically constructed belief net networks. In a singly connected belief network, there is works. These automatically constructed net at most one path (in the undirected sense) between any works can be dynamically extended and mod pair of nodes; in a multiply connected belief network, ified as evidence of new individuals becomes on the other hand, there is at least one pair of nodes available. The main result of this paper is the that has more than one path between them. Despite incremental extension of the singly connect the fact that the general updating problem for mul ed polytree network in such a way that the tiply connected networks is NP-hard (Cooper 1990), network retains its singly connected polytree many propagation algorithms have been applied suc structure after the changes. The algorithm cessfully to multiply connected networks, especially on is deterministic and is guaranteed to have networks that are sparsely connected. These methods a complexity of single node addition that is include clustering (also known as node aggregation) at most of order proportional to the number (Chang and Fung 1989, Pearl 1988), node elimination of nodes (or size) of the network. -
A Framework for the Evaluation and Management of Network Centrality ∗
A Framework for the Evaluation and Management of Network Centrality ∗ Vatche Ishakiany D´oraErd}osz Evimaria Terzix Azer Bestavros{ Abstract total number of shortest paths that go through it. Ever Network-analysis literature is rich in node-centrality mea- since, researchers have proposed different measures of sures that quantify the centrality of a node as a function centrality, as well as algorithms for computing them [1, of the (shortest) paths of the network that go through it. 2, 4, 10, 11]. The common characteristic of these Existing work focuses on defining instances of such mea- measures is that they quantify a node's centrality by sures and designing algorithms for the specific combinato- computing the number (or the fraction) of (shortest) rial problems that arise for each instance. In this work, we paths that go through that node. For example, in a propose a unifying definition of centrality that subsumes all network where packets propagate through nodes, a node path-counting based centrality definitions: e.g., stress, be- with high centrality is one that \sees" (and potentially tweenness or paths centrality. We also define a generic algo- controls) most of the traffic. rithm for computing this generalized centrality measure for In many applications, the centrality of a single node every node and every group of nodes in the network. Next, is not as important as the centrality of a group of we define two optimization problems: k-Group Central- nodes. For example, in a network of lobbyists, one ity Maximization and k-Edge Centrality Boosting. might want to measure the combined centrality of a In the former, the task is to identify the subset of k nodes particular group of lobbyists. -
Lecture 9. Basic Problems of Graph Theory
Lecture 9. Basic Problems of Graph Theory. 1 / 28 Problem of the Seven Bridges of Königsberg Denition An Eulerian path in a multigraph G is a path which contains each edge of G exactly once. If the Eulerian path is closed, then it is called an Euler cycle. If a multigraph contains an Euler cycle, then is called a Eulerian graph. Example Consider graphs z z z y y y w w w t t x x t x a) b) c) in case a the multigraph has an Eulerian cycle, in case b the multigraph has an Eulerian trail, in case c the multigraph hasn't an Eulerian cycle or an Eulerian trail. 2 / 28 Problem of the Seven Bridges of Königsberg In Königsberg, there are two islands A and B on the river Pregola. They are connected each other and with shores C and D by seven bridges. You must set o from any part of the city land: A; B; C or D, go through each of the bridges exactly once and return to the starting point. In 1736 this problem had been solved by the Swiss mathematician Leonhard Euler (1707-1783). He built a graph representing this problem. Shore C River Island A Island B Shore D Leonard Euler answered the important question for citizens "has the resulting graph a closed walk, which contains all edges only once?" Of course the answer was negative. 3 / 28 Problem of the Seven Bridges of Königsberg Theorem Let G be a connected multigraph. G is Eulerian if and only if each vertex of G has even degree. -
582670 Algorithms for Bioinformatics
582670 Algorithms for Bioinformatics Lecture 5: Graph Algorithms and DNA Sequencing 27.9.2012 Adapted from slides by Veli M¨akinen/ Algorithms for Bioinformatics 2011 which are partly from http://bix.ucsd.edu/bioalgorithms/slides.php DNA Sequencing: History Sanger method (1977): Gilbert method (1977): I Labeled ddNTPs terminate I Chemical method to cleave DNA copying at random DNA at specific points (G, points. G+A, T+C, C). I Both methods generate labeled fragments of varying lengths that are further measured by electrophoresis. Sanger Method: Generating a Read 1. Divide sample into four. 2. Each sample will have available all normal nucleotides and modified nucleotides of one type (A, C, G or T) that will terminate DNA strand elongation. 3. Start at primer (restriction site). 4. Grow DNA chain. 5. In each sample the reaction will stop at all points ending with the modified nucleotide. 6. Separate products by length using gel electrophoresis. Sanger Method: Generating a Read DNA Sequencing I Shear DNA into millions of small fragments. I Read 500-700 nucleotides at a time from the small fragments (Sanger method) Fragment Assembly I Computational Challenge: assemble individual short fragments (reads) into a single genomic sequence (\superstring") I Until late 1990s the shotgun fragment assembly of human genome was viewed as intractable problem I Now there exists \complete" sequences of human genomes of several individuals I For small and \easy" genomes, such as bacterial genomes, fragment assembly is tractable with many software tools I Remains -
Graph Algorithms in Bioinformatics an Introduction to Bioinformatics Algorithms Outline
An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Graph Algorithms in Bioinformatics An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Outline 1. Introduction to Graph Theory 2. The Hamiltonian & Eulerian Cycle Problems 3. Basic Biological Applications of Graph Theory 4. DNA Sequencing 5. Shortest Superstring & Traveling Salesman Problems 6. Sequencing by Hybridization 7. Fragment Assembly & Repeats in DNA 8. Fragment Assembly Algorithms An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Section 1: Introduction to Graph Theory An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Knight Tours • Knight Tour Problem: Given an 8 x 8 chessboard, is it possible to find a path for a knight that visits every square exactly once and returns to its starting square? • Note: In chess, a knight may move only by jumping two spaces in one direction, followed by a jump one space in a perpendicular direction. http://www.chess-poster.com/english/laws_of_chess.htm An Introduction to Bioinformatics Algorithms www.bioalgorithms.info 9th Century: Knight Tours Discovered An Introduction to Bioinformatics Algorithms www.bioalgorithms.info 18th Century: N x N Knight Tour Problem • 1759: Berlin Academy of Sciences proposes a 4000 francs prize for the solution of the more general problem of finding a knight tour on an N x N chessboard. • 1766: The problem is solved by Leonhard Euler (pronounced “Oiler”). • The prize was never awarded since Euler was Director of Mathematics at Berlin Academy and was deemed ineligible. Leonhard Euler http://commons.wikimedia.org/wiki/File:Leonhard_Euler_by_Handmann.png An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Introduction to Graph Theory • A graph is a collection (V, E) of two sets: • V is simply a set of objects, which we call the vertices of G. -
1 Plane and Planar Graphs Definition 1 a Graph G(V,E) Is Called Plane If
1 Plane and Planar Graphs Definition 1 A graph G(V,E) is called plane if • V is a set of points in the plane; • E is a set of curves in the plane such that 1. every curve contains at most two vertices and these vertices are the ends of the curve; 2. the intersection of every two curves is either empty, or one, or two vertices of the graph. Definition 2 A graph is called planar, if it is isomorphic to a plane graph. The plane graph which is isomorphic to a given planar graph G is said to be embedded in the plane. A plane graph isomorphic to G is called its drawing. 1 9 2 4 2 1 9 8 3 3 6 8 7 4 5 6 5 7 G is a planar graph H is a plane graph isomorphic to G 1 The adjacency list of graph F . Is it planar? 1 4 56 8 911 2 9 7 6 103 3 7 11 8 2 4 1 5 9 12 5 1 12 4 6 1 2 8 10 12 7 2 3 9 11 8 1 11 36 10 9 7 4 12 12 10 2 6 8 11 1387 12 9546 What happens if we add edge (1,12)? Or edge (7,4)? 2 Definition 3 A set U in a plane is called open, if for every x ∈ U, all points within some distance r from x belong to U. A region is an open set U which contains polygonal u,v-curve for every two points u,v ∈ U. -
Path Finding in Graphs
Path Finding in Graphs Problem Set #2 will be posted by tonight 1 From Last Time Two graphs representing 5-mers from the sequence "GACGGCGGCGCACGGCGCAA" Hamiltonian Path: Eulerian Path: Each k-mer is a vertex. Find a path that Each k-mer is an edge. Find a path that passes through every vertex of this graph passes through every edge of this graph exactly once. exactly once. 2 De Bruijn's Problem Nicolaas de Bruijn Minimal Superstring Problem: (1918-2012) k Find the shortest sequence that contains all |Σ| strings of length k from the alphabet Σ as a substring. Example: All strings of length 3 from the alphabet {'0','1'}. A dutch mathematician noted for his many contributions in the fields of graph theory, number theory, combinatorics and logic. He solved this problem by mapping it to a graph. Note, this particular problem leads to cyclic sequence. 3 De Bruijn's Graphs Minimal Superstrings can be constructed by finding a Or, equivalently, a Eulerian cycle of a Hamiltonian path of an k-dimensional De Bruijn (k−1)-dimensional De Bruijn graph. Here edges k graph. Defined as a graph with |Σ| nodes and edges represent the k-length substrings. from nodes whose k − 1 suffix matches a node's k − 1 prefix 4 Solving Graph Problems on a Computer Graph Representations An example graph: An Adjacency Matrix: Adjacency Lists: A B C D E Edge = [(0,1), (0,4), (1,2), (1,3), A 0 1 0 0 1 (2,0), B 0 0 1 1 0 (3,0), C 1 0 0 0 0 (4,1), (4,2), (4,3)] D 1 0 0 0 0 An array or list of vertex pairs (i,j) E 0 1 1 1 0 indicating an edge from the ith vertex to the jth vertex. -
Eulerian and Hamiltonian Paths
Eulerian and Hamiltonian Paths 1. Euler paths and circuits 1.1. The Könisberg Bridge Problem Könisberg was a town in Prussia, divided in four land regions by the river Pregel. The regions were connected with seven bridges as shown in figure 1(a). The problem is to find a tour through the town that crosses each bridge exactly once. Leonhard Euler gave a formal solution for the problem and –as it is believed- established the graph theory field in mathematics. (a) (b) Figure 1: The bridges of Könisberg (a) and corresponding graph (b) 1.2. Defining Euler paths Obviously, the problem is equivalent with that of finding a path in the graph of figure 1(b) such that it crosses each edge exactly one time. Instead of an exhaustive search of every path, Euler found out a very simple criterion for checking the existence of such paths in a graph. As a result, paths with this property took his name. Definition 1: An Euler path is a path that crosses each edge of the graph exactly once. If the path is closed, we have an Euler circuit. In order to proceed to Euler’s theorem for checking the existence of Euler paths, we define the notion of a vertex’s degree. Definition 2: The degree of a vertex u in a graph equals to the number of edges attached to vertex u. A loop contributes 2 to its vertex’s degree. 1.3. Checking the existence of an Euler path The existence of an Euler path in a graph is directly related to the degrees of the graph’s vertices. -
Combinatorics
Combinatorics Introduction to graph theory Misha Lavrov ARML Practice 11/03/2013 Warm-up 1. How many (unordered) poker hands contain 3 or more aces? 2. 10-digit ISBN codes end in a \check digit": a number 0{9 or the letter X, calculated from the other 9 digits. If a typo is made in a single digit of the code, this can be detected by checking this calculation. Prove that a check digit in the range 1{9 couldn't achieve this goal. 16 3. There are 8 ways to go from (0; 0) to (8; 8) in steps of (0; +1) or (+1; 0). (Do you remember why?) How many of these paths avoid (2; 2), (4; 4), and (6; 6)? You don't have to simplify the expression you get. Warm-up Solutions 4 48 4 48 1. There are 3 · 2 hands with 3 aces, and 4 · 1 hands with 4 aces, for a total of 4560. 2. There are 109 possible ISBN codes (9 digits, which uniquely determine the check digit). If the last digit were in the range 1{9, there would be 9 · 108 possibilities for the last 9 digits. By pigeonhole, two ISBN codes would agree on the last 9 digits, so they'd only differ in the first digit, and an error in that digit couldn't be detected. 3. We use the inclusion-exclusion principle. (Note that there are, 4 12 e.g., 2 · 6 paths from (0; 0) to (8; 8) through (2; 2).) This gives us 16 412 82 428 44 − 2 − + 3 − = 3146: 8 2 6 4 2 4 2 Graphs Definitions A graph is a set of vertices, some of which are joined by edges.