An Efficient Algorithm for Enumerating Eulerian Paths
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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. -
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. -
On Hamiltonian Line-Graphsq
ON HAMILTONIANLINE-GRAPHSQ BY GARY CHARTRAND Introduction. The line-graph L(G) of a nonempty graph G is the graph whose point set can be put in one-to-one correspondence with the line set of G in such a way that two points of L(G) are adjacent if and only if the corresponding lines of G are adjacent. In this paper graphs whose line-graphs are eulerian or hamiltonian are investigated and characterizations of these graphs are given. Furthermore, neces- sary and sufficient conditions are presented for iterated line-graphs to be eulerian or hamiltonian. It is shown that for any connected graph G which is not a path, there exists an iterated line-graph of G which is hamiltonian. Some elementary results on line-graphs. In the course of the article, it will be necessary to refer to several basic facts concerning line-graphs. In this section these results are presented. All the proofs are straightforward and are therefore omitted. In addition a few definitions are given. If x is a Une of a graph G joining the points u and v, written x=uv, then we define the degree of x by deg zz+deg v—2. We note that if w ' the point of L(G) which corresponds to the line x, then the degree of w in L(G) equals the degree of x in G. A point or line is called odd or even depending on whether it has odd or even degree. If G is a connected graph having at least one line, then L(G) is also a connected graph. -
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. -
An Eulerian Path Approach to Global Multiple Alignment for DNA
JOURNAL OFCOMPUTATIONAL BIOLOGY Volume10, Number 6,2003 ©MaryAnn Liebert,Inc. Pp. 803–819 AnEulerian Path Approach to Global Multiple Alignment for DNASequences YU ZHANG1 andMICHAEL S.WATERMAN 2 ABSTRACT With the rapid increase in the datasetof genomesequences, the multiple sequence alignment problemis increasingly importantand frequently involves the alignmentof alargenumber ofsequences. Manyheuristic algorithmshave been proposedto improve the speed ofcom- putationand the qualityof alignment. W eintroduce anovelapproach that is fundamentally different fromall currently availablemethods. Our motivationcomes from the Eulerian methodfor fragment assembly in DNAsequencing thattransforms all DNAfragments into ade Bruijn graphand then reduces sequence assembly toa Eulerian pathproblem. The paperfocuses onglobal multiple alignmentof DNA sequences, whereentire sequences are aligned into onecon guration. Our mainresult is analgorithm with almostlinear compu- tationalspeed with respect tothe totalsize (numberof letters) ofsequences tobe aligned. Fivehundred simulated sequences (averaging500 bases per sequence andas lowas 70% pairwise identity) havebeen aligned within three minutes onapersonal computer,andthe quality ofalignment is satisfactory.As aresult, accurateand simultaneous alignmentof thousandsof long sequences within areasonableamount of time becomespossible. Data froman Arabidopsis sequencing projectis used todemonstrate the performance. Key words: multiple sequencealignment, de Bruijn graph,Eulerian path. 1.INTRODUCTION ultiplesequence -
Graph Theory to Gain a Deeper Understanding of What’S Going On
Graphs Graphs and trees come up everywhere. I We can view the internet as a graph (in many ways) I who is connected to whom I Web search views web pages as a graph I Who points to whom I Niche graphs (Ecology): I The vertices are species I Two vertices are connected by an edge if they compete (use the same food resources, etc.) Niche graphs describe competitiveness. I Influence Graphs I The vertices are people I There is an edge from a to b if a influences b Influence graphs give a visual representation of power structure. I Social networks: who knows whom There are lots of other examples in all fields . By viewing a situation as a graph, we can apply general results of graph theory to gain a deeper understanding of what's going on. We're going to prove some of those general results. But first we need some notation . Directed and Undirected Graphs A graph G is a pair (V ; E), where V is a set of vertices or nodes and E is a set of edges I We sometimes write G(V ; E) instead of G I We sometimes write V (G) and E(G) to denote the vertices/edges of G. In a directed graph (digraph), the edges are ordered pairs (u; v) 2 V × V : I the edge goes from node u to node v In an undirected simple graphs, the edges are sets fu; vg consisting of two nodes. I there's no direction in the edge from u to v I More general (non-simple) undirected graphs (sometimes called multigraphs) allow self-loops and multiple edges between two nodes. -
The Number of Euler Tours of Random Directed Graphs
The number of Euler tours of random directed graphs P´aid´ıCreed∗ Mary Cryanyz School of Mathematical Sciences School of Informatics Queen Mary, University of London University of Edinburgh United Kingdom United Kingdom [email protected] [email protected] Submitted: May 21, 2012; Accepted: Jul 26, 2013; Published: Aug 9, 2013 Mathematics Subject Classifications: 05A16, 05C30, 05C80, 68Q25 Abstract In this paper we obtain the expectation and variance of the number of Euler tours of a random Eulerian directed graph with fixed out-degree sequence. We use this to obtain the asymptotic distribution of the number of Euler tours of a random d-in/d-out graph and prove a concentration result. We are then able to show that a very simple approach for uniform sampling or approximately counting Euler tours yields algorithms running in expected polynomial time for almost every d-in/d-out graph. We make use of the BEST theorem of de Bruijn, van Aardenne-Ehrenfest, Smith and Tutte, which shows that the number of Euler tours of an Eulerian directed graph with out-degree sequence d is the product of the number of arborescences and 1 Q the term jV j [ v2V (dv − 1)!]. Therefore most of our effort is towards estimating the moments of the number of arborescences of a random graph with fixed out-degree sequence. 1 Introduction 1.1 Background Let G = (V; A) be a directed graph. An Euler tour of G is any ordering eπ(1); : : : ; eπ(jAj) of the set of arcs E such that for every 1 6 i < jAj, the target vertex of arc eπ(i) is the source vertex of eπ(i+1), and such that the target vertex of eπ(jAj) is the source of eπ(1). -
A Reverse Aldous–Broder Algorithm
A Reverse Aldous{Broder Algorithm Yiping Hu∗ Russell Lyons† Pengfei Tang‡ October 8, 2020 Abstract The Aldous{Broder algorithm provides a way of sampling a uniformly random spanning tree for finite connected graphs using simple random walk. Namely, start a simple random walk on a connected graph and stop at the cover time. The tree formed by all the first-entrance edges has the law of a uniform spanning tree. Here we show that the tree formed by all the last-exit edges also has the law of a uniform spanning tree. This answers a question of Tom Hayes and Cris Moore from 2010. The proof relies on a bijection that is related to the BEST theorem in graph theory. We also give other applications of our results, including new proofs of the reversibility of loop-erased random walk, of the Aldous{Broder algorithm itself, and of Wilson's algorithm. R´esum´e L'algorithme Aldous{Broder fournit un moyen d'´echantillonner un arbre couvrant uni- form´ement al´eatoirepour des graphes connexes finis en utilisant une marche al´eatoiresimple. A` savoir, commen¸consune marche al´eatoiresimple sur un graphe connexe et arr^etons-nousau moment de la couverture. L'arbre form´epar toutes les ar^etesde la premi`ereentr´eea la loi d'un arbre couvrant uniforme. Nous montrons ici que l'arbre form´epar toutes les ar^etesde derni`ere sortie a ´egalement la loi d'un arbre couvrant uniforme. Cela r´epond `aune question de Tom Hayes et Cris Moore de 2010. La preuve repose sur une bijection qui est li´eeau th´eor`emeBEST de la th´eoriedes graphes.