Special Issue "Graph Algorithms"

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A special issue of Algorithms (ISSN 1999-4893).

Deadline for manuscript submissions: closed (31 October 2012)

Special Issue Editor

Guest Editor
Dr. Jesper Jansson

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics), Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji Campus, Gokasho, Uji, Kyoto 611-0011, Japan
Website | E-Mail
Interests: graph algorithms; phylogenetics; approximation algorithms; combinatorial optimization

Special Issue Information

Dear Colleagues,

This special issue of Algorithms is devoted to the design and analysis of algorithms for solving combinatorial problems of a theoretical or practical nature involving graphs, with a focus on computational complexity. Because of their simplicity and generality, graphs have been used for a long time in many different areas of science and engineering, e.g., to describe how objects such as the atoms of a molecule are connected or to express various types of constraints such as precedence constraints in a complex manufacturing process. More recently, graphs have found new applications in emerging research fields like social network analysis, the design of robust computer network topologies, frequency allocation in wireless networks, and bioinformatics (i.e., to represent metabolic pathways, protein-protein interactions, evolutionary relationships, or other kinds of structured biological information). The amount of data in such applications can be enormous, and therefore, the resulting graphs may be huge, which motivates further development of fast and space-efficient algorithms in the near future for solving various (old and new) graph problems exactly or approximately. We hereby invite papers presenting original research on graph algorithms to this special issue and hope to receive many high-quality submissions.

Dr. Jesper Jansson
Guest Editor

Keywords

  • computational complexity
  • approximation algorithms
  • fixed-parameter tractability
  • compact data structures for graphs
  • pattern matching in graphs
  • graph coloring
  • graph partitioning
  • graph drawing
  • network flow
  • fast algorithms for special graph classes

Published Papers (10 papers)

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Editorial

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Open AccessEditorial Special Issue on Graph Algorithms
Algorithms 2013, 6(3), 457-458; doi:10.3390/a6030457
Received: 9 August 2013 / Revised: 9 August 2013 / Accepted: 9 August 2013 / Published: 12 August 2013
PDF Full-text (38 KB) | HTML Full-text | XML Full-text
Abstract This special issue of Algorithms is devoted to the design and analysis of algorithms for solving combinatorial problems of a theoretical or practical nature involving graphs, with a focus on computational complexity. Full article
(This article belongs to the Special Issue Graph Algorithms)

Research

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Open AccessArticle New Heuristics for Rooted Triplet Consistency
Algorithms 2013, 6(3), 396-406; doi:10.3390/a6030396
Received: 14 April 2013 / Revised: 26 June 2013 / Accepted: 26 June 2013 / Published: 11 July 2013
Cited by 2 | PDF Full-text (222 KB)
Abstract
Rooted triplets are becoming one of the most important types of input for reconstructing rooted phylogenies. A rooted triplet is a phylogenetic tree on three leaves and shows the evolutionary relationship of the corresponding three species. In this paper, we investigate the problem
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Rooted triplets are becoming one of the most important types of input for reconstructing rooted phylogenies. A rooted triplet is a phylogenetic tree on three leaves and shows the evolutionary relationship of the corresponding three species. In this paper, we investigate the problem of inferring the maximum consensus evolutionary tree from a set of rooted triplets. This problem is known to be APX-hard. We present two new heuristic algorithms. For a given set of m triplets on n species, the FastTree algorithm runs in O(m + α(n)n2) time, where α(n) is the functional inverse of Ackermann’s function. This is faster than any other previously known algorithms, although the outcome is less satisfactory. The Best Pair Merge with Total Reconstruction (BPMTR) algorithm runs in O(mn3) time and, on average, performs better than any other previously known algorithms for this problem. Full article
(This article belongs to the Special Issue Graph Algorithms)
Open AccessArticle Computing the Eccentricity Distribution of Large Graphs
Algorithms 2013, 6(1), 100-118; doi:10.3390/a6010100
Received: 1 November 2012 / Revised: 24 January 2013 / Accepted: 31 January 2013 / Published: 18 February 2013
Cited by 9 | PDF Full-text (450 KB) | HTML Full-text | XML Full-text
Abstract
The eccentricity of a node in a graph is defined as the length of a longest shortest path starting at that node. The eccentricity distribution over all nodes is a relevant descriptive property of the graph, and its extreme values allow the derivation
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The eccentricity of a node in a graph is defined as the length of a longest shortest path starting at that node. The eccentricity distribution over all nodes is a relevant descriptive property of the graph, and its extreme values allow the derivation of measures such as the radius, diameter, center and periphery of the graph. This paper describes two new methods for computing the eccentricity distribution of large graphs such as social networks, web graphs, biological networks and routing networks.We first propose an exact algorithm based on eccentricity lower and upper bounds, which achieves significant speedups compared to the straightforward algorithm when computing both the extreme values of the distribution as well as the eccentricity distribution as a whole. The second algorithm that we describe is a hybrid strategy that combines the exact approach with an efficient sampling technique in order to obtain an even larger speedup on the computation of the entire eccentricity distribution. We perform an extensive set of experiments on a number of large graphs in order to measure and compare the performance of our algorithms, and demonstrate how we can efficiently compute the eccentricity distribution of various large real-world graphs. Full article
(This article belongs to the Special Issue Graph Algorithms)
Open AccessArticle A Polynomial-Time Algorithm for Computing the Maximum Common Connected Edge Subgraph of Outerplanar Graphs of Bounded Degree
Algorithms 2013, 6(1), 119-135; doi:10.3390/a6010119
Received: 30 October 2012 / Revised: 27 January 2013 / Accepted: 7 February 2013 / Published: 18 February 2013
Cited by 1 | PDF Full-text (200 KB) | HTML Full-text | XML Full-text
Abstract
The maximum common connected edge subgraph problem is to find a connected graph with the maximum number of edges that is isomorphic to a subgraph of each of the two input graphs, where it has applications in pattern recognition and chemistry. This paper
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The maximum common connected edge subgraph problem is to find a connected graph with the maximum number of edges that is isomorphic to a subgraph of each of the two input graphs, where it has applications in pattern recognition and chemistry. This paper presents a dynamic programming algorithm for the problem when the two input graphs are outerplanar graphs of a bounded vertex degree, where it is known that the problem is NP-hard, even for outerplanar graphs of an unbounded degree. Although the algorithm repeatedly modifies input graphs, it is shown that the number of relevant subproblems is polynomially bounded, and thus, the algorithm works in polynomial time. Full article
(This article belongs to the Special Issue Graph Algorithms)
Open AccessArticle Dubins Traveling Salesman Problem with Neighborhoods: A Graph-Based Approach
Algorithms 2013, 6(1), 84-99; doi:10.3390/a6010084
Received: 31 October 2012 / Revised: 17 January 2013 / Accepted: 18 January 2013 / Published: 4 February 2013
Cited by 6 | PDF Full-text (3056 KB) | HTML Full-text | XML Full-text
Abstract
We study the problem of finding the minimum-length curvature constrained closed path through a set of regions in the plane. This problem is referred to as the Dubins Traveling Salesperson Problem with Neighborhoods (DTSPN). An algorithm is presented that uses sampling to cast
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We study the problem of finding the minimum-length curvature constrained closed path through a set of regions in the plane. This problem is referred to as the Dubins Traveling Salesperson Problem with Neighborhoods (DTSPN). An algorithm is presented that uses sampling to cast this infinite dimensional combinatorial optimization problem as a Generalized Traveling Salesperson Problem (GTSP) with intersecting node sets. The GTSP is then converted to an Asymmetric Traveling Salesperson Problem (ATSP) through a series of graph transformations, thus allowing the use of existing approximation algorithms. This algorithm is shown to perform no worse than the best existing DTSPN algorithm and is shown to perform significantly better when the regions overlap. We report on the application of this algorithm to route an Unmanned Aerial Vehicle (UAV) equipped with a radio to collect data from sparsely deployed ground sensors in a field demonstration of autonomous detection, localization, and verification of multiple acoustic events. Full article
(This article belongs to the Special Issue Graph Algorithms)
Open AccessArticle Tractabilities and Intractabilities on Geometric Intersection Graphs
Algorithms 2013, 6(1), 60-83; doi:10.3390/a6010060
Received: 23 October 2012 / Revised: 10 January 2013 / Accepted: 14 January 2013 / Published: 25 January 2013
Cited by 5 | PDF Full-text (193 KB) | HTML Full-text | XML Full-text
Abstract
A graph is said to be an intersection graph if there is a set of objects such that each vertex corresponds to an object and two vertices are adjacent if and only if the corresponding objects have a nonempty intersection. There are several
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A graph is said to be an intersection graph if there is a set of objects such that each vertex corresponds to an object and two vertices are adjacent if and only if the corresponding objects have a nonempty intersection. There are several natural graph classes that have geometric intersection representations. The geometric representations sometimes help to prove tractability/intractability of problems on graph classes. In this paper, we show some results proved by using geometric representations. Full article
(This article belongs to the Special Issue Graph Algorithms)
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Open AccessArticle Computational Study on a PTAS for Planar Dominating Set Problem
Algorithms 2013, 6(1), 43-59; doi:10.3390/a6010043
Received: 2 November 2012 / Revised: 10 January 2013 / Accepted: 13 January 2013 / Published: 21 January 2013
Cited by 1 | PDF Full-text (150 KB) | HTML Full-text | XML Full-text
Abstract
The dominating set problem is a core NP-hard problem in combinatorial optimization and graph theory, and has many important applications. Baker [JACM 41,1994] introduces a k-outer planar graph decomposition-based framework for designing polynomial time approximation scheme (PTAS) for a class of NP-hard problems
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The dominating set problem is a core NP-hard problem in combinatorial optimization and graph theory, and has many important applications. Baker [JACM 41,1994] introduces a k-outer planar graph decomposition-based framework for designing polynomial time approximation scheme (PTAS) for a class of NP-hard problems in planar graphs. It is mentioned that the framework can be applied to obtain an O(2ckn) time, c is a constant, (1+1/k)-approximation algorithm for the planar dominating set problem. We show that the approximation ratio achieved by the mentioned application of the framework is not bounded by any constant for the planar dominating set problem. We modify the application of the framework to give a PTAS for the planar dominating set problem. With k-outer planar graph decompositions, the modified PTAS has an approximation ratio (1 + 2/k). Using 2k-outer planar graph decompositions, the modified PTAS achieves the approximation ratio (1+1/k) in O(22ckn) time. We report a computational study on the modified PTAS. Our results show that the modified PTAS is practical. Full article
(This article belongs to the Special Issue Graph Algorithms)
Open AccessArticle Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and Tractability
Algorithms 2013, 6(1), 1-11; doi:10.3390/a6010001
Received: 31 October 2012 / Revised: 13 December 2012 / Accepted: 18 December 2012 / Published: 27 December 2012
Cited by 3 | PDF Full-text (189 KB) | HTML Full-text | XML Full-text
Abstract
The problem of finding the maximum number of vertex-disjoint uni-color paths in an edge-colored graph has been recently introduced in literature, motivated by applications in social network analysis. In this paper we investigate the approximation and parameterized complexity of the problem. First, we
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The problem of finding the maximum number of vertex-disjoint uni-color paths in an edge-colored graph has been recently introduced in literature, motivated by applications in social network analysis. In this paper we investigate the approximation and parameterized complexity of the problem. First, we show that, for any constant ε > 0, the problem is not approximable within factor c1-ε, where c is the number of colors, and that the corresponding decision problem is W[1]-hard when parametrized by the number of disjoint paths. Then, we present a fixed-parameter algorithm for the problem parameterized by the number and the length of the disjoint paths. Full article
(This article belongs to the Special Issue Graph Algorithms)
Open AccessArticle Extracting Co-Occurrence Relations from ZDDs
Algorithms 2012, 5(4), 654-667; doi:10.3390/a5040654
Received: 27 September 2012 / Revised: 4 December 2012 / Accepted: 6 December 2012 / Published: 13 December 2012
Cited by 2 | PDF Full-text (154 KB) | HTML Full-text | XML Full-text
Abstract
A zero-suppressed binary decision diagram (ZDD) is a graph representation suitable for handling sparse set families. Given a ZDD representing a set family, we present an efficient algorithm to discover a hidden structure, called a co-occurrence relation, on the ground set. This computation
[...] Read more.
A zero-suppressed binary decision diagram (ZDD) is a graph representation suitable for handling sparse set families. Given a ZDD representing a set family, we present an efficient algorithm to discover a hidden structure, called a co-occurrence relation, on the ground set. This computation can be done in time complexity that is related not to the number of sets, but to some feature values of the ZDD. We furthermore introduce a conditional co-occurrence relation and present an extraction algorithm, which enables us to discover further structural information. Full article
(This article belongs to the Special Issue Graph Algorithms)
Open AccessArticle Exact Algorithms for Maximum Clique: A Computational Study 
Algorithms 2012, 5(4), 545-587; doi:10.3390/a5040545
Received: 11 September 2012 / Revised: 29 October 2012 / Accepted: 29 October 2012 / Published: 19 November 2012
Cited by 24 | PDF Full-text (1432 KB) | HTML Full-text | XML Full-text
Abstract
We investigate a number of recently reported exact algorithms for the maximum clique problem. The program code is presented and analyzed to show how small changes in implementation can have a drastic effect on performance. The computational study demonstrates how problem features and
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We investigate a number of recently reported exact algorithms for the maximum clique problem. The program code is presented and analyzed to show how small changes in implementation can have a drastic effect on performance. The computational study demonstrates how problem features and hardware platforms influence algorithm behaviour. The effect of vertex ordering is investigated. One of the algorithms (MCS) is broken into its constituent parts and we discover that one of these parts frequently degrades performance. It is shown that the standard procedure used for rescaling published results (i.e., adjusting run times based on the calibration of a standard program over a set of benchmarks) is unsafe and can lead to incorrect conclusions being drawn from empirical data. Full article
(This article belongs to the Special Issue Graph Algorithms)

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