Search results for: graph algorithm

Authors: Frank Emmert Streib

Abstract:

The classification of the protein structure is commonly not performed for the whole protein but for structural domains, i.e., compact functional units preserved during evolution. Hence, a first step to a protein structure classification is the separation of the protein into its domains. We approach the problem of protein domain identification by proposing a novel graph theoretical algorithm. We represent the protein structure as an undirected, unweighted and unlabeled graph which nodes correspond the secondary structure elements of the protein. This graph is call the protein graph. The domains are then identified as partitions of the graph corresponding to vertices sets obtained by the maximization of an objective function, which mutually maximizes the cycle distributions found in the partitions of the graph. Our algorithm does not utilize any other kind of information besides the cycle-distribution to find the partitions. If a partition is found, the algorithm is iteratively applied to each of the resulting subgraphs. As stop criterion, we calculate numerically a significance level which indicates the stability of the predicted partition against a random rewiring of the protein graph. Hence, our algorithm terminates automatically its iterative application. We present results for one and two domain proteins and compare our results with the manually assigned domains by the SCOP database and differences are discussed.

Keywords: Graph partitioning, unweighted graph, protein domains.

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Authors: Qiuyi Lyu, Bin Gong

Abstract:

Breadth-First Search (BFS) is a core graph algorithm that is widely used for graph analysis. As it is frequently used in many graph applications, improving the BFS performance is essential. In this paper, we present a graph ordering method that could reorder the graph nodes to achieve better data locality, thus, improving the BFS performance. Our method is based on an observation that the sibling relationships will dominate the cache access pattern during the BFS traversal. Therefore, we propose a frequency-based model to construct the graph order. First, we optimize the graph order according to the nodes’ visit frequency. Nodes with high visit frequency will be processed in priority. Second, we try to maximize the child nodes’ overlap layer by layer. As it is proved to be NP-hard, we propose a heuristic method that could greatly reduce the preprocessing overheads.We conduct extensive experiments on 16 real-world datasets. The result shows that our method could achieve comparable performance with the state-of-the-art methods while the graph ordering overheads are only about 1/15.

Keywords: Breadth-first search, BFS, graph ordering, graph algorithm.

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Authors: Sudhakara G, Hemanth Kumar A.R

Abstract:

In this paper, we define distance partition of vertex set of a graph G with reference to a vertex in it and with the help of the same, a graph with metric dimension two (i.e. β (G) = 2 ) is characterized. In the process, we develop a polynomial time algorithm that verifies if the metric dimension of a given graph G is two. The same algorithm explores all metric bases of graph G whenever β (G) = 2 . We also find a bound for cardinality of any distance partite set with reference to a given vertex, when ever β (G) = 2 . Also, in a graph G with β (G) = 2 , a bound for cardinality of any distance partite set as well as a bound for number of vertices in any sub graph H of G is obtained in terms of diam H .

Keywords: Metric basis, Distance partition, Metric dimension.

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Authors: Do Phuc, Nguyen Thi Kim Phung

Abstract:

In this paper, we represent protein structure by using graph. A protein structure database will become a graph database. Each graph is represented by a spectral vector. We use Jacobi rotation algorithm to calculate the eigenvalues of the normalized Laplacian representation of adjacency matrix of graph. To measure the similarity between two graphs, we calculate the Euclidean distance between two graph spectral vectors. To cluster the graphs, we use M-tree with the Euclidean distance to cluster spectral vectors. Besides, M-tree can be used for graph searching in graph database. Our proposal method was tested with graph database of 100 graphs representing 100 protein structures downloaded from Protein Data Bank (PDB) and we compare the result with the SCOP hierarchical structure.

Keywords: Eigenvalues, m-tree, graph database, protein structure, spectra graph theory.

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Authors: Zhengnan Shi

Abstract:

In the self-stabilizing algorithmic paradigm, each node has a local view of the system, in a finite amount of time the system converges to a global state with desired property. In a graph G = (V, E), a subset S C V is a 2-packing if Vi c V: IN[i] n SI <1. In this paper, an ID-based, constant space, self-stabilizing algorithm that stabilizes to a maximal 2-packing in an arbitrary graph is proposed. It is shown that the algorithm stabilizes in 0(n3) moves under any scheduler (daemon). Specifically, it is shown that the algorithm stabilizes in linear time-steps under a synchronous daemon where every privileged node moves at each time-step.

Keywords: self-stabilization, 2-packing, distributed computing, fault tolerance, graph algorithms

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Authors: Imen Ammari, Mourad Elloumi, Ala Eddine Barouni

Abstract:

Visualizing “Courses – Pre – Required - Architecture" on the screen has proven to be useful and helpful for university actors and specially for students. In fact, these students can easily identify courses and their pre required, perceive the courses to follow in the future, and then can choose rapidly the appropriate course to register in. Given a set of courses and their prerequired, we present an algorithm for visualization a graph entitled “Courses-Pre-Required-Graph" that present courses and their prerequired in order to help students to recognize, lonely, what courses to take in the future and perceive the contain of all courses that they will study. Our algorithm using “Force Directed Placement" technique visualizes the “Courses-Pre-Required-Graph" in such way that courses are easily identifiable. The time complexity of our drawing algorithm is O (n2), where n is the number of courses in the “Courses-Pre-Required-Graph".

Keywords: Courses–Pre-Required-Architecture, Courses-Pre- Required-Graph, Courses-Pre-Required-Visualization, Force directed Placement, Resolution.

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Authors: Z.Farhadpour, Mohammad.R.Meybodi

Abstract:

A number of routing algorithms based on learning automata technique have been proposed for communication networks. How ever, there has been little work on the effects of variation of graph scarcity on the performance of these algorithms. In this paper, a comprehensive study is launched to investigate the performance of LASPA, the first learning automata based solution to the dynamic shortest path routing, across different graph structures with varying scarcities. The sensitivity of three main performance parameters of the algorithm, being average number of processed nodes, scanned edges and average time per update, to variation in graph scarcity is reported. Simulation results indicate that the LASPA algorithm can adapt well to the scarcity variation in graph structure and gives much better outputs than the existing dynamic and fixed algorithms in terms of performance criteria.

Keywords: Learning automata, routing, algorithm, sparse graph

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Authors: Stefan Wagenpfeil, Felix Engel, Paul McKevitt, Matthias Hemmje

Abstract:

Multimedia Indexing and Retrieval is generally de-signed and implemented by employing feature graphs. These graphs typically contain a significant number of nodes and edges to reflect the level of detail in feature detection. A higher level of detail increases the effectiveness of the results but also leads to more complex graph structures. However, graph-traversal-based algorithms for similarity are quite inefficient and computation intensive, espe-cially for large data structures. To deliver fast and effective retrieval, an efficient similarity algorithm, particularly for large graphs, is mandatory. Hence, in this paper, we define a graph-projection into a 2D space (Graph Code) as well as the corresponding algorithms for indexing and retrieval. We show that calculations in this space can be performed more efficiently than graph-traversals due to a simpler processing model and a high level of parallelisation. In consequence, we prove that the effectiveness of retrieval also increases substantially, as Graph Codes facilitate more levels of detail in feature fusion. Thus, Graph Codes provide a significant increase in efficiency and effectiveness (especially for Multimedia indexing and retrieval) and can be applied to images, videos, audio, and text information.

Keywords: indexing, retrieval, multimedia, graph code, graph algorithm

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Authors: D. P. Sharma, A. Chaturvedi, G.Purohit , R.Shivarudraswamy

Abstract:

In today scenario, to meet enhanced demand imposed by domestic, commercial and industrial consumers, various operational & control activities of Radial Distribution Network (RDN) requires a focused attention. Irrespective of sub-domains research aspects of RDN like network reconfiguration, reactive power compensation and economic load scheduling etc, network performance parameters are usually estimated by an iterative process and is commonly known as load (power) flow algorithm. In this paper, a simple mechanism is presented to implement the load flow analysis (LFA) algorithm. The reported algorithm utilizes graph theory principles and is tested on a 69- bus RDN.

Keywords: Radial Distribution network, Graph, Load-flow, Array.

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Authors: Xiantong Li, Jianzhong Li

Abstract:

Graph has become increasingly important in modeling complicated structures and schemaless data such as proteins, chemical compounds, and XML documents. Given a graph query, it is desirable to retrieve graphs quickly from a large database via graph-based indices. Different from the existing methods, our approach, called VFM (Vertex to Frequent Feature Mapping), makes use of vertices and decision features as the basic indexing feature. VFM constructs two mappings between vertices and frequent features to answer graph queries. The VFM approach not only provides an elegant solution to the graph indexing problem, but also demonstrates how database indexing and query processing can benefit from data mining, especially frequent pattern mining. The results show that the proposed method not only avoids the enumeration method of getting subgraphs of query graph, but also effectively reduces the subgraph isomorphism tests between the query graph and graphs in candidate answer set in verification stage.

Keywords: Decision Feature, Frequent Feature, Graph Dataset, Graph Query

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Authors: S. Balaji, V. Swaminathan, K. Kannan

Abstract:

The Minimum Weighted Vertex Cover (MWVC) problem is a classic graph optimization NP - complete problem. Given an undirected graph G = (V, E) and weighting function defined on the vertex set, the minimum weighted vertex cover problem is to find a vertex set S V whose total weight is minimum subject to every edge of G has at least one end point in S. In this paper an effective algorithm, called Support Ratio Algorithm (SRA), is designed to find the minimum weighted vertex cover of a graph. Computational experiments are designed and conducted to study the performance of our proposed algorithm. Extensive simulation results show that the SRA can yield better solutions than other existing algorithms found in the literature for solving the minimum vertex cover problem.

Keywords: Weighted vertex cover, vertex support, approximation algorithms, NP-complete problem.

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Authors: S. Balaji, V. Swaminathan, K. Kannan

Abstract:

The Maximum Weighted Independent Set (MWIS) problem is a classic graph optimization NP-hard problem. Given an undirected graph G = (V, E) and weighting function defined on the vertex set, the MWIS problem is to find a vertex set S V whose total weight is maximum subject to no two vertices in S are adjacent. This paper presents a novel approach to approximate the MWIS of a graph using minimum weighted vertex cover of the graph. Computational experiments are designed and conducted to study the performance of our proposed algorithm. Extensive simulation results show that the proposed algorithm can yield better solutions than other existing algorithms found in the literature for solving the MWIS.

Keywords: weighted independent set, vertex cover, vertex support, heuristic, NP - hard problem.

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Authors: Marek Skomorowski

Abstract:

In syntactic pattern recognition a pattern can be represented by a graph. Given an unknown pattern represented by a graph g, the problem of recognition is to determine if the graph g belongs to a language L(G) generated by a graph grammar G. The so-called IE graphs have been defined in [1] for a description of patterns. The IE graphs are generated by so-called ETPL(k) graph grammars defined in [1]. An efficient, parsing algorithm for ETPL(k) graph grammars for syntactic recognition of patterns represented by IE graphs has been presented in [1]. In practice, structural descriptions may contain pattern distortions, so that the assignment of a graph g, representing an unknown pattern, to a graph language L(G) generated by an ETPL(k) graph grammar G is rejected by the ETPL(k) type parsing. Therefore, there is a need for constructing effective parsing algorithms for recognition of distorted patterns. The purpose of this paper is to present a new approach to syntactic recognition of distorted patterns. To take into account all variations of a distorted pattern under study, a probabilistic description of the pattern is needed. A random IE graph approach is proposed here for such a description ([2]).

Keywords: Syntactic pattern recognition, Distorted patterns, Random graphs, Graph grammars.

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Authors: M. Farshbaf, M. R. Feizi-Derakhshi

Abstract:

Graph partitioning is a NP-hard problem with multiple conflicting objectives. The graph partitioning should minimize the inter-partition relationship while maximizing the intra-partition relationship. Furthermore, the partition load should be evenly distributed over the respective partitions. Therefore this is a multiobjective optimization problem (MOO). One of the approaches to MOO is Pareto optimization which has been used in this paper. The proposed methods of this paper used to improve the performance are injecting best solutions of previous runs into the first generation of next runs and also storing the non-dominated set of previous generations to combine with later generation's non-dominated set. These improvements prevent the GA from getting stuck in the local optima and increase the probability of finding more optimal solutions. Finally, a simulation research is carried out to investigate the effectiveness of the proposed algorithm. The simulation results confirm the effectiveness of the proposed method.

Keywords: Graph partitioning, Genetic algorithm, Multiobjective optimization, Pareto front.

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Authors: Aicha Majda, Abdelhamid El Hassani

Abstract:

Lung CT image segmentation is a prerequisite in lung CT image analysis. Most of the conventional methods need a post-processing to deal with the abnormal lung CT scans such as lung nodules or other lesions. The simplest similarity measure in the standard Graph Cuts Algorithm consists of directly comparing the pixel values of the two neighboring regions, which is not accurate because this kind of metrics is extremely sensitive to minor transformations such as noise or other artifacts problems. In this work, we propose an improved version of the standard graph cuts algorithm based on the Patch-Based similarity metric. The boundary penalty term in the graph cut algorithm is defined Based on Patch-Based similarity measurement instead of the simple intensity measurement in the standard method. The weights between each pixel and its neighboring pixels are Based on the obtained new term. The graph is then created using theses weights between its nodes. Finally, the segmentation is completed with the minimum cut/Max-Flow algorithm. Experimental results show that the proposed method is very accurate and efficient, and can directly provide explicit lung regions without any post-processing operations compared to the standard method.

Keywords: Graph cuts, lung CT scan, lung parenchyma segmentation, patch based similarity metric.

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Authors: Udaya Kumar Reddy K. R, K. Viswanathan Iyer

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Given a simple connected unweighted undirected graph G = (V (G), E(G)) with |V (G)| = n and |E(G)| = m, we present a new algorithm for the all-pairs shortest-path (APSP) problem. The running time of our algorithm is in O(n2 log n). This bound is an improvement over previous best known O(n2.376) time bound of Raimund Seidel (1995) for general graphs. The algorithm presented does not rely on fast matrix multiplication. Our algorithm with slight modifications, enables us to compute the APSP problem for unweighted directed graph in time O(n2 log n), improving a previous best known O(n2.575) time bound of Uri Zwick (2002).

Keywords: Distance in graphs, Dynamic programming, Graphalgorithms, Shortest paths.

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Authors: Nileshkumar Vaishnav, Aditya Tatu

Abstract:

An algebraic framework for processing graph signals axiomatically designates the graph adjacency matrix as the shift operator. In this setup, we often encounter a problem wherein we know the filtered output and the filter coefficients, and need to find out the input graph signal. Solution to this problem using direct approach requires O(N3) operations, where N is the number of vertices in graph. In this paper, we adapt the spectral graph partitioning method for partitioning of graphs and use it to reduce the computational cost of the filtering problem. We use the example of denoising of the temperature data to illustrate the efficacy of the approach.

Keywords: Graph signal processing, graph partitioning, inverse filtering on graphs, algebraic signal processing.

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Authors: So-Jeong Youn, Kyung-Whan Oh

Abstract:

The human friendly interaction is the key function of a human-centered system. Over the years, it has received much attention to develop the convenient interaction through intention recognition. Intention recognition processes multimodal inputs including speech, face images, and body gestures. In this paper, we suggest a novel approach of intention recognition using a graph representation called Intention Graph. A concept of valid intention is proposed, as a target of intention recognition. Our approach has two phases: goal recognition phase and intention recognition phase. In the goal recognition phase, we generate an action graph based on the observed actions, and then the candidate goals and their plans are recognized. In the intention recognition phase, the intention is recognized with relevant goals and user profile. We show that the algorithm has polynomial time complexity. The intention graph is applied to a simple briefcase domain to test our model.

Keywords: Intention recognition, intention, graph, HCI.

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Authors: Jehad Al Dallal

Abstract:

Program slicing is the task of finding all statements in a program that directly or indirectly influence the value of a variable occurrence. The set of statements that can affect the value of a variable at some point in a program is called a program backward slice. In several software engineering applications, such as program debugging and measuring program cohesion and parallelism, several slices are computed at different program points. The existing algorithms for computing program slices are introduced to compute a slice at a program point. In these algorithms, the program, or the model that represents the program, is traversed completely or partially once. To compute more than one slice, the same algorithm is applied for every point of interest in the program. Thus, the same program, or program representation, is traversed several times. In this paper, an algorithm is introduced to compute all forward static slices of a computer program by traversing the program representation graph once. Therefore, the introduced algorithm is useful for software engineering applications that require computing program slices at different points of a program. The program representation graph used in this paper is called Program Dependence Graph (PDG).

Keywords: Program slicing, static slicing, forward slicing, program dependence graph (PDG).

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Authors: Y. Wang

Abstract:

Traveling salesman problem (TSP) is hard to resolve when the number of cities and routes become large. The frequency graph is constructed to tackle the problem. A frequency graph maintains the topological relationships of the original weighted graph. The numbers on the edges are the frequencies of the edges emulated from the local optimal Hamiltonian paths. The simplest kind of local optimal Hamiltonian paths are computed based on the four vertices and three lines inequality. The search algorithm is given to find the optimal Hamiltonian circuit based on the frequency graph. The experiments show that the method can find the optimal Hamiltonian circuit within several trials.

Keywords: Traveling salesman problem, frequency graph, local optimal Hamiltonian path, four vertices and three lines inequality.

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Authors: Zohreh O. Akbari

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In this paper a deterministic polynomial-time algorithm is presented for the Clique problem. The case is considered as the problem of omitting the minimum number of vertices from the input graph so that none of the zeroes on the graph-s adjacency matrix (except the main diagonal entries) would remain on the adjacency matrix of the resulting subgraph. The existence of a deterministic polynomial-time algorithm for the Clique problem, as an NP-complete problem will prove the equality of P and NP complexity classes.

Keywords: Clique problem, Deterministic Polynomial-time Algorithm, Equality of P and NP Complexity Classes.

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Authors: Sizhong Zhou, Hongxia Liu

Abstract:

Abstract–Let k ≥ 3 be an integer, and let G be a graph of order n with n ≥ 9k +3- 42(k - 1)2 + 2. Then a spanning subgraph F of G is called a k-factor if dF (x) = k for each x ∈ V (G). A fractional k-factor is a way of assigning weights to the edges of a graph G (with all weights between 0 and 1) such that for each vertex the sum of the weights of the edges incident with that vertex is k. A graph G is a fractional k-deleted graph if there exists a fractional k-factor after deleting any edge of G. In this paper, it is proved that G is a fractional k-deleted graph if G satisfies δ(G) ≥ k + 1 and |NG(x) ∪ NG(y)| ≥ 1 2 (n + k - 2) for each pair of nonadjacent vertices x, y of G.

Keywords: Graph, minimum degree, neighborhood union, fractional k-factor, fractional k-deleted graph.

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Authors: Zhihan Li

Abstract:

Nowadays, most universities use the course enrollment system considering students’ registration orders. However, the students’ preference level to certain courses is also one important factor to consider. In this research, the possibility of applying a preference-first system has been discussed and analyzed compared to the order-first system. A bipartite graph is applied to resemble the relationship between students and courses they tend to register. With the graph set up, we apply Ford-Fulkerson (F.F.) Algorithm to maximize parings between two sets of nodes, in our case, students and courses. Two models are proposed in this paper: the one considered students’ order first, and the one considered students’ preference first. By comparing and contrasting the two models, we highlight the usability of models which potentially leads to better designs for school course registration systems.

Keywords: Bipartite graph, Ford-Fulkerson Algorithm, graph theory, maximum matching.

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Authors: M. S. Haghighat, A. Dolati, M. Tabari, E. Mohseni

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The Merrifield-Simmons index of a graph G is defined as the total number of its independent sets. A (n, n + 2)-graph is a connected simple graph with n vertices and n + 2 edges. In this paper we characterize the (n, n+2)-graph with the largest Merrifield- Simmons index. We show that its Merrifield-Simmons index i.e. the upper bound of the Merrifield-Simmons index of the (n, n+2)-graphs is 9 × 2n-5 +1 for n ≥ 5.

Keywords: Merrifield-Simmons index, (n, n+2)-graph.

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Authors: Jean-Christophe Sibel, Sylvain Reynal, David Declercq

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In the context of channel coding, the Generalized Belief Propagation (GBP) is an iterative algorithm used to recover the transmission bits sent through a noisy channel. To ensure a reliable transmission, we apply a map on the bits, that is called a code. This code induces artificial correlations between the bits to send, and it can be modeled by a graph whose nodes are the bits and the edges are the correlations. This graph, called Tanner graph, is used for most of the decoding algorithms like Belief Propagation or Gallager-B. The GBP is based on a non unic transformation of the Tanner graph into a so called region-graph. A clear advantage of the GBP over the other algorithms is the freedom in the construction of this graph. In this article, we explain a particular construction for specific graph topologies that involves relevant performance of the GBP. Moreover, we investigate the behavior of the GBP considered as a dynamic system in order to understand the way it evolves in terms of the time and in terms of the noise power of the channel. To this end we make use of classical measures and we introduce a new measure called the hyperspheres method that enables to know the size of the attractors.

Keywords: iterative decoder, LDPC, region-graph, chaos.

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Authors: S.L. Loh, S. Salleh, N.H. Sarmin

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A spanning tree of a connected graph is a tree which consists the set of vertices and some or perhaps all of the edges from the connected graph. In this paper, a model for spanning tree transformation of connected graphs into single-row networks, namely Spanning Tree of Connected Graph Modeling (STCGM) will be introduced. Path-Growing Tree-Forming algorithm applied with Vertex-Prioritized is contained in the model to produce the spanning tree from the connected graph. Paths are produced by Path-Growing and they are combined into a spanning tree by Tree-Forming. The spanning tree that is produced from the connected graph is then transformed into single-row network using Tree Sequence Modeling (TSM). Finally, the single-row routing problem is solved using a method called Enhanced Simulated Annealing for Single-Row Routing (ESSR).

Keywords: Graph theory, simulated annealing, single-rowrouting and spanning tree.

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Authors: R. Anitha, R. S. Lekshmi

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Graph decompositions are vital in the study of combinatorial design theory. A decomposition of a graph G is a partition of its edge set. An n-sun graph is a cycle Cn with an edge terminating in a vertex of degree one attached to each vertex. In this paper, we define n-sun decomposition of some even order graphs with a perfect matching. We have proved that the complete graph K2n, complete bipartite graph K2n, 2n and the Harary graph H4, 2n have n-sun decompositions. A labeling scheme is used to construct the n-suns.

Keywords: Decomposition, Hamilton cycle, n-sun graph, perfect matching, spanning tree.

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Authors: S. Balaji, V. Swaminathan, K. Kannan

Abstract:

The Minimum Vertex Cover (MVC) problem is a classic graph optimization NP - complete problem. In this paper a competent algorithm, called Vertex Support Algorithm (VSA), is designed to find the smallest vertex cover of a graph. The VSA is tested on a large number of random graphs and DIMACS benchmark graphs. Comparative study of this algorithm with the other existing methods has been carried out. Extensive simulation results show that the VSA can yield better solutions than other existing algorithms found in the literature for solving the minimum vertex cover problem.

Keywords: vertex cover, vertex support, approximation algorithms, NP - complete problem.

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Authors: Weng Ming Chu

Abstract:

When faced with stochastic networks with an uncertain duration for their activities, the securing of network completion time becomes problematical, not only because of the non-identical pdf of duration for each node, but also because of the interdependence of network paths. As evidenced by Adlakha & Kulkarni [1], many methods and algorithms have been put forward in attempt to resolve this issue, but most have encountered this same large-size network problem. Therefore, in this research, we focus on network reduction through a Series/Parallel combined mechanism. Our suggested algorithm, named the Activity Network Reduction Algorithm (ANRA), can efficiently transfer a large-size network into an S/P Irreducible Network (SPIN). SPIN can enhance stochastic network analysis, as well as serve as the judgment of symmetry for the Graph Theory.

Keywords: Series/Parallel network, Stochastic network, Network reduction, Interdictive Graph, Complexity Index.

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Authors: Tarasankar Pramanik, Sukumar Mondal, Madhumangal Pal

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In an interval graph G = (V,E) the distance between two vertices u, v is de£ned as the smallest number of edges in a path joining u and v. The eccentricity of a vertex v is the maximum among distances from all other vertices of V . The diameter (δ) and radius (ρ) of the graph G is respectively the maximum and minimum among all the eccentricities of G. The center of the graph G is the set C(G) of vertices with eccentricity ρ. In this context our aim is to establish the relation ρ = δ 2  for an interval graph and to determine the center of it.

Keywords: Interval graph, interval tree, radius, center.

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