Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 12186

Search results for: elemental graph data model

12186 Elemental Graph Data Model: A Semantic and Topological Representation of Building Elements

Authors: Yasmeen A. S. Essawy, Khaled Nassar

Abstract:

With the rapid increase of complexity in the building industry, professionals in the A/E/C industry were forced to adopt Building Information Modeling (BIM) in order to enhance the communication between the different project stakeholders throughout the project life cycle and create a semantic object-oriented building model that can support geometric-topological analysis of building elements during design and construction. This paper presents a model that extracts topological relationships and geometrical properties of building elements from an existing fully designed BIM, and maps this information into a directed acyclic Elemental Graph Data Model (EGDM). The model incorporates BIM-based search algorithms for automatic deduction of geometrical data and topological relationships for each building element type. Using graph search algorithms, such as Depth First Search (DFS) and topological sortings, all possible construction sequences can be generated and compared against production and construction rules to generate an optimized construction sequence and its associated schedule. The model is implemented in a C# platform.

Keywords: Building information modeling, elemental graph data model, geometric and topological data models, and graph theory.

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12185 Concurrency in Web Access Patterns Mining

Authors: Jing Lu, Malcolm Keech, Weiru Chen

Abstract:

Web usage mining is an interesting application of data mining which provides insight into customer behaviour on the Internet. An important technique to discover user access and navigation trails is based on sequential patterns mining. One of the key challenges for web access patterns mining is tackling the problem of mining richly structured patterns. This paper proposes a novel model called Web Access Patterns Graph (WAP-Graph) to represent all of the access patterns from web mining graphically. WAP-Graph also motivates the search for new structural relation patterns, i.e. Concurrent Access Patterns (CAP), to identify and predict more complex web page requests. Corresponding CAP mining and modelling methods are proposed and shown to be effective in the search for and representation of concurrency between access patterns on the web. From experiments conducted on large-scale synthetic sequence data as well as real web access data, it is demonstrated that CAP mining provides a powerful method for structural knowledge discovery, which can be visualised through the CAP-Graph model.

Keywords: concurrent access patterns (CAP), CAP mining and modelling, CAP-Graph, web access patterns (WAP), WAP-Graph, Web usage mining.

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12184 Efficient Filtering of Graph Based Data Using Graph Partitioning

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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12183 Speedup Breadth-First Search by Graph Ordering

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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12182 Topological Queries on Graph-structured XML Data: Models and Implementations

Authors: Hongzhi Wang, Jianzhong Li, Jizhou Luo

Abstract:

In many applications, data is in graph structure, which can be naturally represented as graph-structured XML. Existing queries defined on tree-structured and graph-structured XML data mainly focus on subgraph matching, which can not cover all the requirements of querying on graph. In this paper, a new kind of queries, topological query on graph-structured XML is presented. This kind of queries consider not only the structure of subgraph but also the topological relationship between subgraphs. With existing subgraph query processing algorithms, efficient algorithms for topological query processing are designed. Experimental results show the efficiency of implementation algorithms.

Keywords: XML, Graph Structure, Topological query.

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12181 Using Spectral Vectors and M-Tree for Graph Clustering and Searching in Graph Databases of Protein Structures

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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12180 Formal Modeling and Verification of Software Models

Authors: Siamak Rasulzadeh

Abstract:

Graph transformation has recently become more and more popular as a general visual modeling language to formally state the dynamic semantics of the designed models. Especially, it is a very natural formalism for languages which basically are graph (e.g. UML). Using this technique, we present a highly understandable yet precise approach to formally model and analyze the behavioral semantics of UML 2.0 Activity diagrams. In our proposal, AGG is used to design Activities, then using our previous approach to model checking graph transformation systems, designers can verify and analyze designed Activity diagrams by checking the interesting properties as combination of graph rules and LTL (Linear Temporal Logic) formulas on the Activities.

Keywords: UML 2.0 Activity, Verification, Model Checking, Graph Transformation, Dynamic Semantics.

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12179 An Efficient Graph Query Algorithm Based on Important Vertices and Decision Features

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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12178 Phasor Analysis of a Synchronous Generator: A Bond Graph Approach

Authors: Israel Núñez-Hernández, Peter C. Breedveld, Paul B. T. Weustink, Gilberto Gonzalez-A

Abstract:

This paper presents the use of phasor bond graphs to obtain the steady-state behavior of a synchronous generator. The phasor bond graph elements are built using 2D multibonds, which represent the real and imaginary part of the phasor. The dynamic bond graph model of a salient-pole synchronous generator is showed, and verified viz. a sudden short-circuit test. The reduction of the dynamic model into a phasor representation is described. The previous test is executed on the phasor bond graph model, and its steady-state values are compared with the dynamic response. Besides, the widely used power (torque)-angle curves are obtained by means of the phasor bond graph model, to test the usefulness of this model.

Keywords: Bond graphs, complex power, phasors, synchronous generator, short-circuit, open-circuit, power-angle curve.

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12177 Bond Graph Modeling of Inter-Actuator Interactions in a Multi-Cylinder Hydraulic System

Authors: Mutuku Muvengei, John Kihiu

Abstract:

In this paper, a bond graph dynamic model for a valvecontrolled hydraulic cylinder has been developed. A simplified bond graph model of the inter-actuator interactions in a multi-cylinder hydraulic system has also been presented. The overall bond graph model of a valve-controlled hydraulic cylinder was developed by combining the bond graph sub-models of the pump, spool valve and the actuator using junction structures. Causality was then assigned in order to obtain a computational model which could be simulated. The causal bond graph model of the hydraulic cylinder was verified by comparing the open loop state responses to those of an ODE model which had been developed in literature based on the same assumptions. The results were found to correlate very well both in the shape of the curves, magnitude and the response times, thus indicating that the developed model represents the hydraulic dynamics of a valve-controlled cylinder. A simplified model for interactuator interaction was presented by connecting an effort source with constant pump pressure to the zero-junction from which the cylinders in a multi-cylinder system are supplied with a constant pressure from the pump. On simulating the state responses of the developed model under different situations of cylinder operations, indicated that such a simple model can be used to predict the inter-actuator interactions.

Keywords: Bond graphs, Inter-actuator interactions, Valvecontrolledhydraulic cylinder.

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12176 Analysis of Electrical Networks Using Phasors: A Bond Graph Approach

Authors: Israel Núñez-Hernández, Peter C. Breedveld, Paul B. T. Weustink, Gilberto Gonzalez-A

Abstract:

This paper proposes a phasor representation of electrical networks by using bond graph methodology. A so-called phasor bond graph is built up by means of two-dimensional bonds, which represent the complex plane. Impedances or admittances are used instead of the standard bond graph elements. A procedure to obtain the steady-state values from a phasor bond graph model is presented. Besides the presentation of a phasor bond graph library in SIDOPS code, also an application example is discussed.

Keywords: Bond graphs, phasor theory, steady-state, complex power, electrical networks.

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12175 Model Inversion of a Two Degrees of Freedom Linearized PUMA from Bicausal Bond Graphs

Authors: Gilberto Gonzalez-A, Ignacio Rodríguez- A., Dunia Nuñez-P

Abstract:

A bond graph model of a two degrees of freedom PUMA is described. System inversion gives the system input required to generate a given system output. In order to get the system inversion of the PUMA manipulator, a linearization of the nonlinear bond graph is obtained. Hence, the bicausality of the linearized bond graph of the PUMA manipulator is applied. Thus, the bicausal bond graph provides a systematic way of generating the equations of the system inversion. Simulation results to verify the calculated input for a given output are shown.

Keywords: Bond graph, system inversion, bicausality, PUMA manipulator

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12174 Analyzing the Factors that Cause Parallel Performance Degradation in Parallel Graph-Based Computations Using Graph500

Authors: Mustafa Elfituri, Jonathan Cook

Abstract:

Recently, graph-based computations have become more important in large-scale scientific computing as they can provide a methodology to model many types of relations between independent objects. They are being actively used in fields as varied as biology, social networks, cybersecurity, and computer networks. At the same time, graph problems have some properties such as irregularity and poor locality that make their performance different than regular applications performance. Therefore, parallelizing graph algorithms is a hard and challenging task. Initial evidence is that standard computer architectures do not perform very well on graph algorithms. Little is known exactly what causes this. The Graph500 benchmark is a representative application for parallel graph-based computations, which have highly irregular data access and are driven more by traversing connected data than by computation. In this paper, we present results from analyzing the performance of various example implementations of Graph500, including a shared memory (OpenMP) version, a distributed (MPI) version, and a hybrid version. We measured and analyzed all the factors that affect its performance in order to identify possible changes that would improve its performance. Results are discussed in relation to what factors contribute to performance degradation.

Keywords: Graph computation, Graph500 benchmark, parallel architectures, parallel programming, workload characterization.

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12173 Spanning Tree Transformation of Connected Graphs into Single-Row Networks

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

Abstract:

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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12172 Automatic Fingerprint Classification Using Graph Theory

Authors: Mana Tarjoman, Shaghayegh Zarei

Abstract:

Using efficient classification methods is necessary for automatic fingerprint recognition system. This paper introduces a new structural approach to fingerprint classification by using the directional image of fingerprints to increase the number of subclasses. In this method, the directional image of fingerprints is segmented into regions consisting of pixels with the same direction. Afterwards the relational graph to the segmented image is constructed and according to it, the super graph including prominent information of this graph is formed. Ultimately we apply a matching technique to compare obtained graph with the model graphs in order to classify fingerprints by using cost function. Increasing the number of subclasses with acceptable accuracy in classification and faster processing in fingerprints recognition, makes this system superior.

Keywords: Classification, Directional image, Fingerprint, Graph, Super graph.

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12171 Analysis of a Hydroelectric Plant connected to Electrical Power System in the Physical Domain

Authors: Gilberto Gonzalez-A, Octavio Barriga

Abstract:

A bond graph model of a hydroelectric plant is proposed. In order to analyze the system some structural properties of a bond graph are used. The structural controllability of the hydroelctric plant is described. Also, the steady state of the state variables applying the bond graph in a derivative causality assignment is obtained. Finally, simulation results of the system are shown.

Keywords: Bond graph, hydraulic plant, steady state.

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12170 On the Use of Correlated Binary Model in Social Network Analysis

Authors: Elsayed A. Habib Elamir

Abstract:

In social network analysis the mean nodal degree and density of the graph can be considered as a measure of the activity of all actors in the network and this is an important property of a graph and for making comparisons among networks. Since subjects in a family or organization are subject to common environment factors, it is prime interest to study the association between responses. Therefore, we study the distribution of the mean nodal degree and density of the graph under correlated binary units. The cross product ratio is used to capture the intra-units association among subjects. Computer program and an application are given to show the benefits of the method.

Keywords: Correlated Binary data, cross product ratio, densityof the graph, multiplicative binomial distribution.

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12169 A Neighborhood Condition for Fractional k-deleted Graphs

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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12168 The Extremal Graph with the Largest Merrifield-Simmons Index of (n, n + 2)-graphs

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

Abstract:

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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12167 N-Sun Decomposition of Complete, Complete Bipartite and Some Harary Graphs

Authors: R. Anitha, R. S. Lekshmi

Abstract:

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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12166 Intention Recognition using a Graph Representation

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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12165 Connected Vertex Cover in 2-Connected Planar Graph with Maximum Degree 4 is NP-complete

Authors: Priyadarsini P. L. K, Hemalatha T.

Abstract:

This paper proves that the problem of finding connected vertex cover in a 2-connected planar graph ( CVC-2 ) with maximum degree 4 is NP-complete. The motivation for proving this result is to give a shorter and simpler proof of NP-Completeness of TRA-MLC (the Top Right Access point Minimum-Length Corridor) problem [1], by finding the reduction from CVC-2. TRA-MLC has many applications in laying optical fibre cables for data communication and electrical wiring in floor plans.The problem of finding connected vertex cover in any planar graph ( CVC ) with maximum degree 4 is NP-complete [2]. We first show that CVC-2 belongs to NP and then we find a polynomial reduction from CVC to CVC-2. Let a graph G0 and an integer K form an instance of CVC, where G0 is a planar graph and K is an upper bound on the size of the connected vertex cover in G0. We construct a 2-connected planar graph, say G, by identifying the blocks and cut vertices of G0, and then finding the planar representation of all the blocks of G0, leading to a plane graph G1. We replace the cut vertices with cycles in such a way that the resultant graph G is a 2-connected planar graph with maximum degree 4. We consider L = K -2t+3 t i=1 di where t is the number of cut vertices in G1 and di is the number of blocks for which ith cut vertex is common. We prove that G will have a connected vertex cover with size less than or equal to L if and only if G0 has a connected vertex cover of size less than or equal to K.

Keywords: NP-complete, 2-Connected planar graph, block, cut vertex

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12164 The Diameter of an Interval Graph is Twice of its Radius

Authors: Tarasankar Pramanik, Sukumar Mondal, Madhumangal Pal

Abstract:

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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12163 Completion Number of a Graph

Authors: Sudhakar G

Abstract:

In this paper a new concept of partial complement of a graph G is introduced and using the same a new graph parameter, called completion number of a graph G, denoted by c(G) is defined. Some basic properties of graph parameter, completion number, are studied and upperbounds for completion number of classes of graphs are obtained , the paper includes the characterization also.

Keywords: Completion Number, Maximum Independent subset, Partial complements, Partial self complementary

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12162 On Fractional (k,m)-Deleted Graphs with Constrains Conditions

Authors: Sizhong Zhou, Hongxia Liu

Abstract:

Let G be a graph of order n, and let k  2 and m  0 be two integers. Let h : E(G)  [0, 1] be a function. If e∋x h(e) = k holds for each x  V (G), then we call G[Fh] a fractional k-factor of G with indicator function h where Fh = {e  E(G) : h(e) > 0}. A graph G is called a fractional (k,m)-deleted graph if there exists a fractional k-factor G[Fh] of G with indicator function h such that h(e) = 0 for any e  E(H), where H is any subgraph of G with m edges. In this paper, it is proved that G is a fractional (k,m)-deleted graph if (G)  k + m + m k+1 , n  4k2 + 2k − 6 + (4k 2 +6k−2)m−2 k−1 and max{dG(x), dG(y)}  n 2 for any vertices x and y of G with dG(x, y) = 2. Furthermore, it is shown that the result in this paper is best possible in some sense.

Keywords: Graph, degree condition, fractional k-factor, fractional (k, m)-deleted graph.

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12161 Face Recognition using a Kernelization of Graph Embedding

Authors: Pang Ying Han, Hiew Fu San, Ooi Shih Yin

Abstract:

Linearization of graph embedding has been emerged as an effective dimensionality reduction technique in pattern recognition. However, it may not be optimal for nonlinearly distributed real world data, such as face, due to its linear nature. So, a kernelization of graph embedding is proposed as a dimensionality reduction technique in face recognition. In order to further boost the recognition capability of the proposed technique, the Fisher-s criterion is opted in the objective function for better data discrimination. The proposed technique is able to characterize the underlying intra-class structure as well as the inter-class separability. Experimental results on FRGC database validate the effectiveness of the proposed technique as a feature descriptor.

Keywords: Face recognition, Fisher discriminant, graph embedding, kernelization.

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12160 Metric Dimension on Line Graph of Honeycomb Networks

Authors: M. Hussain, Aqsa Farooq

Abstract:

Let G = (V,E) be a connected graph and distance between any two vertices a and b in G is a−b geodesic and is denoted by d(a, b). A set of vertices W resolves a graph G if each vertex is uniquely determined by its vector of distances to the vertices in W. A metric dimension of G is the minimum cardinality of a resolving set of G. In this paper line graph of honeycomb network has been derived and then we calculated the metric dimension on line graph of honeycomb network.

Keywords: Resolving set, metric dimension, honeycomb network, line graph.

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12159 Comparison of Full Graph Methods of Switched Circuits Solution

Authors: Zdeňka Dostálová, David Matoušek, Bohumil Brtnik

Abstract:

As there are also graph methods of circuit analysis in addition to algebraic methods, it is, in theory, clearly possible to carry out an analysis of a whole switched circuit in two-phase switching exclusively by the graph method as well. This article deals with two methods of full-graph solving of switched circuits: by transformation graphs and by two-graphs. It deals with the circuit switched capacitors and the switched current, too. All methods are presented in an equally detailed steps to be able to compare.

Keywords: Switched capacitors of two phases, switched currents of two phases, transformation graph, two-graph, Mason's formula, voltage transfer, summary graph.

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12158 On Detour Spectra of Some Graphs

Authors: S.K.Ayyaswamy, S.Balachandran

Abstract:

The Detour matrix (DD) of a graph has for its ( i , j) entry the length of the longest path between vertices i and j. The DD-eigenvalues of a connected graph G are the eigenvalues for its detour matrix, and they form the DD-spectrum of G. The DD-energy EDD of the graph G is the sum of the absolute values of its DDeigenvalues. Two connected graphs are said to be DD- equienergetic if they have equal DD-energies. In this paper, the DD- spectra of a variety of graphs and their DD-energies are calculated.

Keywords: Detour eigenvalue (of a graph), detour spectrum(of a graph), detour energy(of a graph), detour - equienergetic graphs.

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12157 SIMGraph: Simplifying Contig Graph to Improve de Novo Genome Assembly Using Next-generation Sequencing Data

Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

Abstract:

De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

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