Search results for: Graph computation

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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Authors: Farooq Ahmad, Hejiao Huang, Xiaolong Wang

Abstract:

Reachability graph (RG) generation suffers from the problem of exponential space and time complexity. To alleviate the more critical problem of time complexity, this paper presents the new approach for RG generation for the Petri net (PN) models of parallel processes. Independent RGs for each parallel process in the PN structure are generated in parallel and cross-product of these RGs turns into the exhaustive state space from which the RG of given parallel system is determined. The complexity analysis of the presented algorithm illuminates significant decrease in the time complexity cost of RG generation. The proposed technique is applicable to parallel programs having multiple threads with the synchronization problem.

Keywords: Parallel processes, Petri net, reachability graph, time complexity.

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Authors: Matthias Dehmer, Frank Emmert Streib, Alexander Mehler, Jürgen Kilian, Max Mühlhauser

Abstract:

Due to the tremendous amount of information provided by the World Wide Web (WWW) developing methods for mining the structure of web-based documents is of considerable interest. In this paper we present a similarity measure for graphs representing web-based hypertext structures. Our similarity measure is mainly based on a novel representation of a graph as linear integer strings, whose components represent structural properties of the graph. The similarity of two graphs is then defined as the optimal alignment of the underlying property strings. In this paper we apply the well known technique of sequence alignments for solving a novel and challenging problem: Measuring the structural similarity of generalized trees. In other words: We first transform our graphs considered as high dimensional objects in linear structures. Then we derive similarity values from the alignments of the property strings in order to measure the structural similarity of generalized trees. Hence, we transform a graph similarity problem to a string similarity problem for developing a efficient graph similarity measure. We demonstrate that our similarity measure captures important structural information by applying it to two different test sets consisting of graphs representing web-based document structures.

Keywords: Graph similarity, hierarchical and directed graphs, hypertext, generalized trees, web structure mining.

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Authors: Raida El Mansouri, Elhillali Kerkouche, Allaoua Chaoui

Abstract:

The Petri net tool INA is a well known tool by the Petri net community. However, it lacks a graphical environment to cerate and analyse INA models. Building a modelling tool for the design and analysis from scratch (for INA tool for example) is generally a prohibitive task. Meta-Modelling approach is useful to deal with such problems since it allows the modelling of the formalisms themselves. In this paper, we propose an approach based on the combined use of Meta-modelling and Graph Grammars to automatically generate a visual modelling tool for INA for analysis purposes. In our approach, the UML Class diagram formalism is used to define a meta-model of INA models. The meta-modelling tool ATOM3 is used to generate a visual modelling tool according to the proposed INA meta-model. We have also proposed a graph grammar to automatically generate INA description of the graphically specified Petri net models. This allows the user to avoid the errors when this description is done manually. Then the INA tool is used to perform the simulation and the analysis of the resulted INA description. Our environment is illustrated through an example.

Keywords: INA, Meta-modelling, Graph Grammars, AToM3, Automatic Code Generation.

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Authors: Lin Cheng, Zijiang Yang

Abstract:

Program synthesis is the task to automatically generate programs based on user specification. In this paper, we present a framework that synthesizes programs from flow charts that serve as accurate and intuitive specification. In order doing so, we propose a deep neural network called GRCNN that recognizes graph structure from its image. GRCNN is trained end-to-end, which can predict edge and node information of the flow chart simultaneously. Experiments show that the accuracy rate to synthesize a program is 66.4%, and the accuracy rates to recognize edge and node are 94.1% and 67.9%, respectively. On average, it takes about 60 milliseconds to synthesize a program.

Keywords: program synthesis, flow chart, specification, graph recognition, CNN.

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Authors: S.K.Ayyaswamy, S.Balachandran, K.Kannan

Abstract:

Let G be a graph of order n. The second stage adjacency matrix of G is the symmetric n × n matrix for which the ijth entry is 1 if the vertices vi and vj are of distance two; otherwise 0. The sum of the absolute values of this second stage adjacency matrix is called the second stage energy of G. In this paper we investigate a few properties and determine some upper bounds for the largest eigenvalue.

Keywords: Second stage spectral radius, Irreducible matrix, Derived graph

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Authors: Mahdi Taheri, Mehrana Niroumand

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In this paper a new definition of adjacency matrix in the simple graphs is presented that is called fuzzy adjacency matrix, so that elements of it are in the form of 0 and n N n 1 , ∈ that are in the interval [0, 1], and then some charactristics of this matrix are presented with the related examples . This form matrix has complete of information of a graph.

Keywords: Graph, adjacency matrix, fuzzy numbers

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Authors: Gilberto Gonzalez-A, Gerardo Jaimes-A

Abstract:

A methodology to design a nonlinear observer in a bond graph approach is proposed. The class of nonlinear observer with multivariable nonlinearities is considered. A junction structure of the bond graph observer is proposed. The proposed methodology to an electrical transformer and a DC motor including the nonlinear saturation is applied. Nonlinear observers for the transformer and DC motor based on multivariable circle criterion in the physical domain are proposed. In order to show the saturation effects on the transformer and DC motor, simulation results are obtained. Finally, the paper describes that convergence of the estimates to the true states is achieved.

Keywords: Bond graph, nonlinear observer, electrical transformer, nonlinear saturation

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Authors: Victor Krebss

Abstract:

Task of object localization is one of the major challenges in creating intelligent transportation. Unfortunately, in densely built-up urban areas, localization based on GPS only produces a large error, or simply becomes impossible. New opportunities arise for the localization due to the rapidly emerging concept of a wireless ad-hoc network. Such network, allows estimating potential distance between these objects measuring received signal level and construct a graph of distances in which nodes are the localization objects, and edges - estimates of the distances between pairs of nodes. Due to the known coordinates of individual nodes (anchors), it is possible to determine the location of all (or part) of the remaining nodes of the graph. Moreover, road map, available in digital format can provide localization routines with valuable additional information to narrow node location search. However, despite abundance of well-known algorithms for solving the problem of localization and significant research efforts, there are still many issues that currently are addressed only partially. In this paper, we propose localization approach based on the graph mapped distances on the digital road map data basis. In fact, problem is reduced to distance graph embedding into the graph representing area geo location data. It makes possible to localize objects, in some cases even if only one reference point is available. We propose simple embedding algorithm and sample implementation as spatial queries over sensor network data stored in spatial database, allowing employing effectively spatial indexing, optimized spatial search routines and geometry functions.

Keywords: Intelligent Transportation System, Sensor Network, Localization, Spatial Query, GIS, Graph Embedding.

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Authors: Patrick Cummings, Laura Cassani, Deirdre Kelliher

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In this paper we present findings from a research effort to apply a hybrid collaborative-context approach for a system focused on Marine Corps civil affairs data collection, aggregation, and analysis called the Marine Civil Information Management System (MARCIMS). The goal of this effort is to provide operators with information to make sense of the interconnectedness of entities and relationships in their area of operation and discover existing data to support civil military operations. Our approach to build a recommendation engine was designed to overcome several technical challenges, including 1) ensuring models were robust to the relatively small amount of data collected by the Marine Corps civil affairs community; 2) finding methods to recommend novel data for which there are no interactions captured; and 3) overcoming confirmation bias by ensuring content was recommended that was relevant for the mission despite being obscure or less well known. We solve this by implementing a combination of collective matrix factorization (CMF) and graph-based random walks to provide recommendations to civil military operations users. We also present a method to resolve the challenge of computation complexity inherent from highly connected nodes through a precomputed process.

Keywords: Recommendation engine, collaborative filtering, context based recommendation, graph analysis, coverage, civil affairs operations, Marine Corps.

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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: Irene Luque Ruiz, Manuel Urbano Cuadrado, Miguel Ángel Gómez-Nieto

Abstract:

New graph similarity methods have been proposed in this work with the aim to refining the chemical information extracted from molecules matching. For this purpose, data fusion of the isomorphic and nonisomorphic subgraphs into a new similarity measure, the Approximate Similarity, was carried out by several approaches. The application of the proposed method to the development of quantitative structure-activity relationships (QSAR) has provided reliable tools for predicting several pharmacological parameters: binding of steroids to the globulin-corticosteroid receptor, the activity of benzodiazepine receptor compounds, and the blood brain barrier permeability. Acceptable results were obtained for the models presented here.

Keywords: Graph similarity, Nonisomorphic dissimilarity, Approximate similarity, Drug activity prediction.

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Authors: XueSong Yu, JiaFeng Liu, XiangLong Tang, JianHua Huang

Abstract:

For improving the efficiency of human 3D tracking, we present an algorithm to track 3D Arm Motion. First, the Hierarchy Limb Model (HLM) is proposed based on the human 3D skeleton model. Second, via graph decomposition, the arm motion state space, modeled by HLM, can be discomposed into two low dimension subspaces: root nodes and leaf nodes. Finally, Rao-Blackwellised Particle Filter is used to estimate the 3D arm motion. The result of experiment shows that our algorithm can advance the computation efficiency.

Keywords: Hierarchy Limb Model; Rao-Blackwellised Particle Filter; 3D tracking

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Authors: Sizhong Zhou, Bingyuan Pu

Abstract:

Let G be a graph of order n, and let a, b and m be positive integers with 1 ≤ a<b. An [a, b]-factor of G is defined as a spanning subgraph F of G such that a ≤ dF (x) ≤ b for each x ∈ V (G). In this paper, it is proved that if n ≥ (a+b−1+√(a+b+1)m−2)2−1 b and δ(G) > n + a + b − 2 √bn+ 1, then for any subgraph H of G with m edges, G has an [a, b]-factor F such that E(H)∩ E(F) = ∅. This result is an extension of thatof Egawa [2].

Keywords: graph, minimum degree, [a, b]-factor.

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Authors: Jayadevan R., Jayant V. Kulkarni, Suresh N. Mali, Hemant K. Abhyankar

Abstract:

An important step in studying the statistics of fingerprint minutia features is to reliably extract minutia features from the fingerprint images. A new reliable method of computation for minutiae feature extraction from fingerprint images is presented. A fingerprint image is treated as a textured image. An orientation flow field of the ridges is computed for the fingerprint image. To accurately locate ridges, a new ridge orientation based computation method is proposed. After ridge segmentation a new method of computation is proposed for smoothing the ridges. The ridge skeleton image is obtained and then smoothed using morphological operators to detect the features. A post processing stage eliminates a large number of false features from the detected set of minutiae features. The detected features are observed to be reliable and accurate.

Keywords: Minutia, orientation field, ridge segmentation, textured image.

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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: Ahmad Salehi

Abstract:

An acyclic coloring of a graph G is a coloring of its vertices such that:(i) no two neighbors in G are assigned the same color and (ii) no bicolored cycle can exist in G. The acyclic chromatic number of G is the least number of colors necessary to acyclically color G. Recently it has been proved that any graph of maximum degree 5 has an acyclic chromatic number at most 8. In this paper we present another proof for this result.

Keywords: Acyclic Coloring, Vertex coloring.

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Authors: Vikas Rastogi, Vipan Kumar, Loveleen Kumar Bhagi

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The present work deals with the structural analysis of turbine blades and modeling of turbine blades. A common failure mode for turbine machines is high cycle of fatigue of compressor and turbine blades due to high dynamic stresses caused by blade vibration and resonance within the operation range of the machinery. In this work, proper damping system will be analyzed to reduce the vibrating blade. The main focus of the work is the modeling of under platform damper to evaluate the dynamic analysis of turbine-blade vibrations. The system is analyzed using Bond graph technique. Bond graph is one of the most convenient ways to represent a system from the physical aspect in foreground. It has advantage of putting together multi-energy domains of a system in a single representation in a unified manner. The bond graph model of dry friction damper is simulated on SYMBOLS-shakti® software. In this work, the blades are modeled as Timoshenko beam. Blade Vibrations under different working conditions are being analyzed numerically.

Keywords: Turbine blade vibrations, Friction dampers, Timoshenko Beam, Bond graph modeling.

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Authors: H. Y. Pourali, V. V. Joshi, B. N. Waphare.

Abstract:

In this paper, we verify the diameter of zero divisor graphs with respect to direct product.

Keywords: Atomic lattice, complement of graph, diameter, direct product of lattices, 0-distributive lattice, girth, product of graphs, prime ideal, zero divisor graph.

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Authors: Jiajun Wang, Xiaoge Li

Abstract:

The purpose of the aspect-level sentiment analysis task is to identify the sentiment polarity of aspects in a sentence. Currently, most methods mainly focus on using neural networks and attention mechanisms to model the relationship between aspects and context, but they ignore the dependence of words in different ranges in the sentence, resulting in deviation when assigning relationship weight to other words other than aspect words. To solve these problems, we propose an aspect-level sentiment analysis model that combines a multi-channel convolutional network and graph convolutional network (GCN). Firstly, the context and the degree of association between words are characterized by Long Short-Term Memory (LSTM) and self-attention mechanism. Besides, a multi-channel convolutional network is used to extract the features of words in different ranges. Finally, a convolutional graph network is used to associate the node information of the dependency tree structure. We conduct experiments on four benchmark datasets. The experimental results are compared with those of other models, which shows that our model is better and more effective.

Keywords: Aspect-level sentiment analysis, attention, multi-channel convolution network, graph convolution network, dependency tree.

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Authors: Sungju Yun, Anjin Park, Keechul Jung

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Motion capture devices have been utilized in producing several contents, such as movies and video games. However, since motion capture devices are expensive and inconvenient to use, motions segmented from captured data was recycled and synthesized to utilize it in another contents, but the motions were generally segmented by contents producers in manual. Therefore, automatic motion segmentation is recently getting a lot of attentions. Previous approaches are divided into on-line and off-line, where on-line approaches segment motions based on similarities between neighboring frames and off-line approaches segment motions by capturing the global characteristics in feature space. In this paper, we propose a graph-based high-level motion segmentation method. Since high-level motions consist of several repeated frames within temporal distances, we consider all similarities among all frames within the temporal distance. This is achieved by constructing a graph, where each vertex represents a frame and the edges between the frames are weighted by their similarity. Then, normalized cuts algorithm is used to partition the constructed graph into several sub-graphs by globally finding minimum cuts. In the experiments, the results using the proposed method showed better performance than PCA-based method in on-line and GMM-based method in off-line, as the proposed method globally segment motions from the graph constructed based similarities between neighboring frames as well as similarities among all frames within temporal distances.

Keywords: Capture Devices, High-Level Motion, Motion Segmentation, Normalized Cuts

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Authors: Chun-I Fan, Ming-Te Chen

Abstract:

This manuscript presents a fast blind signature scheme with extremely low computation for users. Only several modular additions and multiplications are required for a user to obtain and verify a signature in the proposed scheme. Comparing with the existing ones in the literature, the scheme greatly reduces the computations for users.

Keywords: Blind signatures, Untraceable electronic cash, Security & privacy, Electronic commerce

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Authors: Hans H. Diel

Abstract:

This paper describes a computer model of Quantum Field Theory (QFT), referred to in this paper as QTModel. After specifying the initial configuration for a QFT process (e.g. scattering) the model generates the possible applicable processes in terms of Feynman diagrams, the equations for the scattering matrix, and evaluates probability amplitudes for the scattering matrix and cross sections. The computations of probability amplitudes are performed numerically. The equations generated by QTModel are provided for demonstration purposes only. They are not directly used as the base for the computations of probability amplitudes. The computer model supports two modes for the computation of the probability amplitudes: (1) computation according to standard QFT, and (2) computation according to a proposed functional interpretation of quantum theory.

Keywords: Computational Modeling, Simulation of Quantum Theory, Quantum Field Theory, Quantum Electrodynamics

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Authors: Hassan Noori, Abdolali Basiri, Sajjad Rahmany

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In this paper we will introduce a brief introduction to theory of Gr¨obner bases and some applications of Gr¨obner bases to graph coloring problem, automatic geometric theorem proving and cryptography.

Keywords: Gr¨obner bases, Application of Gr¨obner bases, Automatic Geometric Theorem Proving, Graph Coloring, Cryptography.

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Authors: Quoc-Nam Tran

Abstract:

The theory of Groebner Bases, which has recently been honored with the ACM Paris Kanellakis Theory and Practice Award, has become a crucial building block to computer algebra, and is widely used in science, engineering, and computer science. It is wellknown that Groebner bases computation is EXP-SPACE in a general setting. In this paper, we give an algorithm to show that Groebner bases computation is P-SPACE in Boolean rings. We also show that with this discovery, the Groebner bases method can theoretically be as efficient as other methods for automated verification of hardware and software. Additionally, many useful and interesting properties of Groebner bases including the ability to efficiently convert the bases for different orders of variables making Groebner bases a promising method in automated verification.

Keywords: Algorithm, Complexity, Groebner basis, Applications of Computer Science.

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Authors: Hae-Yeoun Lee

Abstract:

Quantification of cardiac function is performed by calculating blood volume and ejection fraction in routine clinical practice. However, these works have been performed by manual contouring, which requires computational costs and varies on the observer. In this paper, an automatic left ventricle segmentation algorithm on cardiac magnetic resonance images (MRI) is presented. Using knowledge on cardiac MRI, a K-mean clustering technique is applied to segment blood region on a coil-sensitivity corrected image. Then, a graph searching technique is used to correct segmentation errors from coil distortion and noises. Finally, blood volume and ejection fraction are calculated. Using cardiac MRI from 15 subjects, the presented algorithm is tested and compared with manual contouring by experts to show outstanding performance.

Keywords: Cardiac MRI, Graph searching, Left ventricle segmentation, K-means clustering.

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Authors: Omar Gaci, Stefan Balev

Abstract:

In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure.

Keywords: interaction network, protein structure, small-world network.

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Authors: A. Badoud, M. Khemliche, S. Latreche

Abstract:

The main objective developed in this paper is to find a graphic technique for modeling, simulation and diagnosis of the industrial systems. This importance is much apparent when it is about a complex system such as the nuclear reactor with pressurized water of several form with various several non-linearity and time scales. In this case the analytical approach is heavy and does not give a fast idea on the evolution of the system. The tool Bond Graph enabled us to transform the analytical model into graphic model and the software of simulation SYMBOLS 2000 specific to the Bond Graphs made it possible to validate and have the results given by the technical specifications. We introduce the analysis of the problem involved in the faults localization and identification in the complex industrial processes. We propose a method of fault detection applied to the diagnosis and to determine the gravity of a detected fault. We show the possibilities of application of the new diagnosis approaches to the complex system control. The industrial systems became increasingly complex with the faults diagnosis procedures in the physical systems prove to become very complex as soon as the systems considered are not elementary any more. Indeed, in front of this complexity, we chose to make recourse to Fault Detection and Isolation method (FDI) by the analysis of the problem of its control and to conceive a reliable system of diagnosis making it possible to apprehend the complex dynamic systems spatially distributed applied to the standard pressurized water nuclear reactor.

Keywords: Bond Graph, Modeling, Simulation, Monitoring, Analytical Redundancy Relations, Pressurized Water Reactor, Directed Graph.

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Authors: A.Y. Bani Hashim, N.A. Abu Osman, W.A.B. Wan Abas, L. Abdul Latif

Abstract:

The unique structural configuration found in human foot allows easy walking. Similar movement is hard to imitate even for an ape. It is obvious that human ambulation relates to the foot structure itself. Suppose the bones are represented as vertices and the joints as edges. This leads to the development of a special graph that represents human foot. On a footprint there are point-ofcontacts which have contact with the ground. It involves specific vertices. Theoretically, for an ideal ambulation, these points provide reactions onto the ground or the static equilibrium forces. They are arranged in sequence in form of a path. The ambulating footprint follows this path. Having the human foot graph and the path crossbred, it results in a representation that describes the profile of an ideal ambulation. This profile cites the locations where the point-of-contact experience normal reaction forces. It highlights the significant of these points.

Keywords: Ambulation, edge, foot, graph, vertex.

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Authors: Matthias Dehmer, Frank Emmert Streib, Jürgen Kilian, Andreas Zulauf

Abstract:

Methods for organizing web data into groups in order to analyze web-based hypertext data and facilitate data availability are very important in terms of the number of documents available online. Thereby, the task of clustering web-based document structures has many applications, e.g., improving information retrieval on the web, better understanding of user navigation behavior, improving web users requests servicing, and increasing web information accessibility. In this paper we investigate a new approach for clustering web-based hypertexts on the basis of their graph structures. The hypertexts will be represented as so called generalized trees which are more general than usual directed rooted trees, e.g., DOM-Trees. As a important preprocessing step we measure the structural similarity between the generalized trees on the basis of a similarity measure d. Then, we apply agglomerative clustering to the obtained similarity matrix in order to create clusters of hypertext graph patterns representing navigation structures. In the present paper we will run our approach on a data set of hypertext structures and obtain good results in Web Structure Mining. Furthermore we outline the application of our approach in Web Usage Mining as future work.

Keywords: Clustering methods, graph-based patterns, graph similarity, hypertext structures, web structure mining

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