WorldWideScience

Sample records for graph pattern matching

  1. Pattern graph rewrite systems

    Directory of Open Access Journals (Sweden)

    Aleks Kissinger

    2014-03-01

    Full Text Available String diagrams are a powerful tool for reasoning about physical processes, logic circuits, tensor networks, and many other compositional structures. Dixon, Duncan and Kissinger introduced string graphs, which are a combinatoric representations of string diagrams, amenable to automated reasoning about diagrammatic theories via graph rewrite systems. In this extended abstract, we show how the power of such rewrite systems can be greatly extended by introducing pattern graphs, which provide a means of expressing infinite families of rewrite rules where certain marked subgraphs, called !-boxes ("bang boxes", on both sides of a rule can be copied any number of times or removed. After reviewing the string graph formalism, we show how string graphs can be extended to pattern graphs and how pattern graphs and pattern rewrite rules can be instantiated to concrete string graphs and rewrite rules. We then provide examples demonstrating the expressive power of pattern graphs and how they can be applied to study interacting algebraic structures that are central to categorical quantum mechanics.

  2. Dynamic Matchings in Convex Bipartite Graphs

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Georgiadis, Loukas; Hansen, Kristoffer Arnsfelt

    2007-01-01

    We consider the problem of maintaining a maximum matching in a convex bipartite graph G = (V,E) under a set of update operations which includes insertions and deletions of vertices and edges. It is not hard to show that it is impossible to maintain an explicit representation of a maximum matching...

  3. POOR TEXTURAL IMAGE MATCHING BASED ON GRAPH THEORY

    Directory of Open Access Journals (Sweden)

    S. Chen

    2016-06-01

    Full Text Available Image matching lies at the heart of photogrammetry and computer vision. For poor textural images, the matching result is affected by low contrast, repetitive patterns, discontinuity or occlusion, few or homogeneous textures. Recently, graph matching became popular for its integration of geometric and radiometric information. Focused on poor textural image matching problem, it is proposed an edge-weight strategy to improve graph matching algorithm. A series of experiments have been conducted including 4 typical landscapes: Forest, desert, farmland, and urban areas. And it is experimentally found that our new algorithm achieves better performance. Compared to SIFT, doubled corresponding points were acquired, and the overall recall rate reached up to 68%, which verifies the feasibility and effectiveness of the algorithm.

  4. Characterizing graphs of maximum matching width at most 2

    DEFF Research Database (Denmark)

    Jeong, Jisu; Ok, Seongmin; Suh, Geewon

    2017-01-01

    The maximum matching width is a width-parameter that is de ned on a branch-decomposition over the vertex set of a graph. The size of a maximum matching in the bipartite graph is used as a cut-function. In this paper, we characterize the graphs of maximum matching width at most 2 using the minor o...

  5. Poor textural image tie point matching via graph theory

    Science.gov (United States)

    Yuan, Xiuxiao; Chen, Shiyu; Yuan, Wei; Cai, Yang

    2017-07-01

    Feature matching aims to find corresponding points to serve as tie points between images. Robust matching is still a challenging task when input images are characterized by low contrast or contain repetitive patterns, occlusions, or homogeneous textures. In this paper, a novel feature matching algorithm based on graph theory is proposed. This algorithm integrates both geometric and radiometric constraints into an edge-weighted (EW) affinity tensor. Tie points are then obtained by high-order graph matching. Four pairs of poor textural images covering forests, deserts, bare lands, and urban areas are tested. For comparison, three state-of-the-art matching techniques, namely, scale-invariant feature transform (SIFT), speeded up robust features (SURF), and features from accelerated segment test (FAST), are also used. The experimental results show that the matching recall obtained by SIFT, SURF, and FAST varies from 0 to 35% in different types of poor textures. However, through the integration of both geometry and radiometry and the EW strategy, the recall obtained by the proposed algorithm is better than 50% in all four image pairs. The better matching recall improves the number of correct matches, dispersion, and positional accuracy.

  6. Polytypic pattern matching

    NARCIS (Netherlands)

    Jeuring, J.T.

    1995-01-01

    The pattern matching problem can be informally specified as follows: given a pattern and a text, find all occurrences of the pattern in the text. The pattern and the text may both be lists, or they may both be trees, or they may both be multi-dimensional arrays, etc. This paper describes a general

  7. The complexity of the matching-cut problem for planar graphs and other graph classes

    NARCIS (Netherlands)

    Bonsma, P.S.

    2009-01-01

    The Matching-Cut problem is the problem to decide whether a graph has an edge cut that is also a matching. Previously this problem was studied under the name of the Decomposable Graph Recognition problem, and proved to be -complete when restricted to graphs with maximum degree four. In this paper it

  8. Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching

    Science.gov (United States)

    2013-01-01

    REPORT Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The stable matching...Franceschetti 858-822-2284 3. DATES COVERED (From - To) Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 - Jealousy Graphs: Structure and...market. Using this structure, we are able to provide a ner analysis of the complexity of a subclass of decentralized matching markets. Jealousy

  9. Fingerprint recognition system by use of graph matching

    Science.gov (United States)

    Shen, Wei; Shen, Jun; Zheng, Huicheng

    2001-09-01

    Fingerprint recognition is an important subject in biometrics to identify or verify persons by physiological characteristics, and has found wide applications in different domains. In the present paper, we present a finger recognition system that combines singular points and structures. The principal steps of processing in our system are: preprocessing and ridge segmentation, singular point extraction and selection, graph representation, and finger recognition by graphs matching. Our fingerprint recognition system is implemented and tested for many fingerprint images and the experimental result are satisfactory. Different techniques are used in our system, such as fast calculation of orientation field, local fuzzy dynamical thresholding, algebraic analysis of connections and fingerprints representation and matching by graphs. Wed find that for fingerprint database that is not very large, the recognition rate is very high even without using a prior coarse category classification. This system works well for both one-to-few and one-to-many problems.

  10. Percolator: Scalable Pattern Discovery in Dynamic Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Choudhury, Sutanay; Purohit, Sumit; Lin, Peng; Wu, Yinghui; Holder, Lawrence B.; Agarwal, Khushbu

    2018-02-06

    We demonstrate Percolator, a distributed system for graph pattern discovery in dynamic graphs. In contrast to conventional mining systems, Percolator advocates efficient pattern mining schemes that (1) support pattern detection with keywords; (2) integrate incremental and parallel pattern mining; and (3) support analytical queries such as trend analysis. The core idea of Percolator is to dynamically decide and verify a small fraction of patterns and their in- stances that must be inspected in response to buffered updates in dynamic graphs, with a total mining cost independent of graph size. We demonstrate a) the feasibility of incremental pattern mining by walking through each component of Percolator, b) the efficiency and scalability of Percolator over the sheer size of real-world dynamic graphs, and c) how the user-friendly GUI of Percolator inter- acts with users to support keyword-based queries that detect, browse and inspect trending patterns. We also demonstrate two user cases of Percolator, in social media trend analysis and academic collaboration analysis, respectively.

  11. Pattern recognition and string matching

    CERN Document Server

    Cheng, Xiuzhen

    2002-01-01

    The research and development of pattern recognition have proven to be of importance in science, technology, and human activity. Many useful concepts and tools from different disciplines have been employed in pattern recognition. Among them is string matching, which receives much theoretical and practical attention. String matching is also an important topic in combinatorial optimization. This book is devoted to recent advances in pattern recognition and string matching. It consists of twenty eight chapters written by different authors, addressing a broad range of topics such as those from classifica­ tion, matching, mining, feature selection, and applications. Each chapter is self-contained, and presents either novel methodological approaches or applications of existing theories and techniques. The aim, intent, and motivation for publishing this book is to pro­ vide a reference tool for the increasing number of readers who depend upon pattern recognition or string matching in some way. This includes student...

  12. Kolmogorov and Zabih’s Graph Cuts Stereo Matching Algorithm

    Directory of Open Access Journals (Sweden)

    Vladimir Kolmogorov

    2014-10-01

    Full Text Available Binocular stereovision estimates the three-dimensional shape of a scene from two photographs taken from different points of view. In rectified epipolar geometry, this is equivalent to a matching problem. This article describes a method proposed by Kolmogorov and Zabih in 2001, which puts forward an energy-based formulation. The aim is to minimize a four-term-energy. This energy is not convex and cannot be minimized except among a class of perturbations called expansion moves, in which case an exact minimization can be done with graph cuts techniques. One noteworthy feature of this method is that it handles occlusion: The algorithm detects points that cannot be matched with any point in the other image. In this method displacements are pixel accurate (no subpixel refinement.

  13. GraMi: Generalized Frequent Pattern Mining in a Single Large Graph

    KAUST Repository

    Saeedy, Mohammed El

    2011-11-01

    Mining frequent subgraphs is an important operation on graphs. Most existing work assumes a database of many small graphs, but modern applications, such as social networks, citation graphs or protein-protein interaction in bioinformatics, are modeled as a single large graph. Interesting interactions in such applications may be transitive (e.g., friend of a friend). Existing methods, however, search for frequent isomorphic (i.e., exact match) subgraphs and cannot discover many useful patterns. In this paper the authors propose GRAMI, a framework that generalizes frequent subgraph mining in a large single graph. GRAMI discovers frequent patterns. A pattern is a graph where edges are generalized to distance-constrained paths. Depending on the definition of the distance function, many instantiations of the framework are possible. Both directed and undirected graphs, as well as multiple labels per vertex, are supported. The authors developed an efficient implementation of the framework that models the frequency resolution phase as a constraint satisfaction problem, in order to avoid the costly enumeration of all instances of each pattern in the graph. The authors also implemented CGRAMI, a version that supports structural and semantic constraints; and AGRAMI, an approximate version that supports very large graphs. The experiments on real data demonstrate that the authors framework is up to 3 orders of magnitude faster and discovers more interesting patterns than existing approaches.

  14. Effectiveness of Vertex Nomination via Seeded Graph Matching to Find Bijections Between Similar Networks

    Science.gov (United States)

    2018-02-01

    Information Directorate This report is published in the interest of scientific and technical information exchange, and its publication does not...the current prototype. 15. SUBJECT TERMS Vertex Nomination via Seeded Graph Matching (VN via SGM), Seeded Graph Matching (SGM), Vertex of Interest (VOI...Author’s Example ................................................................................................................. 4 4.2.2 Simple

  15. Matching of renewable source of energy generation graphs and electrical load in local energy system

    Science.gov (United States)

    Lezhniuk, Petro; Komar, Vyacheslav; Sobchuk, Dmytro; Kravchuk, Sergiy; Kacejko, Piotr; Zavidsky, Vladislav

    2017-08-01

    The paper contains the method of matching generation graph of photovoltaic electric stations and consumers. Characteristic feature of this method is the application of morphometric analysis for assessment of non-uniformity of the integrated graph of energy supply, optimal coefficients of current distribution, that enables by mean of refining the powers, transferring in accordance with the graph , to provide the decrease of electric energy losses in the grid and transport task, as the optimization tool.

  16. Structural pattern matching of nonribosomal peptides

    Directory of Open Access Journals (Sweden)

    Leclère Valérie

    2009-03-01

    Full Text Available Abstract Background Nonribosomal peptides (NRPs, bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents. NRPs are mainly composed of amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there are several hundred different monomers that can be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently stores more than 700 NRPs annotated with their monomeric peptide structure encoded by undirected labeled graphs. This opens a way to a systematic analysis of structural patterns occurring in NRPs. Such studies can investigate the functional role of some monomeric chains, or analyse NRPs that have been computationally predicted from the synthetase protein sequence. A basic operation in such analyses is the search for a given structural pattern in the database. Results We developed an efficient method that allows for a quick search for a structural pattern in the NORINE database. The method identifies all peptides containing a pattern substructure of a given size. This amounts to solving a variant of the maximum common subgraph problem on pattern and peptide graphs, which is done by computing cliques in an appropriate compatibility graph. Conclusion The method has been incorporated into the NORINE database, available at http://bioinfo.lifl.fr/norine. Less than one second is needed to search for a pattern in the entire database.

  17. Computational Comparison of Several Greedy Algorithms for the Minimum Cost Perfect Matching Problem on Large Graphs

    DEFF Research Database (Denmark)

    Wøhlk, Sanne; Laporte, Gilbert

    2017-01-01

    The aim of this paper is to computationally compare several algorithms for the Minimum Cost Perfect Matching Problem on an undirected complete graph. Our work is motivated by the need to solve large instances of the Capacitated Arc Routing Problem (CARP) arising in the optimization of garbage...... collection in Denmark. Common heuristics for the CARP involve the optimal matching of the odd-degree nodes of a graph. The algorithms used in the comparison include the CPLEX solution of an exact formulation, the LEDA matching algorithm, a recent implementation of the Blossom algorithm, as well as six...

  18. GRAMI: Frequent subgraph and pattern mining in a single large graph

    KAUST Repository

    Elseidy, M.

    2014-01-01

    Mining frequent subgraphs is an important operation on graphs; it is defined as finding all subgraphs that appear frequently in a database according to a given frequency threshold. Most existing work assumes a database of many small graphs, but modern applications, such as social networks, citation graphs, or proteinprotein interactions in bioinformatics, are modeled as a single large graph. In this paper we present GRAMI, a novel framework for frequent subgraph mining in a single large graph. GRAMI undertakes a novel approach that only finds the minimal set of instances to satisfy the frequency threshold and avoids the costly enumeration of all instances required by previous approaches. We accompany our approach with a heuristic and optimizations that significantly improve performance. Additionally, we present an extension of GRAMI that mines frequent patterns. Compared to subgraphs, patterns offer a more powerful version of matching that captures transitive interactions between graph nodes (like friend of a friend) which are very common in modern applications. Finally, we present CGRAMI, a version supporting structural and semantic constraints, and AGRAMI, an approximate version producing results with no false positives. Our experiments on real data demonstrate that our framework is up to 2 orders of magnitude faster and discovers more interesting patterns than existing approaches. 2014 VLDB Endowment.

  19. Privacy-Preserving Profile Matching Using the Social Graph

    NARCIS (Netherlands)

    Jeckmans, Arjan; Tang, Qiang; Hartel, Pieter H.

    2011-01-01

    We present a privacy-preserving protocol for users to test a match with potential new friends in an environment where all users cryptographically encrypt their private information. The following scenario is considered. Suppose that user Alice thinks that Bob might be a good new friend. So, Alice and

  20. Fuzzy automata and pattern matching

    Science.gov (United States)

    Setzer, C. B.; Warsi, N. A.

    1986-01-01

    A wide-ranging search for articles and books concerned with fuzzy automata and syntactic pattern recognition is presented. A number of survey articles on image processing and feature detection were included. Hough's algorithm is presented to illustrate the way in which knowledge about an image can be used to interpret the details of the image. It was found that in hand generated pictures, the algorithm worked well on following the straight lines, but had great difficulty turning corners. An algorithm was developed which produces a minimal finite automaton recognizing a given finite set of strings. One difficulty of the construction is that, in some cases, this minimal automaton is not unique for a given set of strings and a given maximum length. This algorithm compares favorably with other inference algorithms. More importantly, the algorithm produces an automaton with a rigorously described relationship to the original set of strings that does not depend on the algorithm itself.

  1. A review on compressed pattern matching

    Directory of Open Access Journals (Sweden)

    Surya Prakash Mishra

    2016-09-01

    Full Text Available Compressed pattern matching (CPM refers to the task of locating all the occurrences of a pattern (or set of patterns inside the body of compressed text. In this type of matching, pattern may or may not be compressed. CPM is very useful in handling large volume of data especially over the network. It has many applications in computational biology, where it is useful in finding similar trends in DNA sequences; intrusion detection over the networks, big data analytics etc. Various solutions have been provided by researchers where pattern is matched directly over the uncompressed text. Such solution requires lot of space and consumes lot of time when handling the big data. Various researchers have proposed the efficient solutions for compression but very few exist for pattern matching over the compressed text. Considering the future trend where data size is increasing exponentially day-by-day, CPM has become a desirable task. This paper presents a critical review on the recent techniques on the compressed pattern matching. The covered techniques includes: Word based Huffman codes, Word Based Tagged Codes; Wavelet Tree Based Indexing. We have presented a comparative analysis of all the techniques mentioned above and highlighted their advantages and disadvantages.

  2. Quantum Experiments and Graphs: Multiparty States as Coherent Superpositions of Perfect Matchings

    Science.gov (United States)

    Krenn, Mario; Gu, Xuemei; Zeilinger, Anton

    2017-12-01

    We show a surprising link between experimental setups to realize high-dimensional multipartite quantum states and graph theory. In these setups, the paths of photons are identified such that the photon-source information is never created. We find that each of these setups corresponds to an undirected graph, and every undirected graph corresponds to an experimental setup. Every term in the emerging quantum superposition corresponds to a perfect matching in the graph. Calculating the final quantum state is in the #P-complete complexity class, thus it cannot be done efficiently. To strengthen the link further, theorems from graph theory—such as Hall's marriage problem—are rephrased in the language of pair creation in quantum experiments. We show explicitly how this link allows one to answer questions about quantum experiments (such as which classes of entangled states can be created) with graph theoretical methods, and how to potentially simulate properties of graphs and networks with quantum experiments (such as critical exponents and phase transitions).

  3. Quantum Experiments and Graphs: Multiparty States as Coherent Superpositions of Perfect Matchings.

    Science.gov (United States)

    Krenn, Mario; Gu, Xuemei; Zeilinger, Anton

    2017-12-15

    We show a surprising link between experimental setups to realize high-dimensional multipartite quantum states and graph theory. In these setups, the paths of photons are identified such that the photon-source information is never created. We find that each of these setups corresponds to an undirected graph, and every undirected graph corresponds to an experimental setup. Every term in the emerging quantum superposition corresponds to a perfect matching in the graph. Calculating the final quantum state is in the #P-complete complexity class, thus it cannot be done efficiently. To strengthen the link further, theorems from graph theory-such as Hall's marriage problem-are rephrased in the language of pair creation in quantum experiments. We show explicitly how this link allows one to answer questions about quantum experiments (such as which classes of entangled states can be created) with graph theoretical methods, and how to potentially simulate properties of graphs and networks with quantum experiments (such as critical exponents and phase transitions).

  4. A direct mining approach to efficient constrained graph pattern discovery

    DEFF Research Database (Denmark)

    Zhu, Feida; Zhang, Zequn; Qu, Qiang

    2013-01-01

    Despite the wealth of research on frequent graph pattern mining, how to efficiently mine the complete set of those with constraints still poses a huge challenge to the existing algorithms mainly due to the inherent bottleneck in the mining paradigm. In essence, mining requests with explicitly-spe...

  5. Computing Maximum Cardinality Matchings in Parallel on Bipartite Graphs via Tree-Grafting

    International Nuclear Information System (INIS)

    Azad, Ariful; Buluc, Aydn; Pothen, Alex

    2016-01-01

    It is difficult to obtain high performance when computing matchings on parallel processors because matching algorithms explicitly or implicitly search for paths in the graph, and when these paths become long, there is little concurrency. In spite of this limitation, we present a new algorithm and its shared-memory parallelization that achieves good performance and scalability in computing maximum cardinality matchings in bipartite graphs. This algorithm searches for augmenting paths via specialized breadth-first searches (BFS) from multiple source vertices, hence creating more parallelism than single source algorithms. Algorithms that employ multiple-source searches cannot discard a search tree once no augmenting path is discovered from the tree, unlike algorithms that rely on single-source searches. We describe a novel tree-grafting method that eliminates most of the redundant edge traversals resulting from this property of multiple-source searches. We also employ the recent direction-optimizing BFS algorithm as a subroutine to discover augmenting paths faster. Our algorithm compares favorably with the current best algorithms in terms of the number of edges traversed, the average augmenting path length, and the number of iterations. Here, we provide a proof of correctness for our algorithm. Our NUMA-aware implementation is scalable to 80 threads of an Intel multiprocessor and to 240 threads on an Intel Knights Corner coprocessor. On average, our parallel algorithm runs an order of magnitude faster than the fastest algorithms available. The performance improvement is more significant on graphs with small matching number.

  6. FPFH-based graph matching for 3D point cloud registration

    Science.gov (United States)

    Zhao, Jiapeng; Li, Chen; Tian, Lihua; Zhu, Jihua

    2018-04-01

    Correspondence detection is a vital step in point cloud registration and it can help getting a reliable initial alignment. In this paper, we put forward an advanced point feature-based graph matching algorithm to solve the initial alignment problem of rigid 3D point cloud registration with partial overlap. Specifically, Fast Point Feature Histograms are used to determine the initial possible correspondences firstly. Next, a new objective function is provided to make the graph matching more suitable for partially overlapping point cloud. The objective function is optimized by the simulated annealing algorithm for final group of correct correspondences. Finally, we present a novel set partitioning method which can transform the NP-hard optimization problem into a O(n3)-solvable one. Experiments on the Stanford and UWA public data sets indicates that our method can obtain better result in terms of both accuracy and time cost compared with other point cloud registration methods.

  7. On Tree Pattern Matching by Pushdown Automata

    Directory of Open Access Journals (Sweden)

    T. Flouri

    2009-01-01

    Full Text Available Tree pattern matching is an important operation in Computer Science on which a number of tasks such as mechanical theorem proving, term-rewriting, symbolic computation and non-procedural programming languages are based on. Work has begun on a systematic approach to the construction of tree pattern matchers by deterministic pushdown automata which read subject trees in prefix notation. The method is analogous to the construction of string pattern matchers: for given patterns, a non-deterministic pushdown automaton is created and then it is determinised. In this first paper, we present the proposed non-deterministic pushdown automaton which will serve as a basis for the determinisation process, and prove its correctness. 

  8. AN INTEGRATED RANSAC AND GRAPH BASED MISMATCH ELIMINATION APPROACH FOR WIDE-BASELINE IMAGE MATCHING

    Directory of Open Access Journals (Sweden)

    M. Hasheminasab

    2015-12-01

    Full Text Available In this paper we propose an integrated approach in order to increase the precision of feature point matching. Many different algorithms have been developed as to optimizing the short-baseline image matching while because of illumination differences and viewpoints changes, wide-baseline image matching is so difficult to handle. Fortunately, the recent developments in the automatic extraction of local invariant features make wide-baseline image matching possible. The matching algorithms which are based on local feature similarity principle, using feature descriptor as to establish correspondence between feature point sets. To date, the most remarkable descriptor is the scale-invariant feature transform (SIFT descriptor , which is invariant to image rotation and scale, and it remains robust across a substantial range of affine distortion, presence of noise, and changes in illumination. The epipolar constraint based on RANSAC (random sample consensus method is a conventional model for mismatch elimination, particularly in computer vision. Because only the distance from the epipolar line is considered, there are a few false matches in the selected matching results based on epipolar geometry and RANSAC. Aguilariu et al. proposed Graph Transformation Matching (GTM algorithm to remove outliers which has some difficulties when the mismatched points surrounded by the same local neighbor structure. In this study to overcome these limitations, which mentioned above, a new three step matching scheme is presented where the SIFT algorithm is used to obtain initial corresponding point sets. In the second step, in order to reduce the outliers, RANSAC algorithm is applied. Finally, to remove the remained mismatches, based on the adjacent K-NN graph, the GTM is implemented. Four different close range image datasets with changes in viewpoint are utilized to evaluate the performance of the proposed method and the experimental results indicate its robustness and

  9. A hierarchical graph neuron scheme for real-time pattern recognition.

    Science.gov (United States)

    Nasution, B B; Khan, A I

    2008-02-01

    The hierarchical graph neuron (HGN) implements a single cycle memorization and recall operation through a novel algorithmic design. The HGN is an improvement on the already published original graph neuron (GN) algorithm. In this improved approach, it recognizes incomplete/noisy patterns. It also resolves the crosstalk problem, which is identified in the previous publications, within closely matched patterns. To accomplish this, the HGN links multiple GN networks for filtering noise and crosstalk out of pattern data inputs. Intrinsically, the HGN is a lightweight in-network processing algorithm which does not require expensive floating point computations; hence, it is very suitable for real-time applications and tiny devices such as the wireless sensor networks. This paper describes that the HGN's pattern matching capability and the small response time remain insensitive to the increases in the number of stored patterns. Moreover, the HGN does not require definition of rules or setting of thresholds by the operator to achieve the desired results nor does it require heuristics entailing iterative operations for memorization and recall of patterns.

  10. 1 / n Expansion for the Number of Matchings on Regular Graphs and Monomer-Dimer Entropy

    Science.gov (United States)

    Pernici, Mario

    2017-08-01

    Using a 1 / n expansion, that is an expansion in descending powers of n, for the number of matchings in regular graphs with 2 n vertices, we study the monomer-dimer entropy for two classes of graphs. We study the difference between the extensive monomer-dimer entropy of a random r-regular graph G (bipartite or not) with 2 n vertices and the average extensive entropy of r-regular graphs with 2 n vertices, in the limit n → ∞. We find a series expansion for it in the numbers of cycles; with probability 1 it converges for dimer density p diverges as |ln(1-p)| for p → 1. In the case of regular lattices, we similarly expand the difference between the specific monomer-dimer entropy on a lattice and the one on the Bethe lattice; we write down its Taylor expansion in powers of p through the order 10, expressed in terms of the number of totally reducible walks which are not tree-like. We prove through order 6 that its expansion coefficients in powers of p are non-negative.

  11. Rewrite Systems, Pattern Matching, and Code Generation

    Science.gov (United States)

    1988-06-09

    fmd a local set L’ which includes L and define the transformation on L’ instead of on L. 11 The straightforward way to define tree transformations...Proposition 2.19 Both B-ftt and T-ftt include: REL relabelings FTA (t ,t) such that t e RECOG HOM homomorphisms LHOM linear homomorphisms The capabilities...fsa for the set of the structures of the original pattern set. The LB-fsa IS used to fmd the structural subpatterns matching a: each node of the

  12. Graph configuration model based evaluation of the education-occupation match.

    Science.gov (United States)

    Gadar, Laszlo; Abonyi, Janos

    2018-01-01

    To study education-occupation matchings we developed a bipartite network model of education to work transition and a graph configuration model based metric. We studied the career paths of 15 thousand Hungarian students based on the integrated database of the National Tax Administration, the National Health Insurance Fund, and the higher education information system of the Hungarian Government. A brief analysis of gender pay gap and the spatial distribution of over-education is presented to demonstrate the background of the research and the resulted open dataset. We highlighted the hierarchical and clustered structure of the career paths based on the multi-resolution analysis of the graph modularity. The results of the cluster analysis can support policymakers to fine-tune the fragmented program structure of higher education.

  13. Data Acquisition Based on Stable Matching of Bipartite Graph in Cooperative Vehicle-Infrastructure Systems.

    Science.gov (United States)

    Tang, Xiaolan; Hong, Donghui; Chen, Wenlong

    2017-06-08

    Existing studies on data acquisition in vehicular networks often take the mobile vehicular nodes as data carriers. However, their autonomous movements, limited resources and security risks impact the quality of services. In this article, we propose a data acquisition model using stable matching of bipartite graph in cooperative vehicle-infrastructure systems, namely, DAS. Contents are distributed to roadside units, while vehicular nodes support supplementary storage. The original distribution problem is formulated as a stable matching problem of bipartite graph, where the data and the storage cells compose two sides of vertices. Regarding the factors relevant with the access ratio and delay, the preference rankings for contents and roadside units are calculated, respectively. With a multi-replica preprocessing algorithm to handle the potential one-to-many mapping, the matching problem is addressed in polynomial time. In addition, vehicular nodes carry and forward assistant contents to deliver the failed packets because of bandwidth competition. Furthermore, an incentive strategy is put forward to boost the vehicle cooperation and to achieve a fair bandwidth allocation at roadside units. Experiments show that DAS achieves a high access ratio and a small storage cost with an acceptable delay.

  14. Quick Mining of Isomorphic Exact Large Patterns from Large Graphs

    KAUST Repository

    Almasri, Islam

    2014-12-01

    The applications of the sub graph isomorphism search are growing with the growing number of areas that model their systems using graphs or networks. Specifically, many biological systems, such as protein interaction networks, molecular structures and protein contact maps, are modeled as graphs. The sub graph isomorphism search is concerned with finding all sub graphs that are isomorphic to a relevant query graph, the existence of such sub graphs can reflect on the characteristics of the modeled system. The most computationally expensive step in the search for isomorphic sub graphs is the backtracking algorithm that traverses the nodes of the target graph. In this paper, we propose a pruning approach that is inspired by the minimum remaining value heuristic that achieves greater scalability over large query and target graphs. Our testing on various biological networks shows that performance enhancement of our approach over existing state-of-the-art approaches varies between 6x and 53x. © 2014 IEEE.

  15. Quick Mining of Isomorphic Exact Large Patterns from Large Graphs

    KAUST Repository

    Almasri, Islam; Gao, Xin; Fedoroff, Nina V.

    2014-01-01

    The applications of the sub graph isomorphism search are growing with the growing number of areas that model their systems using graphs or networks. Specifically, many biological systems, such as protein interaction networks, molecular structures and protein contact maps, are modeled as graphs. The sub graph isomorphism search is concerned with finding all sub graphs that are isomorphic to a relevant query graph, the existence of such sub graphs can reflect on the characteristics of the modeled system. The most computationally expensive step in the search for isomorphic sub graphs is the backtracking algorithm that traverses the nodes of the target graph. In this paper, we propose a pruning approach that is inspired by the minimum remaining value heuristic that achieves greater scalability over large query and target graphs. Our testing on various biological networks shows that performance enhancement of our approach over existing state-of-the-art approaches varies between 6x and 53x. © 2014 IEEE.

  16. The Smallest Valid Extension-Based Efficient, Rare Graph Pattern Mining, Considering Length-Decreasing Support Constraints and Symmetry Characteristics of Graphs

    Directory of Open Access Journals (Sweden)

    Unil Yun

    2016-05-01

    Full Text Available Frequent graph mining has been proposed to find interesting patterns (i.e., frequent sub-graphs from databases composed of graph transaction data, which can effectively express complex and large data in the real world. In addition, various applications for graph mining have been suggested. Traditional graph pattern mining methods use a single minimum support threshold factor in order to check whether or not mined patterns are interesting. However, it is not a sufficient factor that can consider valuable characteristics of graphs such as graph sizes and features of graph elements. That is, previous methods cannot consider such important characteristics in their mining operations since they only use a fixed minimum support threshold in the mining process. For this reason, in this paper, we propose a novel graph mining algorithm that can consider various multiple, minimum support constraints according to the types of graph elements and changeable minimum support conditions, depending on lengths of graph patterns. In addition, the proposed algorithm performs in mining operations more efficiently because it can minimize duplicated operations and computational overheads by considering symmetry features of graphs. Experimental results provided in this paper demonstrate that the proposed algorithm outperforms previous mining approaches in terms of pattern generation, runtime and memory usage.

  17. A Selectivity based approach to Continuous Pattern Detection in Streaming Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Choudhury, Sutanay; Holder, Larry; Chin, George; Agarwal, Khushbu; Feo, John T.

    2015-05-27

    Cyber security is one of the most significant technical challenges in current times. Detecting adversarial activities, prevention of theft of intellectual properties and customer data is a high priority for corporations and government agencies around the world. Cyber defenders need to analyze massive-scale, high-resolution network flows to identify, categorize, and mitigate attacks involving networks spanning institutional and national boundaries. Many of the cyber attacks can be described as subgraph patterns, with prominent examples being insider infiltrations (path queries), denial of service (parallel paths) and malicious spreads (tree queries). This motivates us to explore subgraph matching on streaming graphs in a continuous setting. The novelty of our work lies in using the subgraph distributional statistics collected from the streaming graph to determine the query processing strategy. We introduce a ``Lazy Search" algorithm where the search strategy is decided on a vertex-to-vertex basis depending on the likelihood of a match in the vertex neighborhood. We also propose a metric named ``Relative Selectivity" that is used to select between different query processing strategies. Our experiments performed on real online news, network traffic stream and a synthetic social network benchmark demonstrate 10-100x speedups over non-incremental, selectivity agnostic approaches.

  18. Computationally Secure Pattern Matching in the Presence of Malicious Adversaries

    DEFF Research Database (Denmark)

    Hazay, Carmit; Toft, Tomas

    2014-01-01

    for important variations of the secure pattern matching problem that are significantly more efficient than the current state of art solutions: First, we deal with secure pattern matching with wildcards. In this variant the pattern may contain wildcards that match both 0 and 1. Our protocol requires O......We propose a protocol for the problem of secure two-party pattern matching, where Alice holds a text t∈{0,1}∗ of length n, while Bob has a pattern p∈{0,1}∗ of length m. The goal is for Bob to (only) learn where his pattern occurs in Alice’s text, while Alice learns nothing. Private pattern matching...... is an important problem that has many applications in the area of DNA search, computational biology and more. Our construction guarantees full simulation in the presence of malicious, polynomial-time adversaries (assuming the hardness of DDH assumption) and exhibits computation and communication costs of O...

  19. High Performance Embedded System for Real-Time Pattern Matching

    CERN Document Server

    Sotiropoulou, Calliope Louisa; The ATLAS collaboration; Gkaitatzis, Stamatios; Citraro, Saverio; Giannetti, Paola; Dell'Orso, Mauro

    2016-01-01

    In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics (HEP) and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturised version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory (AM) chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering...

  20. A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly.

    Science.gov (United States)

    Dinh, Hieu; Rajasekaran, Sanguthevar

    2011-07-15

    Exact-match overlap graphs have been broadly used in the context of DNA assembly and the shortest super string problem where the number of strings n ranges from thousands to billions. The length ℓ of the strings is from 25 to 1000, depending on the DNA sequencing technologies. However, many DNA assemblers using overlap graphs suffer from the need for too much time and space in constructing the graphs. It is nearly impossible for these DNA assemblers to handle the huge amount of data produced by the next-generation sequencing technologies where the number n of strings could be several billions. If the overlap graph is explicitly stored, it would require Ω(n(2)) memory, which could be prohibitive in practice when n is greater than a hundred million. In this article, we propose a novel data structure using which the overlap graph can be compactly stored. This data structure requires only linear time to construct and and linear memory to store. For a given set of input strings (also called reads), we can informally define an exact-match overlap graph as follows. Each read is represented as a node in the graph and there is an edge between two nodes if the corresponding reads overlap sufficiently. A formal description follows. The maximal exact-match overlap of two strings x and y, denoted by ov(max)(x, y), is the longest string which is a suffix of x and a prefix of y. The exact-match overlap graph of n given strings of length ℓ is an edge-weighted graph in which each vertex is associated with a string and there is an edge (x, y) of weight ω=ℓ-|ov(max)(x, y)| if and only if ω ≤ λ, where |ov(max)(x, y)| is the length of ov(max)(x, y) and λ is a given threshold. In this article, we show that the exact-match overlap graphs can be represented by a compact data structure that can be stored using at most (2λ-1)(2⌈logn⌉+⌈logλ⌉)n bits with a guarantee that the basic operation of accessing an edge takes O(log λ) time. We also propose two algorithms for

  1. Statistical density modification using local pattern matching

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.

    2003-01-01

    Statistical density modification can make use of local patterns of density found in protein structures to improve crystallographic phases. A method for improving crystallographic phases is presented that is based on the preferential occurrence of certain local patterns of electron density in macromolecular electron-density maps. The method focuses on the relationship between the value of electron density at a point in the map and the pattern of density surrounding this point. Patterns of density that can be superimposed by rotation about the central point are considered equivalent. Standard templates are created from experimental or model electron-density maps by clustering and averaging local patterns of electron density. The clustering is based on correlation coefficients after rotation to maximize the correlation. Experimental or model maps are also used to create histograms relating the value of electron density at the central point to the correlation coefficient of the density surrounding this point with each member of the set of standard patterns. These histograms are then used to estimate the electron density at each point in a new experimental electron-density map using the pattern of electron density at points surrounding that point and the correlation coefficient of this density to each of the set of standard templates, again after rotation to maximize the correlation. The method is strengthened by excluding any information from the point in question from both the templates and the local pattern of density in the calculation. A function based on the origin of the Patterson function is used to remove information about the electron density at the point in question from nearby electron density. This allows an estimation of the electron density at each point in a map, using only information from other points in the process. The resulting estimates of electron density are shown to have errors that are nearly independent of the errors in the original map using

  2. Loose Graph Simulations

    DEFF Research Database (Denmark)

    Mansutti, Alessio; Miculan, Marino; Peressotti, Marco

    2017-01-01

    We introduce loose graph simulations (LGS), a new notion about labelled graphs which subsumes in an intuitive and natural way subgraph isomorphism (SGI), regular language pattern matching (RLPM) and graph simulation (GS). Being a unification of all these notions, LGS allows us to express directly...... also problems which are “mixed” instances of previous ones, and hence which would not fit easily in any of them. After the definition and some examples, we show that the problem of finding loose graph simulations is NP-complete, we provide formal translation of SGI, RLPM, and GS into LGSs, and we give...

  3. GraMi: Generalized Frequent Pattern Mining in a Single Large Graph

    KAUST Repository

    Saeedy, Mohammed El; Kalnis, Panos

    2011-01-01

    resolution phase as a constraint satisfaction problem, in order to avoid the costly enumeration of all instances of each pattern in the graph. The authors also implemented CGRAMI, a version that supports structural and semantic constraints; and AGRAMI

  4. High performance embedded system for real-time pattern matching

    International Nuclear Information System (INIS)

    Sotiropoulou, C.-L.; Luciano, P.; Gkaitatzis, S.; Citraro, S.; Giannetti, P.; Dell'Orso, M.

    2017-01-01

    In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton–proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering) are also implemented on the FPGA. The pattern matching can be executed on a 2D or 3D space, on black and white or grayscale images, depending on the application and thus increasing exponentially the processing requirements of the system. We present the firmware implementation of the training and pattern matching algorithm, performance and results on a latest generation Xilinx Kintex Ultrascale FPGA device. - Highlights: • A high performance embedded system for real-time pattern matching is proposed. • It is based on a system developed for High Energy Physics experiment triggers. • It mimics the operation of the human brain (cognitive image processing). • The process can be executed on 2D and 3D, black and white or grayscale images. • The implementation uses FPGAs and custom designed associative memory (AM) chips.

  5. High performance embedded system for real-time pattern matching

    Energy Technology Data Exchange (ETDEWEB)

    Sotiropoulou, C.-L., E-mail: c.sotiropoulou@cern.ch [University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa (Italy); INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Luciano, P. [University of Cassino and Southern Lazio, Gaetano di Biasio 43, Cassino 03043 (Italy); INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Gkaitatzis, S. [Aristotle University of Thessaloniki, 54124 Thessaloniki (Greece); Citraro, S. [University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa (Italy); INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Giannetti, P. [INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Dell' Orso, M. [University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa (Italy); INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy)

    2017-02-11

    In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton–proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering) are also implemented on the FPGA. The pattern matching can be executed on a 2D or 3D space, on black and white or grayscale images, depending on the application and thus increasing exponentially the processing requirements of the system. We present the firmware implementation of the training and pattern matching algorithm, performance and results on a latest generation Xilinx Kintex Ultrascale FPGA device. - Highlights: • A high performance embedded system for real-time pattern matching is proposed. • It is based on a system developed for High Energy Physics experiment triggers. • It mimics the operation of the human brain (cognitive image processing). • The process can be executed on 2D and 3D, black and white or grayscale images. • The implementation uses FPGAs and custom designed associative memory (AM) chips.

  6. High Performance Embedded System for Real-Time Pattern Matching

    CERN Document Server

    Sotiropoulou, Calliope Louisa; The ATLAS collaboration; Gkaitatzis, Stamatios; Citraro, Saverio; Giannetti, Paola; Dell'Orso, Mauro

    2016-01-01

    We present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics (HEP) and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The design uses the flexibility of Field Programmable Gate Arrays (FPGAs) and the powerful Associative Memory Chip (ASIC) to achieve real-time performance. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain.

  7. Sleep patterns and match performance in elite Australian basketball athletes.

    Science.gov (United States)

    Staunton, Craig; Gordon, Brett; Custovic, Edhem; Stanger, Jonathan; Kingsley, Michael

    2017-08-01

    To assess sleep patterns and associations between sleep and match performance in elite Australian female basketball players. Prospective cohort study. Seventeen elite female basketball players were monitored across two consecutive in-season competitions (30 weeks). Total sleep time and sleep efficiency were determined using triaxial accelerometers for Baseline, Pre-match, Match-day and Post-match timings. Match performance was determined using the basketball efficiency statistic (EFF). The effects of match schedule (Regular versus Double-Header; Home versus Away) and sleep on EFF were assessed. The Double-Header condition changed the pattern of sleep when compared with the Regular condition (F (3,48) =3.763, P=0.017), where total sleep time Post-match was 11% less for Double-Header (mean±SD; 7.2±1.4h) compared with Regular (8.0±1.3h; P=0.007). Total sleep time for Double-Header was greater Pre-match (8.2±1.7h) compared with Baseline (7.1±1.6h; P=0.022) and Match-day (7.3±1.5h; P=0.007). Small correlations existed between sleep metrics at Pre-match and EFF for pooled data (r=-0.39 to -0.22; P≥0.238). Relationships between total sleep time and EFF ranged from moderate negative to large positive correlations for individual players (r=-0.37 to 0.62) and reached significance for one player (r=0.60; P=0.025). Match schedule can affect the sleep patterns of elite female basketball players. A large degree of inter-individual variability existed in the relationship between sleep and match performance; nevertheless, sleep monitoring might assist in the optimisation of performance for some athletes. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  8. Betting on Illusory Patterns: Probability Matching in Habitual Gamblers.

    Science.gov (United States)

    Gaissmaier, Wolfgang; Wilke, Andreas; Scheibehenne, Benjamin; McCanney, Paige; Barrett, H Clark

    2016-03-01

    Why do people gamble? A large body of research suggests that cognitive distortions play an important role in pathological gambling. Many of these distortions are specific cases of a more general misperception of randomness, specifically of an illusory perception of patterns in random sequences. In this article, we provide further evidence for the assumption that gamblers are particularly prone to perceiving illusory patterns. In particular, we compared habitual gamblers to a matched sample of community members with regard to how much they exhibit the choice anomaly 'probability matching'. Probability matching describes the tendency to match response proportions to outcome probabilities when predicting binary outcomes. It leads to a lower expected accuracy than the maximizing strategy of predicting the most likely event on each trial. Previous research has shown that an illusory perception of patterns in random sequences fuels probability matching. So does impulsivity, which is also reported to be higher in gamblers. We therefore hypothesized that gamblers will exhibit more probability matching than non-gamblers, which was confirmed in a controlled laboratory experiment. Additionally, gamblers scored much lower than community members on the cognitive reflection task, which indicates higher impulsivity. This difference could account for the difference in probability matching between the samples. These results suggest that gamblers are more willing to bet impulsively on perceived illusory patterns.

  9. Maximum-entropy networks pattern detection, network reconstruction and graph combinatorics

    CERN Document Server

    Squartini, Tiziano

    2017-01-01

    This book is an introduction to maximum-entropy models of random graphs with given topological properties and their applications. Its original contribution is the reformulation of many seemingly different problems in the study of both real networks and graph theory within the unified framework of maximum entropy. Particular emphasis is put on the detection of structural patterns in real networks, on the reconstruction of the properties of networks from partial information, and on the enumeration and sampling of graphs with given properties.  After a first introductory chapter explaining the motivation, focus, aim and message of the book, chapter 2 introduces the formal construction of maximum-entropy ensembles of graphs with local topological constraints. Chapter 3 focuses on the problem of pattern detection in real networks and provides a powerful way to disentangle nontrivial higher-order structural features from those that can be traced back to simpler local constraints. Chapter 4 focuses on the problem o...

  10. A robust approach towards unknown transformation, regional adjacency graphs, multigraph matching, segmentation video frames from unnamed aerial vehicles (UAV)

    Science.gov (United States)

    Gohatre, Umakant Bhaskar; Patil, Venkat P.

    2018-04-01

    In computer vision application, the multiple object detection and tracking, in real-time operation is one of the important research field, that have gained a lot of attentions, in last few years for finding non stationary entities in the field of image sequence. The detection of object is advance towards following the moving object in video and then representation of object is step to track. The multiple object recognition proof is one of the testing assignment from detection multiple objects from video sequence. The picture enrollment has been for quite some time utilized as a reason for the location the detection of moving multiple objects. The technique of registration to discover correspondence between back to back casing sets in view of picture appearance under inflexible and relative change. The picture enrollment is not appropriate to deal with event occasion that can be result in potential missed objects. In this paper, for address such problems, designs propose novel approach. The divided video outlines utilizing area adjancy diagram of visual appearance and geometric properties. Then it performed between graph sequences by using multi graph matching, then getting matching region labeling by a proposed graph coloring algorithms which assign foreground label to respective region. The plan design is robust to unknown transformation with significant improvement in overall existing work which is related to moving multiple objects detection in real time parameters.

  11. Kangaroo – A pattern-matching program for biological sequences

    Directory of Open Access Journals (Sweden)

    Betel Doron

    2002-07-01

    Full Text Available Abstract Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats.

  12. PATTERN CLASSIFICATION APPROACHES TO MATCHING BUILDING POLYGONS AT MULTIPLE SCALES

    Directory of Open Access Journals (Sweden)

    X. Zhang

    2012-07-01

    Full Text Available Matching of building polygons with different levels of detail is crucial in the maintenance and quality assessment of multi-representation databases. Two general problems need to be addressed in the matching process: (1 Which criteria are suitable? (2 How to effectively combine different criteria to make decisions? This paper mainly focuses on the second issue and views data matching as a supervised pattern classification. Several classifiers (i.e. decision trees, Naive Bayes and support vector machines are evaluated for the matching task. Four criteria (i.e. position, size, shape and orientation are used to extract information for these classifiers. Evidence shows that these classifiers outperformed the weighted average approach.

  13. A new taxonomy of sublinear keyword pattern matching algorithms

    NARCIS (Netherlands)

    Cleophas, L.G.W.A.; Watson, B.W.; Zwaan, G.

    2004-01-01

    Abstract This paper presents a new taxonomy of sublinear (multiple) keyword pattern matching algorithms. Based on an earlier taxonomy by Watson and Zwaan [WZ96, WZ95], this new taxonomy includes not only suffix-based algorithms related to the Boyer-Moore, Commentz-Walter and Fan-Su algorithms, but

  14. Construction of basic match schedules for sports competitions by using graph theory

    NARCIS (Netherlands)

    van Weert, Arjan; Schreuder, J.A.M.; Burke, Edmund; Carter, Michael

    1997-01-01

    Basic Match Schedules are important for constructing sports timetables. Firstly these schedules guarantee the fairness of the sports competitions and secondly they reduce the complexity of the problem. This paper presents an approach to the problem of finding Basic Match Schedules for sports

  15. Evaluating structural pattern recognition for handwritten math via primitive label graphs

    Science.gov (United States)

    Zanibbi, Richard; Mouchère, Harold; Viard-Gaudin, Christian

    2013-01-01

    Currently, structural pattern recognizer evaluations compare graphs of detected structure to target structures (i.e. ground truth) using recognition rates, recall and precision for object segmentation, classification and relationships. In document recognition, these target objects (e.g. symbols) are frequently comprised of multiple primitives (e.g. connected components, or strokes for online handwritten data), but current metrics do not characterize errors at the primitive level, from which object-level structure is obtained. Primitive label graphs are directed graphs defined over primitives and primitive pairs. We define new metrics obtained by Hamming distances over label graphs, which allow classification, segmentation and parsing errors to be characterized separately, or using a single measure. Recall and precision for detected objects may also be computed directly from label graphs. We illustrate the new metrics by comparing a new primitive-level evaluation to the symbol-level evaluation performed for the CROHME 2012 handwritten math recognition competition. A Python-based set of utilities for evaluating, visualizing and translating label graphs is publicly available.

  16. Functional classification of protein structures by local structure matching in graph representation.

    Science.gov (United States)

    Mills, Caitlyn L; Garg, Rohan; Lee, Joslynn S; Tian, Liang; Suciu, Alexandru; Cooperman, Gene; Beuning, Penny J; Ondrechen, Mary Jo

    2018-03-31

    As a result of high-throughput protein structure initiatives, over 14,400 protein structures have been solved by structural genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP-Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP-Func method to our previously reported method, structurally aligned local sites of activity (SALSA), using the ribulose phosphate binding barrel (RPBB), 6-hairpin glycosidase (6-HG), and Concanavalin A-like Lectins/Glucanase (CAL/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP-Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP-Func methods to predict function. Forty-one SG proteins in the RPBB superfamily, nine SG proteins in the 6-HG superfamily, and one SG protein in the CAL/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  17. REGULAR PATTERN MINING (WITH JITTER ON WEIGHTED-DIRECTED DYNAMIC GRAPHS

    Directory of Open Access Journals (Sweden)

    A. GUPTA

    2017-02-01

    Full Text Available Real world graphs are mostly dynamic in nature, exhibiting time-varying behaviour in structure of the graph, weight on the edges and direction of the edges. Mining regular patterns in the occurrence of edge parameters gives an insight into the consumer trends over time in ecommerce co-purchasing networks. But such patterns need not necessarily be precise as in the case when some product goes out of stock or a group of customers becomes unavailable for a short period of time. Ignoring them may lead to loss of useful information and thus taking jitter into account becomes vital. To the best of our knowledge, no work has been yet reported to extract regular patterns considering a jitter of length greater than unity. In this article, we propose a novel method to find quasi regular patterns on weight and direction sequences of such graphs. The method involves analysing the dynamic network considering the inconsistencies in the occurrence of edges. It utilizes the relation between the occurrence sequence and the corresponding weight and direction sequences to speed up this process. Further, these patterns are used to determine the most central nodes (such as the most profit yielding products. To accomplish this we introduce the concept of dynamic closeness centrality and dynamic betweenness centrality. Experiments on Enron e-mail dataset and a synthetic dynamic network show that the presented approach is efficient, so it can be used to find patterns in large scale networks consisting of many timestamps.

  18. Incremental View Maintenance for Deductive Graph Databases Using Generalized Discrimination Networks

    Directory of Open Access Journals (Sweden)

    Thomas Beyhl

    2016-12-01

    Full Text Available Nowadays, graph databases are employed when relationships between entities are in the scope of database queries to avoid performance-critical join operations of relational databases. Graph queries are used to query and modify graphs stored in graph databases. Graph queries employ graph pattern matching that is NP-complete for subgraph isomorphism. Graph database views can be employed that keep ready answers in terms of precalculated graph pattern matches for often stated and complex graph queries to increase query performance. However, such graph database views must be kept consistent with the graphs stored in the graph database. In this paper, we describe how to use incremental graph pattern matching as technique for maintaining graph database views. We present an incremental maintenance algorithm for graph database views, which works for imperatively and declaratively specified graph queries. The evaluation shows that our maintenance algorithm scales when the number of nodes and edges stored in the graph database increases. Furthermore, our evaluation shows that our approach can outperform existing approaches for the incremental maintenance of graph query results.

  19. Attention Modulates Visual-Tactile Interaction in Spatial Pattern Matching

    Science.gov (United States)

    Göschl, Florian; Engel, Andreas K.; Friese, Uwe

    2014-01-01

    Factors influencing crossmodal interactions are manifold and operate in a stimulus-driven, bottom-up fashion, as well as via top-down control. Here, we evaluate the interplay of stimulus congruence and attention in a visual-tactile task. To this end, we used a matching paradigm requiring the identification of spatial patterns that were concurrently presented visually on a computer screen and haptically to the fingertips by means of a Braille stimulator. Stimulation in our paradigm was always bimodal with only the allocation of attention being manipulated between conditions. In separate blocks of the experiment, participants were instructed to (a) focus on a single modality to detect a specific target pattern, (b) pay attention to both modalities to detect a specific target pattern, or (c) to explicitly evaluate if the patterns in both modalities were congruent or not. For visual as well as tactile targets, congruent stimulus pairs led to quicker and more accurate detection compared to incongruent stimulation. This congruence facilitation effect was more prominent under divided attention. Incongruent stimulation led to behavioral decrements under divided attention as compared to selectively attending a single sensory channel. Additionally, when participants were asked to evaluate congruence explicitly, congruent stimulation was associated with better performance than incongruent stimulation. Our results extend previous findings from audiovisual studies, showing that stimulus congruence also resulted in behavioral improvements in visuotactile pattern matching. The interplay of stimulus processing and attentional control seems to be organized in a highly flexible fashion, with the integration of signals depending on both bottom-up and top-down factors, rather than occurring in an ‘all-or-nothing’ manner. PMID:25203102

  20. Attention modulates visual-tactile interaction in spatial pattern matching.

    Directory of Open Access Journals (Sweden)

    Florian Göschl

    Full Text Available Factors influencing crossmodal interactions are manifold and operate in a stimulus-driven, bottom-up fashion, as well as via top-down control. Here, we evaluate the interplay of stimulus congruence and attention in a visual-tactile task. To this end, we used a matching paradigm requiring the identification of spatial patterns that were concurrently presented visually on a computer screen and haptically to the fingertips by means of a Braille stimulator. Stimulation in our paradigm was always bimodal with only the allocation of attention being manipulated between conditions. In separate blocks of the experiment, participants were instructed to (a focus on a single modality to detect a specific target pattern, (b pay attention to both modalities to detect a specific target pattern, or (c to explicitly evaluate if the patterns in both modalities were congruent or not. For visual as well as tactile targets, congruent stimulus pairs led to quicker and more accurate detection compared to incongruent stimulation. This congruence facilitation effect was more prominent under divided attention. Incongruent stimulation led to behavioral decrements under divided attention as compared to selectively attending a single sensory channel. Additionally, when participants were asked to evaluate congruence explicitly, congruent stimulation was associated with better performance than incongruent stimulation. Our results extend previous findings from audiovisual studies, showing that stimulus congruence also resulted in behavioral improvements in visuotactile pattern matching. The interplay of stimulus processing and attentional control seems to be organized in a highly flexible fashion, with the integration of signals depending on both bottom-up and top-down factors, rather than occurring in an 'all-or-nothing' manner.

  1. Matching theory

    CERN Document Server

    Plummer, MD

    1986-01-01

    This study of matching theory deals with bipartite matching, network flows, and presents fundamental results for the non-bipartite case. It goes on to study elementary bipartite graphs and elementary graphs in general. Further discussed are 2-matchings, general matching problems as linear programs, the Edmonds Matching Algorithm (and other algorithmic approaches), f-factors and vertex packing.

  2. Automatic micropropagation of plants--the vision-system: graph rewriting as pattern recognition

    Science.gov (United States)

    Schwanke, Joerg; Megnet, Roland; Jensch, Peter F.

    1993-03-01

    The automation of plant-micropropagation is necessary to produce high amounts of biomass. Plants have to be dissected on particular cutting-points. A vision-system is needed for the recognition of the cutting-points on the plants. With this background, this contribution is directed to the underlying formalism to determine cutting-points on abstract-plant models. We show the usefulness of pattern recognition by graph-rewriting along with some examples in this context.

  3. Highly Parallelized Pattern Matching Execution for the ATLAS Experiment

    CERN Document Server

    Citraro, Saverio; The ATLAS collaboration

    2015-01-01

    The trigger system of the ATLAS experiment at LHC will extend its rejection capabilities during operations in 2015-2018 by introducing the Fast TracKer system (FTK). FTK is a hardware based system capable of finding charged particle tracks by analyzing hits in silicon detectors at the rate of 105 events per second. The core of track reconstruction is performed into two pipelined steps. At first step the candidate tracks are found by matching combination of low resolution hits to predefined patterns; then they are used in the second step to seed a more precise track fitting algorithm. The key FTK component is an Associative Memory (AM) system that is used to perform pattern matching with high degree of parallelism. The AM system implementation, the AM Serial Link Processor, is based on an extremely powerful network of 2 Gb/s serial links to sustain a huge traffic of data. We report on the design of the Serial Link Processor consisting of two types of boards, the Little Associative Memory Board (LAMB), a mezzan...

  4. Highly Parallelized Pattern Matching Execution for the ATLAS Experiment

    CERN Document Server

    Citraro, Saverio; The ATLAS collaboration

    2015-01-01

    Abstract– The Associative Memory (AM) system of the Fast Tracker (FTK) processor has been designed to perform pattern matching using as input the data from the silicon tracker in the ATLAS experiment. The AM is the primary component of the FTK system and is designed using ASIC technology (the AM chip) to execute pattern matching with a high degree of parallelism. The FTK system finds track candidates at low resolution that are seeds for a full resolution track fitting. The AM system implementation is named “Serial Link Processor” and is based on an extremely powerful network of 2 Gb/s serial links to sustain a huge traffic of data. This paper reports on the design of the Serial Link Processor consisting of two types of boards, the Little Associative Memory Board (LAMB), a mezzanine where the AM chips are mounted, and the Associative Memory Board (AMB), a 9U VME motherboard which hosts four LAMB daughterboards. We also report on the performance of the prototypes (both hardware and firmware) produced and ...

  5. Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2

    Science.gov (United States)

    da Silva Figueiredo Celestino Gomes, Priscila; Da Silva, Franck; Bret, Guillaume; Rognan, Didier

    2018-01-01

    A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the public release of their bound X-ray structures and potencies. In a first phase, 36 agonists were docked to 26 Protein Data Bank (PDB) structures of the FXR receptor, and next rescored using the in-house developed GRIM method. GRIM aligns protein-ligand interaction patterns of docked poses to those of available PDB templates for the target protein, and rescore poses by a graph matching method. In agreement with results obtained during the previous 2015 docking challenge, we clearly show that GRIM rescoring improves the overall quality of top-ranked poses by prioritizing interaction patterns already visited in the PDB. Importantly, this challenge enables us to refine the applicability domain of the method by better defining the conditions of its success. We notably show that rescoring apolar ligands in hydrophobic pockets leads to frequent GRIM failures. In the second phase, 102 FXR agonists were ranked by decreasing affinity according to the Gibbs free energy of the corresponding GRIM-selected poses, computed by the HYDE scoring function. Interestingly, this fast and simple rescoring scheme provided the third most accurate ranking method among 57 contributions. Although the obtained ranking is still unsuitable for hit to lead optimization, the GRIM-HYDE scoring scheme is accurate and fast enough to post-process virtual screening data.

  6. On the exactness of the cavity method for weighted b-matchings on arbitrary graphs and its relation to linear programs

    International Nuclear Information System (INIS)

    Bayati, Mohsen; Borgs, Christian; Chayes, Jennifer; Zecchina, Riccardo

    2008-01-01

    We consider the general problem of finding the minimum weight b-matching on arbitrary graphs. We prove that, whenever the linear programing relaxation of the problem has no fractional solutions, then the cavity or belief propagation equations converge to the correct solution both for synchronous and asynchronous updating. (letter)

  7. EEG analysis of seizure patterns using visibility graphs for detection of generalized seizures.

    Science.gov (United States)

    Wang, Lei; Long, Xi; Arends, Johan B A M; Aarts, Ronald M

    2017-10-01

    The traditional EEG features in the time and frequency domain show limited seizure detection performance in the epileptic population with intellectual disability (ID). In addition, the influence of EEG seizure patterns on detection performance was less studied. A single-channel EEG signal can be mapped into visibility graphs (VGS), including basic visibility graph (VG), horizontal VG (HVG), and difference VG (DVG). These graphs were used to characterize different EEG seizure patterns. To demonstrate its effectiveness in identifying EEG seizure patterns and detecting generalized seizures, EEG recordings of 615h on one EEG channel from 29 epileptic patients with ID were analyzed. A novel feature set with discriminative power for seizure detection was obtained by using the VGS method. The degree distributions (DDs) of DVG can clearly distinguish EEG of each seizure pattern. The degree entropy and power-law degree power in DVG were proposed here for the first time, and they show significant difference between seizure and non-seizure EEG. The connecting structure measured by HVG can better distinguish seizure EEG from background than those by VG and DVG. A traditional EEG feature set based on frequency analysis was used here as a benchmark feature set. With a support vector machine (SVM) classifier, the seizure detection performance of the benchmark feature set (sensitivity of 24%, FD t /h of 1.8s) can be improved by combining our proposed VGS features extracted from one EEG channel (sensitivity of 38%, FD t /h of 1.4s). The proposed VGS-based features can help improve seizure detection for ID patients. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Pragmatic Graph Rewriting Modifications

    OpenAIRE

    Rodgers, Peter; Vidal, Natalia

    1999-01-01

    We present new pragmatic constructs for easing programming in visual graph rewriting programming languages. The first is a modification to the rewriting process for nodes the host graph, where nodes specified as 'Once Only' in the LHS of a rewrite match at most once with a corresponding node in the host graph. This reduces the previously common use of tags to indicate the progress of matching in the graph. The second modification controls the application of LHS graphs, where those specified a...

  9. Pattern analysis of directed graphs using DEDICOM: an application to Enron email.

    Energy Technology Data Exchange (ETDEWEB)

    Bader, Brett William; Harshman, Richard A. (University of Western Ontario London, Ontario, Canada); Kolda, Tamara Gibson (Sandia National Labs, Livermore, CA)

    2006-12-01

    DEDICOM is a linear algebra model for analyzing intrinsically asymmetric relationships, such as trade among nations or the exchange of emails among individuals. DEDICOM decomposes a complex pattern of observed relations among objects into a sum of simpler patterns of inferred relations among latent components of the objects. Three-way DEDICOM is a higher-order extension of the model that incorporates a third mode of the data, such as time, giving it stronger uniqueness properties and consequently enhancing interpretability of solutions. In this paper, we present algorithms for computing these decompositions on large, sparse data as well as a variant for computing an asymmetric nonnegative factorization. When we apply these techniques to adjacency arrays arising from directed graphs with edges labeled by time, we obtain a smaller graph on latent semantic dimensions and gain additional information about their changing relationships over time. We demonstrate these techniques on the Enron email corpus to learn about the social networks and their transient behavior. The mixture of roles assigned to individuals by DEDICOM showed strong correspondence with known job classifications and revealed the patterns of communication between these roles. Changes in the communication pattern over time, e.g., between top executives and the legal department, were also apparent in the solutions.

  10. Optimizing Fukushima Emissions Through Pattern Matching and Genetic Algorithms

    Science.gov (United States)

    Lucas, D. D.; Simpson, M. D.; Philip, C. S.; Baskett, R.

    2017-12-01

    Hazardous conditions during the Fukushima Daiichi nuclear power plant (NPP) accident hindered direct observations of the emissions of radioactive materials into the atmosphere. A wide range of emissions are estimated from bottom-up studies using reactor inventories and top-down approaches based on inverse modeling. We present a new inverse modeling estimate of cesium-137 emitted from the Fukushima NPP. Our estimate considers weather uncertainty through a large ensemble of Weather Research and Forecasting model simulations and uses the FLEXPART atmospheric dispersion model to transport and deposit cesium. The simulations are constrained by observations of the spatial distribution of cumulative cesium deposited on the surface of Japan through April 2, 2012. Multiple spatial metrics are used to quantify differences between observed and simulated deposition patterns. In order to match the observed pattern, we use a multi-objective genetic algorithm to optimize the time-varying emissions. We find that large differences with published bottom-up estimates are required to explain the observations. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  11. Recognition of building group patterns in topographic maps based on graph partitioning and random forest

    Science.gov (United States)

    He, Xianjin; Zhang, Xinchang; Xin, Qinchuan

    2018-02-01

    Recognition of building group patterns (i.e., the arrangement and form exhibited by a collection of buildings at a given mapping scale) is important to the understanding and modeling of geographic space and is hence essential to a wide range of downstream applications such as map generalization. Most of the existing methods develop rigid rules based on the topographic relationships between building pairs to identify building group patterns and thus their applications are often limited. This study proposes a method to identify a variety of building group patterns that allow for map generalization. The method first identifies building group patterns from potential building clusters based on a machine-learning algorithm and further partitions the building clusters with no recognized patterns based on the graph partitioning method. The proposed method is applied to the datasets of three cities that are representative of the complex urban environment in Southern China. Assessment of the results based on the reference data suggests that the proposed method is able to recognize both regular (e.g., the collinear, curvilinear, and rectangular patterns) and irregular (e.g., the L-shaped, H-shaped, and high-density patterns) building group patterns well, given that the correctness values are consistently nearly 90% and the completeness values are all above 91% for three study areas. The proposed method shows promises in automated recognition of building group patterns that allows for map generalization.

  12. Generalised power graph compression reveals dominant relationship patterns in complex networks.

    Science.gov (United States)

    Ahnert, Sebastian E

    2014-03-25

    We introduce a framework for the discovery of dominant relationship patterns in complex networks, by compressing the networks into power graphs with overlapping power nodes. When paired with enrichment analysis of node classification terms, the most compressible sets of edges provide a highly informative sketch of the dominant relationship patterns that define the network. In addition, this procedure also gives rise to a novel, link-based definition of overlapping node communities in which nodes are defined by their relationships with sets of other nodes, rather than through connections within the community. We show that this completely general approach can be applied to undirected, directed, and bipartite networks, yielding valuable insights into the large-scale structure of real-world networks, including social networks and food webs. Our approach therefore provides a novel way in which network architecture can be studied, defined and classified.

  13. Chromatic graph theory

    CERN Document Server

    Chartrand, Gary; Rosen, Kenneth H

    2008-01-01

    Beginning with the origin of the four color problem in 1852, the field of graph colorings has developed into one of the most popular areas of graph theory. Introducing graph theory with a coloring theme, Chromatic Graph Theory explores connections between major topics in graph theory and graph colorings as well as emerging topics. This self-contained book first presents various fundamentals of graph theory that lie outside of graph colorings, including basic terminology and results, trees and connectivity, Eulerian and Hamiltonian graphs, matchings and factorizations, and graph embeddings. The remainder of the text deals exclusively with graph colorings. It covers vertex colorings and bounds for the chromatic number, vertex colorings of graphs embedded on surfaces, and a variety of restricted vertex colorings. The authors also describe edge colorings, monochromatic and rainbow edge colorings, complete vertex colorings, several distinguishing vertex and edge colorings, and many distance-related vertex coloring...

  14. GRAMI: Frequent subgraph and pattern mining in a single large graph

    KAUST Repository

    Elseidy, M.; Abdelhamid, Ehab; Skiadopoulos, S.; Kalnis, Panos

    2014-01-01

    Mining frequent subgraphs is an important operation on graphs; it is defined as finding all subgraphs that appear frequently in a database according to a given frequency threshold. Most existing work assumes a database of many small graphs

  15. The effect of football matches on crime patterns in Barcelona

    OpenAIRE

    Struse, Simon Planells; Montolio, Daniel

    2014-01-01

    Given the actual debate, in many European countries, about the need for public administrations to raise their revenues through taxing the crime externalities generated by some private leisure activities, this article analyzes the effect of football matches on crime focusing both on property crimes and interpersonal violent crimes. Our aim is to determine up to what extent a private leisure activity, such as football matches, induces negative crime externalities to the whole society. Using dat...

  16. Graph theoretical analysis reveals the reorganization of the brain network pattern in primary open angle glaucoma patients

    International Nuclear Information System (INIS)

    Wang, Jieqiong; Li, Ting; Xian, Junfang; Wang, Ningli; He, Huiguang

    2016-01-01

    Most previous glaucoma studies with resting-state fMRI have focused on the neuronal activity in the individual structure of the brain, yet ignored the functional communication of anatomically separated structures. The purpose of this study is to investigate the efficiency of the functional communication change or not in glaucoma patients. We applied the resting-state fMRI data to construct the connectivity network of 25 normal controls and 25 age-gender-matched primary open angle glaucoma patients. Graph theoretical analysis was performed to assess brain network pattern differences between the two groups. No significant differences of the global network measures were found between the two groups. However, the local measures were radically reorganized in glaucoma patients. Comparing with the hub regions in normal controls' network, we found that six hub regions disappeared and nine hub regions appeared in the network of patients. In addition, the betweenness centralities of two altered hub regions, right fusiform gyrus and right lingual gyrus, were significantly correlated with the visual field mean deviation. Although the efficiency of functional communication is preserved in the brain network of the glaucoma at the global level, the efficiency of functional communication is altered in some specialized regions of the glaucoma. (orig.)

  17. Graph theoretical analysis reveals the reorganization of the brain network pattern in primary open angle glaucoma patients

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jieqiong [Chinese Academy of Sciences, State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Beijing (China); Li, Ting; Xian, Junfang [Capital Medical University, Department of Radiology, Beijing Tongren Hospital, Beijing (China); Wang, Ningli [Capital Medical University, Department of Ophthalmology, Beijing Tongren Hospital, Beijing (China); He, Huiguang [Chinese Academy of Sciences, State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Beijing (China); Chinese Academy of Sciences, Research Center for Brain-Inspired Intelligence, Institute of Automation, Beijing (China)

    2016-11-15

    Most previous glaucoma studies with resting-state fMRI have focused on the neuronal activity in the individual structure of the brain, yet ignored the functional communication of anatomically separated structures. The purpose of this study is to investigate the efficiency of the functional communication change or not in glaucoma patients. We applied the resting-state fMRI data to construct the connectivity network of 25 normal controls and 25 age-gender-matched primary open angle glaucoma patients. Graph theoretical analysis was performed to assess brain network pattern differences between the two groups. No significant differences of the global network measures were found between the two groups. However, the local measures were radically reorganized in glaucoma patients. Comparing with the hub regions in normal controls' network, we found that six hub regions disappeared and nine hub regions appeared in the network of patients. In addition, the betweenness centralities of two altered hub regions, right fusiform gyrus and right lingual gyrus, were significantly correlated with the visual field mean deviation. Although the efficiency of functional communication is preserved in the brain network of the glaucoma at the global level, the efficiency of functional communication is altered in some specialized regions of the glaucoma. (orig.)

  18. RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

    Science.gov (United States)

    Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

    2015-01-01

    Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619

  19. Rotation and scale change invariant point pattern relaxation matching by the Hopfield neural network

    Science.gov (United States)

    Sang, Nong; Zhang, Tianxu

    1997-12-01

    Relaxation matching is one of the most relevant methods for image matching. The original relaxation matching technique using point patterns is sensitive to rotations and scale changes. We improve the original point pattern relaxation matching technique to be invariant to rotations and scale changes. A method that makes the Hopfield neural network perform this matching process is discussed. An advantage of this is that the relaxation matching process can be performed in real time with the neural network's massively parallel capability to process information. Experimental results with large simulated images demonstrate the effectiveness and feasibility of the method to perform point patten relaxation matching invariant to rotations and scale changes and the method to perform this matching by the Hopfield neural network. In addition, we show that the method presented can be tolerant to small random error.

  20. Strategy and pattern recognition in expert\\ud comprehension of 2 × 2 interaction graphs

    OpenAIRE

    Peebles, David

    2013-01-01

    I present a model of expert comprehension performance for 2 × 2 "interaction" graphs typically used to present data from two-way factorial research designs. Developed using the ACT-R cognitive architecture, the model simulates the cognitive and perceptual operations involved in interpreting interaction graphs and provides a detailed characterisation of the information\\ud extracted from the diagram, the prior knowledge required to interpret interaction graphs, and the knowledge generated durin...

  1. LPaMI: A Graph-Based Lifestyle Pattern Mining Application Using Personal Image Collections in Smartphones

    Directory of Open Access Journals (Sweden)

    Kifayat Ullah Khan

    2017-11-01

    Full Text Available Normally, individuals use smartphones for a variety of purposes like photography, schedule planning, playing games, and so on, apart from benefiting from the core tasks of call-making and short messaging. These services are sources of personal data generation. Therefore, any application that utilises personal data of a user from his/her smartphone is truly a great witness of his/her interests and this information can be used for various personalised services. In this paper, we present Lifestyle Pattern MIning (LPaMI, which is a personalised application for mining the lifestyle patterns of a smartphone user. LPaMI uses the personal photograph collections of a user, which reflect the day-to-day photos taken by a smartphone, to recognise scenes (called objects of interest in our work. These are then mined to discover lifestyle patterns. The uniqueness of LPaMI lies in our graph-based approach to mining the patterns of interest. Modelling of data in the form of graphs is effective in preserving the lifestyle behaviour maintained over the passage of time. Graph-modelled lifestyle data enables us to apply variety of graph mining techniques for pattern discovery. To demonstrate the effectiveness of our proposal, we have developed a prototype system for LPaMI to implement its end-to-end pipeline. We have also conducted an extensive evaluation for various phases of LPaMI using different real-world datasets. We understand that the output of LPaMI can be utilised for variety of pattern discovery application areas like trip and food recommendations, shopping, and so on.

  2. What makes a pattern? Matching decoding methods to data in multivariate pattern analysis

    Directory of Open Access Journals (Sweden)

    Philip A Kragel

    2012-11-01

    Full Text Available Research in neuroscience faces the challenge of integrating information across different spatial scales of brain function. A promising technique for harnessing information at a range of spatial scales is multivariate pattern analysis (MVPA of functional magnetic resonance imaging (fMRI data. While the prevalence of MVPA has increased dramatically in recent years, its typical implementations for classification of mental states utilize only a subset of the information encoded in local fMRI signals. We review published studies employing multivariate pattern classification since the technique’s introduction, which reveal an extensive focus on the improved detection power that linear classifiers provide over traditional analysis techniques. We demonstrate using simulations and a searchlight approach, however, that nonlinear classifiers are capable of extracting distinct information about interactions within a local region. We conclude that for spatially localized analyses, such as searchlight and region of interest, multiple classification approaches should be compared in order to match fMRI analyses to the properties of local circuits.

  3. Rating Algorithm for Pronunciation of English Based on Audio Feature Pattern Matching

    Directory of Open Access Journals (Sweden)

    Li Kun

    2015-01-01

    Full Text Available With the increasing internationalization of China, language communication has become an important channel for us to adapt to the political and economic environment. How to improve English learners’ language learning efficiency in limited conditions has turned into a problem demanding prompt solution at present. This paper applies two pronunciation patterns according to the actual needs of English pronunciation rating: to-be-evaluated pronunciation pattern and standard pronunciation pattern. It will translate the patterns into English pronunciation rating results through European distance. Besides, this paper will introduce the design philosophy of the whole algorithm in combination with CHMM matching pattern. Each link of the CHMM pattern will be given selective analysis while a contrast experiment between the CHMM matching pattern and the other two patterns will be conducted. From the experiment results, it can be concluded that CHMM pattern is the best option.

  4. A Vision Chip for Color Segmentation and Pattern Matching

    Directory of Open Access Journals (Sweden)

    Ralph Etienne-Cummings

    2003-06-01

    Full Text Available A 128(H × 64(V × RGB CMOS imager is integrated with region-of-interest selection, RGB-to-HSI transformation, HSI-based pixel segmentation, (36bins × 12bits-HSI histogramming, and sum-of-absolute-difference (SAD template matching. Thirty-two learned color templates are stored and compared to each image. The chip captures the R, G, and B images using in-pixel storage before passing the pixel content to a multiplying digital-to-analog converter (DAC for white balancing. The DAC can also be used to pipe in images for a PC. The color processing uses a biologically inspired color opponent representation and an analog lookup table to determine the Hue (H of each pixel. Saturation (S is computed using a loser-take-all circuit. Intensity (I is given by the sum of the color components. A histogram of the segments of the image, constructed by counting the number of pixels falling into 36 Hue intervals of 10 degrees, is stored on a chip and compared against the histograms of new segments using SAD comparisons. We demonstrate color-based image segmentation and object recognition with this chip. Running at 30 fps, it uses 1 mW. To our knowledge, this is the first chip that integrates imaging, color segmentation, and color-based object recognition at the focal plane.

  5. Cryptically patterned moths perceive bark structure when choosing body orientations that match wing color pattern to the bark pattern.

    Directory of Open Access Journals (Sweden)

    Chang-Ku Kang

    Full Text Available Many moths have wing patterns that resemble bark of trees on which they rest. The wing patterns help moths to become camouflaged and to avoid predation because the moths are able to assume specific body orientations that produce a very good match between the pattern on the bark and the pattern on the wings. Furthermore, after landing on a bark moths are able to perceive stimuli that correlate with their crypticity and are able to re-position their bodies to new more cryptic locations and body orientations. However, the proximate mechanisms, i.e. how a moth finds an appropriate resting position and orientation, are poorly studied. Here, we used a geometrid moth Jankowskia fuscaria to examine i whether a choice of resting orientation by moths depends on the properties of natural background, and ii what sensory cues moths use. We studied moths' behavior on natural (a tree log and artificial backgrounds, each of which was designed to mimic one of the hypothetical cues that moths may perceive on a tree trunk (visual pattern, directional furrow structure, and curvature. We found that moths mainly used structural cues from the background when choosing their resting position and orientation. Our findings highlight the possibility that moths use information from one type of sensory modality (structure of furrows is probably detected through tactile channel to achieve crypticity in another sensory modality (visual. This study extends our knowledge of how behavior, sensory systems and morphology of animals interact to produce crypsis.

  6. Cryptically patterned moths perceive bark structure when choosing body orientations that match wing color pattern to the bark pattern.

    Science.gov (United States)

    Kang, Chang-Ku; Moon, Jong-Yeol; Lee, Sang-Im; Jablonski, Piotr G

    2013-01-01

    Many moths have wing patterns that resemble bark of trees on which they rest. The wing patterns help moths to become camouflaged and to avoid predation because the moths are able to assume specific body orientations that produce a very good match between the pattern on the bark and the pattern on the wings. Furthermore, after landing on a bark moths are able to perceive stimuli that correlate with their crypticity and are able to re-position their bodies to new more cryptic locations and body orientations. However, the proximate mechanisms, i.e. how a moth finds an appropriate resting position and orientation, are poorly studied. Here, we used a geometrid moth Jankowskia fuscaria to examine i) whether a choice of resting orientation by moths depends on the properties of natural background, and ii) what sensory cues moths use. We studied moths' behavior on natural (a tree log) and artificial backgrounds, each of which was designed to mimic one of the hypothetical cues that moths may perceive on a tree trunk (visual pattern, directional furrow structure, and curvature). We found that moths mainly used structural cues from the background when choosing their resting position and orientation. Our findings highlight the possibility that moths use information from one type of sensory modality (structure of furrows is probably detected through tactile channel) to achieve crypticity in another sensory modality (visual). This study extends our knowledge of how behavior, sensory systems and morphology of animals interact to produce crypsis.

  7. Fast Partial Evaluation of Pattern Matching in Strings

    DEFF Research Database (Denmark)

    Ager, Mads Sig; Danvy, Olivier; Rohde, Henning Korsholm

    2006-01-01

    We show how to obtain all of Knuth, Morris, and Pratt's linear-time string matcher by specializing a quadratic-time string matcher with respect to a pattern string. Although it has been known for 15 years how to obtain this linear matcher by partial evaluation of a quadratic one, how to obtain...... it in linear time has remained an open problem. Obtaining a linear matcher by partial evaluation of a quadratic one is achieved by performing its backtracking at specialization time and memoizing its results. We show (1) how to rewrite the source matcher such that its static intermediate computations can...... be shared at specialization time and (2) how to extend the memoization capabilities of a partial evaluator to static functions. Such an extended partial evaluator, if its memoization is implemented efficiently, specializes the rewritten source matcher in linear time. Finally, we show that the method also...

  8. Fast Partial Evaluation of Pattern Matching in Strings

    DEFF Research Database (Denmark)

    Ager, Mads Sig; Danvy, Olivier; Rohde, Henning Korsholm

    2003-01-01

    We show how to obtain all of Knuth, Morris, and Pratt's linear-time string matcher by specializing a quadratic-time string matcher with respect to a pattern string. Although it has been known for 15 years how to obtain this linear matcher by partial evaluation of a quadratic one, how to obtain...... it in linear time has remained an open problem. Obtaining a linear matcher by partial evaluation of a quadratic one is achieved by performing its backtracking at specialization time and memoizing its results. We show (1) how to rewrite the source matcher such that its static intermediate computations can...... be shared at specialization time and (2) how to extend the memoization capabilities of a partial evaluator to static functions. Such an extended partial evaluator, if its memoization is implemented efficiently, specializes the rewritten source matcher in linear time. Finally, we show that the method also...

  9. Fast Partial Evaluation of Pattern Matching in Strings

    DEFF Research Database (Denmark)

    Ager, Mads Sig; Danvy, Olivier; Rohde, Henning Korsholm

    2003-01-01

    We show how to obtain all of Knuth, Morris, and Pratt's linear-time string matcher by partial evaluation of a quadratic-time string matcher with respect to a pattern string. Although it has been known for 15 years how to obtain this linear matcher by partial evaluation of a quadratic one, how...... to obtain it in linear time has remained an open problem.Obtaining a linear matcher by partial evaluation of a quadratic one is achieved by performing its backtracking at specialization time and memoizing its results. We show (1) how to rewrite the source matcher such that its static intermediate...... computations can be shared at specialization time and (2) how to extend the memoization capabilities of a partial evaluator to static functions. Such an extended partial evaluator, if its memoization is implemented efficiently, specializes the rewritten source matcher in linear time....

  10. Fan fault diagnosis based on symmetrized dot pattern analysis and image matching

    Science.gov (United States)

    Xu, Xiaogang; Liu, Haixiao; Zhu, Hao; Wang, Songling

    2016-07-01

    To detect the mechanical failure of fans, a new diagnostic method based on the symmetrized dot pattern (SDP) analysis and image matching is proposed. Vibration signals of 13 kinds of running states are acquired on a centrifugal fan test bed and reconstructed by the SDP technique. The SDP pattern templates of each running state are established. An image matching method is performed to diagnose the fault. In order to improve the diagnostic accuracy, the single template, multiple templates and clustering fault templates are used to perform the image matching.

  11. A multi-pattern hash-binary hybrid algorithm for URL matching in the HTTP protocol.

    Directory of Open Access Journals (Sweden)

    Ping Zeng

    Full Text Available In this paper, based on our previous multi-pattern uniform resource locator (URL binary-matching algorithm called HEM, we propose an improved multi-pattern matching algorithm called MH that is based on hash tables and binary tables. The MH algorithm can be applied to the fields of network security, data analysis, load balancing, cloud robotic communications, and so on-all of which require string matching from a fixed starting position. Our approach effectively solves the performance problems of the classical multi-pattern matching algorithms. This paper explores ways to improve string matching performance under the HTTP protocol by using a hash method combined with a binary method that transforms the symbol-space matching problem into a digital-space numerical-size comparison and hashing problem. The MH approach has a fast matching speed, requires little memory, performs better than both the classical algorithms and HEM for matching fields in an HTTP stream, and it has great promise for use in real-world applications.

  12. GRAMI: Generalized Frequent Subgraph Mining in Large Graphs

    KAUST Repository

    El Saeedy, Mohammed El Sayed

    2011-07-24

    Mining frequent subgraphs is an important operation on graphs. Most existing work assumes a database of many small graphs, but modern applications, such as social networks, citation graphs or protein-protein interaction in bioinformatics, are modeled as a single large graph. Interesting interactions in such applications may be transitive (e.g., friend of a friend). Existing methods, however, search for frequent isomorphic (i.e., exact match) subgraphs and cannot discover many useful patterns. In this paper we propose GRAMI, a framework that generalizes frequent subgraph mining in a large single graph. GRAMI discovers frequent patterns. A pattern is a graph where edges are generalized to distance-constrained paths. Depending on the definition of the distance function, many instantiations of the framework are possible. Both directed and undirected graphs, as well as multiple labels per vertex, are supported. We developed an efficient implementation of the framework that models the frequency resolution phase as a constraint satisfaction problem, in order to avoid the costly enumeration of all instances of each pattern in the graph. We also implemented CGRAMI, a version that supports structural and semantic constraints; and AGRAMI, an approximate version that supports very large graphs. Our experiments on real data demonstrate that our framework is up to 3 orders of magnitude faster and discovers more interesting patterns than existing approaches.

  13. A Boyer-Moore (or Watson-Watson) type algorithm for regular tree pattern matching

    NARCIS (Netherlands)

    Watson, B.W.; Aarts, E.H.L.; Eikelder, ten H.M.M.; Hemerik, C.; Rem, M.

    1995-01-01

    In this chapter, I outline a new algorithm for regular tree pattern matching. The existence of this algorithm was first mentioned in the statements accompanying my dissertation, [2]. In order to avoid repeating the material in my dissertation, it is assumed that the reader is familiar with Chapters

  14. Length-Bounded Hybrid CPU/GPU Pattern Matching Algorithm for Deep Packet Inspection

    Directory of Open Access Journals (Sweden)

    Yi-Shan Lin

    2017-01-01

    Full Text Available Since frequent communication between applications takes place in high speed networks, deep packet inspection (DPI plays an important role in the network application awareness. The signature-based network intrusion detection system (NIDS contains a DPI technique that examines the incoming packet payloads by employing a pattern matching algorithm that dominates the overall inspection performance. Existing studies focused on implementing efficient pattern matching algorithms by parallel programming on software platforms because of the advantages of lower cost and higher scalability. Either the central processing unit (CPU or the graphic processing unit (GPU were involved. Our studies focused on designing a pattern matching algorithm based on the cooperation between both CPU and GPU. In this paper, we present an enhanced design for our previous work, a length-bounded hybrid CPU/GPU pattern matching algorithm (LHPMA. In the preliminary experiment, the performance and comparison with the previous work are displayed, and the experimental results show that the LHPMA can achieve not only effective CPU/GPU cooperation but also higher throughput than the previous method.

  15. Two related algorithms for root-to-frontier tree pattern matching

    NARCIS (Netherlands)

    Cleophas, L.G.W.A.; Hemerik, C.; Zwaan, G.

    2006-01-01

    Tree pattern matching (TPM) algorithms on ordered, ranked trees play an important role in applications such as compilers and term rewriting systems. Many TPM algorithms appearing in the literature are based on tree automata. For efficiency, these automata should be deterministic, yet deterministic

  16. Post-decomposition optimizations using pattern matching and rule-based clustering for multi-patterning technology

    Science.gov (United States)

    Wang, Lynn T.-N.; Madhavan, Sriram

    2018-03-01

    A pattern matching and rule-based polygon clustering methodology with DFM scoring is proposed to detect decomposition-induced manufacturability detractors and fix the layout designs prior to manufacturing. A pattern matcher scans the layout for pre-characterized patterns from a library. If a pattern were detected, rule-based clustering identifies the neighboring polygons that interact with those captured by the pattern. Then, DFM scores are computed for the possible layout fixes: the fix with the best score is applied. The proposed methodology was applied to two 20nm products with a chip area of 11 mm2 on the metal 2 layer. All the hotspots were resolved. The number of DFM spacing violations decreased by 7-15%.

  17. Phase-locked patterns of the Kuramoto model on 3-regular graphs

    Science.gov (United States)

    DeVille, Lee; Ermentrout, Bard

    2016-09-01

    We consider the existence of non-synchronized fixed points to the Kuramoto model defined on sparse networks: specifically, networks where each vertex has degree exactly three. We show that "most" such networks support multiple attracting phase-locked solutions that are not synchronized and study the depth and width of the basins of attraction of these phase-locked solutions. We also show that it is common in "large enough" graphs to find phase-locked solutions where one or more of the links have angle difference greater than π/2.

  18. Graph Aggregation

    NARCIS (Netherlands)

    Endriss, U.; Grandi, U.

    Graph aggregation is the process of computing a single output graph that constitutes a good compromise between several input graphs, each provided by a different source. One needs to perform graph aggregation in a wide variety of situations, e.g., when applying a voting rule (graphs as preference

  19. Effects of Pattern Matching, Pattern Discrimination, and Experience in the Development of Diagnostic Expertise.

    Science.gov (United States)

    Papa, Frank; And Others

    1990-01-01

    In this study an artificial intelligence assessment tool used disease-by-feature frequency estimates to create disease prototypes for nine common causes of acute chest pain. The tool then used each subject's prototypes and a pattern-recognition-based decision-making mechanism to diagnose 18 myocardial infarction cases. (MLW)

  20. Distorted Pattern Recognition and Analysis with the Help of IEf Graph Representation

    Directory of Open Access Journals (Sweden)

    Adam Sedziwy

    2002-01-01

    Full Text Available An algorithm for distorted pattern recognition is presented. lt's generalization of M Flasinski results (Pattern Recognition, 27, 1-16, 1992. A new formalism allows to make both qualitative and quantitive distortion analysis. It also enlarges parser flexibility by extending the set of patterns which may be recognized.

  1. Receptive fields of locust brain neurons are matched to polarization patterns of the sky.

    Science.gov (United States)

    Bech, Miklós; Homberg, Uwe; Pfeiffer, Keram

    2014-09-22

    Many animals, including insects, are able to use celestial cues as a reference for spatial orientation and long-distance navigation [1]. In addition to direct sunlight, the chromatic gradient of the sky and its polarization pattern are suited to serve as orientation cues [2-5]. Atmospheric scattering of sunlight causes a regular pattern of E vectors in the sky, which are arranged along concentric circles around the sun [5, 6]. Although certain insects rely predominantly on sky polarization for spatial orientation [7], it has been argued that detection of celestial E vector orientation may not suffice to differentiate between solar and antisolar directions [8, 9]. We show here that polarization-sensitive (POL) neurons in the brain of the desert locust Schistocerca gregaria can overcome this ambiguity. Extracellular recordings from POL units in the central complex and lateral accessory lobes revealed E vector tunings arranged in concentric circles within large receptive fields, matching the sky polarization pattern at certain solar positions. Modeling of neuronal responses under an idealized sky polarization pattern (Rayleigh sky) suggests that these "matched filter" properties allow locusts to unambiguously determine the solar azimuth by relying solely on the sky polarization pattern for compass navigation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Data-Driven Engineering of Social Dynamics: Pattern Matching and Profit Maximization.

    Science.gov (United States)

    Peng, Huan-Kai; Lee, Hao-Chih; Pan, Jia-Yu; Marculescu, Radu

    2016-01-01

    In this paper, we define a new problem related to social media, namely, the data-driven engineering of social dynamics. More precisely, given a set of observations from the past, we aim at finding the best short-term intervention that can lead to predefined long-term outcomes. Toward this end, we propose a general formulation that covers two useful engineering tasks as special cases, namely, pattern matching and profit maximization. By incorporating a deep learning model, we derive a solution using convex relaxation and quadratic-programming transformation. Moreover, we propose a data-driven evaluation method in place of the expensive field experiments. Using a Twitter dataset, we demonstrate the effectiveness of our dynamics engineering approach for both pattern matching and profit maximization, and study the multifaceted interplay among several important factors of dynamics engineering, such as solution validity, pattern-matching accuracy, and intervention cost. Finally, the method we propose is general enough to work with multi-dimensional time series, so it can potentially be used in many other applications.

  3. Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

    Science.gov (United States)

    Inoue, Kentaro; Shimozono, Shinichi; Yoshida, Hideaki; Kurata, Hiroyuki

    2012-01-01

    For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

  4. Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

    Directory of Open Access Journals (Sweden)

    Kentaro Inoue

    Full Text Available BACKGROUND: For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. RESULTS: We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. CONCLUSIONS: Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

  5. Data-Driven Engineering of Social Dynamics: Pattern Matching and Profit Maximization.

    Directory of Open Access Journals (Sweden)

    Huan-Kai Peng

    Full Text Available In this paper, we define a new problem related to social media, namely, the data-driven engineering of social dynamics. More precisely, given a set of observations from the past, we aim at finding the best short-term intervention that can lead to predefined long-term outcomes. Toward this end, we propose a general formulation that covers two useful engineering tasks as special cases, namely, pattern matching and profit maximization. By incorporating a deep learning model, we derive a solution using convex relaxation and quadratic-programming transformation. Moreover, we propose a data-driven evaluation method in place of the expensive field experiments. Using a Twitter dataset, we demonstrate the effectiveness of our dynamics engineering approach for both pattern matching and profit maximization, and study the multifaceted interplay among several important factors of dynamics engineering, such as solution validity, pattern-matching accuracy, and intervention cost. Finally, the method we propose is general enough to work with multi-dimensional time series, so it can potentially be used in many other applications.

  6. Data-Driven Engineering of Social Dynamics: Pattern Matching and Profit Maximization

    Science.gov (United States)

    Peng, Huan-Kai; Lee, Hao-Chih; Pan, Jia-Yu; Marculescu, Radu

    2016-01-01

    In this paper, we define a new problem related to social media, namely, the data-driven engineering of social dynamics. More precisely, given a set of observations from the past, we aim at finding the best short-term intervention that can lead to predefined long-term outcomes. Toward this end, we propose a general formulation that covers two useful engineering tasks as special cases, namely, pattern matching and profit maximization. By incorporating a deep learning model, we derive a solution using convex relaxation and quadratic-programming transformation. Moreover, we propose a data-driven evaluation method in place of the expensive field experiments. Using a Twitter dataset, we demonstrate the effectiveness of our dynamics engineering approach for both pattern matching and profit maximization, and study the multifaceted interplay among several important factors of dynamics engineering, such as solution validity, pattern-matching accuracy, and intervention cost. Finally, the method we propose is general enough to work with multi-dimensional time series, so it can potentially be used in many other applications. PMID:26771830

  7. A distributed query execution engine of big attributed graphs.

    Science.gov (United States)

    Batarfi, Omar; Elshawi, Radwa; Fayoumi, Ayman; Barnawi, Ahmed; Sakr, Sherif

    2016-01-01

    A graph is a popular data model that has become pervasively used for modeling structural relationships between objects. In practice, in many real-world graphs, the graph vertices and edges need to be associated with descriptive attributes. Such type of graphs are referred to as attributed graphs. G-SPARQL has been proposed as an expressive language, with a centralized execution engine, for querying attributed graphs. G-SPARQL supports various types of graph querying operations including reachability, pattern matching and shortest path where any G-SPARQL query may include value-based predicates on the descriptive information (attributes) of the graph edges/vertices in addition to the structural predicates. In general, a main limitation of centralized systems is that their vertical scalability is always restricted by the physical limits of computer systems. This article describes the design, implementation in addition to the performance evaluation of DG-SPARQL, a distributed, hybrid and adaptive parallel execution engine of G-SPARQL queries. In this engine, the topology of the graph is distributed over the main memory of the underlying nodes while the graph data are maintained in a relational store which is replicated on the disk of each of the underlying nodes. DG-SPARQL evaluates parts of the query plan via SQL queries which are pushed to the underlying relational stores while other parts of the query plan, as necessary, are evaluated via indexless memory-based graph traversal algorithms. Our experimental evaluation shows the efficiency and the scalability of DG-SPARQL on querying massive attributed graph datasets in addition to its ability to outperform the performance of Apache Giraph, a popular distributed graph processing system, by orders of magnitudes.

  8. Robust real-time pattern matching using bayesian sequential hypothesis testing.

    Science.gov (United States)

    Pele, Ofir; Werman, Michael

    2008-08-01

    This paper describes a method for robust real time pattern matching. We first introduce a family of image distance measures, the "Image Hamming Distance Family". Members of this family are robust to occlusion, small geometrical transforms, light changes and non-rigid deformations. We then present a novel Bayesian framework for sequential hypothesis testing on finite populations. Based on this framework, we design an optimal rejection/acceptance sampling algorithm. This algorithm quickly determines whether two images are similar with respect to a member of the Image Hamming Distance Family. We also present a fast framework that designs a near-optimal sampling algorithm. Extensive experimental results show that the sequential sampling algorithm performance is excellent. Implemented on a Pentium 4 3 GHz processor, detection of a pattern with 2197 pixels, in 640 x 480 pixel frames, where in each frame the pattern rotated and was highly occluded, proceeds at only 0.022 seconds per frame.

  9. A novel iris patterns matching algorithm of weighted polar frequency correlation

    Science.gov (United States)

    Zhao, Weijie; Jiang, Linhua

    2014-11-01

    Iris recognition is recognized as one of the most accurate techniques for biometric authentication. In this paper, we present a novel correlation method - Weighted Polar Frequency Correlation(WPFC) - to match and evaluate two iris images, actually it can also be used for evaluating the similarity of any two images. The WPFC method is a novel matching and evaluating method for iris image matching, which is complete different from the conventional methods. For instance, the classical John Daugman's method of iris recognition uses 2D Gabor wavelets to extract features of iris image into a compact bit stream, and then matching two bit streams with hamming distance. Our new method is based on the correlation in the polar coordinate system in frequency domain with regulated weights. The new method is motivated by the observation that the pattern of iris that contains far more information for recognition is fine structure at high frequency other than the gross shapes of iris images. Therefore, we transform iris images into frequency domain and set different weights to frequencies. Then calculate the correlation of two iris images in frequency domain. We evaluate the iris images by summing the discrete correlation values with regulated weights, comparing the value with preset threshold to tell whether these two iris images are captured from the same person or not. Experiments are carried out on both CASIA database and self-obtained images. The results show that our method is functional and reliable. Our method provides a new prospect for iris recognition system.

  10. Graph Theoretical Analysis of Developmental Patterns of the White Matter Network

    Directory of Open Access Journals (Sweden)

    Zhang eChen

    2013-11-01

    Full Text Available Understanding the development of human brain organization is critical for gaining insight into how the enhancement of cognitive processes is related to the fine-tuning of the brain network. However, the developmental trajectory of the large-scale white matter (WM network is not fully understood. Here, using graph theory, we examine developmental changes in the organization of WM networks in 180 typically-developing participants. WM networks were constructed using whole brain tractography and 78 cortical regions of interest were extracted from each participant. The subjects were first divided into 5 equal sample size (n=36 groups (early childhood: 6.0-9.7 years; late childhood: 9.8-12.7 years; adolescence: 12.9-17.5 years; young adult: 17.6-21.8 years; adult: 21.9-29.6 years. Most prominent changes in the topological properties of developing brain networks occur at late childhood and adolescence. During late childhood period, the structural brain network showed significant increase in the global efficiency but decrease in modularity, suggesting a shift of topological organization toward a more randomized configuration. However, while preserving most topological features, there was a significant increase in the local efficiency at adolescence, suggesting the dynamic process of rewiring and rebalancing brain connections at different growth stages. In addition, several pivotal hubs were identified that are vital for the global coordination of information flow over the whole brain network across all age groups. Significant increases of nodal efficiency were present in several regions such as precuneus at late childhood. Finally, a stable and functionally/anatomically related modular organization was identified throughout the development of the WM network. This study used network analysis to elucidate the topological changes in brain maturation, paving the way for developing novel methods for analyzing disrupted brain connectivity in

  11. Skew-adjacency matrices of graphs

    NARCIS (Netherlands)

    Cavers, M.; Cioaba, S.M.; Fallat, S.; Gregory, D.A.; Haemers, W.H.; Kirkland, S.J.; McDonald, J.J.; Tsatsomeros, M.

    2012-01-01

    The spectra of the skew-adjacency matrices of a graph are considered as a possible way to distinguish adjacency cospectral graphs. This leads to the following topics: graphs whose skew-adjacency matrices are all cospectral; relations between the matchings polynomial of a graph and the characteristic

  12. Practical graph mining with R

    CERN Document Server

    Hendrix, William; Jenkins, John; Padmanabhan, Kanchana; Chakraborty, Arpan

    2014-01-01

    Practical Graph Mining with R presents a "do-it-yourself" approach to extracting interesting patterns from graph data. It covers many basic and advanced techniques for the identification of anomalous or frequently recurring patterns in a graph, the discovery of groups or clusters of nodes that share common patterns of attributes and relationships, the extraction of patterns that distinguish one category of graphs from another, and the use of those patterns to predict the category of new graphs. Hands-On Application of Graph Data Mining Each chapter in the book focuses on a graph mining task, such as link analysis, cluster analysis, and classification. Through applications using real data sets, the book demonstrates how computational techniques can help solve real-world problems. The applications covered include network intrusion detection, tumor cell diagnostics, face recognition, predictive toxicology, mining metabolic and protein-protein interaction networks, and community detection in social networks. De...

  13. Improving the Communication Pattern in Matrix-Vector Operations for Large Scale-Free Graphs by Disaggregation

    Energy Technology Data Exchange (ETDEWEB)

    Kuhlemann, Verena [Emory Univ., Atlanta, GA (United States); Vassilevski, Panayot S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2013-10-28

    Matrix-vector multiplication is the key operation in any Krylov-subspace iteration method. We are interested in Krylov methods applied to problems associated with the graph Laplacian arising from large scale-free graphs. Furthermore, computations with graphs of this type on parallel distributed-memory computers are challenging. This is due to the fact that scale-free graphs have a degree distribution that follows a power law, and currently available graph partitioners are not efficient for such an irregular degree distribution. The lack of a good partitioning leads to excessive interprocessor communication requirements during every matrix-vector product. Here, we present an approach to alleviate this problem based on embedding the original irregular graph into a more regular one by disaggregating (splitting up) vertices in the original graph. The matrix-vector operations for the original graph are performed via a factored triple matrix-vector product involving the embedding graph. And even though the latter graph is larger, we are able to decrease the communication requirements considerably and improve the performance of the matrix-vector product.

  14. Graph sampling

    OpenAIRE

    Zhang, L.-C.; Patone, M.

    2017-01-01

    We synthesise the existing theory of graph sampling. We propose a formal definition of sampling in finite graphs, and provide a classification of potential graph parameters. We develop a general approach of Horvitz–Thompson estimation to T-stage snowball sampling, and present various reformulations of some common network sampling methods in the literature in terms of the outlined graph sampling theory.

  15. EEG analysis of seizure patterns using visibility graphs for detection of generalized seizures

    NARCIS (Netherlands)

    Wang, Lei; Long, Xi; Arends, J.B.A.M.; Aarts, R.M.

    2017-01-01

    Background The traditional EEG features in the time and frequency domain show limited seizure detection performance in the epileptic population with intellectual disability (ID). In addition, the influence of EEG seizure patterns on detection performance was less studied. New method A single-channel

  16. Dietary pattern analysis: a comparison between matched vegetarian and omnivorous subjects.

    Science.gov (United States)

    Clarys, Peter; Deriemaeker, Peter; Huybrechts, Inge; Hebbelinck, Marcel; Mullie, Patrick

    2013-06-13

    Dietary pattern analysis, based on the concept that foods eaten together are as important as a reductive methodology characterized by a single food or nutrient analysis, has emerged as an alternative approach to study the relation between nutrition and disease. The aim of the present study was to compare nutritional intake and the results of dietary pattern analysis in properly matched vegetarian and omnivorous subjects. Vegetarians (n = 69) were recruited via purposeful sampling and matched non-vegetarians (n = 69) with same age, gender, health and lifestyle characteristics were searched for via convenience sampling. Two dietary pattern analysis methods, the Healthy Eating Index-2010 (HEI-2010) and the Mediterranean Diet Score (MDS) were calculated and analysed in function of the nutrient intake. Mean total energy intake was comparable between vegetarians and omnivorous subjects (p > 0.05). Macronutrient analysis revealed significant differences between the mean values for vegetarians and omnivorous subjects (absolute and relative protein and total fat intake were significantly lower in vegetarians, while carbohydrate and fibre intakes were significantly higher in vegetarians than in omnivorous subjects). The HEI and MDS were significantly higher for the vegetarians (HEI = 53.8.1 ± 11.2; MDS = 4.3 ± 1.3) compared to the omnivorous subjects (HEI = 46.4 ± 15.3; MDS = 3.8 ± 1.4). Our results indicate a more nutrient dense pattern, closer to the current dietary recommendations for the vegetarians compared to the omnivorous subjects. Both indexing systems were able to discriminate between the vegetarians and the non-vegetarians with higher scores for the vegetarian subjects.

  17. Handbook of graph grammars and computing by graph transformation

    CERN Document Server

    Engels, G; Kreowski, H J; Rozenberg, G

    1999-01-01

    Graph grammars originated in the late 60s, motivated by considerations about pattern recognition and compiler construction. Since then, the list of areas which have interacted with the development of graph grammars has grown quite impressively. Besides the aforementioned areas, it includes software specification and development, VLSI layout schemes, database design, modeling of concurrent systems, massively parallel computer architectures, logic programming, computer animation, developmental biology, music composition, visual languages, and many others.The area of graph grammars and graph tran

  18. Crack displacement sensing and measurement in concrete using circular grating moire fringes and pattern matching

    Science.gov (United States)

    Chan, H. M.; Yen, K. S.; Ratnam, M. M.

    2008-09-01

    The moire method has been extensively studied in the past and applied in various engineering applications. Several techniques are available for generating the moire fringes in these applications, which include moire interferometry, projection moire, shadow moire, moire deflectometry etc. Most of these methods use the superposition of linear gratings to generate the moire patterns. The use of non-linear gratings, such as circular, radial and elongated gratings has received less attention from the research community. The potential of non-linear gratings in engineering measurement has been realized in a limited number of applications, such as rotation measurement, measurement of linear displacement, measurement of expansion coefficients of materials and measurement of strain distribution. In this work, circular gratings of different pitch were applied to the sensing and measurement of crack displacement in concrete structures. Gratings of pitch 0.50 mm and 0.55 mm were generated using computer software and attached to two overlapping acrylic plates that were bonded to either side of the crack. The resulting moire patterns were captured using a standard digital camera and compared with a set of reference patterns generated using a precision positioning stage. Using several image pre-processing stages, such as filtering and morphological operations, and pattern matching the magnitude displacements along two orthogonal axes can be detected with a resolution of 0.05 mm.

  19. Ontology Matching Across Domains

    Science.gov (United States)

    2010-05-01

    matching include GMO [1], Anchor-Prompt [2], and Similarity Flooding [3]. GMO is an iterative structural matcher, which uses RDF bipartite graphs to...AFRL under contract# FA8750-09-C-0058. References [1] Hu, W., Jian, N., Qu, Y., Wang, Y., “ GMO : a graph matching for ontologies”, in: Proceedings of

  20. Nutritional Status and Daytime Pattern of Protein Intake on Match, Post-Match, Rest and Training Days in Senior Professional and Youth Elite Soccer Players.

    Science.gov (United States)

    Bettonviel A, E O; Brinkmans N, Y J; Russcher, Kris; Wardenaar, Floris C; Witard, Oliver C

    2016-06-01

    The nutritional status of elite soccer players across match, postmatch, training and rest days has not been defined. Recent evidence suggests the pattern of dietary protein intake impacts the daytime turnover of muscle proteins and, as such, influences muscle recovery. We assessed the nutritional status and daytime pattern of protein intake in senior professional and elite youth soccer players and compared findings against published recommendations. Fourteen senior professional (SP) and 15 youth elite (YP) soccer players from the Dutch premier division completed nutritional assessments using a 24-hr web-based recall method. Recall days consisted of a match, postmatch, rest, and training day. Daily energy intake over the 4-day period was similar between SP (2988 ± 583 kcal/day) and YP (2938 ± 465 kcal/day; p = .800). Carbohydrate intake over the combined 4-day period was lower in SP (4.7 ± 0.7 g·kg-1 BM·day-1) vs. YP (6.0 ± 1.5 g·kg-1 BM·day-1, p = .006) and SP failed to meet recommended carbohydrate intakes on match and training days. Conversely, recommended protein intakes were met for SP (1.9 ± 0.3 g·kg-1 BM·day-1) and YP (1.7 ± 0.4 g·kg-1 BM·day-1), with no differences between groups (p = .286). Accordingly, both groups met or exceeded recommended daily protein intakes on individual match, postmatch, rest and training days. A similar "balanced" daytime pattern of protein intake was observed in SP and YP. To conclude, SP increased protein intake on match and training days to a greater extent than YP, however at the expense of carbohydrate intake. The daytime distribution of protein intake for YP and SP aligned with current recommendations of a balanced protein meal pattern.

  1. Graph spectrum

    NARCIS (Netherlands)

    Brouwer, A.E.; Haemers, W.H.; Brouwer, A.E.; Haemers, W.H.

    2012-01-01

    This chapter presents some simple results on graph spectra.We assume the reader is familiar with elementary linear algebra and graph theory. Throughout, J will denote the all-1 matrix, and 1 is the all-1 vector.

  2. Pattern Matching Framework to Estimate the Urgency of Off-Normal Situations in NPPs

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jin Soo; Park, Sang Jun; Heo, Gyun Young [Kyung Hee University, Yongin (Korea, Republic of); Park, Jin Kyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Kim, Hyo Jin; Park, Soon Yeol [Korea Hydro and Nuclear Power, Yeonggwang (Korea, Republic of)

    2010-10-15

    According to power plant operators, it was said that they could quite well recognize off-normal situations from an incipient stage and also anticipate the possibility of upcoming trips in case of skilled operators, even though it is difficult to clarify the cause of the off-normal situation. From the interview, we could assure the feasibility of two assumptions for the diagnosis of off-normal conditions: One is that we can predict whether an accidental shutdown happens or not if we observe the early stage when an off-normal starts to grow. The other is the observation at the early stage can provide the remaining time to a trip as well as the cause of such an off-normal situation. For this purpose, the development of on-line monitoring systems using various data processing techniques in nuclear power plants (NPPs) has been the subject of increasing attention and becomes important contributor to improve performance and economics. Many of studies have suggested the diagnostic methodologies. One of representative methods was to use the distance discrimination as a similarity measure, for example, such as the Euclidean distance. A variety of artificial intelligence techniques such as a neural network have been developed as well. In addition, some of these methodologies were to reduce the data dimensions for more effectively work. While sharing the same motivation with the previous achievements, this study proposed non-parametric pattern matching techniques to reduce the uncertainty in pursuance of selection of models and modeling processes. This could be characterized by the following two aspects: First, for overcoming considering only a few typical scenarios in the most of the studies, this study is getting the entire sets of off-normal situations which are anticipated in NPPs, which are created by a full-scope simulator. Second, many of the existing researches adopted the process of forming a diagnosis model which is so-called a training technique or a parametric

  3. Pattern Matching Framework to Estimate the Urgency of Off-Normal Situations in NPPs

    International Nuclear Information System (INIS)

    Shin, Jin Soo; Park, Sang Jun; Heo, Gyun Young; Park, Jin Kyun; Kim, Hyo Jin; Park, Soon Yeol

    2010-01-01

    According to power plant operators, it was said that they could quite well recognize off-normal situations from an incipient stage and also anticipate the possibility of upcoming trips in case of skilled operators, even though it is difficult to clarify the cause of the off-normal situation. From the interview, we could assure the feasibility of two assumptions for the diagnosis of off-normal conditions: One is that we can predict whether an accidental shutdown happens or not if we observe the early stage when an off-normal starts to grow. The other is the observation at the early stage can provide the remaining time to a trip as well as the cause of such an off-normal situation. For this purpose, the development of on-line monitoring systems using various data processing techniques in nuclear power plants (NPPs) has been the subject of increasing attention and becomes important contributor to improve performance and economics. Many of studies have suggested the diagnostic methodologies. One of representative methods was to use the distance discrimination as a similarity measure, for example, such as the Euclidean distance. A variety of artificial intelligence techniques such as a neural network have been developed as well. In addition, some of these methodologies were to reduce the data dimensions for more effectively work. While sharing the same motivation with the previous achievements, this study proposed non-parametric pattern matching techniques to reduce the uncertainty in pursuance of selection of models and modeling processes. This could be characterized by the following two aspects: First, for overcoming considering only a few typical scenarios in the most of the studies, this study is getting the entire sets of off-normal situations which are anticipated in NPPs, which are created by a full-scope simulator. Second, many of the existing researches adopted the process of forming a diagnosis model which is so-called a training technique or a parametric

  4. GPUs for fast triggering and pattern matching at the CERN experiment NA62

    International Nuclear Information System (INIS)

    Lamanna, Gianluca; Collazuol, Gianmaria; Sozzi, Marco

    2011-01-01

    In rare decays experiments an effective trigger is crucial to reduce both the quantity of data written on tape and the bandwidth requirements for the DAQ (Data Acquisition) system. A multilevel architecture is commonly used to achieve a higher reduction factor, exploiting dedicated custom hardware and flexible software in standard computers. In this paper we discuss the possibility to use commercial video card processors (GPU) to build a fast and effective trigger system, both at hardware and software level. The case of fast pattern matching in the RICH detector of the NA62 experiment at CERN aiming at measuring the Branching Ratio of the ultra rare decay K + →π + νν-bar is considered as use case although the versatility and the customizability of this approach easily allow exporting the concept to different contexts.

  5. ISOLATED SPEECH RECOGNITION SYSTEM FOR TAMIL LANGUAGE USING STATISTICAL PATTERN MATCHING AND MACHINE LEARNING TECHNIQUES

    Directory of Open Access Journals (Sweden)

    VIMALA C.

    2015-05-01

    Full Text Available In recent years, speech technology has become a vital part of our daily lives. Various techniques have been proposed for developing Automatic Speech Recognition (ASR system and have achieved great success in many applications. Among them, Template Matching techniques like Dynamic Time Warping (DTW, Statistical Pattern Matching techniques such as Hidden Markov Model (HMM and Gaussian Mixture Models (GMM, Machine Learning techniques such as Neural Networks (NN, Support Vector Machine (SVM, and Decision Trees (DT are most popular. The main objective of this paper is to design and develop a speaker-independent isolated speech recognition system for Tamil language using the above speech recognition techniques. The background of ASR system, the steps involved in ASR, merits and demerits of the conventional and machine learning algorithms and the observations made based on the experiments are presented in this paper. For the above developed system, highest word recognition accuracy is achieved with HMM technique. It offered 100% accuracy during training process and 97.92% for testing process.

  6. A Hybrid CPU/GPU Pattern-Matching Algorithm for Deep Packet Inspection.

    Directory of Open Access Journals (Sweden)

    Chun-Liang Lee

    Full Text Available The large quantities of data now being transferred via high-speed networks have made deep packet inspection indispensable for security purposes. Scalable and low-cost signature-based network intrusion detection systems have been developed for deep packet inspection for various software platforms. Traditional approaches that only involve central processing units (CPUs are now considered inadequate in terms of inspection speed. Graphic processing units (GPUs have superior parallel processing power, but transmission bottlenecks can reduce optimal GPU efficiency. In this paper we describe our proposal for a hybrid CPU/GPU pattern-matching algorithm (HPMA that divides and distributes the packet-inspecting workload between a CPU and GPU. All packets are initially inspected by the CPU and filtered using a simple pre-filtering algorithm, and packets that might contain malicious content are sent to the GPU for further inspection. Test results indicate that in terms of random payload traffic, the matching speed of our proposed algorithm was 3.4 times and 2.7 times faster than those of the AC-CPU and AC-GPU algorithms, respectively. Further, HPMA achieved higher energy efficiency than the other tested algorithms.

  7. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.

    Science.gov (United States)

    Du, Pan; Kibbe, Warren A; Lin, Simon M

    2006-09-01

    A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially problematic in detecting peaks with low amplitudes. Usually, various baseline correction algorithms and smoothing methods are applied before attempting peak detection. This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods. Most peak detection algorithms simply identify peaks based on amplitude, ignoring the additional information present in the shape of the peaks in a spectrum. In our experience, 'true' peaks have characteristic shapes, and providing a shape-matching function that provides a 'goodness of fit' coefficient should provide a more robust peak identification method. Based on these observations, a continuous wavelet transform (CWT)-based peak detection algorithm has been devised that identifies peaks with different scales and amplitudes. By transforming the spectrum into wavelet space, the pattern-matching problem is simplified and in addition provides a powerful technique for identifying and separating the signal from the spike noise and colored noise. This transformation, with the additional information provided by the 2D CWT coefficients can greatly enhance the effective signal-to-noise ratio. Furthermore, with this technique no baseline removal or peak smoothing preprocessing steps are required before peak detection, and this improves the robustness of peak detection under a variety of conditions. The algorithm was evaluated with SELDI-TOF spectra with known polypeptide positions. Comparisons with two other popular algorithms were performed. The results show the CWT-based algorithm can identify both strong and weak peaks while keeping false positive rate low. The algorithm is implemented in R and will be

  8. A Data-Driven Modeling Strategy for Smart Grid Power Quality Coupling Assessment Based on Time Series Pattern Matching

    Directory of Open Access Journals (Sweden)

    Hao Yu

    2018-01-01

    Full Text Available This study introduces a data-driven modeling strategy for smart grid power quality (PQ coupling assessment based on time series pattern matching to quantify the influence of single and integrated disturbance among nodes in different pollution patterns. Periodic and random PQ patterns are constructed by using multidimensional frequency-domain decomposition for all disturbances. A multidimensional piecewise linear representation based on local extreme points is proposed to extract the patterns features of single and integrated disturbance in consideration of disturbance variation trend and severity. A feature distance of pattern (FDP is developed to implement pattern matching on univariate PQ time series (UPQTS and multivariate PQ time series (MPQTS to quantify the influence of single and integrated disturbance among nodes in the pollution patterns. Case studies on a 14-bus distribution system are performed and analyzed; the accuracy and applicability of the FDP in the smart grid PQ coupling assessment are verified by comparing with other time series pattern matching methods.

  9. Oscillatory signatures of crossmodal congruence effects: An EEG investigation employing a visuotactile pattern matching paradigm.

    Science.gov (United States)

    Göschl, Florian; Friese, Uwe; Daume, Jonathan; König, Peter; Engel, Andreas K

    2015-08-01

    Coherent percepts emerge from the accurate combination of inputs from the different sensory systems. There is an ongoing debate about the neurophysiological mechanisms of crossmodal interactions in the brain, and it has been proposed that transient synchronization of neurons might be of central importance. Oscillatory activity in lower frequency ranges (congruence. Analysis of the behavioral data showed benefits for congruent visuotactile stimulus combinations. Differences in oscillatory dynamics related to crossmodal congruence within the two tasks were observed in the beta-band for crossmodal target detection, as well as in the theta-band for congruence evaluation. Contrasting ongoing activity preceding visuotactile stimulation between the two tasks revealed differences in the alpha- and beta-bands. Source reconstruction of between-task differences showed prominent involvement of premotor cortex, supplementary motor area, somatosensory association cortex and the supramarginal gyrus. These areas not only exhibited more involvement in the pre-stimulus interval for target detection compared to congruence evaluation, but were also crucially involved in post-stimulus differences related to crossmodal stimulus congruence within the detection task. These results add to the increasing evidence that low frequency oscillations are functionally relevant for integration in distributed brain networks, as demonstrated for crossmodal interactions in visuotactile pattern matching in the current study. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Infiltration patterns in monoclonal plasma cell disorders: correlation of magnetic resonance imaging with matched bone marrow histology

    Energy Technology Data Exchange (ETDEWEB)

    Andrulis, Mindaugas [Institute of Pathology, University of Heidelberg, Heidelberg (Germany); Bäuerle, Tobias [Department of Diagnostic and Interventional Radiology, University of Hamburg, Hamburg (Germany); Goldschmidt, Hartmut [Department of Hematology and Oncology, University of Heidelberg, Heidelberg (Germany); Delorme, Stefan [Department of Radiology, German Cancer Research Center (DKFZ), Heidelberg (Germany); Landgren, Ola [Multiple Myeloma Section, Metabolism Branch, National Cancer Institute, Bethesda (United States); Schirmacher, Peter [Institute of Pathology, University of Heidelberg, Heidelberg (Germany); Hillengass, Jens, E-mail: jens.hillengass@med.uni-heidelberg.de [Department of Hematology and Oncology, University of Heidelberg, Heidelberg (Germany); Department of Radiology, German Cancer Research Center (DKFZ), Heidelberg (Germany)

    2014-06-15

    Objectives: To investigate how plasma cell infiltration patterns detected by MRI match the plasma cell distribution in bone marrow biopsy. Methods: We assessed 50 patients with monoclonal plasma cell disorders of all clinical stages. MRI infiltration pattern was compared with matched BM histology from the same anatomic region. Results: MRI revealed a minimal (n = 11, 22%), focal (n = 5, 10%), diffuse (n = 14, 28%) and mixed (n = 20, 40%) infiltration pattern. Diffuse MRI pattern was predominant in smoldering myeloma patients whereas the MRI patterns with “focal component” (i.e. focal and mixed) were most common in symptomatic myeloma (p < 0.01). In histology an interstitial (n = 13, 26%), nodular (n = 23, 46%) and packed marrow (n = 14, 28%) was found respectively. All three histological types of infiltration were observed in patients with diffuse and mixed MRI patterns. Minimal MRI pattern was found in all MGUS patients and was associated with an interstitial BM infiltration. In two patients with minimal MRI pattern an extensive micro-nodular BM infiltration was found in histology. Conclusions: Infiltration patterns in MRI represent different histological growth patterns of plasma cells, but the MRI resolution is not sufficient to visualize micro-nodular aggregates of plasma cells.

  11. Infiltration patterns in monoclonal plasma cell disorders: correlation of magnetic resonance imaging with matched bone marrow histology

    International Nuclear Information System (INIS)

    Andrulis, Mindaugas; Bäuerle, Tobias; Goldschmidt, Hartmut; Delorme, Stefan; Landgren, Ola; Schirmacher, Peter; Hillengass, Jens

    2014-01-01

    Objectives: To investigate how plasma cell infiltration patterns detected by MRI match the plasma cell distribution in bone marrow biopsy. Methods: We assessed 50 patients with monoclonal plasma cell disorders of all clinical stages. MRI infiltration pattern was compared with matched BM histology from the same anatomic region. Results: MRI revealed a minimal (n = 11, 22%), focal (n = 5, 10%), diffuse (n = 14, 28%) and mixed (n = 20, 40%) infiltration pattern. Diffuse MRI pattern was predominant in smoldering myeloma patients whereas the MRI patterns with “focal component” (i.e. focal and mixed) were most common in symptomatic myeloma (p < 0.01). In histology an interstitial (n = 13, 26%), nodular (n = 23, 46%) and packed marrow (n = 14, 28%) was found respectively. All three histological types of infiltration were observed in patients with diffuse and mixed MRI patterns. Minimal MRI pattern was found in all MGUS patients and was associated with an interstitial BM infiltration. In two patients with minimal MRI pattern an extensive micro-nodular BM infiltration was found in histology. Conclusions: Infiltration patterns in MRI represent different histological growth patterns of plasma cells, but the MRI resolution is not sufficient to visualize micro-nodular aggregates of plasma cells

  12. Modern graph theory

    CERN Document Server

    Bollobás, Béla

    1998-01-01

    The time has now come when graph theory should be part of the education of every serious student of mathematics and computer science, both for its own sake and to enhance the appreciation of mathematics as a whole. This book is an in-depth account of graph theory, written with such a student in mind; it reflects the current state of the subject and emphasizes connections with other branches of pure mathematics. The volume grew out of the author's earlier book, Graph Theory -- An Introductory Course, but its length is well over twice that of its predecessor, allowing it to reveal many exciting new developments in the subject. Recognizing that graph theory is one of several courses competing for the attention of a student, the book contains extensive descriptive passages designed to convey the flavor of the subject and to arouse interest. In addition to a modern treatment of the classical areas of graph theory such as coloring, matching, extremal theory, and algebraic graph theory, the book presents a detailed ...

  13. Equipackable graphs

    DEFF Research Database (Denmark)

    Vestergaard, Preben Dahl; Hartnell, Bert L.

    2006-01-01

    There are many results dealing with the problem of decomposing a fixed graph into isomorphic subgraphs. There has also been work on characterizing graphs with the property that one can delete the edges of a number of edge disjoint copies of the subgraph and, regardless of how that is done, the gr...

  14. Constructs for Programming with Graph Rewrites

    OpenAIRE

    Rodgers, Peter

    2000-01-01

    Graph rewriting is becoming increasingly popular as a method for programming with graph based data structures. We present several modifications to a basic serial graph rewriting paradigm and discuss how they improve coding programs in the Grrr graph rewriting programming language. The constructs we present are once only nodes, attractor nodes and single match rewrites. We illustrate the operation of the constructs by example. The advantages of adding these new rewrite modifiers is to reduce t...

  15. CERN Computing Colloquia Spring Series: IT Security - A High-Performance Pattern Matching Engine for Intrusion Detection

    CERN Multimedia

    CERN. Geneva

    2006-01-01

    The flexible and modular design of the engine allows a broad spectrum of applications, ranging from high-end enterprise level network devices that need to match hundreds of thousands of patterns at speeds of tens of gigabits per second, to low-end dev...

  16. Two tree-formation methods for fast pattern search using nearest-neighbour and nearest-centroid matching

    NARCIS (Netherlands)

    Schomaker, Lambertus; Mangalagiu, D.; Vuurpijl, Louis; Weinfeld, M.; Schomaker, Lambert; Vuurpijl, Louis

    2000-01-01

    This paper describes tree­based classification of character images, comparing two methods of tree formation and two methods of matching: nearest neighbor and nearest centroid. The first method, Preprocess Using Relative Distances (PURD) is a tree­based reorganization of a flat list of patterns,

  17. GPUs for fast pattern matching in the RICH of the NA62 experiment

    International Nuclear Information System (INIS)

    Lamanna, Gianluca; Collazuol, Gianmaria; Sozzi, Marco

    2011-01-01

    In rare decays experiments an effective online selection is a fundamental part of the data acquisition system (DAQ) in order to reduce both the quantity of data written on tape and the bandwidth requirements for the DAQ system. A multilevel architecture is commonly used to achieve a higher reduction factor, exploiting dedicated custom hardware and flexible software in standard computers. In this paper we discuss the possibility to use commercial video card processors (GPU) to build a fast and effective trigger system, both at hardware and software level. The computing power of the GPUs allows to design a real-time system in which trigger decisions are taken directly in the video processor with a defined maximum latency. This allows building lowest trigger levels based on standard off-the-shelf PCs with CPU and GPU (instead of the commonly adopted solutions based on custom electronics with FPGA or ASICs) with enhanced and high performance computation capabilities, resulting in high rejection power, high efficiency and simpler low level triggers. The ongoing work presented here shows the results achieved in the case of fast pattern matching in the RICH detector of the NA62 at CERN, aiming at measuring the Branching Ratio of the ultra rare decay K + →π + νν-bar, is considered as use case, although the versatility and the customizability of this approach easily allow exporting the concept to different contexts. In particular the application is related to particle identification in the RICH detector of the NA62 experiment, where the rate of events to be analyzed will be around 10 MHz. The results obtained in lab tests are very encouraging to go towards a working prototype. Due to the use of off-the-shelf technology, in continuous development for other purposes (Video Games, image editing,...), the architecture described would be easily exported into other experiments, for building powerful, flexible and fully customizable trigger systems.

  18. GPUs for fast pattern matching in the RICH of the NA62 experiment

    Energy Technology Data Exchange (ETDEWEB)

    Lamanna, Gianluca, E-mail: gianluca.lamanna@cern.c [CERN, 1211 Geneve 23 (Switzerland); Collazuol, Gianmaria, E-mail: gianmaria.collazuol@cern.c [INFN Pisa, Largo Pontecorvo 3, 56127 Pisa (Italy); Sozzi, Marco, E-mail: marco.sozzi@cern.c [University and INFN Pisa, Largo Pontecorvo 3, 56127 Pisa (Italy)

    2011-05-21

    In rare decays experiments an effective online selection is a fundamental part of the data acquisition system (DAQ) in order to reduce both the quantity of data written on tape and the bandwidth requirements for the DAQ system. A multilevel architecture is commonly used to achieve a higher reduction factor, exploiting dedicated custom hardware and flexible software in standard computers. In this paper we discuss the possibility to use commercial video card processors (GPU) to build a fast and effective trigger system, both at hardware and software level. The computing power of the GPUs allows to design a real-time system in which trigger decisions are taken directly in the video processor with a defined maximum latency. This allows building lowest trigger levels based on standard off-the-shelf PCs with CPU and GPU (instead of the commonly adopted solutions based on custom electronics with FPGA or ASICs) with enhanced and high performance computation capabilities, resulting in high rejection power, high efficiency and simpler low level triggers. The ongoing work presented here shows the results achieved in the case of fast pattern matching in the RICH detector of the NA62 at CERN, aiming at measuring the Branching Ratio of the ultra rare decay K{sup +}{yields}{pi}{sup +}{nu}{nu}-bar, is considered as use case, although the versatility and the customizability of this approach easily allow exporting the concept to different contexts. In particular the application is related to particle identification in the RICH detector of the NA62 experiment, where the rate of events to be analyzed will be around 10 MHz. The results obtained in lab tests are very encouraging to go towards a working prototype. Due to the use of off-the-shelf technology, in continuous development for other purposes (Video Games, image editing,...), the architecture described would be easily exported into other experiments, for building powerful, flexible and fully customizable trigger systems.

  19. Advanced optical correlation and digital methods for pattern matching—50th anniversary of Vander Lugt matched filter

    Science.gov (United States)

    Millán, María S.

    2012-10-01

    On the verge of the 50th anniversary of Vander Lugt’s formulation for pattern matching based on matched filtering and optical correlation, we acknowledge the very intense research activity developed in the field of correlation-based pattern recognition during this period of time. The paper reviews some domains that appeared as emerging fields in the last years of the 20th century and have been developed later on in the 21st century. Such is the case of three-dimensional (3D) object recognition, biometric pattern matching, optical security and hybrid optical-digital processors. 3D object recognition is a challenging case of multidimensional image recognition because of its implications in the recognition of real-world objects independent of their perspective. Biometric recognition is essentially pattern recognition for which the personal identification is based on the authentication of a specific physiological characteristic possessed by the subject (e.g. fingerprint, face, iris, retina, and multifactor combinations). Biometric recognition often appears combined with encryption-decryption processes to secure information. The optical implementations of correlation-based pattern recognition processes still rely on the 4f-correlator, the joint transform correlator, or some of their variants. But the many applications developed in the field have been pushing the systems for a continuous improvement of their architectures and algorithms, thus leading towards merged optical-digital solutions.

  20. Advanced optical correlation and digital methods for pattern matching—50th anniversary of Vander Lugt matched filter

    International Nuclear Information System (INIS)

    Millán, María S

    2012-01-01

    On the verge of the 50th anniversary of Vander Lugt’s formulation for pattern matching based on matched filtering and optical correlation, we acknowledge the very intense research activity developed in the field of correlation-based pattern recognition during this period of time. The paper reviews some domains that appeared as emerging fields in the last years of the 20th century and have been developed later on in the 21st century. Such is the case of three-dimensional (3D) object recognition, biometric pattern matching, optical security and hybrid optical–digital processors. 3D object recognition is a challenging case of multidimensional image recognition because of its implications in the recognition of real-world objects independent of their perspective. Biometric recognition is essentially pattern recognition for which the personal identification is based on the authentication of a specific physiological characteristic possessed by the subject (e.g. fingerprint, face, iris, retina, and multifactor combinations). Biometric recognition often appears combined with encryption–decryption processes to secure information. The optical implementations of correlation-based pattern recognition processes still rely on the 4f-correlator, the joint transform correlator, or some of their variants. But the many applications developed in the field have been pushing the systems for a continuous improvement of their architectures and algorithms, thus leading towards merged optical–digital solutions. (review article)

  1. Network-level accident-mapping: Distance based pattern matching using artificial neural network.

    Science.gov (United States)

    Deka, Lipika; Quddus, Mohammed

    2014-04-01

    The objective of an accident-mapping algorithm is to snap traffic accidents onto the correct road segments. Assigning accidents onto the correct segments facilitate to robustly carry out some key analyses in accident research including the identification of accident hot-spots, network-level risk mapping and segment-level accident risk modelling. Existing risk mapping algorithms have some severe limitations: (i) they are not easily 'transferable' as the algorithms are specific to given accident datasets; (ii) they do not perform well in all road-network environments such as in areas of dense road network; and (iii) the methods used do not perform well in addressing inaccuracies inherent in and type of road environment. The purpose of this paper is to develop a new accident mapping algorithm based on the common variables observed in most accident databases (e.g. road name and type, direction of vehicle movement before the accident and recorded accident location). The challenges here are to: (i) develop a method that takes into account uncertainties inherent to the recorded traffic accident data and the underlying digital road network data, (ii) accurately determine the type and proportion of inaccuracies, and (iii) develop a robust algorithm that can be adapted for any accident set and road network of varying complexity. In order to overcome these challenges, a distance based pattern-matching approach is used to identify the correct road segment. This is based on vectors containing feature values that are common in the accident data and the network data. Since each feature does not contribute equally towards the identification of the correct road segments, an ANN approach using the single-layer perceptron is used to assist in "learning" the relative importance of each feature in the distance calculation and hence the correct link identification. The performance of the developed algorithm was evaluated based on a reference accident dataset from the UK confirming that

  2. A pattern-matched Twitter analysis of US cancer-patient sentiments.

    Science.gov (United States)

    Crannell, W Christian; Clark, Eric; Jones, Chris; James, Ted A; Moore, Jesse

    2016-12-01

    Twitter has been recognized as an important source of organic sentiment and opinion. This study aimed to (1) characterize the content of tweets authored by the United States cancer patients; and (2) use patient tweets to compute the average happiness of cancer patients for each cancer diagnosis. A large sample of English tweets from March 2014 through December 2014 was obtained from Twitter. Using regular expression software pattern matching, the tweets were filtered by cancer diagnosis. For each cancer-specific tweetset, individual patients were extracted, and the content of the tweet was categorized. The patients' Twitter identification numbers were used to gather all tweets for each patient, and happiness values for patient tweets were calculated using a quantitative hedonometric analysis. The most frequently tweeted cancers were breast (n = 15,421, 11% of total cancer tweets), lung (n = 2928, 2.0%), prostate (n = 1036, 0.7%), and colorectal (n = 773, 0.5%). Patient tweets pertained to the treatment course (n = 73, 26%), diagnosis (n = 65, 23%), and then surgery and/or biopsy (n = 42, 15%). Computed happiness values for each cancer diagnosis revealed higher average happiness values for thyroid (h_avg = 6.1625), breast (h_avg = 6.1485), and lymphoma (h_avg = 6.0977) cancers and lower average happiness values for pancreatic (h_avg = 5.8766), lung (h_avg = 5.8733), and kidney (h_avg = 5.8464) cancers. The study confirms that patients are expressing themselves openly on social media about their illness and that unique cancer diagnoses are correlated with varying degrees of happiness. Twitter can be employed as a tool to identify patient needs and as a means to gauge the cancer patient experience. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Movement patterns and muscle damage during simulated rugby sevens matches in National team players.

    Science.gov (United States)

    Pereira, Lucas A; Nakamura, Fábio Y; Moraes, José E; Kitamura, Katia; Ramos, Solange P; Loturco, Irineu

    2017-02-23

    The aim of this study was to analyze the match performance (i.e., distance covered in different intensities), signs of muscle damage (assessed by means of creatine kinase [CK] activity and rate of force development [RFD]), and neuromuscular fatigue (using linear sprint and vertical jump performances) following three single-day simulated matches performed by rugby sevens players from the Brazilian National Team. Ten male rugby sevens players (25.2 ± 3.6 years; 88.7 ± 7.1 kg; 182.2 ± 6.3 cm) participated in this study. On the day prior to the matches, the athletes performed a 40-m sprint, a vertical jump assessment and a maximal isometric force test. In the morning of the match day, blood samples were collected to analyze the CK activity. Afterwards, three simulated rugby sevens' matches were performed with 2-h intermission periods. The match performance (encompassing total distance and distance covered in different velocity ranges and body loads [BL]) were obtained from global positioning system units. The statistical analysis was performed by using a mixed model approach and the effect sizes (ES) of the differences. The statistical significance level was set at P0.8) and significant (P< 0.05) reductions were demonstrated in the total distance and BL when comparing the 2 with the 1 halves. Decrements in the explosive force capacity (assessed by means of RFD) and the squat jump were noticed (ES varying from 0.55 to 1.14; P< 0.05). The CK activity increased after the matches (ES = 1.29; P< 0.05). The rugby sevens players were able to maintain the physical performance across three successive matches simulating the first day of a tournament. The augmented CK activity and the decreases in the squat jump and RFD suggest that increased levels of muscle damage were experienced on the day after the matches. Therefore, the technical staff are encouraged to implement recovery strategies and planned substitutions during multi-day tournaments in order to reduce the impact of

  4. Neural coding in graphs of bidirectional associative memories.

    Science.gov (United States)

    Bouchain, A David; Palm, Günther

    2012-01-24

    In the last years we have developed large neural network models for the realization of complex cognitive tasks in a neural network architecture that resembles the network of the cerebral cortex. We have used networks of several cortical modules that contain two populations of neurons (one excitatory, one inhibitory). The excitatory populations in these so-called "cortical networks" are organized as a graph of Bidirectional Associative Memories (BAMs), where edges of the graph correspond to BAMs connecting two neural modules and nodes of the graph correspond to excitatory populations with associative feedback connections (and inhibitory interneurons). The neural code in each of these modules consists essentially of the firing pattern of the excitatory population, where mainly it is the subset of active neurons that codes the contents to be represented. The overall activity can be used to distinguish different properties of the patterns that are represented which we need to distinguish and control when performing complex tasks like language understanding with these cortical networks. The most important pattern properties or situations are: exactly fitting or matching input, incomplete information or partially matching pattern, superposition of several patterns, conflicting information, and new information that is to be learned. We show simple simulations of these situations in one area or module and discuss how to distinguish these situations based on the overall internal activation of the module. This article is part of a Special Issue entitled "Neural Coding". Copyright © 2011 Elsevier B.V. All rights reserved.

  5. How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches

    Directory of Open Access Journals (Sweden)

    Barbara Diana

    2017-08-01

    Full Text Available The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance. This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013—First Leg. The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann–Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

  6. How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches.

    Science.gov (United States)

    Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M; Jonsson, Gudberg K; Anguera, M Teresa

    2017-01-01

    The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013-First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann-Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

  7. Neuraminidase and hemagglutinin matching patterns of a highly pathogenic avian and two pandemic H1N1 influenza A viruses.

    Directory of Open Access Journals (Sweden)

    Yonghui Zhang

    Full Text Available BACKGROUND: Influenza A virus displays strong reassortment characteristics, which enable it to achieve adaptation in human infection. Surveying the reassortment and virulence of novel viruses is important in the prevention and control of an influenza pandemic. Meanwhile, studying the mechanism of reassortment may accelerate the development of anti-influenza strategies. METHODOLOGY/PRINCIPAL FINDINGS: The hemagglutinin (HA and neuraminidase (NA matching patterns of two pandemic H1N1 viruses (the 1918 and current 2009 strains and a highly pathogenic avian influenza A virus (H5N1 were studied using a pseudotyped particle (pp system. Our data showed that four of the six chimeric HA/NA combinations could produce infectious pps, and that some of the chimeric pps had greater infectivity than did their ancestors, raising the possibility of reassortment among these viruses. The NA of H5N1 (A/Anhui/1/2005 could hardly reassort with the HAs of the two H1N1 viruses. Many biological characteristics of HA and NA, including infectivity, hemagglutinating ability, and NA activity, are dependent on their matching pattern. CONCLUSIONS/SIGNIFICANCE: Our data suggest the existence of an interaction between HA and NA, and the HA NA matching pattern is critical for valid viral reassortment.

  8. Interaction graphs

    DEFF Research Database (Denmark)

    Seiller, Thomas

    2016-01-01

    Interaction graphs were introduced as a general, uniform, construction of dynamic models of linear logic, encompassing all Geometry of Interaction (GoI) constructions introduced so far. This series of work was inspired from Girard's hyperfinite GoI, and develops a quantitative approach that should...... be understood as a dynamic version of weighted relational models. Until now, the interaction graphs framework has been shown to deal with exponentials for the constrained system ELL (Elementary Linear Logic) while keeping its quantitative aspect. Adapting older constructions by Girard, one can clearly define...... "full" exponentials, but at the cost of these quantitative features. We show here that allowing interpretations of proofs to use continuous (yet finite in a measure-theoretic sense) sets of states, as opposed to earlier Interaction Graphs constructions were these sets of states were discrete (and finite...

  9. Introduction to graph theory

    CERN Document Server

    Trudeau, Richard J

    1994-01-01

    Preface1. Pure Mathematics Introduction; Euclidean Geometry as Pure Mathematics; Games; Why Study Pure Mathematics?; What's Coming; Suggested Reading2. Graphs Introduction; Sets; Paradox; Graphs; Graph diagrams; Cautions; Common Graphs; Discovery; Complements and Subgraphs; Isomorphism; Recognizing Isomorphic Graphs; Semantics The Number of Graphs Having a Given nu; Exercises; Suggested Reading3. Planar Graphs Introduction; UG, K subscript 5, and the Jordan Curve Theorem; Are there More Nonplanar Graphs?; Expansions; Kuratowski's Theorem; Determining Whether a Graph is Planar or

  10. Generalized Phase contrast and matched filtering for speckle‐free patterned illumination

    DEFF Research Database (Denmark)

    Palima, Darwin; Bañas, Andrew Rafael; Villangca, Mark Jayson

    2013-01-01

    Generalized Phase Contrast (GPC) and matched‐filtering GPC use tandem diffractive phase elements on Fourier‐conjugate planes of a 4f optical processor to efficiently reshape incident light into a pattern that resembles the input phase modulation pattern. The synthesized patterns are inherently...... to optically trap and mechanically manipulate microparticles, GPC has also been applied for laser beamshaping, optical phase cryptography, and greyscale image projection. Recent reports from our collaborators highlight that GPC‐based spatial lightshaping, when combined with temporal focusing and multiphoton...... excitation, exhibits some robustness against light scattering and, hence, makes a promising tool for spatially precise targeting of deeper subsurface neurons using minimally speckled patterned illumination for multiphoton excitation....

  11. Graph theory

    CERN Document Server

    Diestel, Reinhard

    2017-01-01

    This standard textbook of modern graph theory, now in its fifth edition, combines the authority of a classic with the engaging freshness of style that is the hallmark of active mathematics. It covers the core material of the subject with concise yet reliably complete proofs, while offering glimpses of more advanced methods in each field by one or two deeper results, again with proofs given in full detail. The book can be used as a reliable text for an introductory course, as a graduate text, and for self-study. From the reviews: “This outstanding book cannot be substituted with any other book on the present textbook market. It has every chance of becoming the standard textbook for graph theory.”Acta Scientiarum Mathematiciarum “Deep, clear, wonderful. This is a serious book about the heart of graph theory. It has depth and integrity. ”Persi Diaconis & Ron Graham, SIAM Review “The book has received a very enthusiastic reception, which it amply deserves. A masterly elucidation of modern graph theo...

  12. Pattern formation without diffraction matching in optical parametric oscillators with a metamaterial.

    Science.gov (United States)

    Tassin, Philippe; Van der Sande, Guy; Veretennicoff, Irina; Kockaert, Pascal; Tlidi, Mustapha

    2009-05-25

    We consider a degenerate optical parametric oscillator containing a left-handed material. We show that the inclusion of a left-handed material layer allows for controlling the strength and sign of the diffraction coefficient at either the pump or the signal frequency. Subsequently, we demonstrate the existence of stable dissipative structures without diffraction matching, i.e., without the usual relationship between the diffraction coefficients of the signal and pump fields. Finally, we investigate the size scaling of these light structures with decreasing diffraction strength.

  13. A Clustering Graph Generator

    Energy Technology Data Exchange (ETDEWEB)

    Winlaw, Manda [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); De Sterck, Hans [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-10-26

    In very simple terms a network can be de ned as a collection of points joined together by lines. Thus, networks can be used to represent connections between entities in a wide variety of elds including engi- neering, science, medicine, and sociology. Many large real-world networks share a surprising number of properties, leading to a strong interest in model development research and techniques for building synthetic networks have been developed, that capture these similarities and replicate real-world graphs. Modeling these real-world networks serves two purposes. First, building models that mimic the patterns and prop- erties of real networks helps to understand the implications of these patterns and helps determine which patterns are important. If we develop a generative process to synthesize real networks we can also examine which growth processes are plausible and which are not. Secondly, high-quality, large-scale network data is often not available, because of economic, legal, technological, or other obstacles [7]. Thus, there are many instances where the systems of interest cannot be represented by a single exemplar network. As one example, consider the eld of cybersecurity, where systems require testing across diverse threat scenarios and validation across diverse network structures. In these cases, where there is no single exemplar network, the systems must instead be modeled as a collection of networks in which the variation among them may be just as important as their common features. By developing processes to build synthetic models, so-called graph generators, we can build synthetic networks that capture both the essential features of a system and realistic variability. Then we can use such synthetic graphs to perform tasks such as simulations, analysis, and decision making. We can also use synthetic graphs to performance test graph analysis algorithms, including clustering algorithms and anomaly detection algorithms.

  14. Spatio-temporal dynamics of global H5N1 outbreaks match bird migration patterns

    Directory of Open Access Journals (Sweden)

    Yali Si

    2009-11-01

    Full Text Available The global spread of highly pathogenic avian influenza H5N1 in poultry, wild birds and humans, poses a significant pandemic threat and a serious public health risk. An efficient surveillance and disease control system relies on the understanding of the dispersion patterns and spreading mechanisms of the virus. A space-time cluster analysis of H5N1 outbreaks was used to identify spatio-temporal patterns at a global scale and over an extended period of time. Potential mechanisms explaining the spread of the H5N1 virus, and the role of wild birds, were analyzed. Between December 2003 and December 2006, three global epidemic phases of H5N1 influenza were identified. These H5N1 outbreaks showed a clear seasonal pattern, with a high density of outbreaks in winter and early spring (i.e., October to March. In phase I and II only the East Asia Australian flyway was affected. During phase III, the H5N1 viruses started to appear in four other flyways: the Central Asian flyway, the Black Sea Mediterranean flyway, the East Atlantic flyway and the East Africa West Asian flyway. Six disease cluster patterns along these flyways were found to be associated with the seasonal migration of wild birds. The spread of the H5N1 virus, as demonstrated by the space-time clusters, was associated with the patterns of migration of wild birds. Wild birds may therefore play an important role in the spread of H5N1 over long distances. Disease clusters were also detected at sites where wild birds are known to overwinter and at times when migratory birds were present. This leads to the suggestion that wild birds may also be involved in spreading the H5N1 virus over short distances.

  15. Enlisting Clustering and Graph-Traversal Methods for Cutting Pattern and Net Topology Design in Pneumatic Hybrids

    DEFF Research Database (Denmark)

    Ayres, Phil; Vestartas, Petras; Ramsgaard Thomsen, Mette

    2017-01-01

    Cutting patterns for architectural membranes are generally characterised by rational approaches to surface discretisation and minimisation of geometric deviation between discrete elements that comprise the membrane. In this paper, we present an alternative approach for cutting pattern generation...... to the cutting pattern generation method and the net topology generation method used to produce a constraint net for a given membrane. We test our computational design approach through an iterative cycle of digital and physical prototyping before realising an air-inflated cable restrained pneumatic structural...

  16. Coloring sums of extensions of certain graphs

    Directory of Open Access Journals (Sweden)

    Johan Kok

    2017-12-01

    Full Text Available We recall that the minimum number of colors that allow a proper coloring of graph $G$ is called the chromatic number of $G$ and denoted $\\chi(G$. Motivated by the introduction of the concept of the $b$-chromatic sum of a graph the concept of $\\chi'$-chromatic sum and $\\chi^+$-chromatic sum are introduced in this paper. The extended graph $G^x$ of a graph $G$ was recently introduced for certain regular graphs. This paper furthers the concepts of $\\chi'$-chromatic sum and $\\chi^+$-chromatic sum to extended paths and cycles. Bipartite graphs also receive some attention. The paper concludes with patterned structured graphs. These last said graphs are typically found in chemical and biological structures.

  17. Graph theory

    CERN Document Server

    Gould, Ronald

    2012-01-01

    This introduction to graph theory focuses on well-established topics, covering primary techniques and including both algorithmic and theoretical problems. The algorithms are presented with a minimum of advanced data structures and programming details. This thoroughly corrected 1988 edition provides insights to computer scientists as well as advanced undergraduates and graduate students of topology, algebra, and matrix theory. Fundamental concepts and notation and elementary properties and operations are the first subjects, followed by examinations of paths and searching, trees, and networks. S

  18. Graphs & digraphs

    CERN Document Server

    Chartrand, Gary; Zhang, Ping

    2010-01-01

    Gary Chartrand has influenced the world of Graph Theory for almost half a century. He has supervised more than a score of Ph.D. dissertations and written several books on the subject. The most widely known of these texts, Graphs and Digraphs, … has much to recommend it, with clear exposition, and numerous challenging examples [that] make it an ideal textbook for the advanced undergraduate or beginning graduate course. The authors have updated their notation to reflect the current practice in this still-growing area of study. By the authors' estimation, the 5th edition is approximately 50% longer than the 4th edition. … the legendary Frank Harary, author of the second graph theory text ever produced, is one of the figures profiled. His book was the standard in the discipline for several decades. Chartrand, Lesniak and Zhang have produced a worthy successor.-John T. Saccoman, MAA Reviews, June 2012 (This book is in the MAA's basic library list.)As with the earlier editions, the current text emphasizes clear...

  19. Neural network based pattern matching and spike detection tools and services--in the CARMEN neuroinformatics project.

    Science.gov (United States)

    Fletcher, Martyn; Liang, Bojian; Smith, Leslie; Knowles, Alastair; Jackson, Tom; Jessop, Mark; Austin, Jim

    2008-10-01

    In the study of information flow in the nervous system, component processes can be investigated using a range of electrophysiological and imaging techniques. Although data is difficult and expensive to produce, it is rarely shared and collaboratively exploited. The Code Analysis, Repository and Modelling for e-Neuroscience (CARMEN) project addresses this challenge through the provision of a virtual neuroscience laboratory: an infrastructure for sharing data, tools and services. Central to the CARMEN concept are federated CARMEN nodes, which provide: data and metadata storage, new, thirdparty and legacy services, and tools. In this paper, we describe the CARMEN project as well as the node infrastructure and an associated thick client tool for pattern visualisation and searching, the Signal Data Explorer (SDE). We also discuss new spike detection methods, which are central to the services provided by CARMEN. The SDE is a client application which can be used to explore data in the CARMEN repository, providing data visualization, signal processing and a pattern matching capability. It performs extremely fast pattern matching and can be used to search for complex conditions composed of many different patterns across the large datasets that are typical in neuroinformatics. Searches can also be constrained by specifying text based metadata filters. Spike detection services which use wavelet and morphology techniques are discussed, and have been shown to outperform traditional thresholding and template based systems. A number of different spike detection and sorting techniques will be deployed as services within the CARMEN infrastructure, to allow users to benchmark their performance against a wide range of reference datasets.

  20. Patterns of somatic alterations between matched primary and metastatic colorectal tumors characterized by whole-genome sequencing.

    Science.gov (United States)

    Xie, Tao; Cho, Yong Beom; Wang, Kai; Huang, Donghui; Hong, Hye Kyung; Choi, Yoon-La; Ko, Young Hyeh; Nam, Do-Hyun; Jin, Juyoun; Yang, Heekyoung; Fernandez, Julio; Deng, Shibing; Rejto, Paul A; Lee, Woo Yong; Mao, Mao

    2014-10-01

    Colorectal cancer (CRC) patients have poor prognosis after formation of distant metastasis. Understanding the molecular mechanisms by which genetic changes facilitate metastasis is critical for the development of targeted therapeutic strategies aimed at controlling disease progression while minimizing toxic side effects. A comprehensive portrait of somatic alterations in CRC and the changes between primary and metastatic tumors has yet to be developed. We performed whole genome sequencing of two primary CRC tumors and their matched liver metastases. By comparing to matched germline DNA, we catalogued somatic alterations at multiple scales, including single nucleotide variations, small insertions and deletions, copy number aberrations and structural variations in both the primary and matched metastasis. We found that the majority of these somatic alterations are present in both sites. Despite the overall similarity, several de novo alterations in the metastases were predicted to be deleterious, in genes including FBXW7, DCLK1 and FAT2, which might contribute to the initiation and progression of distant metastasis. Through careful examination of the mutation prevalence among tumor cells at each site, we also proposed distinct clonal evolution patterns between primary and metastatic tumors in the two cases. These results suggest that somatic alterations may play an important role in driving the development of colorectal cancer metastasis and present challenges and opportunities when considering the choice of treatment. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Hierarchy of modular graph identities

    International Nuclear Information System (INIS)

    D’Hoker, Eric; Kaidi, Justin

    2016-01-01

    The low energy expansion of Type II superstring amplitudes at genus one is organized in terms of modular graph functions associated with Feynman graphs of a conformal scalar field on the torus. In earlier work, surprising identities between two-loop graphs at all weights, and between higher-loop graphs of weights four and five were constructed. In the present paper, these results are generalized in two complementary directions. First, all identities at weight six and all dihedral identities at weight seven are obtained and proven. Whenever the Laurent polynomial at the cusp is available, the form of these identities confirms the pattern by which the vanishing of the Laurent polynomial governs the full modular identity. Second, the family of modular graph functions is extended to include all graphs with derivative couplings and worldsheet fermions. These extended families of modular graph functions are shown to obey a hierarchy of inhomogeneous Laplace eigenvalue equations. The eigenvalues are calculated analytically for the simplest infinite sub-families and obtained by Maple for successively more complicated sub-families. The spectrum is shown to consist solely of eigenvalues s(s−1) for positive integers s bounded by the weight, with multiplicities which exhibit rich representation-theoretic patterns.

  2. Hierarchy of modular graph identities

    Energy Technology Data Exchange (ETDEWEB)

    D’Hoker, Eric; Kaidi, Justin [Mani L. Bhaumik Institute for Theoretical Physics, Department of Physics and Astronomy,University of California,Los Angeles, CA 90095 (United States)

    2016-11-09

    The low energy expansion of Type II superstring amplitudes at genus one is organized in terms of modular graph functions associated with Feynman graphs of a conformal scalar field on the torus. In earlier work, surprising identities between two-loop graphs at all weights, and between higher-loop graphs of weights four and five were constructed. In the present paper, these results are generalized in two complementary directions. First, all identities at weight six and all dihedral identities at weight seven are obtained and proven. Whenever the Laurent polynomial at the cusp is available, the form of these identities confirms the pattern by which the vanishing of the Laurent polynomial governs the full modular identity. Second, the family of modular graph functions is extended to include all graphs with derivative couplings and worldsheet fermions. These extended families of modular graph functions are shown to obey a hierarchy of inhomogeneous Laplace eigenvalue equations. The eigenvalues are calculated analytically for the simplest infinite sub-families and obtained by Maple for successively more complicated sub-families. The spectrum is shown to consist solely of eigenvalues s(s−1) for positive integers s bounded by the weight, with multiplicities which exhibit rich representation-theoretic patterns.

  3. Pattern Matching for Volcano Status Assessment: what monitoring data alone can say about Mt. Etna activity

    Science.gov (United States)

    Cannavo, F.; Cannata, A.; Cassisi, C.

    2017-12-01

    The importance of assessing the ongoing status of active volcanoes is crucial not only for exposures to the local population but due to possible presence of tephra also for airline traffic. Adequately monitoring of active volcanoes, hence, plays a key role for civil protection purposes. In last decades, in order to properly monitor possible threats, continuous measuring networks have been designed and deployed on most of potentially hazardous volcanos. Nevertheless, at the present, volcano real-time surveillance is basically delegated to one or more human experts in volcanology, who interpret data coming from different kind of monitoring networks using their experience and non-measurable information (e.g. information from the field) to infer the volcano status. In some cases, raw data are used in some models to obtain more clues on the ongoing activity. In the last decades, with the development of volcano monitoring networks, huge amount of data of different geophysical, geochemical and volcanological types have been collected and stored in large databases. Having such big data sets with many examples of volcanic activity allows us to study volcano monitoring from a machine learning perspective. Thus, exploiting opportunities offered by the abundance of volcano monitoring time-series data we can try to address the following questions: Are the monitored parameters sufficient to discriminate the volcano status? Is it possible to infer/distinguish the volcano status only from the multivariate patterns of measurements? Are all the kind of measurements in the pattern equally useful for status assessment? How accurate would be an automatic system of status inference based only on pattern recognition of data? Here we present preliminary results of the data analysis we performed on a set of data and activity covering the period 2011-2017 at Mount Etna (Italy). In the considered period, we had 52 events of lava fountaining and long periods of Strombolian activity. We

  4. Estimation of subcriticality and fuel concentration by using 'pattern matching' of neutron flux distribution under non uniformed system

    International Nuclear Information System (INIS)

    Ishitani, Kazuki; Yamane, Yoshihiro

    1999-01-01

    In nuclear fuel reprocessing plants, monitoring the spatial profile of neutron flux to infer subcriticality and distribution of fuel concentration using detectors such as PSPC, is very beneficial in sight of criticality safety. In this paper a method of subcriticality and fuel concentration estimation which is supposed to use under non-uniformed system is proposed. Its basic concept is the pattern matching between measured neutron flux distribution and beforehand calculated one. In any kind of subcriticality estimation, we can regard that measured neutron counts put any kind of black box, and then this black box outputs subcriticality. We proposed the use of artificial neural network or 'pattern matching' as black box which have no theoretical clear base. These method are wholly based on the calculated value as recently advancement of computer code accuracy for criticality safety. The most difference between indirect bias estimation method and our method is that our new approach target are the unknown non-uniform system. (J.P.N.)

  5. Investigation of cortical thickness abnormalities in lithium-free adults with bipolar type I disorder using cortical pattern matching

    Science.gov (United States)

    Foland-Ross, Lara C.; Thompson, Paul M.; Sugar, Catherine A.; Madsen, Sarah K.; Shen, Jim K.; Penfold, Conor; Ahlf, Kyle; Rasser, Paul E.; Fischer, Jeffrey; Yang, Yilan; Townsend, Jennifer; Bookheimer, Susan Y.; Altshuler, Lori L.

    2013-01-01

    Objective Several lines of evidence implicate gray matter abnormalities in the prefrontal cortex and anterior cingulate cortex in patients with bipolar disorder. Findings however, have been largely inconsistent across studies. Differences in patients’ medication status or mood state, or the application of traditional volumetric methods that are insensitive to subtle neuroanatomic differences may have contributed to these inconsistent findings. Given this, we used magnetic resonance imaging (MRI) in conjunction with cortical pattern matching methods to assess cortical thickness abnormalities in euthymic bipolar subjects who were not treated with lithium. Method Sixty-five subjects, including 34 lithium-free euthymic subjects with bipolar (type I) disorder and 31 healthy subjects were scanned using magnetic resonance imaging (MRI). Data were processed to measure cortical gray matter thickness. Cortical pattern matching methods associated homologous brain regions across subjects. Spatially normalized thickness maps were analyzed to assess illness effects and associations with clinical variables. Results Relative to healthy subjects, euthymic bipolar I subjects had significantly thinner gray matter in bilateral prefrontal cortex (Brodmann Areas 11, 10, 8 and 44) and left anterior cingulate cortex (Brodmann Areas 24/32). Additionally, thinning in these regions was more pronounced in patients with a history of psychosis. No areas of thicker cortex were detected in bipolar subjects versus healthy subjects. Conclusions Using a technique that is highly sensitive to subtle neuroanatomic differences, significant regional cortical thinning was found in euthymic subjects with bipolar disorder. Clinical implications are discussed. PMID:21285139

  6. Contracting a planar graph efficiently

    DEFF Research Database (Denmark)

    Holm, Jacob; Italiano, Giuseppe F.; Karczmarz, Adam

    2017-01-01

    the data structure, we can achieve optimal running times for decremental bridge detection, 2-edge connectivity, maximal 3-edge connected components, and the problem of finding a unique perfect matching for a static planar graph. Furthermore, we improve the running times of algorithms for several planar...

  7. Improving the Pattern Reproducibility of Multiple-Point-Based Prior Models Using Frequency Matching

    DEFF Research Database (Denmark)

    Cordua, Knud Skou; Hansen, Thomas Mejer; Mosegaard, Klaus

    2014-01-01

    Some multiple-point-based sampling algorithms, such as the snesim algorithm, rely on sequential simulation. The conditional probability distributions that are used for the simulation are based on statistics of multiple-point data events obtained from a training image. During the simulation, data...... events with zero probability in the training image statistics may occur. This is handled by pruning the set of conditioning data until an event with non-zero probability is found. The resulting probability distribution sampled by such algorithms is a pruned mixture model. The pruning strategy leads...... to a probability distribution that lacks some of the information provided by the multiple-point statistics from the training image, which reduces the reproducibility of the training image patterns in the outcome realizations. When pruned mixture models are used as prior models for inverse problems, local re...

  8. Analyses of Crime Patterns in NIBRS Data Based on a Novel Graph Theory Clustering Method: Virginia as a Case Study

    Directory of Open Access Journals (Sweden)

    Peixin Zhao

    2014-01-01

    Full Text Available This paper suggests a novel clustering method for analyzing the National Incident-Based Reporting System (NIBRS data, which include the determination of correlation of different crime types, the development of a likelihood index for crimes to occur in a jurisdiction, and the clustering of jurisdictions based on crime type. The method was tested by using the 2005 assault data from 121 jurisdictions in Virginia as a test case. The analyses of these data show that some different crime types are correlated and some different crime parameters are correlated with different crime types. The analyses also show that certain jurisdictions within Virginia share certain crime patterns. This information assists with constructing a pattern for a specific crime type and can be used to determine whether a jurisdiction may be more likely to see this type of crime occur in their area.

  9. Graph Theory to Pure Mathematics: Some Illustrative Examples

    Indian Academy of Sciences (India)

    Graph Theory to Pure Mathematics: Some. Illustrative Examples v Yegnanarayanan is a. Professor of Mathematics at MNM Jain Engineering. College, Chennai. His research interests include graph theory and its applications to both pure maths and theoretical computer science. Keywords. Graph theory, matching theory,.

  10. Continuous Acetylsalicylic Acid Treatment Does Not Influence Bleeding Pattern or Outcome of Aneurysmal Subarachnoid Hemorrhage: A Matched-Pair Analysis.

    Science.gov (United States)

    Bruder, Markus; Won, Sae-Yeon; Wagner, Marlies; Brawanski, Nina; Dinc, Nazife; Kashefiolasl, Sepide; Seifert, Volker; Konczalla, Juergen

    2018-05-01

    Demographic changes are leading to an aging society with a growing number of patients with cardiovascular diseases, relying on antiplatelet drugs like acetylsalicylic acid (ASA). Although antiplatelet agents are suspected to be protective not only in the cardiologic but in the neurovascular field, the alteration of the coagulating process could have a major impact on the course and outcome after rupture of intracranial aneurysms. Between June 1999 and December 2014, 1422 patients were treated for aneurysmal SAH in our institution, 144 (10.1%) with continuous ASA at the time of aneurysm rupture. A matched-pair analysis was performed. The rate of patients with continuous ASA treatment while rupture of the aneurysm is rising significantly (P bleeding pattern. Outcome was not different in the matched-pair analysis. There was no statistical difference in treatment related-complication rates of microsurgical and endovascular procedures. Therefore, ASA use should not influence treatment decision of the ruptured aneurysm. Copyright © 2018 Elsevier Inc. All rights reserved.

  11. Fixed-pattern noise correction method based on improved moment matching for a TDI CMOS image sensor.

    Science.gov (United States)

    Xu, Jiangtao; Nie, Huafeng; Nie, Kaiming; Jin, Weimin

    2017-09-01

    In this paper, an improved moment matching method based on a spatial correlation filter (SCF) and bilateral filter (BF) is proposed to correct the fixed-pattern noise (FPN) of a time-delay-integration CMOS image sensor (TDI-CIS). First, the values of row FPN (RFPN) and column FPN (CFPN) are estimated and added to the original image through SCF and BF, respectively. Then the filtered image will be processed by an improved moment matching method with a moving window. Experimental results based on a 128-stage TDI-CIS show that, after correcting the FPN in the image captured under uniform illumination, the standard deviation of row mean vector (SDRMV) decreases from 5.6761 LSB to 0.1948 LSB, while the standard deviation of the column mean vector (SDCMV) decreases from 15.2005 LSB to 13.1949LSB. In addition, for different images captured by different TDI-CISs, the average decrease of SDRMV and SDCMV is 5.4922/2.0357 LSB, respectively. Comparative experimental results indicate that the proposed method can effectively correct the FPNs of different TDI-CISs while maintaining image details without any auxiliary equipment.

  12. [Propensity score matching in SPSS].

    Science.gov (United States)

    Huang, Fuqiang; DU, Chunlin; Sun, Menghui; Ning, Bing; Luo, Ying; An, Shengli

    2015-11-01

    To realize propensity score matching in PS Matching module of SPSS and interpret the analysis results. The R software and plug-in that could link with the corresponding versions of SPSS and propensity score matching package were installed. A PS matching module was added in the SPSS interface, and its use was demonstrated with test data. Score estimation and nearest neighbor matching was achieved with the PS matching module, and the results of qualitative and quantitative statistical description and evaluation were presented in the form of a graph matching. Propensity score matching can be accomplished conveniently using SPSS software.

  13. Human Identification by Cross-Correlation and Pattern Matching of Personalized Heartbeat: Influence of ECG Leads and Reference Database Size.

    Science.gov (United States)

    Jekova, Irena; Krasteva, Vessela; Schmid, Ramun

    2018-01-27

    Human identification (ID) is a biometric task, comparing single input sample to many stored templates to identify an individual in a reference database. This paper aims to present the perspectives of personalized heartbeat pattern for reliable ECG-based identification. The investigations are using a database with 460 pairs of 12-lead resting electrocardiograms (ECG) with 10-s durations recorded at time-instants T1 and T2 > T1 + 1 year. Intra-subject long-term ECG stability and inter-subject variability of personalized PQRST (500 ms) and QRS (100 ms) patterns is quantified via cross-correlation, amplitude ratio and pattern matching between T1 and T2 using 7 features × 12-leads. Single and multi-lead ID models are trained on the first 230 ECG pairs. Their validation on 10, 20, ... 230 reference subjects (RS) from the remaining 230 ECG pairs shows: (i) two best single-lead ID models using lead II for a small population RS = (10-140) with identification accuracy AccID = (89.4-67.2)% and aVF for a large population RS = (140-230) with AccID = (67.2-63.9)%; (ii) better performance of the 6-lead limb vs. the 6-lead chest ID model-(91.4-76.1)% vs. (90.9-70)% for RS = (10-230); (iii) best performance of the 12-lead ID model-(98.4-87.4)% for RS = (10-230). The tolerable reference database size, keeping AccID > 80%, is RS = 30 in the single-lead ID scenario (II); RS = 50 (6 chest leads); RS = 100 (6 limb leads), RS > 230-maximal population in this study (12-lead ECG).

  14. Outsourced pattern matching

    DEFF Research Database (Denmark)

    Faust, Sebastian; Hazay, Carmit; Venturi, Daniele

    2013-01-01

    In secure delegatable computation, computationally weak devices (or clients) wish to outsource their computation and data to an untrusted server in the cloud. While most earlier work considers the general question of how to securely outsource any computation to the cloud server, we focus...... that contain confidential data (e.g., health related data about patient history). Our constructions offer simulation-based security in the presence of semi-honest and malicious adversaries (in the random oracle model) and limit the communication in the query phase to O(m) bits plus the number of occurrences...

  15. Boxed Permutation Pattern Matching

    DEFF Research Database (Denmark)

    Amit, Mika; Bille, Philip; Cording, Patrick Hagge

    2016-01-01

    the goal is to only find the boxed subsequences of T that are order-isomorphic to P. This problem was introduced by Bruner and Lackner who showed that it can be solved in O(n3) time. Cho et al. [CPM 2015] gave an O(n2m) time algorithm and improved it to O(n2 logm). In this paper we present a solution...

  16. Graphs, Ideal Flow, and the Transportation Network

    OpenAIRE

    Teknomo, Kardi

    2016-01-01

    This lecture discusses the mathematical relationship between network structure and network utilization of transportation network. Network structure means the graph itself. Network utilization represent the aggregation of trajectories of agents in using the network graph. I show the similarity and relationship between the structural pattern of the network and network utilization.

  17. Graph visualization (Invited talk)

    NARCIS (Netherlands)

    Wijk, van J.J.; Kreveld, van M.J.; Speckmann, B.

    2012-01-01

    Black and white node link diagrams are the classic method to depict graphs, but these often fall short to give insight in large graphs or when attributes of nodes and edges play an important role. Graph visualization aims obtaining insight in such graphs using interactive graphical representations.

  18. Robust Point Matching for Non-Rigid Shapes: A Relaxation Labeling Based Approach

    National Research Council Canada - National Science Library

    Zheng, Yefeng; Doermann, David S

    2004-01-01

    .... Based on this observation, we formulate point matching as a graph matching problem. Each point is a node in the graph, and two nodes are connected by an edge if their Euclidean distance is less...

  19. Graphs and matrices

    CERN Document Server

    Bapat, Ravindra B

    2014-01-01

    This new edition illustrates the power of linear algebra in the study of graphs. The emphasis on matrix techniques is greater than in other texts on algebraic graph theory. Important matrices associated with graphs (for example, incidence, adjacency and Laplacian matrices) are treated in detail. Presenting a useful overview of selected topics in algebraic graph theory, early chapters of the text focus on regular graphs, algebraic connectivity, the distance matrix of a tree, and its generalized version for arbitrary graphs, known as the resistance matrix. Coverage of later topics include Laplacian eigenvalues of threshold graphs, the positive definite completion problem and matrix games based on a graph. Such an extensive coverage of the subject area provides a welcome prompt for further exploration. The inclusion of exercises enables practical learning throughout the book. In the new edition, a new chapter is added on the line graph of a tree, while some results in Chapter 6 on Perron-Frobenius theory are reo...

  20. Inferring ontology graph structures using OWL reasoning

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel; Hoehndorf, Robert

    2018-01-01

    ' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies

  1. Specific Patterns of Emotion Recognition from Faces in Children with ASD: Results of a Cross-Modal Matching Paradigm

    Science.gov (United States)

    Golan, Ofer; Gordon, Ilanit; Fichman, Keren; Keinan, Giora

    2018-01-01

    Children with ASD show emotion recognition difficulties, as part of their social communication deficits. We examined facial emotion recognition (FER) in intellectually disabled children with ASD and in younger typically developing (TD) controls, matched on mental age. Our emotion-matching paradigm employed three different modalities: facial, vocal…

  2. Adaptive Graph Convolutional Neural Networks

    OpenAIRE

    Li, Ruoyu; Wang, Sheng; Zhu, Feiyun; Huang, Junzhou

    2018-01-01

    Graph Convolutional Neural Networks (Graph CNNs) are generalizations of classical CNNs to handle graph data such as molecular data, point could and social networks. Current filters in graph CNNs are built for fixed and shared graph structure. However, for most real data, the graph structures varies in both size and connectivity. The paper proposes a generalized and flexible graph CNN taking data of arbitrary graph structure as input. In that way a task-driven adaptive graph is learned for eac...

  3. On middle cube graphs

    Directory of Open Access Journals (Sweden)

    C. Dalfo

    2015-10-01

    Full Text Available We study a family of graphs related to the $n$-cube. The middle cube graph of parameter k is the subgraph of $Q_{2k-1}$ induced by the set of vertices whose binary representation has either $k-1$ or $k$ number of ones. The middle cube graphs can be obtained from the well-known odd graphs by doubling their vertex set. Here we study some of the properties of the middle cube graphs in the light of the theory of distance-regular graphs. In particular, we completely determine their spectra (eigenvalues and their multiplicities, and associated eigenvectors.

  4. Application of graph theory to the morphological analysis of settlements

    OpenAIRE

    Szmytkie Robert

    2017-01-01

    In the following paper, the analyses of morphology of settlements were conducted using graph methods. The intention of the author was to create a quantifiable and simple measure, which, in a quantitative way, would express the degree of development of a graph (the spatial pattern of settlement). When analysing examples of graphs assigned to a set of small towns and large villages, it was noticed that the graph development index should depend on: a relative number of edges in relation to the n...

  5. Using Graph Components Derived from an Associative Concept Dictionary to Predict fMRI Neural Activation Patterns that Represent the Meaning of Nouns.

    Directory of Open Access Journals (Sweden)

    Hiroyuki Akama

    Full Text Available In this study, we introduce an original distance definition for graphs, called the Markov-inverse-F measure (MiF. This measure enables the integration of classical graph theory indices with new knowledge pertaining to structural feature extraction from semantic networks. MiF improves the conventional Jaccard and/or Simpson indices, and reconciles both the geodesic information (random walk and co-occurrence adjustment (degree balance and distribution. We measure the effectiveness of graph-based coefficients through the application of linguistic graph information for a neural activity recorded during conceptual processing in the human brain. Specifically, the MiF distance is computed between each of the nouns used in a previous neural experiment and each of the in-between words in a subgraph derived from the Edinburgh Word Association Thesaurus of English. From the MiF-based information matrix, a machine learning model can accurately obtain a scalar parameter that specifies the degree to which each voxel in (the MRI image of the brain is activated by each word or each principal component of the intermediate semantic features. Furthermore, correlating the voxel information with the MiF-based principal components, a new computational neurolinguistics model with a network connectivity paradigm is created. This allows two dimensions of context space to be incorporated with both semantic and neural distributional representations.

  6. Tutte sets in graphs I: Maximal tutte sets and D-graphs

    NARCIS (Netherlands)

    Bauer, D.; Broersma, Haitze J.; Morgana, A.; Schmeichel, E.

    A well-known formula of Tutte and Berge expresses the size of a maximum matching in a graph $G$ in terms of what is usually called the deficiency of $G$. A subset $X$ of $V(G)$ for which this deficiency is attained is called a Tutte set of $G$. While much is known about maximum matchings, less is

  7. Price competition on graphs

    NARCIS (Netherlands)

    Soetevent, A.R.

    2010-01-01

    This paper extends Hotelling's model of price competition with quadratic transportation costs from a line to graphs. I propose an algorithm to calculate firm-level demand for any given graph, conditional on prices and firm locations. One feature of graph models of price competition is that spatial

  8. Graphing Inequalities, Connecting Meaning

    Science.gov (United States)

    Switzer, J. Matt

    2014-01-01

    Students often have difficulty with graphing inequalities (see Filloy, Rojano, and Rubio 2002; Drijvers 2002), and J. Matt Switzer's students were no exception. Although students can produce graphs for simple inequalities, they often struggle when the format of the inequality is unfamiliar. Even when producing a correct graph of an…

  9. Similarity Measure of Graphs

    Directory of Open Access Journals (Sweden)

    Amine Labriji

    2017-07-01

    Full Text Available The topic of identifying the similarity of graphs was considered as highly recommended research field in the Web semantic, artificial intelligence, the shape recognition and information research. One of the fundamental problems of graph databases is finding similar graphs to a graph query. Existing approaches dealing with this problem are usually based on the nodes and arcs of the two graphs, regardless of parental semantic links. For instance, a common connection is not identified as being part of the similarity of two graphs in cases like two graphs without common concepts, the measure of similarity based on the union of two graphs, or the one based on the notion of maximum common sub-graph (SCM, or the distance of edition of graphs. This leads to an inadequate situation in the context of information research. To overcome this problem, we suggest a new measure of similarity between graphs, based on the similarity measure of Wu and Palmer. We have shown that this new measure satisfies the properties of a measure of similarities and we applied this new measure on examples. The results show that our measure provides a run time with a gain of time compared to existing approaches. In addition, we compared the relevance of the similarity values obtained, it appears that this new graphs measure is advantageous and  offers a contribution to solving the problem mentioned above.

  10. Distance-regular graphs

    NARCIS (Netherlands)

    van Dam, Edwin R.; Koolen, Jack H.; Tanaka, Hajime

    2016-01-01

    This is a survey of distance-regular graphs. We present an introduction to distance-regular graphs for the reader who is unfamiliar with the subject, and then give an overview of some developments in the area of distance-regular graphs since the monograph 'BCN'[Brouwer, A.E., Cohen, A.M., Neumaier,

  11. Fuzzy Graph Language Recognizability

    OpenAIRE

    Kalampakas , Antonios; Spartalis , Stefanos; Iliadis , Lazaros

    2012-01-01

    Part 5: Fuzzy Logic; International audience; Fuzzy graph language recognizability is introduced along the lines of the established theory of syntactic graph language recognizability by virtue of the algebraic structure of magmoids. The main closure properties of the corresponding class are investigated and several interesting examples of fuzzy graph languages are examined.

  12. Spectra of Graphs

    NARCIS (Netherlands)

    Brouwer, A.E.; Haemers, W.H.

    2012-01-01

    This book gives an elementary treatment of the basic material about graph spectra, both for ordinary, and Laplace and Seidel spectra. The text progresses systematically, by covering standard topics before presenting some new material on trees, strongly regular graphs, two-graphs, association

  13. The Index-Based Subgraph Matching Algorithm (ISMA): Fast Subgraph Enumeration in Large Networks Using Optimized Search Trees

    OpenAIRE

    Demeyer, Sofie; Michoel, Tom; Fostier, Jan; Audenaert, Pieter; Pickavet, Mario; Demeester, Piet

    2013-01-01

    Subgraph matching algorithms are designed to find all instances of predefined subgraphs in a large graph or network and play an important role in the discovery and analysis of so-called network motifs, subgraph patterns which occur more often than expected by chance. We present the index-based subgraph matching algorithm (ISMA), a novel tree-based algorithm. ISMA realizes a speedup compared to existing algorithms by carefully selecting the order in which the nodes of a query subgraph are inve...

  14. OPEX: Optimized Eccentricity Computation in Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, Keith [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2011-11-14

    Real-world graphs have many properties of interest, but often these properties are expensive to compute. We focus on eccentricity, radius and diameter in this work. These properties are useful measures of the global connectivity patterns in a graph. Unfortunately, computing eccentricity for all nodes is O(n2) for a graph with n nodes. We present OPEX, a novel combination of optimizations which improves computation time of these properties by orders of magnitude in real-world experiments on graphs of many different sizes. We run OPEX on graphs with up to millions of links. OPEX gives either exact results or bounded approximations, unlike its competitors which give probabilistic approximations or sacrifice node-level information (eccentricity) to compute graphlevel information (diameter).

  15. Graphs and Homomorphisms

    CERN Document Server

    Hell, Pavol

    2004-01-01

    This is a book about graph homomorphisms. Graph theory is now an established discipline but the study of graph homomorphisms has only recently begun to gain wide acceptance and interest. The subject gives a useful perspective in areas such as graph reconstruction, products, fractional and circular colourings, and has applications in complexity theory, artificial intelligence, telecommunication, and, most recently, statistical physics.Based on the authors' lecture notes for graduate courses, this book can be used as a textbook for a second course in graph theory at 4th year or master's level an

  16. Simplicial complexes of graphs

    CERN Document Server

    Jonsson, Jakob

    2008-01-01

    A graph complex is a finite family of graphs closed under deletion of edges. Graph complexes show up naturally in many different areas of mathematics, including commutative algebra, geometry, and knot theory. Identifying each graph with its edge set, one may view a graph complex as a simplicial complex and hence interpret it as a geometric object. This volume examines topological properties of graph complexes, focusing on homotopy type and homology. Many of the proofs are based on Robin Forman's discrete version of Morse theory. As a byproduct, this volume also provides a loosely defined toolbox for attacking problems in topological combinatorics via discrete Morse theory. In terms of simplicity and power, arguably the most efficient tool is Forman's divide and conquer approach via decision trees; it is successfully applied to a large number of graph and digraph complexes.

  17. Introduction to quantum graphs

    CERN Document Server

    Berkolaiko, Gregory

    2012-01-01

    A "quantum graph" is a graph considered as a one-dimensional complex and equipped with a differential operator ("Hamiltonian"). Quantum graphs arise naturally as simplified models in mathematics, physics, chemistry, and engineering when one considers propagation of waves of various nature through a quasi-one-dimensional (e.g., "meso-" or "nano-scale") system that looks like a thin neighborhood of a graph. Works that currently would be classified as discussing quantum graphs have been appearing since at least the 1930s, and since then, quantum graphs techniques have been applied successfully in various areas of mathematical physics, mathematics in general and its applications. One can mention, for instance, dynamical systems theory, control theory, quantum chaos, Anderson localization, microelectronics, photonic crystals, physical chemistry, nano-sciences, superconductivity theory, etc. Quantum graphs present many non-trivial mathematical challenges, which makes them dear to a mathematician's heart. Work on qu...

  18. Graph Theory in Paris : Conference in Memory of Claude Berge

    CERN Document Server

    Fonlupt, Jean; Fouquet, Jean-Luc; Fournier, Jean-Claude; Alfonsín, Jorge

    2007-01-01

    In July 2004, a conference on graph theory was held in Paris in memory of Claude Berge, one of the pioneers of the field. The event brought together many prominent specialists on topics, such as perfect graphs and matching theory, upon which Claude Berge's work has had a major impact. This volume includes contributions to these and other topics from many of the participants.

  19. Connections between the matching and chromatic polynomials

    Directory of Open Access Journals (Sweden)

    E. J. Farrell

    1992-01-01

    Full Text Available The main results established are (i a connection between the matching and chromatic polynomials and (ii a formula for the matching polynomial of a general complement of a subgraph of a graph. Some deductions on matching and chromatic equivalence and uniqueness are made.

  20. Graph Processing on GPUs: A Survey

    DEFF Research Database (Denmark)

    Shi, Xuanhua; Zheng, Zhigao; Zhou, Yongluan

    2018-01-01

    hundreds of billions, has attracted much attention in both industry and academia. It still remains a great challenge to process such large-scale graphs. Researchers have been seeking for new possible solutions. Because of the massive degree of parallelism and the high memory access bandwidth in GPU......, utilizing GPU to accelerate graph processing proves to be a promising solution. This article surveys the key issues of graph processing on GPUs, including data layout, memory access pattern, workload mapping, and specific GPU programming. In this article, we summarize the state-of-the-art research on GPU...

  1. Graphing trillions of triangles.

    Science.gov (United States)

    Burkhardt, Paul

    2017-07-01

    The increasing size of Big Data is often heralded but how data are transformed and represented is also profoundly important to knowledge discovery, and this is exemplified in Big Graph analytics. Much attention has been placed on the scale of the input graph but the product of a graph algorithm can be many times larger than the input. This is true for many graph problems, such as listing all triangles in a graph. Enabling scalable graph exploration for Big Graphs requires new approaches to algorithms, architectures, and visual analytics. A brief tutorial is given to aid the argument for thoughtful representation of data in the context of graph analysis. Then a new algebraic method to reduce the arithmetic operations in counting and listing triangles in graphs is introduced. Additionally, a scalable triangle listing algorithm in the MapReduce model will be presented followed by a description of the experiments with that algorithm that led to the current largest and fastest triangle listing benchmarks to date. Finally, a method for identifying triangles in new visual graph exploration technologies is proposed.

  2. Outer-totalistic cellular automata on graphs

    International Nuclear Information System (INIS)

    Marr, Carsten; Huett, Marc-Thorsten

    2009-01-01

    We present an intuitive formalism for implementing cellular automata on arbitrary topologies. By that means, we identify a symmetry operation in the class of elementary cellular automata. Moreover, we determine the subset of topologically sensitive elementary cellular automata and find that the overall number of complex patterns decreases under increasing neighborhood size in regular graphs. As exemplary applications, we apply the formalism to complex networks and compare the potential of scale-free graphs and metabolic networks to generate complex dynamics

  3. Inferring ontology graph structures using OWL reasoning

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2018-01-05

    Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies\\' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies\\' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph .Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

  4. Inferring ontology graph structures using OWL reasoning.

    Science.gov (United States)

    Rodríguez-García, Miguel Ángel; Hoehndorf, Robert

    2018-01-05

    Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies' semantic content remains a challenge. We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph . Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

  5. Identifying patients with Alzheimer's disease using resting-state fMRI and graph theory.

    Science.gov (United States)

    Khazaee, Ali; Ebrahimzadeh, Ata; Babajani-Feremi, Abbas

    2015-11-01

    Study of brain network on the basis of resting-state functional magnetic resonance imaging (fMRI) has provided promising results to investigate changes in connectivity among different brain regions because of diseases. Graph theory can efficiently characterize different aspects of the brain network by calculating measures of integration and segregation. In this study, we combine graph theoretical approaches with advanced machine learning methods to study functional brain network alteration in patients with Alzheimer's disease (AD). Support vector machine (SVM) was used to explore the ability of graph measures in diagnosis of AD. We applied our method on the resting-state fMRI data of twenty patients with AD and twenty age and gender matched healthy subjects. The data were preprocessed and each subject's graph was constructed by parcellation of the whole brain into 90 distinct regions using the automated anatomical labeling (AAL) atlas. The graph measures were then calculated and used as the discriminating features. Extracted network-based features were fed to different feature selection algorithms to choose most significant features. In addition to the machine learning approach, statistical analysis was performed on connectivity matrices to find altered connectivity patterns in patients with AD. Using the selected features, we were able to accurately classify patients with AD from healthy subjects with accuracy of 100%. Results of this study show that pattern recognition and graph of brain network, on the basis of the resting state fMRI data, can efficiently assist in the diagnosis of AD. Classification based on the resting-state fMRI can be used as a non-invasive and automatic tool to diagnosis of Alzheimer's disease. Copyright © 2015 International Federation of Clinical Neurophysiology. All rights reserved.

  6. Introductory graph theory

    CERN Document Server

    Chartrand, Gary

    1984-01-01

    Graph theory is used today in the physical sciences, social sciences, computer science, and other areas. Introductory Graph Theory presents a nontechnical introduction to this exciting field in a clear, lively, and informative style. Author Gary Chartrand covers the important elementary topics of graph theory and its applications. In addition, he presents a large variety of proofs designed to strengthen mathematical techniques and offers challenging opportunities to have fun with mathematics. Ten major topics - profusely illustrated - include: Mathematical Models, Elementary Concepts of Grap

  7. Price Competition on Graphs

    OpenAIRE

    Adriaan R. Soetevent

    2010-01-01

    This paper extends Hotelling's model of price competition with quadratic transportation costs from a line to graphs. I propose an algorithm to calculate firm-level demand for any given graph, conditional on prices and firm locations. One feature of graph models of price competition is that spatial discontinuities in firm-level demand may occur. I show that the existence result of D'Aspremont et al. (1979) does not extend to simple star graphs. I conjecture that this non-existence result holds...

  8. Price Competition on Graphs

    OpenAIRE

    Pim Heijnen; Adriaan Soetevent

    2014-01-01

    This paper extends Hotelling's model of price competition with quadratic transportation costs from a line to graphs. We derive an algorithm to calculate firm-level demand for any given graph, conditional on prices and firm locations. These graph models of price competition may lead to spatial discontinuities in firm-level demand. We show that the existence result of D'Aspremont et al. (1979) does not extend to simple star graphs and conjecture that this non-existence result holds more general...

  9. Functions and graphs

    CERN Document Server

    Gelfand, I M; Shnol, E E

    1969-01-01

    The second in a series of systematic studies by a celebrated mathematician I. M. Gelfand and colleagues, this volume presents students with a well-illustrated sequence of problems and exercises designed to illuminate the properties of functions and graphs. Since readers do not have the benefit of a blackboard on which a teacher constructs a graph, the authors abandoned the customary use of diagrams in which only the final form of the graph appears; instead, the book's margins feature step-by-step diagrams for the complete construction of each graph. The first part of the book employs simple fu

  10. Creating more effective graphs

    CERN Document Server

    Robbins, Naomi B

    2012-01-01

    A succinct and highly readable guide to creating effective graphs The right graph can be a powerful tool for communicating information, improving a presentation, or conveying your point in print. If your professional endeavors call for you to present data graphically, here's a book that can help you do it more effectively. Creating More Effective Graphs gives you the basic knowledge and techniques required to choose and create appropriate graphs for a broad range of applications. Using real-world examples everyone can relate to, the author draws on her years of experience in gr

  11. Graph Generator Survey

    Energy Technology Data Exchange (ETDEWEB)

    Lothian, Joshua [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Powers, Sarah S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sullivan, Blair D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Baker, Matthew B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Schrock, Jonathan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Poole, Stephen W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-10-01

    The benchmarking effort within the Extreme Scale Systems Center at Oak Ridge National Laboratory seeks to provide High Performance Computing benchmarks and test suites of interest to the DoD sponsor. The work described in this report is a part of the effort focusing on graph generation. A previously developed benchmark, SystemBurn, allowed the emulation of different application behavior profiles within a single framework. To complement this effort, similar capabilities are desired for graph-centric problems. This report examines existing synthetic graph generator implementations in preparation for further study on the properties of their generated synthetic graphs.

  12. Graph Compression by BFS

    Directory of Open Access Journals (Sweden)

    Alberto Apostolico

    2009-08-01

    Full Text Available The Web Graph is a large-scale graph that does not fit in main memory, so that lossless compression methods have been proposed for it. This paper introduces a compression scheme that combines efficient storage with fast retrieval for the information in a node. The scheme exploits the properties of the Web Graph without assuming an ordering of the URLs, so that it may be applied to more general graphs. Tests on some datasets of use achieve space savings of about 10% over existing methods.

  13. TrajGraph: A Graph-Based Visual Analytics Approach to Studying Urban Network Centralities Using Taxi Trajectory Data.

    Science.gov (United States)

    Huang, Xiaoke; Zhao, Ye; Yang, Jing; Zhang, Chong; Ma, Chao; Ye, Xinyue

    2016-01-01

    We propose TrajGraph, a new visual analytics method, for studying urban mobility patterns by integrating graph modeling and visual analysis with taxi trajectory data. A special graph is created to store and manifest real traffic information recorded by taxi trajectories over city streets. It conveys urban transportation dynamics which can be discovered by applying graph analysis algorithms. To support interactive, multiscale visual analytics, a graph partitioning algorithm is applied to create region-level graphs which have smaller size than the original street-level graph. Graph centralities, including Pagerank and betweenness, are computed to characterize the time-varying importance of different urban regions. The centralities are visualized by three coordinated views including a node-link graph view, a map view and a temporal information view. Users can interactively examine the importance of streets to discover and assess city traffic patterns. We have implemented a fully working prototype of this approach and evaluated it using massive taxi trajectories of Shenzhen, China. TrajGraph's capability in revealing the importance of city streets was evaluated by comparing the calculated centralities with the subjective evaluations from a group of drivers in Shenzhen. Feedback from a domain expert was collected. The effectiveness of the visual interface was evaluated through a formal user study. We also present several examples and a case study to demonstrate the usefulness of TrajGraph in urban transportation analysis.

  14. Graph Theory. 1. Fragmentation of Structural Graphs

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2002-12-01

    Full Text Available The investigation of structural graphs has many fields of applications in engineering, especially in applied sciences like as applied chemistry and physics, computer sciences and automation, electronics and telecommunication. The main subject of the paper is to express fragmentation criteria in graph using a new method of investigation: terminal paths. Using terminal paths are defined most of the fragmentation criteria that are in use in molecular topology, but the fields of applications are more generally than that, as I mentioned before. Graphical examples of fragmentation are given for every fragmentation criteria. Note that all fragmentation is made with a computer program that implements a routine for every criterion.[1] A web routine for tracing all terminal paths in graph can be found at the address: http://vl.academicdirect.ro/molecular_topology/tpaths/ [1] M. V. Diudea, I. Gutman, L. Jäntschi, Molecular Topology, Nova Science, Commack, New York, 2001, 2002.

  15. Quantum complexity of graph and algebraic problems

    International Nuclear Information System (INIS)

    Doern, Sebastian

    2008-01-01

    This thesis is organized as follows: In Chapter 2 we give some basic notations, definitions and facts from linear algebra, graph theory, group theory and quantum computation. In Chapter 3 we describe three important methods for the construction of quantum algorithms. We present the quantum search algorithm by Grover, the quantum amplitude amplification and the quantum walk search technique by Magniez et al. These three tools are the basis for the development of our new quantum algorithms for graph and algebra problems. In Chapter 4 we present two tools for proving quantum query lower bounds. We present the quantum adversary method by Ambainis and the polynomial method introduced by Beals et al. The quantum adversary tool is very useful to prove good lower bounds for many graph and algebra problems. The part of the thesis containing the original results is organized in two parts. In the first part we consider the graph problems. In Chapter 5 we give a short summary of known quantum graph algorithms. In Chapter 6 to 8 we study the complexity of our new algorithms for matching problems, graph traversal and independent set problems on quantum computers. In the second part of our thesis we present new quantum algorithms for algebraic problems. In Chapter 9 to 10 we consider group testing problems and prove quantum complexity bounds for important problems from linear algebra. (orig.)

  16. Quantum complexity of graph and algebraic problems

    Energy Technology Data Exchange (ETDEWEB)

    Doern, Sebastian

    2008-02-04

    This thesis is organized as follows: In Chapter 2 we give some basic notations, definitions and facts from linear algebra, graph theory, group theory and quantum computation. In Chapter 3 we describe three important methods for the construction of quantum algorithms. We present the quantum search algorithm by Grover, the quantum amplitude amplification and the quantum walk search technique by Magniez et al. These three tools are the basis for the development of our new quantum algorithms for graph and algebra problems. In Chapter 4 we present two tools for proving quantum query lower bounds. We present the quantum adversary method by Ambainis and the polynomial method introduced by Beals et al. The quantum adversary tool is very useful to prove good lower bounds for many graph and algebra problems. The part of the thesis containing the original results is organized in two parts. In the first part we consider the graph problems. In Chapter 5 we give a short summary of known quantum graph algorithms. In Chapter 6 to 8 we study the complexity of our new algorithms for matching problems, graph traversal and independent set problems on quantum computers. In the second part of our thesis we present new quantum algorithms for algebraic problems. In Chapter 9 to 10 we consider group testing problems and prove quantum complexity bounds for important problems from linear algebra. (orig.)

  17. Representation of activity in images using geospatial temporal graphs

    Science.gov (United States)

    Brost, Randolph; McLendon, III, William C.; Parekh, Ojas D.; Rintoul, Mark Daniel; Watson, Jean-Paul; Strip, David R.; Diegert, Carl

    2018-05-01

    Various technologies pertaining to modeling patterns of activity observed in remote sensing images using geospatial-temporal graphs are described herein. Graphs are constructed by representing objects in remote sensing images as nodes, and connecting nodes with undirected edges representing either distance or adjacency relationships between objects and directed edges representing changes in time. Activity patterns may be discerned from the graphs by coding nodes representing persistent objects like buildings differently from nodes representing ephemeral objects like vehicles, and examining the geospatial-temporal relationships of ephemeral nodes within the graph.

  18. Computing solutions for matching games

    NARCIS (Netherlands)

    Biró, Péter; Kern, Walter; Paulusma, Daniël

    2012-01-01

    A matching game is a cooperative game (N, v) defined on a graph G = (N, E) with an edge weighting w : E → R+. The player set is N and the value of a coalition S ⊆ N is defined as the maximum weight of a matching in the subgraph induced by S. First we present an O(nm+n2 log n) algorithm that tests if

  19. Foods Served in Child Care Facilities Participating in the Child and Adult Care Food Program: Menu Match and Agreement with the New Meal Patterns and Best Practices.

    Science.gov (United States)

    Dave, Jayna M; Cullen, Karen W

    2018-02-20

    To assess the agreement of posted menus with foods served to 3- to 5-year-old children attending federal Child and Adult Care Food Program (CACFP)-enrolled facilities, and the degree to which the facilities met the new meal patterns and best practices. On-site observations and menu coding. Nine early care and education centers. Agreement of posted menus with foods served, and comparison of foods served and consumed with the new CACFP meal guidelines and best practices. Data were compiled for each meal (breakfast, lunch, and snacks). Frequencies and percentages of agreement with the posted menu (coded matches, substitutions, additions, and omissions) were calculated for each food component in the CACFP menu guidelines. Menu total match was created by summing the menu match plus acceptable substitutions. Menus were compared with the new CACFP meal guidelines and best practices. The match between the posted menus and foods actually served to children at breakfast, lunch, and snack was high when the acceptable menu substitutions were considered (approximately 94% to 100% total match). Comparing the menus with the new meal guidelines and best practices, the 1 guideline that was fully implemented was serving only unflavored, low-fat, or 1% milk; fruit and vegetable guidelines were partially met; fruit juice was not served often, nor were legumes; the guideline for 1 whole grain-rich serving/d was not met; and regular beef and full-fat cheese products were commonly served. Early care and education centers enrolled in CACFP provided meals that met the current CACFP guidelines. Some menu improvements are needed for the centers to meet the new guidelines and best practices. Copyright © 2018 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

  20. Canonical Skeletons for Shape Matching

    NARCIS (Netherlands)

    Eede, M. van; Macrini, D.; Telea, A.; Sminchisescu, C.; Dickinson, S.

    2006-01-01

    Skeletal representations of 2-D shape, including shock graphs, have become increasingly popular for shape matching and object recognition. However, it is well known that skeletal structure can be unstable under minor boundary deformation, part articulation, and minor shape deformation (due to, for

  1. Matched filtering Generalized Phase Contrast using binary phase for dynamic spot- and line patterns in biophotonics and structured lighting

    DEFF Research Database (Denmark)

    Bañas, Andrew Rafael; Aabo, Thomas; Palima, Darwin

    2013-01-01

    as a combination of Generalized Phase Contrast and phase-only correlation. Such an analysis makes it convenient to optimize an mGPC system for different setup conditions. Results showing binary-only phase generation of dynamic spot arrays and line patterns are presented. © 201 Optical Society of America...

  2. A graph rewriting programming language for graph drawing

    OpenAIRE

    Rodgers, Peter

    1998-01-01

    This paper describes Grrr, a prototype visual graph drawing tool. Previously there were no visual languages for programming graph drawing algorithms despite the inherently visual nature of the process. The languages which gave a diagrammatic view of graphs were not computationally complete and so could not be used to implement complex graph drawing algorithms. Hence current graph drawing tools are all text based. Recent developments in graph rewriting systems have produced computationally com...

  3. Graph Transforming Java Data

    NARCIS (Netherlands)

    de Mol, M.J.; Rensink, Arend; Hunt, James J.

    This paper introduces an approach for adding graph transformation-based functionality to existing JAVA programs. The approach relies on a set of annotations to identify the intended graph structure, as well as on user methods to manipulate that structure, within the user’s own JAVA class

  4. Distance-transitive graphs

    NARCIS (Netherlands)

    Cohen, A.M.; Beineke, L.W.; Wilson, R.J.; Cameron, P.J.

    2004-01-01

    In this chapter we investigate the classification of distance-transitive graphs: these are graphs whose automorphism groups are transitive on each of the sets of pairs of vertices at distance i, for i = 0, 1,.... We provide an introduction into the field. By use of the classification of finite

  5. Adventures in graph theory

    CERN Document Server

    Joyner, W David

    2017-01-01

    This textbook acts as a pathway to higher mathematics by seeking and illuminating the connections between graph theory and diverse fields of mathematics, such as calculus on manifolds, group theory, algebraic curves, Fourier analysis, cryptography and other areas of combinatorics. An overview of graph theory definitions and polynomial invariants for graphs prepares the reader for the subsequent dive into the applications of graph theory. To pique the reader’s interest in areas of possible exploration, recent results in mathematics appear throughout the book, accompanied with examples of related graphs, how they arise, and what their valuable uses are. The consequences of graph theory covered by the authors are complicated and far-reaching, so topics are always exhibited in a user-friendly manner with copious graphs, exercises, and Sage code for the computation of equations. Samples of the book’s source code can be found at github.com/springer-math/adventures-in-graph-theory. The text is geared towards ad...

  6. Recognition of fractal graphs

    NARCIS (Netherlands)

    Perepelitsa, VA; Sergienko, [No Value; Kochkarov, AM

    1999-01-01

    Definitions of prefractal and fractal graphs are introduced, and they are used to formulate mathematical models in different fields of knowledge. The topicality of fractal-graph recognition from the point of view, of fundamental improvement in the efficiency of the solution of algorithmic problems

  7. Graph Colouring Algorithms

    DEFF Research Database (Denmark)

    Husfeldt, Thore

    2015-01-01

    This chapter presents an introduction to graph colouring algorithms. The focus is on vertex-colouring algorithms that work for general classes of graphs with worst-case performance guarantees in a sequential model of computation. The presentation aims to demonstrate the breadth of available...

  8. Packing Degenerate Graphs Greedily

    Czech Academy of Sciences Publication Activity Database

    Allen, P.; Böttcher, J.; Hladký, J.; Piguet, Diana

    2017-01-01

    Roč. 61, August (2017), s. 45-51 ISSN 1571-0653 R&D Projects: GA ČR GJ16-07822Y Institutional support: RVO:67985807 Keywords : tree packing conjecture * graph packing * graph processes Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics

  9. Generalized connectivity of graphs

    CERN Document Server

    Li, Xueliang

    2016-01-01

    Noteworthy results, proof techniques, open problems and conjectures in generalized (edge-) connectivity are discussed in this book. Both theoretical and practical analyses for generalized (edge-) connectivity of graphs are provided. Topics covered in this book include: generalized (edge-) connectivity of graph classes, algorithms, computational complexity, sharp bounds, Nordhaus-Gaddum-type results, maximum generalized local connectivity, extremal problems, random graphs, multigraphs, relations with the Steiner tree packing problem and generalizations of connectivity. This book enables graduate students to understand and master a segment of graph theory and combinatorial optimization. Researchers in graph theory, combinatorics, combinatorial optimization, probability, computer science, discrete algorithms, complexity analysis, network design, and the information transferring models will find this book useful in their studies.

  10. The many faces of graph dynamics

    Science.gov (United States)

    Pignolet, Yvonne Anne; Roy, Matthieu; Schmid, Stefan; Tredan, Gilles

    2017-06-01

    The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is known today about the network dynamics: indeed, complex networks in reality are not static, but rather dynamically evolve over time. Our paper is motivated by the empirical observation that network evolution patterns seem far from random, but exhibit structure. Moreover, the specific patterns appear to depend on the network type, contradicting the existence of a ‘one fits it all’ model. However, we still lack observables to quantify these intuitions, as well as metrics to compare graph evolutions. Such observables and metrics are needed for extrapolating or predicting evolutions, as well as for interpolating graph evolutions. To explore the many faces of graph dynamics and to quantify temporal changes, this paper suggests to build upon the concept of centrality, a measure of node importance in a network. In particular, we introduce the notion of centrality distance, a natural similarity measure for two graphs which depends on a given centrality, characterizing the graph type. Intuitively, centrality distances reflect the extent to which (non-anonymous) node roles are different or, in case of dynamic graphs, have changed over time, between two graphs. We evaluate the centrality distance approach for five evolutionary models and seven real-world social and physical networks. Our results empirically show the usefulness of centrality distances for characterizing graph dynamics compared to a null-model of random evolution, and highlight the differences between the considered scenarios. Interestingly, our approach allows us to compare the dynamics of very different networks, in terms of scale and evolution speed.

  11. Autoregressive Moving Average Graph Filtering

    OpenAIRE

    Isufi, Elvin; Loukas, Andreas; Simonetto, Andrea; Leus, Geert

    2016-01-01

    One of the cornerstones of the field of signal processing on graphs are graph filters, direct analogues of classical filters, but intended for signals defined on graphs. This work brings forth new insights on the distributed graph filtering problem. We design a family of autoregressive moving average (ARMA) recursions, which (i) are able to approximate any desired graph frequency response, and (ii) give exact solutions for tasks such as graph signal denoising and interpolation. The design phi...

  12. Evolutionary games on graphs

    Science.gov (United States)

    Szabó, György; Fáth, Gábor

    2007-07-01

    Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.

  13. MOSS-5: A Fast Method of Approximating Counts of 5-Node Graphlets in Large Graphs

    KAUST Repository

    Wang, Pinghui; Zhao, Junzhou; Zhang, Xiangliang; Li, Zhenguo; Cheng, Jiefeng; Lui, John C.S.; Towsley, Don; Tao, Jing; Guan, Xiaohong

    2017-01-01

    Counting 3-, 4-, and 5-node graphlets in graphs is important for graph mining applications such as discovering abnormal/evolution patterns in social and biology networks. In addition, it is recently widely used for computing similarities between

  14. What Would a Graph Look Like in this Layout? A Machine Learning Approach to Large Graph Visualization.

    Science.gov (United States)

    Kwon, Oh-Hyun; Crnovrsanin, Tarik; Ma, Kwan-Liu

    2018-01-01

    Using different methods for laying out a graph can lead to very different visual appearances, with which the viewer perceives different information. Selecting a "good" layout method is thus important for visualizing a graph. The selection can be highly subjective and dependent on the given task. A common approach to selecting a good layout is to use aesthetic criteria and visual inspection. However, fully calculating various layouts and their associated aesthetic metrics is computationally expensive. In this paper, we present a machine learning approach to large graph visualization based on computing the topological similarity of graphs using graph kernels. For a given graph, our approach can show what the graph would look like in different layouts and estimate their corresponding aesthetic metrics. An important contribution of our work is the development of a new framework to design graph kernels. Our experimental study shows that our estimation calculation is considerably faster than computing the actual layouts and their aesthetic metrics. Also, our graph kernels outperform the state-of-the-art ones in both time and accuracy. In addition, we conducted a user study to demonstrate that the topological similarity computed with our graph kernel matches perceptual similarity assessed by human users.

  15. Parameterized Verification of Graph Transformation Systems with Whole Neighbourhood Operations

    OpenAIRE

    Delzanno, Giorgio; Stückrath, Jan

    2014-01-01

    We introduce a new class of graph transformation systems in which rewrite rules can be guarded by universally quantified conditions on the neighbourhood of nodes. These conditions are defined via special graph patterns which may be transformed by the rule as well. For the new class for graph rewrite rules, we provide a symbolic procedure working on minimal representations of upward closed sets of configurations. We prove correctness and effectiveness of the procedure by a categorical presenta...

  16. Local gradient Gabor pattern (LGGP) with applications in face recognition, cross-spectral matching, and soft biometrics

    Science.gov (United States)

    Chen, Cunjian; Ross, Arun

    2013-05-01

    Researchers in face recognition have been using Gabor filters for image representation due to their robustness to complex variations in expression and illumination. Numerous methods have been proposed to model the output of filter responses by employing either local or global descriptors. In this work, we propose a novel but simple approach for encoding Gradient information on Gabor-transformed images to represent the face, which can be used for identity, gender and ethnicity assessment. Extensive experiments on the standard face benchmark FERET (Visible versus Visible), as well as the heterogeneous face dataset HFB (Near-infrared versus Visible), suggest that the matching performance due to the proposed descriptor is comparable against state-of-the-art descriptor-based approaches in face recognition applications. Furthermore, the same feature set is used in the framework of a Collaborative Representation Classification (CRC) scheme for deducing soft biometric traits such as gender and ethnicity from face images in the AR, Morph and CAS-PEAL databases.

  17. Subgraph detection using graph signals

    KAUST Repository

    Chepuri, Sundeep Prabhakar

    2017-03-06

    In this paper we develop statistical detection theory for graph signals. In particular, given two graphs, namely, a background graph that represents an usual activity and an alternative graph that represents some unusual activity, we are interested in answering the following question: To which of the two graphs does the observed graph signal fit the best? To begin with, we assume both the graphs are known, and derive an optimal Neyman-Pearson detector. Next, we derive a suboptimal detector for the case when the alternative graph is not known. The developed theory is illustrated with numerical experiments.

  18. Subgraph detection using graph signals

    KAUST Repository

    Chepuri, Sundeep Prabhakar; Leus, Geert

    2017-01-01

    In this paper we develop statistical detection theory for graph signals. In particular, given two graphs, namely, a background graph that represents an usual activity and an alternative graph that represents some unusual activity, we are interested in answering the following question: To which of the two graphs does the observed graph signal fit the best? To begin with, we assume both the graphs are known, and derive an optimal Neyman-Pearson detector. Next, we derive a suboptimal detector for the case when the alternative graph is not known. The developed theory is illustrated with numerical experiments.

  19. Dynamic planar embeddings of dynamic graphs

    DEFF Research Database (Denmark)

    Holm, Jacob; Rotenberg, Eva

    2015-01-01

    -flip-linkable(u, v) providing a suggestion for a flip that will make them linkable if one exists. We will support all updates and queries in O(log2 n) time. Our time bounds match those of Italiano et al. for a static (flipless) embedding of a dynamic graph. Our new algorithm is simpler, exploiting...... that the complement of a spanning tree of a connected plane graph is a spanning tree of the dual graph. The primal and dual trees are interpreted as having the same Euler tour, and a main idea of the new algorithm is an elegant interaction between top trees over the two trees via their common Euler tour....

  20. Dynamic planar embeddings of dynamic graphs

    DEFF Research Database (Denmark)

    Holm, Jacob; Rotenberg, Eva

    2017-01-01

    query, one-flip- linkable(u,v) providing a suggestion for a flip that will make them linkable if one exists. We support all updates and queries in O(log 2 n) time. Our time bounds match those of Italiano et al. for a static (flipless) embedding of a dynamic graph. Our new algorithm is simpler......, exploiting that the complement of a spanning tree of a connected plane graph is a spanning tree of the dual graph. The primal and dual trees are interpreted as having the same Euler tour, and a main idea of the new algorithm is an elegant interaction between top trees over the two trees via their common...

  1. Mining a database of single amplified genomes from Red Sea brine pool extremophiles—improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA)

    Science.gov (United States)

    Grötzinger, Stefan W.; Alam, Intikhab; Ba Alawi, Wail; Bajic, Vladimir B.; Stingl, Ulrich; Eppinger, Jörg

    2014-01-01

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  2. Mining a database of single amplified genomes from Red Sea brine pool extremophiles – Improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA

    Directory of Open Access Journals (Sweden)

    Stefan Wolfgang Grötzinger

    2014-04-01

    Full Text Available Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs and poor homology of novel extremophile’s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the INDIGO data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes may translate into false positives when searching for specific functions. The Profile & Pattern Matching (PPM strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO-terms (which represent enzyme function profiles and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern. The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2,577 E.C. numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from 6 different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter and PROSITE IDs (pattern filter. Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns are present. Scripts for annotation, as well as for the PPM algorithm, are available through the INDIGO website.

  3. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

    KAUST Repository

    Grötzinger, Stefan W.

    2014-04-07

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile\\'s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  4. Extremal graph theory

    CERN Document Server

    Bollobas, Bela

    2004-01-01

    The ever-expanding field of extremal graph theory encompasses a diverse array of problem-solving methods, including applications to economics, computer science, and optimization theory. This volume, based on a series of lectures delivered to graduate students at the University of Cambridge, presents a concise yet comprehensive treatment of extremal graph theory.Unlike most graph theory treatises, this text features complete proofs for almost all of its results. Further insights into theory are provided by the numerous exercises of varying degrees of difficulty that accompany each chapter. A

  5. Ring-enhancement pattern on contrast-enhanced CT predicts adenosquamous carcinoma of the pancreas: a matched case-control study.

    Science.gov (United States)

    Imaoka, Hiroshi; Shimizu, Yasuhiro; Mizuno, Nobumasa; Hara, Kazuo; Hijioka, Susumu; Tajika, Masahiro; Tanaka, Tsutomu; Ishihara, Makoto; Ogura, Takeshi; Obayashi, Tomohiko; Shinagawa, Akihide; Sakaguchi, Masafumi; Yamaura, Hidekazu; Kato, Mina; Niwa, Yasumasa; Yamao, Kenji

    2014-01-01

    Adenosquamous carcinoma of the pancreas (ASC) is a rare malignant neoplasm of the pancreas, exhibiting both glandular and squamous differentiation. However, little is known about its imaging features. This study examined the imaging features of pancreatic ASC. We evaluated images of contrast-enhanced computed tomography (CT) and endoscopic ultrasonography (EUS). As controls, solid pancreatic neoplasms matched in a 2:1 ratio to ASC cases for age, sex and tumor location were also evaluated. Twenty-three ASC cases were examined, and 46 solid pancreatic neoplasms (43 pancreatic ductal adenocarcinomas, two pancreatic neuroendocrine tumors and one acinar cell carcinoma) were matched as controls. Univariate analysis demonstrated significant differences in the outline and vascularity of tumors on contrast-enhanced CT in the ASC and control groups (P outline, cystic changes, and the ring-enhancement pattern on contrast-enhanced CT were seen to have significant predictive powers by stepwise forward logistic regression analysis (P = 0.044, P = 0.010, and P = 0.001, respectively). Of the three, the ring-enhancement pattern was the most useful, and its predictive diagnostic sensitivity, specificity, positive predictive value and negative predictive value for diagnosis of ASC were 65.2%, 89.6%, 75.0% and 84.3%, respectively. These results demonstrate that presence of the ring-enhancement pattern on contrast-enhanced CT is the most useful predictive factor for ASC. Copyright © 2014 IAP and EPC. Published by Elsevier B.V. All rights reserved.

  6. On solution concepts for matching games

    NARCIS (Netherlands)

    Biro, Peter; Kern, Walter; Paulusma, Daniël; Kratochvil, J.; Li, A.; Fiala, J.; Kolman, P.

    A matching game is a cooperative game $(N,v)$ defined on a graph $G = (N,E)$ with an edge weighting $\\omega : E \\to {\\Bbb R}_+$ . The player set is $N$ and the value of a coalition $S \\subseteq  N$ is defined as the maximum weight of a matching in the subgraph induced by $S$. First we present an

  7. Downhill Domination in Graphs

    Directory of Open Access Journals (Sweden)

    Haynes Teresa W.

    2014-08-01

    Full Text Available A path π = (v1, v2, . . . , vk+1 in a graph G = (V,E is a downhill path if for every i, 1 ≤ i ≤ k, deg(vi ≥ deg(vi+1, where deg(vi denotes the degree of vertex vi ∈ V. The downhill domination number equals the minimum cardinality of a set S ⊆ V having the property that every vertex v ∈ V lies on a downhill path originating from some vertex in S. We investigate downhill domination numbers of graphs and give upper bounds. In particular, we show that the downhill domination number of a graph is at most half its order, and that the downhill domination number of a tree is at most one third its order. We characterize the graphs obtaining each of these bounds

  8. Tailored Random Graph Ensembles

    International Nuclear Information System (INIS)

    Roberts, E S; Annibale, A; Coolen, A C C

    2013-01-01

    Tailored graph ensembles are a developing bridge between biological networks and statistical mechanics. The aim is to use this concept to generate a suite of rigorous tools that can be used to quantify and compare the topology of cellular signalling networks, such as protein-protein interaction networks and gene regulation networks. We calculate exact and explicit formulae for the leading orders in the system size of the Shannon entropies of random graph ensembles constrained with degree distribution and degree-degree correlation. We also construct an ergodic detailed balance Markov chain with non-trivial acceptance probabilities which converges to a strictly uniform measure and is based on edge swaps that conserve all degrees. The acceptance probabilities can be generalized to define Markov chains that target any alternative desired measure on the space of directed or undirected graphs, in order to generate graphs with more sophisticated topological features.

  9. Cycles in graphs

    CERN Document Server

    Alspach, BR

    1985-01-01

    This volume deals with a variety of problems involving cycles in graphs and circuits in digraphs. Leading researchers in this area present here 3 survey papers and 42 papers containing new results. There is also a collection of unsolved problems.

  10. Introduction to graph theory

    CERN Document Server

    Wilson, Robin J

    1985-01-01

    Graph Theory has recently emerged as a subject in its own right, as well as being an important mathematical tool in such diverse subjects as operational research, chemistry, sociology and genetics. This book provides a comprehensive introduction to the subject.

  11. Hyperbolicity in median graphs

    Indian Academy of Sciences (India)

    mic problems in hyperbolic spaces and hyperbolic graphs have been .... that in general the main obstacle is that we do not know the location of ...... [25] Jonckheere E and Lohsoonthorn P, A hyperbolic geometry approach to multipath routing,.

  12. Measuring Two-Event Structural Correlations on Graphs

    Science.gov (United States)

    2012-08-01

    2012 to 00-00-2012 4. TITLE AND SUBTITLE Measuring Two-Event Structural Correlations on Graphs 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ...by event simulation on the DBLP graph. Then we examine the efficiency and scala - bility of the framework with a Twitter network. The third part of...correlation pattern mining for large graphs. In Proc. of the 8th Workshop on Mining and Learning with Graphs, pages 119–126, 2010. [23] T. Smith. A

  13. Uniform Single Valued Neutrosophic Graphs

    Directory of Open Access Journals (Sweden)

    S. Broumi

    2017-09-01

    Full Text Available In this paper, we propose a new concept named the uniform single valued neutrosophic graph. An illustrative example and some properties are examined. Next, we develop an algorithmic approach for computing the complement of the single valued neutrosophic graph. A numerical example is demonstrated for computing the complement of single valued neutrosophic graphs and uniform single valued neutrosophic graph.

  14. Collective Rationality in Graph Aggregation

    NARCIS (Netherlands)

    Endriss, U.; Grandi, U.; Schaub, T.; Friedrich, G.; O'Sullivan, B.

    2014-01-01

    Suppose a number of agents each provide us with a directed graph over a common set of vertices. Graph aggregation is the problem of computing a single “collective” graph that best represents the information inherent in this profile of individual graphs. We consider this aggregation problem from the

  15. Classical dynamics on graphs

    International Nuclear Information System (INIS)

    Barra, F.; Gaspard, P.

    2001-01-01

    We consider the classical evolution of a particle on a graph by using a time-continuous Frobenius-Perron operator that generalizes previous propositions. In this way, the relaxation rates as well as the chaotic properties can be defined for the time-continuous classical dynamics on graphs. These properties are given as the zeros of some periodic-orbit zeta functions. We consider in detail the case of infinite periodic graphs where the particle undergoes a diffusion process. The infinite spatial extension is taken into account by Fourier transforms that decompose the observables and probability densities into sectors corresponding to different values of the wave number. The hydrodynamic modes of diffusion are studied by an eigenvalue problem of a Frobenius-Perron operator corresponding to a given sector. The diffusion coefficient is obtained from the hydrodynamic modes of diffusion and has the Green-Kubo form. Moreover, we study finite but large open graphs that converge to the infinite periodic graph when their size goes to infinity. The lifetime of the particle on the open graph is shown to correspond to the lifetime of a system that undergoes a diffusion process before it escapes

  16. In-Storage Embedded Accelerator for Sparse Pattern Processing

    OpenAIRE

    Jun, Sang-Woo; Nguyen, Huy T.; Gadepally, Vijay N.; Arvind

    2016-01-01

    We present a novel architecture for sparse pattern processing, using flash storage with embedded accelerators. Sparse pattern processing on large data sets is the essence of applications such as document search, natural language processing, bioinformatics, subgraph matching, machine learning, and graph processing. One slice of our prototype accelerator is capable of handling up to 1TB of data, and experiments show that it can outperform C/C++ software solutions on a 16-core system at a fracti...

  17. Adaptive Discrete Hypergraph Matching.

    Science.gov (United States)

    Yan, Junchi; Li, Changsheng; Li, Yin; Cao, Guitao

    2018-02-01

    This paper addresses the problem of hypergraph matching using higher-order affinity information. We propose a solver that iteratively updates the solution in the discrete domain by linear assignment approximation. The proposed method is guaranteed to converge to a stationary discrete solution and avoids the annealing procedure and ad-hoc post binarization step that are required in several previous methods. Specifically, we start with a simple iterative discrete gradient assignment solver. This solver can be trapped in an -circle sequence under moderate conditions, where is the order of the graph matching problem. We then devise an adaptive relaxation mechanism to jump out this degenerating case and show that the resulting new path will converge to a fixed solution in the discrete domain. The proposed method is tested on both synthetic and real-world benchmarks. The experimental results corroborate the efficacy of our method.

  18. Proxy Graph: Visual Quality Metrics of Big Graph Sampling.

    Science.gov (United States)

    Nguyen, Quan Hoang; Hong, Seok-Hee; Eades, Peter; Meidiana, Amyra

    2017-06-01

    Data sampling has been extensively studied for large scale graph mining. Many analyses and tasks become more efficient when performed on graph samples of much smaller size. The use of proxy objects is common in software engineering for analysis and interaction with heavy objects or systems. In this paper, we coin the term 'proxy graph' and empirically investigate how well a proxy graph visualization can represent a big graph. Our investigation focuses on proxy graphs obtained by sampling; this is one of the most common proxy approaches. Despite the plethora of data sampling studies, this is the first evaluation of sampling in the context of graph visualization. For an objective evaluation, we propose a new family of quality metrics for visual quality of proxy graphs. Our experiments cover popular sampling techniques. Our experimental results lead to guidelines for using sampling-based proxy graphs in visualization.

  19. Cellular Automata on Graphs: Topological Properties of ER Graphs Evolved towards Low-Entropy Dynamics

    Directory of Open Access Journals (Sweden)

    Marc-Thorsten Hütt

    2012-06-01

    Full Text Available Cellular automata (CA are a remarkably  efficient tool for exploring general properties of complex systems and spatiotemporal patterns arising from local rules. Totalistic cellular automata,  where the update  rules depend  only on the density of neighboring states, are at the same time a versatile  tool for exploring  dynamical  processes on graphs. Here we briefly review our previous results on cellular automata on graphs, emphasizing some systematic relationships between network architecture and dynamics identified in this way. We then extend the investigation  towards graphs obtained in a simulated-evolution procedure, starting from Erdő s–Rényi (ER graphs and selecting for low entropies of the CA dynamics. Our key result is a strong association of low Shannon entropies with a broadening of the graph’s degree distribution.

  20. Word Similarity from Dictionaries: Inferring Fuzzy Measures from Fuzzy Graphs

    Directory of Open Access Journals (Sweden)

    Vicenc Torra

    2008-01-01

    Full Text Available WORD SIMILARITY FROM DICTIONARIES: INFERRING FUZZY MEASURES FROM FUZZY GRAPHS The computation of similarities between words is a basic element of information retrieval systems, when retrieval is not solely based on word matching. In this work we consider a measure between words based on dictionaries. This is achieved assuming that a dictionary is formalized as a fuzzy graph. We show that the approach permits to compute measures not only for pairs of words but for sets of them.

  1. On some covering graphs of a graph

    Directory of Open Access Journals (Sweden)

    Shariefuddin Pirzada

    2016-10-01

    Full Text Available For a graph $G$ with vertex set $V(G=\\{v_1, v_2, \\dots, v_n\\}$, let $S$ be the covering set of $G$ having the maximum degree over all the minimum covering sets of $G$. Let $N_S[v]=\\{u\\in S : uv \\in E(G \\}\\cup \\{v\\}$ be the closed neighbourhood of the vertex $v$ with respect to $S.$ We define a square matrix $A_S(G= (a_{ij},$ by $a_{ij}=1,$ if $\\left |N_S[v_i]\\cap N_S[v_j] \\right| \\geq 1, i\

  2. Application of graph theory to the morphological analysis of settlements

    Directory of Open Access Journals (Sweden)

    Szmytkie Robert

    2017-12-01

    Full Text Available In the following paper, the analyses of morphology of settlements were conducted using graph methods. The intention of the author was to create a quantifiable and simple measure, which, in a quantitative way, would express the degree of development of a graph (the spatial pattern of settlement. When analysing examples of graphs assigned to a set of small towns and large villages, it was noticed that the graph development index should depend on: a relative number of edges in relation to the number of nodes (β index, the number of cycles (urban blocks, which evidences the complexity of the spatial pattern of settlement, and the average rank of nodes of a graph, which expresses the degree of complexity of a street network.

  3. Matching fields and lattice points of simplices

    OpenAIRE

    Loho, Georg; Smith, Ben

    2018-01-01

    We show that the Chow covectors of a linkage matching field define a bijection of lattice points and we demonstrate how one can recover the linkage matching field from this bijection. This resolves two open questions from Sturmfels & Zelevinsky (1993) on linkage matching fields. For this, we give an explicit construction that associates a bipartite incidence graph of an ordered partition of a common set to all lattice points in a dilated simplex. Given a triangulation of a product of two simp...

  4. Fundamentals of algebraic graph transformation

    CERN Document Server

    Ehrig, Hartmut; Prange, Ulrike; Taentzer, Gabriele

    2006-01-01

    Graphs are widely used to represent structural information in the form of objects and connections between them. Graph transformation is the rule-based manipulation of graphs, an increasingly important concept in computer science and related fields. This is the first textbook treatment of the algebraic approach to graph transformation, based on algebraic structures and category theory. Part I is an introduction to the classical case of graph and typed graph transformation. In Part II basic and advanced results are first shown for an abstract form of replacement systems, so-called adhesive high-level replacement systems based on category theory, and are then instantiated to several forms of graph and Petri net transformation systems. Part III develops typed attributed graph transformation, a technique of key relevance in the modeling of visual languages and in model transformation. Part IV contains a practical case study on model transformation and a presentation of the AGG (attributed graph grammar) tool envir...

  5. The STAPL Parallel Graph Library

    KAUST Repository

    Harshvardhan,

    2013-01-01

    This paper describes the stapl Parallel Graph Library, a high-level framework that abstracts the user from data-distribution and parallelism details and allows them to concentrate on parallel graph algorithm development. It includes a customizable distributed graph container and a collection of commonly used parallel graph algorithms. The library introduces pGraph pViews that separate algorithm design from the container implementation. It supports three graph processing algorithmic paradigms, level-synchronous, asynchronous and coarse-grained, and provides common graph algorithms based on them. Experimental results demonstrate improved scalability in performance and data size over existing graph libraries on more than 16,000 cores and on internet-scale graphs containing over 16 billion vertices and 250 billion edges. © Springer-Verlag Berlin Heidelberg 2013.

  6. Graphs, groups and surfaces

    CERN Document Server

    White, AT

    1985-01-01

    The field of topological graph theory has expanded greatly in the ten years since the first edition of this book appeared. The original nine chapters of this classic work have therefore been revised and updated. Six new chapters have been added, dealing with: voltage graphs, non-orientable imbeddings, block designs associated with graph imbeddings, hypergraph imbeddings, map automorphism groups and change ringing.Thirty-two new problems have been added to this new edition, so that there are now 181 in all; 22 of these have been designated as ``difficult'''' and 9 as ``unsolved''''. Three of the four unsolved problems from the first edition have been solved in the ten years between editions; they are now marked as ``difficult''''.

  7. Profinite graphs and groups

    CERN Document Server

    Ribes, Luis

    2017-01-01

    This book offers a detailed introduction to graph theoretic methods in profinite groups and applications to abstract groups. It is the first to provide a comprehensive treatment of the subject. The author begins by carefully developing relevant notions in topology, profinite groups and homology, including free products of profinite groups, cohomological methods in profinite groups, and fixed points of automorphisms of free pro-p groups. The final part of the book is dedicated to applications of the profinite theory to abstract groups, with sections on finitely generated subgroups of free groups, separability conditions in free and amalgamated products, and algorithms in free groups and finite monoids. Profinite Graphs and Groups will appeal to students and researchers interested in profinite groups, geometric group theory, graphs and connections with the theory of formal languages. A complete reference on the subject, the book includes historical and bibliographical notes as well as a discussion of open quest...

  8. Subdominant pseudoultrametric on graphs

    Energy Technology Data Exchange (ETDEWEB)

    Dovgoshei, A A; Petrov, E A [Institute of Applied Mathematics and Mechanics, National Academy of Sciences of Ukraine, Donetsk (Ukraine)

    2013-08-31

    Let (G,w) be a weighted graph. We find necessary and sufficient conditions under which the weight w:E(G)→R{sup +} can be extended to a pseudoultrametric on V(G), and establish a criterion for the uniqueness of such an extension. We demonstrate that (G,w) is a complete k-partite graph, for k≥2, if and only if for any weight that can be extended to a pseudoultrametric, among all such extensions one can find the least pseudoultrametric consistent with w. We give a structural characterization of graphs for which the subdominant pseudoultrametric is an ultrametric for any strictly positive weight that can be extended to a pseudoultrametric. Bibliography: 14 titles.

  9. Quantitative graph theory mathematical foundations and applications

    CERN Document Server

    Dehmer, Matthias

    2014-01-01

    The first book devoted exclusively to quantitative graph theory, Quantitative Graph Theory: Mathematical Foundations and Applications presents and demonstrates existing and novel methods for analyzing graphs quantitatively. Incorporating interdisciplinary knowledge from graph theory, information theory, measurement theory, and statistical techniques, this book covers a wide range of quantitative-graph theoretical concepts and methods, including those pertaining to real and random graphs such as:Comparative approaches (graph similarity or distance)Graph measures to characterize graphs quantitat

  10. Topics in combinatorial pattern matching

    DEFF Research Database (Denmark)

    Vildhøj, Hjalte Wedel

    Problem. Given m documents of total length n, we consider the problem of finding a longest string common to at least d ≥ 2 of the documents. This problem is known as the longest common substring (LCS) problem and has a classic O(n) space and O(n) time solution (Weiner [FOCS’73], Hui [CPM’92]). However...

  11. Augmented marked graphs

    CERN Document Server

    Cheung, King Sing

    2014-01-01

    Petri nets are a formal and theoretically rich model for the modelling and analysis of systems. A subclass of Petri nets, augmented marked graphs possess a structure that is especially desirable for the modelling and analysis of systems with concurrent processes and shared resources.This monograph consists of three parts: Part I provides the conceptual background for readers who have no prior knowledge on Petri nets; Part II elaborates the theory of augmented marked graphs; finally, Part III discusses the application to system integration. The book is suitable as a first self-contained volume

  12. Graph Query Portal

    OpenAIRE

    Dayal, Amit; Brock, David

    2018-01-01

    Prashant Chandrasekar, a lead developer for the Social Interactome project, has tasked the team with creating a graph representation of the data collected from the social networks involved in that project. The data is currently stored in a MySQL database. The client requested that the graph database be Cayley, but after a literature review, Neo4j was chosen. The reasons for this shift will be explained in the design section. Secondarily, the team was tasked with coming up with three scena...

  13. Spectral radius of graphs

    CERN Document Server

    Stevanovic, Dragan

    2015-01-01

    Spectral Radius of Graphs provides a thorough overview of important results on the spectral radius of adjacency matrix of graphs that have appeared in the literature in the preceding ten years, most of them with proofs, and including some previously unpublished results of the author. The primer begins with a brief classical review, in order to provide the reader with a foundation for the subsequent chapters. Topics covered include spectral decomposition, the Perron-Frobenius theorem, the Rayleigh quotient, the Weyl inequalities, and the Interlacing theorem. From this introduction, the

  14. A simple greedy algorithm for dynamic graph orientation

    DEFF Research Database (Denmark)

    Berglin, Edvin; Brodal, Gerth Stølting

    2017-01-01

    Graph orientations with low out-degree are one of several ways to efficiently store sparse graphs. If the graphs allow for insertion and deletion of edges, one may have to flip the orientation of some edges to prevent blowing up the maximum out-degree. We use arboricity as our sparsity measure....... With an immensely simple greedy algorithm, we get parametrized trade-off bounds between out-degree and worst case number of flips, which previously only existed for amortized number of flips. We match the previous best worst-case algorithm (in O(log n) flips) for general arboricity and beat it for either constant...... or super-logarithmic arboricity. We also match a previous best amortized result for at least logarithmic arboricity, and give the first results with worst-case O(1) and O(sqrt(log n)) flips nearly matching degree bounds to their respective amortized solutions....

  15. Graph embedding with rich information through heterogeneous graph

    KAUST Repository

    Sun, Guolei

    2017-01-01

    Graph embedding, aiming to learn low-dimensional representations for nodes in graphs, has attracted increasing attention due to its critical application including node classification, link prediction and clustering in social network analysis. Most

  16. Using Graph and Vertex Entropy to Compare Empirical Graphs with Theoretical Graph Models

    Directory of Open Access Journals (Sweden)

    Tomasz Kajdanowicz

    2016-09-01

    Full Text Available Over the years, several theoretical graph generation models have been proposed. Among the most prominent are: the Erdős–Renyi random graph model, Watts–Strogatz small world model, Albert–Barabási preferential attachment model, Price citation model, and many more. Often, researchers working with real-world data are interested in understanding the generative phenomena underlying their empirical graphs. They want to know which of the theoretical graph generation models would most probably generate a particular empirical graph. In other words, they expect some similarity assessment between the empirical graph and graphs artificially created from theoretical graph generation models. Usually, in order to assess the similarity of two graphs, centrality measure distributions are compared. For a theoretical graph model this means comparing the empirical graph to a single realization of a theoretical graph model, where the realization is generated from the given model using an arbitrary set of parameters. The similarity between centrality measure distributions can be measured using standard statistical tests, e.g., the Kolmogorov–Smirnov test of distances between cumulative distributions. However, this approach is both error-prone and leads to incorrect conclusions, as we show in our experiments. Therefore, we propose a new method for graph comparison and type classification by comparing the entropies of centrality measure distributions (degree centrality, betweenness centrality, closeness centrality. We demonstrate that our approach can help assign the empirical graph to the most similar theoretical model using a simple unsupervised learning method.

  17. Topics in graph theory graphs and their Cartesian product

    CERN Document Server

    Imrich, Wilfried; Rall, Douglas F

    2008-01-01

    From specialists in the field, you will learn about interesting connections and recent developments in the field of graph theory by looking in particular at Cartesian products-arguably the most important of the four standard graph products. Many new results in this area appear for the first time in print in this book. Written in an accessible way, this book can be used for personal study in advanced applications of graph theory or for an advanced graph theory course.

  18. Partitioning a call graph

    NARCIS (Netherlands)

    Bisseling, R.H.; Byrka, J.; Cerav-Erbas, S.; Gvozdenovic, N.; Lorenz, M.; Pendavingh, R.A.; Reeves, C.; Röger, M.; Verhoeven, A.; Berg, van den J.B.; Bhulai, S.; Hulshof, J.; Koole, G.; Quant, C.; Williams, J.F.

    2006-01-01

    Splitting a large software system into smaller and more manageable units has become an important problem for many organizations. The basic structure of a software system is given by a directed graph with vertices representing the programs of the system and arcs representing calls from one program to

  19. Coloring geographical threshold graphs

    Energy Technology Data Exchange (ETDEWEB)

    Bradonjic, Milan [Los Alamos National Laboratory; Percus, Allon [Los Alamos National Laboratory; Muller, Tobias [EINDHOVEN UNIV. OF TECH

    2008-01-01

    We propose a coloring algorithm for sparse random graphs generated by the geographical threshold graph (GTG) model, a generalization of random geometric graphs (RGG). In a GTG, nodes are distributed in a Euclidean space, and edges are assigned according to a threshold function involving the distance between nodes as well as randomly chosen node weights. The motivation for analyzing this model is that many real networks (e.g., wireless networks, the Internet, etc.) need to be studied by using a 'richer' stochastic model (which in this case includes both a distance between nodes and weights on the nodes). Here, we analyze the GTG coloring algorithm together with the graph's clique number, showing formally that in spite of the differences in structure between GTG and RGG, the asymptotic behavior of the chromatic number is identical: {chi}1n 1n n / 1n n (1 + {omicron}(1)). Finally, we consider the leading corrections to this expression, again using the coloring algorithm and clique number to provide bounds on the chromatic number. We show that the gap between the lower and upper bound is within C 1n n / (1n 1n n){sup 2}, and specify the constant C.

  20. Supermarket model on graphs

    NARCIS (Netherlands)

    Budhiraja, A.S.; Mukherjee, D.; Wu, R.

    2017-01-01

    We consider a variation of the supermarket model in which the servers can communicate with their neighbors and where the neighborhood relationships are described in terms of a suitable graph. Tasks with unit-exponential service time distributions arrive at each vertex as independent Poisson

  1. Basin Hopping Graph

    DEFF Research Database (Denmark)

    Kucharik, Marcel; Hofacker, Ivo; Stadler, Peter

    2014-01-01

    of the folding free energy landscape, however, can provide the relevant information. Results We introduce the basin hopping graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect...

  2. The STAPL Parallel Graph Library

    KAUST Repository

    Harshvardhan,; Fidel, Adam; Amato, Nancy M.; Rauchwerger, Lawrence

    2013-01-01

    This paper describes the stapl Parallel Graph Library, a high-level framework that abstracts the user from data-distribution and parallelism details and allows them to concentrate on parallel graph algorithm development. It includes a customizable

  3. A Maximum Resonant Set of Polyomino Graphs

    Directory of Open Access Journals (Sweden)

    Zhang Heping

    2016-05-01

    Full Text Available A polyomino graph P is a connected finite subgraph of the infinite plane grid such that each finite face is surrounded by a regular square of side length one and each edge belongs to at least one square. A dimer covering of P corresponds to a perfect matching. Different dimer coverings can interact via an alternating cycle (or square with respect to them. A set of disjoint squares of P is a resonant set if P has a perfect matching M so that each one of those squares is M-alternating. In this paper, we show that if K is a maximum resonant set of P, then P − K has a unique perfect matching. We further prove that the maximum forcing number of a polyomino graph is equal to the cardinality of a maximum resonant set. This confirms a conjecture of Xu et al. [26]. We also show that if K is a maximal alternating set of P, then P − K has a unique perfect matching.

  4. Groupies in multitype random graphs

    OpenAIRE

    Shang, Yilun

    2016-01-01

    A groupie in a graph is a vertex whose degree is not less than the average degree of its neighbors. Under some mild conditions, we show that the proportion of groupies is very close to 1/2 in multitype random graphs (such as stochastic block models), which include Erd?s-R?nyi random graphs, random bipartite, and multipartite graphs as special examples. Numerical examples are provided to illustrate the theoretical results.

  5. Groupies in multitype random graphs.

    Science.gov (United States)

    Shang, Yilun

    2016-01-01

    A groupie in a graph is a vertex whose degree is not less than the average degree of its neighbors. Under some mild conditions, we show that the proportion of groupies is very close to 1/2 in multitype random graphs (such as stochastic block models), which include Erdős-Rényi random graphs, random bipartite, and multipartite graphs as special examples. Numerical examples are provided to illustrate the theoretical results.

  6. Temporal Representation in Semantic Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Levandoski, J J; Abdulla, G M

    2007-08-07

    A wide range of knowledge discovery and analysis applications, ranging from business to biological, make use of semantic graphs when modeling relationships and concepts. Most of the semantic graphs used in these applications are assumed to be static pieces of information, meaning temporal evolution of concepts and relationships are not taken into account. Guided by the need for more advanced semantic graph queries involving temporal concepts, this paper surveys the existing work involving temporal representations in semantic graphs.

  7. Quantum walks on quotient graphs

    International Nuclear Information System (INIS)

    Krovi, Hari; Brun, Todd A.

    2007-01-01

    A discrete-time quantum walk on a graph Γ is the repeated application of a unitary evolution operator to a Hilbert space corresponding to the graph. If this unitary evolution operator has an associated group of symmetries, then for certain initial states the walk will be confined to a subspace of the original Hilbert space. Symmetries of the original graph, given by its automorphism group, can be inherited by the evolution operator. We show that a quantum walk confined to the subspace corresponding to this symmetry group can be seen as a different quantum walk on a smaller quotient graph. We give an explicit construction of the quotient graph for any subgroup H of the automorphism group and illustrate it with examples. The automorphisms of the quotient graph which are inherited from the original graph are the original automorphism group modulo the subgroup H used to construct it. The quotient graph is constructed by removing the symmetries of the subgroup H from the original graph. We then analyze the behavior of hitting times on quotient graphs. Hitting time is the average time it takes a walk to reach a given final vertex from a given initial vertex. It has been shown in earlier work [Phys. Rev. A 74, 042334 (2006)] that the hitting time for certain initial states of a quantum walks can be infinite, in contrast to classical random walks. We give a condition which determines whether the quotient graph has infinite hitting times given that they exist in the original graph. We apply this condition for the examples discussed and determine which quotient graphs have infinite hitting times. All known examples of quantum walks with hitting times which are short compared to classical random walks correspond to systems with quotient graphs much smaller than the original graph; we conjecture that the existence of a small quotient graph with finite hitting times is necessary for a walk to exhibit a quantum speedup

  8. A generalization of total graphs

    Indian Academy of Sciences (India)

    M Afkhami

    2018-04-12

    Apr 12, 2018 ... product of any lower triangular matrix with the transpose of any element of U belongs to U. The ... total graph of R, which is denoted by T( (R)), is a simple graph with all elements of R as vertices, and ...... [9] Badawi A, On dot-product graph of a commutative ring, Communications in Algebra 43 (2015). 43–50.

  9. Graph transformation tool contest 2008

    NARCIS (Netherlands)

    Rensink, Arend; van Gorp, Pieter

    This special section is the outcome of the graph transformation tool contest organised during the Graph-Based Tools (GraBaTs) 2008 workshop, which took place as a satellite event of the International Conference on Graph Transformation (ICGT) 2008. The contest involved two parts: three “off-line case

  10. On dominator colorings in graphs

    Indian Academy of Sciences (India)

    colors required for a dominator coloring of G is called the dominator .... Theorem 1.3 shows that the complete graph Kn is the only connected graph of order n ... Conversely, if a graph G satisfies condition (i) or (ii), it is easy to see that χd(G) =.

  11. Topic Model for Graph Mining.

    Science.gov (United States)

    Xuan, Junyu; Lu, Jie; Zhang, Guangquan; Luo, Xiangfeng

    2015-12-01

    Graph mining has been a popular research area because of its numerous application scenarios. Many unstructured and structured data can be represented as graphs, such as, documents, chemical molecular structures, and images. However, an issue in relation to current research on graphs is that they cannot adequately discover the topics hidden in graph-structured data which can be beneficial for both the unsupervised learning and supervised learning of the graphs. Although topic models have proved to be very successful in discovering latent topics, the standard topic models cannot be directly applied to graph-structured data due to the "bag-of-word" assumption. In this paper, an innovative graph topic model (GTM) is proposed to address this issue, which uses Bernoulli distributions to model the edges between nodes in a graph. It can, therefore, make the edges in a graph contribute to latent topic discovery and further improve the accuracy of the supervised and unsupervised learning of graphs. The experimental results on two different types of graph datasets show that the proposed GTM outperforms the latent Dirichlet allocation on classification by using the unveiled topics of these two models to represent graphs.

  12. Matching Message Design and Depressed Cognition: An Exploration of Attention Patterns for Gain- and Loss-Framed Depression Help-Seeking Messages.

    Science.gov (United States)

    Lueck, Jennifer A

    2017-07-01

    Although disproportionally affected by depression, most depressed college students do not seek the help they need. Research has recently uncovered the potential negative effects of depression help-seeking messages if depressed cognition is not considered in the health message design process. It is unclear if depression determines whether and how individuals pay attention to gain- and loss-framed depression help-seeking messages-a mechanism that has significant implications for the strategic planning of health communication interventions. In order to enable the effective matching of message design and audience features, this study investigated attention patterns for gain (n = 75)- and loss (n = 78)-framed depression help-seeking messages using eye-tracking technology and self-report measures. The results confirmed that depression is a characteristic of risk avoidance and negative cognition. Depressed participants tended to pay more attention to disease information that was placed in a loss-framed rather than a gain-framed depression help-seeking message. Using negative message framing strategies for health messages seeking to educate about depression symptoms might therefore be a useful persuasive strategy-particularly when disseminated to vulnerable populations affected by depression. Furthermore, the present study emphasizes the effective use of eye-tracking technology in communication research.

  13. Algorithms for Planar Graphs and Graphs in Metric Spaces

    DEFF Research Database (Denmark)

    Wulff-Nilsen, Christian

    structural properties that can be exploited. For instance, a road network or a wire layout on a microchip is typically (near-)planar and distances in the network are often defined w.r.t. the Euclidean or the rectilinear metric. Specialized algorithms that take advantage of such properties are often orders...... of magnitude faster than the corresponding algorithms for general graphs. The first and main part of this thesis focuses on the development of efficient planar graph algorithms. The most important contributions include a faster single-source shortest path algorithm, a distance oracle with subquadratic...... for geometric graphs and graphs embedded in metric spaces. Roughly speaking, the stretch factor is a real value expressing how well a (geo-)metric graph approximates the underlying complete graph w.r.t. distances. We give improved algorithms for computing the stretch factor of a given graph and for augmenting...

  14. Graph 500 on OpenSHMEM: Using a Practical Survey of Past Work to Motivate Novel Algorithmic Developments

    Energy Technology Data Exchange (ETDEWEB)

    Grossman, Max [Rice Univ., Houston, TX (United States); Pritchard Jr., Howard Porter [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Budimlic, Zoran [Rice Univ., Houston, TX (United States); Sarkar, Vivek [Rice Univ., Houston, TX (United States)

    2016-12-22

    Graph500 [14] is an effort to offer a standardized benchmark across large-scale distributed platforms which captures the behavior of common communicationbound graph algorithms. Graph500 differs from other large-scale benchmarking efforts (such as HPL [6] or HPGMG [7]) primarily in the irregularity of its computation and data access patterns. The core computational kernel of Graph500 is a breadth-first search (BFS) implemented on an undirected graph. The output of Graph500 is a spanning tree of the input graph, usually represented by a predecessor mapping for every node in the graph. The Graph500 benchmark defines several pre-defined input sizes for implementers to test against. This report summarizes investigation into implementing the Graph500 benchmark on OpenSHMEM, and focuses on first building a strong and practical understanding of the strengths and limitations of past work before proposing and developing novel extensions.

  15. Gems of combinatorial optimization and graph algorithms

    CERN Document Server

    Skutella, Martin; Stiller, Sebastian; Wagner, Dorothea

    2015-01-01

    Are you looking for new lectures for your course on algorithms, combinatorial optimization, or algorithmic game theory?  Maybe you need a convenient source of relevant, current topics for a graduate student or advanced undergraduate student seminar?  Or perhaps you just want an enjoyable look at some beautiful mathematical and algorithmic results, ideas, proofs, concepts, and techniques in discrete mathematics and theoretical computer science?   Gems of Combinatorial Optimization and Graph Algorithms is a handpicked collection of up-to-date articles, carefully prepared by a select group of international experts, who have contributed some of their most mathematically or algorithmically elegant ideas.  Topics include longest tours and Steiner trees in geometric spaces, cartograms, resource buying games, congestion games, selfish routing, revenue equivalence and shortest paths, scheduling, linear structures in graphs, contraction hierarchies, budgeted matching problems, and motifs in networks.   This ...

  16. Document organization by means of graphs

    Directory of Open Access Journals (Sweden)

    Santa Vallejo Figueroa

    2016-12-01

    Full Text Available Nowadays documents are the main way to represent information and knowledge in several domains. Continuously users store documents in hard disk or online media according to some personal organization based on topics, but such documents can contain one or more topics. This situation makes hard to access documents when is required. The current search engines are based on the name of file or content, but where the desired term or terms must match exactly as are in the content. In this paper, a method for organize documents by means of graphs is proposed, taking into account the topics of the documents. For this a graph for each document is generated taking into account synonyms, semantic related terms, hyponyms, and hypernyms of nouns and verbs contained in documents. The proposal have been compares against Google Desktop and LogicalDoc with interesting results.

  17. A seminar on graph theory

    CERN Document Server

    Harary, Frank

    2015-01-01

    Presented in 1962-63 by experts at University College, London, these lectures offer a variety of perspectives on graph theory. Although the opening chapters form a coherent body of graph theoretic concepts, this volume is not a text on the subject but rather an introduction to the extensive literature of graph theory. The seminar's topics are geared toward advanced undergraduate students of mathematics.Lectures by this volume's editor, Frank Harary, include ""Some Theorems and Concepts of Graph Theory,"" ""Topological Concepts in Graph Theory,"" ""Graphical Reconstruction,"" and other introduc

  18. Spectral fluctuations of quantum graphs

    International Nuclear Information System (INIS)

    Pluhař, Z.; Weidenmüller, H. A.

    2014-01-01

    We prove the Bohigas-Giannoni-Schmit conjecture in its most general form for completely connected simple graphs with incommensurate bond lengths. We show that for graphs that are classically mixing (i.e., graphs for which the spectrum of the classical Perron-Frobenius operator possesses a finite gap), the generating functions for all (P,Q) correlation functions for both closed and open graphs coincide (in the limit of infinite graph size) with the corresponding expressions of random-matrix theory, both for orthogonal and for unitary symmetry

  19. Dynamic Representations of Sparse Graphs

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf

    1999-01-01

    We present a linear space data structure for maintaining graphs with bounded arboricity—a large class of sparse graphs containing e.g. planar graphs and graphs of bounded treewidth—under edge insertions, edge deletions, and adjacency queries. The data structure supports adjacency queries in worst...... case O(c) time, and edge insertions and edge deletions in amortized O(1) and O(c+log n) time, respectively, where n is the number of nodes in the graph, and c is the bound on the arboricity....

  20. Domination criticality in product graphs

    Directory of Open Access Journals (Sweden)

    M.R. Chithra

    2015-07-01

    Full Text Available A connected dominating set is an important notion and has many applications in routing and management of networks. Graph products have turned out to be a good model of interconnection networks. This motivated us to study the Cartesian product of graphs G with connected domination number, γc(G=2,3 and characterize such graphs. Also, we characterize the k−γ-vertex (edge critical graphs and k−γc-vertex (edge critical graphs for k=2,3 where γ denotes the domination number of G. We also discuss the vertex criticality in grids.

  1. Graph Creation, Visualisation and Transformation

    Directory of Open Access Journals (Sweden)

    Maribel Fernández

    2010-03-01

    Full Text Available We describe a tool to create, edit, visualise and compute with interaction nets - a form of graph rewriting systems. The editor, called GraphPaper, allows users to create and edit graphs and their transformation rules using an intuitive user interface. The editor uses the functionalities of the TULIP system, which gives us access to a wealth of visualisation algorithms. Interaction nets are not only a formalism for the specification of graphs, but also a rewrite-based computation model. We discuss graph rewriting strategies and a language to express them in order to perform strategic interaction net rewriting.

  2. Study of Chromatic parameters of Line, Total, Middle graphs and Graph operators of Bipartite graph

    Science.gov (United States)

    Nagarathinam, R.; Parvathi, N.

    2018-04-01

    Chromatic parameters have been explored on the basis of graph coloring process in which a couple of adjacent nodes receives different colors. But the Grundy and b-coloring executes maximum colors under certain restrictions. In this paper, Chromatic, b-chromatic and Grundy number of some graph operators of bipartite graph has been investigat

  3. Faucet: streaming de novo assembly graph construction.

    Science.gov (United States)

    Rozov, Roye; Goldshlager, Gil; Halperin, Eran; Shamir, Ron

    2018-01-01

    We present Faucet, a two-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed. Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded. We demonstrate this functionality by performing streaming graph assembly of publicly available data, and observe that the ratio of disk use to raw data size decreases as coverage is increased. Faucet pairs the de Bruijn graph obtained from the reads with additional meta-data derived from them. We show these metadata-coverage counts collected at junction k-mers and connections bridging between junction pairs-contain most salient information needed for assembly, and demonstrate they enable cleaning of metagenome assembly graphs, greatly improving contiguity while maintaining accuracy. We compared Fauceted resource use and assembly quality to state of the art metagenome assemblers, as well as leading resource-efficient genome assemblers. Faucet used orders of magnitude less time and disk space than the specialized metagenome assemblers MetaSPAdes and Megahit, while also improving on their memory use; this broadly matched performance of other assemblers optimizing resource efficiency-namely, Minia and LightAssembler. However, on metagenomes tested, Faucet,o outputs had 14-110% higher mean NGA50 lengths compared with Minia, and 2- to 11-fold higher mean NGA50 lengths compared with LightAssembler, the only other streaming assembler available. Faucet is available at https://github.com/Shamir-Lab/Faucet. rshamir@tau.ac.il or eranhalperin@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

  4. Graph Sampling for Covariance Estimation

    KAUST Repository

    Chepuri, Sundeep Prabhakar

    2017-04-25

    In this paper the focus is on subsampling as well as reconstructing the second-order statistics of signals residing on nodes of arbitrary undirected graphs. Second-order stationary graph signals may be obtained by graph filtering zero-mean white noise and they admit a well-defined power spectrum whose shape is determined by the frequency response of the graph filter. Estimating the graph power spectrum forms an important component of stationary graph signal processing and related inference tasks such as Wiener prediction or inpainting on graphs. The central result of this paper is that by sampling a significantly smaller subset of vertices and using simple least squares, we can reconstruct the second-order statistics of the graph signal from the subsampled observations, and more importantly, without any spectral priors. To this end, both a nonparametric approach as well as parametric approaches including moving average and autoregressive models for the graph power spectrum are considered. The results specialize for undirected circulant graphs in that the graph nodes leading to the best compression rates are given by the so-called minimal sparse rulers. A near-optimal greedy algorithm is developed to design the subsampling scheme for the non-parametric and the moving average models, whereas a particular subsampling scheme that allows linear estimation for the autoregressive model is proposed. Numerical experiments on synthetic as well as real datasets related to climatology and processing handwritten digits are provided to demonstrate the developed theory.

  5. Canonical Labelling of Site Graphs

    Directory of Open Access Journals (Sweden)

    Nicolas Oury

    2013-06-01

    Full Text Available We investigate algorithms for canonical labelling of site graphs, i.e. graphs in which edges bind vertices on sites with locally unique names. We first show that the problem of canonical labelling of site graphs reduces to the problem of canonical labelling of graphs with edge colourings. We then present two canonical labelling algorithms based on edge enumeration, and a third based on an extension of Hopcroft's partition refinement algorithm. All run in quadratic worst case time individually. However, one of the edge enumeration algorithms runs in sub-quadratic time for graphs with "many" automorphisms, and the partition refinement algorithm runs in sub-quadratic time for graphs with "few" bisimulation equivalences. This suite of algorithms was chosen based on the expectation that graphs fall in one of those two categories. If that is the case, a combined algorithm runs in sub-quadratic worst case time. Whether this expectation is reasonable remains an interesting open problem.

  6. Learning heat diffusion graphs

    OpenAIRE

    Thanou, Dorina; Dong, Xiaowen; Kressner, Daniel; Frossard, Pascal

    2016-01-01

    Effective information analysis generally boils down to properly identifying the structure or geometry of the data, which is often represented by a graph. In some applications, this structure may be partly determined by design constraints or pre-determined sensing arrangements, like in road transportation networks for example. In general though, the data structure is not readily available and becomes pretty difficult to define. In particular, the global smoothness assumptions, that most of the...

  7. An Unusual Exponential Graph

    Science.gov (United States)

    Syed, M. Qasim; Lovatt, Ian

    2014-01-01

    This paper is an addition to the series of papers on the exponential function begun by Albert Bartlett. In particular, we ask how the graph of the exponential function y = e[superscript -t/t] would appear if y were plotted versus ln t rather than the normal practice of plotting ln y versus t. In answering this question, we find a new way to…

  8. Understanding Charts and Graphs.

    Science.gov (United States)

    1987-07-28

    Farenheit degrees, which have no Onaturalo zero ); finally, ratio scales have numbers that are ordered so that the magnitudes of differences are important and...system. They have to do with the very nature of how marks serve as meaningful symbols. In the ideal case, a chart or graph will be absolutely unambiguous...and these laws comprise this principle (see Stevens, 1974). Absolute discriminability: A minimal magnitude of a mark is necessary for it to be detected

  9. MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

    Science.gov (United States)

    Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

    2011-01-01

    We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

  10. Matching Organs

    Science.gov (United States)

    ... to know FAQ Living donation What is living donation? Organs Types Being a living donor First steps Being ... brochures What Every Patient Needs to Know Living Donation Multiple Listing Visit UNOS Store Learn more How organs are matched How to become a living donor ...

  11. Graphs cospectral with a friendship graph or its complement

    Directory of Open Access Journals (Sweden)

    Alireza Abdollahi

    2013-12-01

    Full Text Available Let $n$ be any positive integer and let $F_n$ be the friendship (or Dutch windmill graph with $2n+1$ vertices and $3n$ edges. Here we study graphs with the same adjacency spectrum as the $F_n$. Two graphs are called cospectral if the eigenvalues multiset of their adjacency matrices are the same. Let $G$ be a graph cospectral with $F_n$. Here we prove that if $G$ has no cycle of length $4$ or $5$, then $Gcong F_n$. Moreover if $G$ is connected and planar then $Gcong F_n$.All but one of connected components of $G$ are isomorphic to $K_2$.The complement $overline{F_n}$ of the friendship graph is determined by its adjacency eigenvalues, that is, if $overline{F_n}$ is cospectral with a graph $H$, then $Hcong overline{F_n}$.

  12. Decomposing Oriented Graphs into Six Locally Irregular Oriented Graphs

    DEFF Research Database (Denmark)

    Bensmail, Julien; Renault, Gabriel

    2016-01-01

    An undirected graph G is locally irregular if every two of its adjacent vertices have distinct degrees. We say that G is decomposable into k locally irregular graphs if there exists a partition E1∪E2∪⋯∪Ek of the edge set E(G) such that each Ei induces a locally irregular graph. It was recently co...

  13. X-Graphs: Language and Algorithms for Heterogeneous Graph Streams

    Science.gov (United States)

    2017-09-01

    are widely used by academia and industry. 15. SUBJECT TERMS Data Analytics, Graph Analytics, High-Performance Computing 16. SECURITY CLASSIFICATION...form the core of the DeepDive Knowledge Construction System. 2 INTRODUCTION The goal of the X-Graphs project was to develop computational techniques...memory multicore machine. Ringo is based on Snap.py and SNAP, and uses Python . Ringo now allows the integration of Delite DSL Framework Graph

  14. Exploring and Making Sense of Large Graphs

    Science.gov (United States)

    2015-08-01

    WWW), Rio de Janeiro , Brazil, pages 119–130. ACM, 2013. [BYH04] Xiao Bai, Hang Yu, and Edwin R. Hancock. Graph Matching Using Spectral Embedding and...grant number DE -AC52-07NA27344, the Defense Advanced Research Projects Agency under grant number W911NF-11-C-0088, the Air Force Research Laboratory...MDL principle) visualizing. Table 3.8: Feature-based comparison of VOG with alternative approaches. So ft clu ste rin g De ns e b lo ck s St ar s Ch ai

  15. Endomorphisms of graph algebras

    DEFF Research Database (Denmark)

    Conti, Roberto; Hong, Jeong Hee; Szymanski, Wojciech

    2012-01-01

    We initiate a systematic investigation of endomorphisms of graph C*-algebras C*(E), extending several known results on endomorphisms of the Cuntz algebras O_n. Most but not all of this study is focused on endomorphisms which permute the vertex projections and globally preserve the diagonal MASA D...... that the restriction to the diagonal MASA of an automorphism which globally preserves both D_E and the core AF-subalgebra eventually commutes with the corresponding one-sided shift. Secondly, we exhibit several properties of proper endomorphisms, investigate invertibility of localized endomorphisms both on C...

  16. Total colourings of graphs

    CERN Document Server

    Yap, Hian-Poh

    1996-01-01

    This book provides an up-to-date and rapid introduction to an important and currently active topic in graph theory. The author leads the reader to the forefront of research in this area. Complete and easily readable proofs of all the main theorems, together with numerous examples, exercises and open problems are given. The book is suitable for use as a textbook or as seminar material for advanced undergraduate and graduate students. The references are comprehensive and so it will also be useful for researchers as a handbook.

  17. Graph Algorithm Animation with Grrr

    OpenAIRE

    Rodgers, Peter; Vidal, Natalia

    2000-01-01

    We discuss geometric positioning, highlighting of visited nodes and user defined highlighting that form the algorithm animation facilities in the Grrr graph rewriting programming language. The main purpose of animation was initially for the debugging and profiling of Grrr code, but recently it has been extended for the purpose of teaching algorithms to undergraduate students. The animation is restricted to graph based algorithms such as graph drawing, list manipulation or more traditional gra...

  18. Optimization Problems on Threshold Graphs

    Directory of Open Access Journals (Sweden)

    Elena Nechita

    2010-06-01

    Full Text Available During the last three decades, different types of decompositions have been processed in the field of graph theory. Among these we mention: decompositions based on the additivity of some characteristics of the graph, decompositions where the adjacency law between the subsets of the partition is known, decompositions where the subgraph induced by every subset of the partition must have predeterminate properties, as well as combinations of such decompositions. In this paper we characterize threshold graphs using the weakly decomposition, determine: density and stability number, Wiener index and Wiener polynomial for threshold graphs.

  19. Eulerian Graphs and Related Topics

    CERN Document Server

    Fleischner, Herbert

    1990-01-01

    The two volumes comprising Part 1 of this work embrace the theme of Eulerian trails and covering walks. They should appeal both to researchers and students, as they contain enough material for an undergraduate or graduate graph theory course which emphasizes Eulerian graphs, and thus can be read by any mathematician not yet familiar with graph theory. But they are also of interest to researchers in graph theory because they contain many recent results, some of which are only partial solutions to more general problems. A number of conjectures have been included as well. Various problems (such a

  20. Quantum Graph Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Maunz, Peter Lukas Wilhelm [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sterk, Jonathan David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lobser, Daniel [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Parekh, Ojas D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ryan-Anderson, Ciaran [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2016-01-01

    In recent years, advanced network analytics have become increasingly important to na- tional security with applications ranging from cyber security to detection and disruption of ter- rorist networks. While classical computing solutions have received considerable investment, the development of quantum algorithms to address problems, such as data mining of attributed relational graphs, is a largely unexplored space. Recent theoretical work has shown that quan- tum algorithms for graph analysis can be more efficient than their classical counterparts. Here, we have implemented a trapped-ion-based two-qubit quantum information proces- sor to address these goals. Building on Sandia's microfabricated silicon surface ion traps, we have designed, realized and characterized a quantum information processor using the hyperfine qubits encoded in two 171 Yb + ions. We have implemented single qubit gates using resonant microwave radiation and have employed Gate set tomography (GST) to characterize the quan- tum process. For the first time, we were able to prove that the quantum process surpasses the fault tolerance thresholds of some quantum codes by demonstrating a diamond norm distance of less than 1 . 9 x 10 [?] 4 . We used Raman transitions in order to manipulate the trapped ions' motion and realize two-qubit gates. We characterized the implemented motion sensitive and insensitive single qubit processes and achieved a maximal process infidelity of 6 . 5 x 10 [?] 5 . We implemented the two-qubit gate proposed by Molmer and Sorensen and achieved a fidelity of more than 97 . 7%.

  1. Graph averaging as a means to compare multichannel EEG coherence networks and its application to the study of mental fatigue and neurodegenerative disease

    NARCIS (Netherlands)

    Crippa, Alessandro; Maurits, Natasha M.; Lorist, Monicque M.; Roerdink, Jos B.T.M.

    A method is proposed for quantifying differences between multichannel EEG coherence networks represented by functional unit (FU) maps. The approach is based on inexact graph matching for attributed relational graphs and graph averaging, adapted to FU-maps. The mean of a set of input FU-maps is

  2. Asymptote Misconception on Graphing Functions: Does Graphing Software Resolve It?

    Directory of Open Access Journals (Sweden)

    Mehmet Fatih Öçal

    2017-01-01

    Full Text Available Graphing function is an important issue in mathematics education due to its use in various areas of mathematics and its potential roles for students to enhance learning mathematics. The use of some graphing software assists students’ learning during graphing functions. However, the display of graphs of functions that students sketched by hand may be relatively different when compared to the correct forms sketched using graphing software. The possible misleading effects of this situation brought a discussion of a misconception (asymptote misconception on graphing functions. The purpose of this study is two- fold. First of all, this study investigated whether using graphing software (GeoGebra in this case helps students to determine and resolve this misconception in calculus classrooms. Second, the reasons for this misconception are sought. The multiple case study was utilized in this study. University students in two calculus classrooms who received instructions with (35 students or without GeoGebra assisted instructions (32 students were compared according to whether they fell into this misconception on graphing basic functions (1/x, lnx, ex. In addition, students were interviewed to reveal the reasons behind this misconception. Data were analyzed by means of descriptive and content analysis methods. The findings indicated that those who received GeoGebra assisted instruction were better in resolving it. In addition, the reasons behind this misconception were found to be teacher-based, exam-based and some other factors.

  3. ON BIPOLAR SINGLE VALUED NEUTROSOPHIC GRAPHS

    OpenAIRE

    Said Broumi; Mohamed Talea; Assia Bakali; Florentin Smarandache

    2016-01-01

    In this article, we combine the concept of bipolar neutrosophic set and graph theory. We introduce the notions of bipolar single valued neutrosophic graphs, strong bipolar single valued neutrosophic graphs, complete bipolar single valued neutrosophic graphs, regular bipolar single valued neutrosophic graphs and investigate some of their related properties.

  4. Neuro-symbolic representation learning on biological knowledge graphs.

    Science.gov (United States)

    Alshahrani, Mona; Khan, Mohammad Asif; Maddouri, Omar; Kinjo, Akira R; Queralt-Rosinach, Núria; Hoehndorf, Robert

    2017-09-01

    Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of Semantic Web based knowledge bases in biology to use in machine learning and data analytics. https://github.com/bio-ontology-research-group/walking-rdf-and-owl. robert.hoehndorf@kaust.edu.sa. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  5. Neuro-symbolic representation learning on biological knowledge graphs

    KAUST Repository

    Alshahrani, Mona

    2017-04-21

    Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge.We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of SemanticWeb based knowledge bases in biology to use in machine learning and data analytics.https://github.com/bio-ontology-research-group/walking-rdf-and-owl.robert.hoehndorf@kaust.edu.sa.Supplementary data are available at Bioinformatics online.

  6. Graph Theory. 2. Vertex Descriptors and Graph Coloring

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2002-12-01

    Full Text Available This original work presents the construction of a set of ten sequence matrices and their applications for ordering vertices in graphs. For every sequence matrix three ordering criteria are applied: lexicographic ordering, based on strings of numbers, corresponding to every vertex, extracted as rows from sequence matrices; ordering by the sum of path lengths from a given vertex; and ordering by the sum of paths, starting from a given vertex. We also examine a graph that has different orderings for the above criteria. We then proceed to demonstrate that every criterion induced its own partition of graph vertex. We propose the following theoretical result: both LAVS and LVDS criteria generate identical partitioning of vertices in any graph. Finally, a coloring of graph vertices according to introduced ordering criteria was proposed.

  7. On an edge partition and root graphs of some classes of line graphs

    Directory of Open Access Journals (Sweden)

    K Pravas

    2017-04-01

    Full Text Available The Gallai and the anti-Gallai graphs of a graph $G$ are complementary pairs of spanning subgraphs of the line graph of $G$. In this paper we find some structural relations between these graph classes by finding a partition of the edge set of the line graph of a graph $G$ into the edge sets of the Gallai and anti-Gallai graphs of $G$. Based on this, an optimal algorithm to find the root graph of a line graph is obtained. Moreover, root graphs of diameter-maximal, distance-hereditary, Ptolemaic and chordal graphs are also discussed.

  8. The planar cubic Cayley graphs

    CERN Document Server

    Georgakopoulos, Agelos

    2018-01-01

    The author obtains a complete description of the planar cubic Cayley graphs, providing an explicit presentation and embedding for each of them. This turns out to be a rich class, comprising several infinite families. He obtains counterexamples to conjectures of Mohar, Bonnington and Watkins. The author's analysis makes the involved graphs accessible to computation, corroborating a conjecture of Droms.

  9. Groupies in random bipartite graphs

    OpenAIRE

    Yilun Shang

    2010-01-01

    A vertex $v$ of a graph $G$ is called a groupie if its degree is notless than the average of the degrees of its neighbors. In thispaper we study the influence of bipartition $(B_1,B_2)$ on groupiesin random bipartite graphs $G(B_1,B_2,p)$ with both fixed $p$ and$p$ tending to zero.

  10. Nested Dynamic Condition Response Graphs

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas; Mukkamala, Raghava Rao; Slaats, Tijs

    2012-01-01

    We present an extension of the recently introduced declarative process model Dynamic Condition Response Graphs ( DCR Graphs) to allow nested subgraphs and a new milestone relation between events. The extension was developed during a case study carried out jointly with our industrial partner...

  11. Bell inequalities for graph states

    International Nuclear Information System (INIS)

    Toth, G.; Hyllus, P.; Briegel, H.J.; Guehne, O.

    2005-01-01

    Full text: In the last years graph states have attracted an increasing interest in the field of quantum information theory. Graph states form a family of multi-qubit states which comprises many popular states such as the GHZ states and the cluster states. They also play an important role in applications. For instance, measurement based quantum computation uses graph states as resources. From a theoretical point of view, it is remarkable that graph states allow for a simple description in terms of stabilizing operators. In this contribution, we investigate the non-local properties of graph states. We derive a family of Bell inequalities which require three measurement settings for each party and are maximally violated by graph states. In turn, any graph state violates at least one of the inequalities. We show that for certain types of graph states the violation of these inequalities increases exponentially with the number of qubits. We also discuss connections to other entanglement properties such as the positively of the partial transpose or the geometric measure of entanglement. (author)

  12. Graph Sampling for Covariance Estimation

    KAUST Repository

    Chepuri, Sundeep Prabhakar; Leus, Geert

    2017-01-01

    specialize for undirected circulant graphs in that the graph nodes leading to the best compression rates are given by the so-called minimal sparse rulers. A near-optimal greedy algorithm is developed to design the subsampling scheme for the non

  13. Network reconstruction via graph blending

    Science.gov (United States)

    Estrada, Rolando

    2016-05-01

    Graphs estimated from empirical data are often noisy and incomplete due to the difficulty of faithfully observing all the components (nodes and edges) of the true graph. This problem is particularly acute for large networks where the number of components may far exceed available surveillance capabilities. Errors in the observed graph can render subsequent analyses invalid, so it is vital to develop robust methods that can minimize these observational errors. Errors in the observed graph may include missing and spurious components, as well fused (multiple nodes are merged into one) and split (a single node is misinterpreted as many) nodes. Traditional graph reconstruction methods are only able to identify missing or spurious components (primarily edges, and to a lesser degree nodes), so we developed a novel graph blending framework that allows us to cast the full estimation problem as a simple edge addition/deletion problem. Armed with this framework, we systematically investigate the viability of various topological graph features, such as the degree distribution or the clustering coefficients, and existing graph reconstruction methods for tackling the full estimation problem. Our experimental results suggest that incorporating any topological feature as a source of information actually hinders reconstruction accuracy. We provide a theoretical analysis of this phenomenon and suggest several avenues for improving this estimation problem.

  14. A cluster algorithm for graphs

    NARCIS (Netherlands)

    S. van Dongen

    2000-01-01

    textabstractA cluster algorithm for graphs called the emph{Markov Cluster algorithm (MCL~algorithm) is introduced. The algorithm provides basically an interface to an algebraic process defined on stochastic matrices, called the MCL~process. The graphs may be both weighted (with nonnegative weight)

  15. Graph theoretical model of a sensorimotor connectome in zebrafish.

    Science.gov (United States)

    Stobb, Michael; Peterson, Joshua M; Mazzag, Borbala; Gahtan, Ethan

    2012-01-01

    Mapping the detailed connectivity patterns (connectomes) of neural circuits is a central goal of neuroscience. The best quantitative approach to analyzing connectome data is still unclear but graph theory has been used with success. We present a graph theoretical model of the posterior lateral line sensorimotor pathway in zebrafish. The model includes 2,616 neurons and 167,114 synaptic connections. Model neurons represent known cell types in zebrafish larvae, and connections were set stochastically following rules based on biological literature. Thus, our model is a uniquely detailed computational representation of a vertebrate connectome. The connectome has low overall connection density, with 2.45% of all possible connections, a value within the physiological range. We used graph theoretical tools to compare the zebrafish connectome graph to small-world, random and structured random graphs of the same size. For each type of graph, 100 randomly generated instantiations were considered. Degree distribution (the number of connections per neuron) varied more in the zebrafish graph than in same size graphs with less biological detail. There was high local clustering and a short average path length between nodes, implying a small-world structure similar to other neural connectomes and complex networks. The graph was found not to be scale-free, in agreement with some other neural connectomes. An experimental lesion was performed that targeted three model brain neurons, including the Mauthner neuron, known to control fast escape turns. The lesion decreased the number of short paths between sensory and motor neurons analogous to the behavioral effects of the same lesion in zebrafish. This model is expandable and can be used to organize and interpret a growing database of information on the zebrafish connectome.

  16. Graph theoretical model of a sensorimotor connectome in zebrafish.

    Directory of Open Access Journals (Sweden)

    Michael Stobb

    Full Text Available Mapping the detailed connectivity patterns (connectomes of neural circuits is a central goal of neuroscience. The best quantitative approach to analyzing connectome data is still unclear but graph theory has been used with success. We present a graph theoretical model of the posterior lateral line sensorimotor pathway in zebrafish. The model includes 2,616 neurons and 167,114 synaptic connections. Model neurons represent known cell types in zebrafish larvae, and connections were set stochastically following rules based on biological literature. Thus, our model is a uniquely detailed computational representation of a vertebrate connectome. The connectome has low overall connection density, with 2.45% of all possible connections, a value within the physiological range. We used graph theoretical tools to compare the zebrafish connectome graph to small-world, random and structured random graphs of the same size. For each type of graph, 100 randomly generated instantiations were considered. Degree distribution (the number of connections per neuron varied more in the zebrafish graph than in same size graphs with less biological detail. There was high local clustering and a short average path length between nodes, implying a small-world structure similar to other neural connectomes and complex networks. The graph was found not to be scale-free, in agreement with some other neural connectomes. An experimental lesion was performed that targeted three model brain neurons, including the Mauthner neuron, known to control fast escape turns. The lesion decreased the number of short paths between sensory and motor neurons analogous to the behavioral effects of the same lesion in zebrafish. This model is expandable and can be used to organize and interpret a growing database of information on the zebrafish connectome.

  17. Planar graphs theory and algorithms

    CERN Document Server

    Nishizeki, T

    1988-01-01

    Collected in this volume are most of the important theorems and algorithms currently known for planar graphs, together with constructive proofs for the theorems. Many of the algorithms are written in Pidgin PASCAL, and are the best-known ones; the complexities are linear or 0(nlogn). The first two chapters provide the foundations of graph theoretic notions and algorithmic techniques. The remaining chapters discuss the topics of planarity testing, embedding, drawing, vertex- or edge-coloring, maximum independence set, subgraph listing, planar separator theorem, Hamiltonian cycles, and single- or multicommodity flows. Suitable for a course on algorithms, graph theory, or planar graphs, the volume will also be useful for computer scientists and graph theorists at the research level. An extensive reference section is included.

  18. Quantum chaos on discrete graphs

    International Nuclear Information System (INIS)

    Smilansky, Uzy

    2007-01-01

    Adapting a method developed for the study of quantum chaos on quantum (metric) graphs (Kottos and Smilansky 1997 Phys. Rev. Lett. 79 4794, Kottos and Smilansky 1999 Ann. Phys., NY 274 76), spectral ζ functions and trace formulae for discrete Laplacians on graphs are derived. This is achieved by expressing the spectral secular equation in terms of the periodic orbits of the graph and obtaining functions which belong to the class of ζ functions proposed originally by Ihara (1966 J. Mat. Soc. Japan 18 219) and expanded by subsequent authors (Stark and Terras 1996 Adv. Math. 121 124, Kotani and Sunada 2000 J. Math. Sci. Univ. Tokyo 7 7). Finally, a model of 'classical dynamics' on the discrete graph is proposed. It is analogous to the corresponding classical dynamics derived for quantum graphs (Kottos and Smilansky 1997 Phys. Rev. Lett. 79 4794, Kottos and Smilansky 1999 Ann. Phys., NY 274 76). (fast track communication)

  19. RJSplot: Interactive Graphs with R.

    Science.gov (United States)

    Barrios, David; Prieto, Carlos

    2018-03-01

    Data visualization techniques provide new methods for the generation of interactive graphs. These graphs allow a better exploration and interpretation of data but their creation requires advanced knowledge of graphical libraries. Recent packages have enabled the integration of interactive graphs in R. However, R provides limited graphical packages that allow the generation of interactive graphs for computational biology applications. The present project has joined the analytical power of R with the interactive graphical features of JavaScript in a new R package (RJSplot). It enables the easy generation of interactive graphs in R, provides new visualization capabilities, and contributes to the advance of computational biology analytical methods. At present, 16 interactive graphics are available in RJSplot, such as the genome viewer, Manhattan plots, 3D plots, heatmaps, dendrograms, networks, and so on. The RJSplot package is freely available online at http://rjsplot.net. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Matching games: the least core and the nucleolus

    NARCIS (Netherlands)

    Kern, Walter; Paulusma, Daniël

    2003-01-01

    A matching game is a cooperative game defined by a graph G = (N, E). The player set is N and the value of a coalition S ⫅ N is defined as the size of a maximum matching in the subgraph induced by S. We show that the nucleolus of such games can be computed efficiently. The result is based on an

  1. On characterizing terrain visibility graphs

    Directory of Open Access Journals (Sweden)

    William Evans

    2015-06-01

    Full Text Available A terrain is an $x$-monotone polygonal line in the $xy$-plane. Two vertices of a terrain are mutually visible if and only if there is no terrain vertex on or above the open line segment connecting them. A graph whose vertices represent terrain vertices and whose edges represent mutually visible pairs of terrain vertices is called a terrain visibility graph. We would like to find properties that are both necessary and sufficient for a graph to be a terrain visibility graph; that is, we would like to characterize terrain visibility graphs.Abello et al. [Discrete and Computational Geometry, 14(3:331--358, 1995] showed that all terrain visibility graphs are “persistent”. They showed that the visibility information of a terrain point set implies some ordering requirements on the slopes of the lines connecting pairs of points in any realization, and as a step towards showing sufficiency, they proved that for any persistent graph $M$ there is a total order on the slopes of the (pseudo lines in a generalized configuration of points whose visibility graph is $M$.We give a much simpler proof of this result by establishing an orientation to every triple of vertices, reflecting some slope ordering requirements that are consistent with $M$ being the visibility graph, and prove that these requirements form a partial order. We give a faster algorithm to construct a total order on the slopes. Our approach attempts to clarify the implications of the graph theoretic properties on the ordering of the slopes, and may be interpreted as defining properties on an underlying oriented matroid that we show is a restricted type of $3$-signotope.

  2. Graph embedding with rich information through heterogeneous graph

    KAUST Repository

    Sun, Guolei

    2017-11-12

    Graph embedding, aiming to learn low-dimensional representations for nodes in graphs, has attracted increasing attention due to its critical application including node classification, link prediction and clustering in social network analysis. Most existing algorithms for graph embedding only rely on the topology information and fail to use the copious information in nodes as well as edges. As a result, their performance for many tasks may not be satisfactory. In this thesis, we proposed a novel and general framework for graph embedding with rich text information (GERI) through constructing a heterogeneous network, in which we integrate node and edge content information with graph topology. Specially, we designed a novel biased random walk to explore the constructed heterogeneous network with the notion of flexible neighborhood. Our sampling strategy can compromise between BFS and DFS local search on heterogeneous graph. To further improve our algorithm, we proposed semi-supervised GERI (SGERI), which learns graph embedding in an discriminative manner through heterogeneous network with label information. The efficacy of our method is demonstrated by extensive comparison experiments with 9 baselines over multi-label and multi-class classification on various datasets including Citeseer, Cora, DBLP and Wiki. It shows that GERI improves the Micro-F1 and Macro-F1 of node classification up to 10%, and SGERI improves GERI by 5% in Wiki.

  3. CORECLUSTER: A Degeneracy Based Graph Clustering Framework

    OpenAIRE

    Giatsidis , Christos; Malliaros , Fragkiskos; Thilikos , Dimitrios M. ,; Vazirgiannis , Michalis

    2014-01-01

    International audience; Graph clustering or community detection constitutes an important task forinvestigating the internal structure of graphs, with a plethora of applications in several domains. Traditional tools for graph clustering, such asspectral methods, typically suffer from high time and space complexity. In thisarticle, we present \\textsc{CoreCluster}, an efficient graph clusteringframework based on the concept of graph degeneracy, that can be used along withany known graph clusteri...

  4. PERSEUS-HUB: Interactive and Collective Exploration of Large-Scale Graphs

    Directory of Open Access Journals (Sweden)

    Di Jin

    2017-07-01

    Full Text Available Graphs emerge naturally in many domains, such as social science, neuroscience, transportation engineering, and more. In many cases, such graphs have millions or billions of nodes and edges, and their sizes increase daily at a fast pace. How can researchers from various domains explore large graphs interactively and efficiently to find out what is ‘important’? How can multiple researchers explore a new graph dataset collectively and “help” each other with their findings? In this article, we present Perseus-Hub, a large-scale graph mining tool that computes a set of graph properties in a distributed manner, performs ensemble, multi-view anomaly detection to highlight regions that are worth investigating, and provides users with uncluttered visualization and easy interaction with complex graph statistics. Perseus-Hub uses a Spark cluster to calculate various statistics of large-scale graphs efficiently, and aggregates the results in a summary on the master node to support interactive user exploration. In Perseus-Hub, the visualized distributions of graph statistics provide preliminary analysis to understand a graph. To perform a deeper analysis, users with little prior knowledge can leverage patterns (e.g., spikes in the power-law degree distribution marked by other users or experts. Moreover, Perseus-Hub guides users to regions of interest by highlighting anomalous nodes and helps users establish a more comprehensive understanding about the graph at hand. We demonstrate our system through the case study on real, large-scale networks.

  5. Image denoising via adaptive eigenvectors of graph Laplacian

    Science.gov (United States)

    Chen, Ying; Tang, Yibin; Xu, Ning; Zhou, Lin; Zhao, Li

    2016-07-01

    An image denoising method via adaptive eigenvectors of graph Laplacian (EGL) is proposed. Unlike the trivial parameter setting of the used eigenvectors in the traditional EGL method, in our method, the eigenvectors are adaptively selected in the whole denoising procedure. In detail, a rough image is first built with the eigenvectors from the noisy image, where the eigenvectors are selected by using the deviation estimation of the clean image. Subsequently, a guided image is effectively restored with a weighted average of the noisy and rough images. In this operation, the average coefficient is adaptively obtained to set the deviation of the guided image to approximately that of the clean image. Finally, the denoised image is achieved by a group-sparse model with the pattern from the guided image, where the eigenvectors are chosen in the error control of the noise deviation. Moreover, a modified group orthogonal matching pursuit algorithm is developed to efficiently solve the above group sparse model. The experiments show that our method not only improves the practicality of the EGL methods with the dependence reduction of the parameter setting, but also can outperform some well-developed denoising methods, especially for noise with large deviations.

  6. Semantic graphs and associative memories

    Science.gov (United States)

    Pomi, Andrés; Mizraji, Eduardo

    2004-12-01

    Graphs have been increasingly utilized in the characterization of complex networks from diverse origins, including different kinds of semantic networks. Human memories are associative and are known to support complex semantic nets; these nets are represented by graphs. However, it is not known how the brain can sustain these semantic graphs. The vision of cognitive brain activities, shown by modern functional imaging techniques, assigns renewed value to classical distributed associative memory models. Here we show that these neural network models, also known as correlation matrix memories, naturally support a graph representation of the stored semantic structure. We demonstrate that the adjacency matrix of this graph of associations is just the memory coded with the standard basis of the concept vector space, and that the spectrum of the graph is a code invariant of the memory. As long as the assumptions of the model remain valid this result provides a practical method to predict and modify the evolution of the cognitive dynamics. Also, it could provide us with a way to comprehend how individual brains that map the external reality, almost surely with different particular vector representations, are nevertheless able to communicate and share a common knowledge of the world. We finish presenting adaptive association graphs, an extension of the model that makes use of the tensor product, which provides a solution to the known problem of branching in semantic nets.

  7. XML Graphs in Program Analysis

    DEFF Research Database (Denmark)

    Møller, Anders; Schwartzbach, Michael I.

    2011-01-01

    of XML graphs against different XML schema languages, and provide a software package that enables others to make use of these ideas. We also survey the use of XML graphs for program analysis with four very different languages: XACT (XML in Java), Java Servlets (Web application programming), XSugar......XML graphs have shown to be a simple and effective formalism for representing sets of XML documents in program analysis. It has evolved through a six year period with variants tailored for a range of applications. We present a unified definition, outline the key properties including validation...

  8. Coloring and The Lonely Graph

    OpenAIRE

    Rabern, Landon

    2007-01-01

    We improve upper bounds on the chromatic number proven independently in \\cite{reedNote} and \\cite{ingo}. Our main lemma gives a sufficient condition for two paths in graph to be completely joined. Using this, we prove that if a graph has an optimal coloring with more than $\\frac{\\omega}{2}$ singleton color classes, then it satisfies $\\chi \\leq \\frac{\\omega + \\Delta + 1}{2}$. It follows that a graph satisfying $n - \\Delta < \\alpha + \\frac{\\omega - 1}{2}$ must also satisfy $\\chi \\leq \\frac{\\ome...

  9. Graphs with Eulerian unit spheres

    OpenAIRE

    Knill, Oliver

    2015-01-01

    d-spheres in graph theory are inductively defined as graphs for which all unit spheres S(x) are (d-1)-spheres and that the removal of one vertex renders the graph contractible. Eulerian d-spheres are geometric d-spheres which are d+1 colorable. We prove here that G is an Eulerian sphere if and only if the degrees of all the (d-2)-dimensional sub-simplices in G are even. This generalizes a Kempe-Heawood result for d=2 and is work related to the conjecture that all d-spheres have chromatic numb...

  10. Fractional graph theory a rational approach to the theory of graphs

    CERN Document Server

    Scheinerman, Edward R

    2013-01-01

    A unified treatment of the most important results in the study of fractional graph concepts, this volume explores the various ways in which integer-valued concepts can be modified to derive nonintegral values. It begins with the general fractional theory of hypergraphs and presents in-depth coverage of fundamental and advanced topics. Subjects include fractional matching, fractional coloring, fractional edge coloring, fractional arboricity via matroid methods, and fractional isomorphism. The final chapter examines additional topics such as fractional domination, fractional intersection numbers

  11. Network graph analysis and visualization with Gephi

    CERN Document Server

    Cherven, Ken

    2013-01-01

    A practical, hands-on guide, that provides you with all the tools you need to visualize and analyze your data using network graphs with Gephi.This book is for data analysts who want to intuitively reveal patterns and trends, highlight outliers, and tell stories with their data using Gephi. It is great for anyone looking to explore interactions within network datasets, whether the data comes from social media or elsewhere. It is also a valuable resource for those seeking to learn more about Gephi without being overwhelmed by technical details.

  12. Eulerian graph embeddings and trails confined to lattice tubes

    International Nuclear Information System (INIS)

    Soteros, C E

    2006-01-01

    Embeddings of graphs in sublattices of the square and simple cubic lattice known as tubes (or prisms) are considered. For such sublattices, two combinatorial bounds are obtained which each relate the number of embeddings of all closed eulerian graphs with k branch points (vertices of degree greater than two) to the number of self-avoiding polygons. From these bounds it is proved that the entropic critical exponent for the number of embeddings of closed eulerian graphs with k branch points is equal to k, and the entropic critical exponent for the number of closed trails with k branch points is equal to k + 1. One of the required combinatorial bounds is obtained via Madras' 1999 lattice cluster pattern theorem, which yields a bound on the number of ways to convert a self-avoiding polygon into a closed eulerian graph embedding with k branch points. The other combinatorial bound is established by constructing a method for sequentially removing branch points from a closed eulerian graph embedding; this yields a bound on the number of ways to convert a closed eulerian graph embedding into a self-avoiding polygon

  13. Tutte sets in graphs II: The complexity of finding maximum Tutte sets

    NARCIS (Netherlands)

    Bauer, D.; Broersma, Haitze J.; Kahl, N.; Morgana, A.; Schmeichel, E.; Surowiec, T.

    2007-01-01

    A well-known formula of Tutte and Berge expresses the size of a maximum matching in a graph $G$ in terms of what is usually called the deficiency. A subset $X$ of $V(G)$ for which this deficiency is attained is called a Tutte set of $G$. While much is known about maximum matchings, less is known

  14. Properly colored connectivity of graphs

    CERN Document Server

    Li, Xueliang; Qin, Zhongmei

    2018-01-01

    A comprehensive survey of proper connection of graphs is discussed in this book with real world applications in computer science and network security. Beginning with a brief introduction, comprising relevant definitions and preliminary results, this book moves on to consider a variety of properties of graphs that imply bounds on the proper connection number. Detailed proofs of significant advancements toward open problems and conjectures are presented with complete references. Researchers and graduate students with an interest in graph connectivity and colorings will find this book useful as it builds upon fundamental definitions towards modern innovations, strategies, and techniques. The detailed presentation lends to use as an introduction to proper connection of graphs for new and advanced researchers, a solid book for a graduate level topics course, or as a reference for those interested in expanding and further developing research in the area.

  15. Graph anomalies in cyber communications

    Energy Technology Data Exchange (ETDEWEB)

    Vander Wiel, Scott A [Los Alamos National Laboratory; Storlie, Curtis B [Los Alamos National Laboratory; Sandine, Gary [Los Alamos National Laboratory; Hagberg, Aric A [Los Alamos National Laboratory; Fisk, Michael [Los Alamos National Laboratory

    2011-01-11

    Enterprises monitor cyber traffic for viruses, intruders and stolen information. Detection methods look for known signatures of malicious traffic or search for anomalies with respect to a nominal reference model. Traditional anomaly detection focuses on aggregate traffic at central nodes or on user-level monitoring. More recently, however, traffic is being viewed more holistically as a dynamic communication graph. Attention to the graph nature of the traffic has expanded the types of anomalies that are being sought. We give an overview of several cyber data streams collected at Los Alamos National Laboratory and discuss current work in modeling the graph dynamics of traffic over the network. We consider global properties and local properties within the communication graph. A method for monitoring relative entropy on multiple correlated properties is discussed in detail.

  16. Open Graphs and Computational Reasoning

    Directory of Open Access Journals (Sweden)

    Lucas Dixon

    2010-06-01

    Full Text Available We present a form of algebraic reasoning for computational objects which are expressed as graphs. Edges describe the flow of data between primitive operations which are represented by vertices. These graphs have an interface made of half-edges (edges which are drawn with an unconnected end and enjoy rich compositional principles by connecting graphs along these half-edges. In particular, this allows equations and rewrite rules to be specified between graphs. Particular computational models can then be encoded as an axiomatic set of such rules. Further rules can be derived graphically and rewriting can be used to simulate the dynamics of a computational system, e.g. evaluating a program on an input. Examples of models which can be formalised in this way include traditional electronic circuits as well as recent categorical accounts of quantum information.

  17. The toughness of split graphs

    NARCIS (Netherlands)

    Woeginger, G.J.

    1998-01-01

    In this short note we argue that the toughness of split graphs can be computed in polynomial time. This solves an open problem from a recent paper by Kratsch et al. (Discrete Math. 150 (1996) 231–245).

  18. Generating random networks and graphs

    CERN Document Server

    Coolen, Ton; Roberts, Ekaterina

    2017-01-01

    This book supports researchers who need to generate random networks, or who are interested in the theoretical study of random graphs. The coverage includes exponential random graphs (where the targeted probability of each network appearing in the ensemble is specified), growth algorithms (i.e. preferential attachment and the stub-joining configuration model), special constructions (e.g. geometric graphs and Watts Strogatz models) and graphs on structured spaces (e.g. multiplex networks). The presentation aims to be a complete starting point, including details of both theory and implementation, as well as discussions of the main strengths and weaknesses of each approach. It includes extensive references for readers wishing to go further. The material is carefully structured to be accessible to researchers from all disciplines while also containing rigorous mathematical analysis (largely based on the techniques of statistical mechanics) to support those wishing to further develop or implement the theory of rand...

  19. Belief propagation and loop series on planar graphs

    International Nuclear Information System (INIS)

    Chertkov, Michael; Teodorescu, Razvan; Chernyak, Vladimir Y

    2008-01-01

    We discuss a generic model of Bayesian inference with binary variables defined on edges of a planar graph. The Loop Calculus approach of Chertkov and Chernyak (2006 Phys. Rev. E 73 065102(R) [cond-mat/0601487]; 2006 J. Stat. Mech. P06009 [cond-mat/0603189]) is used to evaluate the resulting series expansion for the partition function. We show that, for planar graphs, truncating the series at single-connected loops reduces, via a map reminiscent of the Fisher transformation (Fisher 1961 Phys. Rev. 124 1664), to evaluating the partition function of the dimer-matching model on an auxiliary planar graph. Thus, the truncated series can be easily re-summed, using the Pfaffian formula of Kasteleyn (1961 Physics 27 1209). This allows us to identify a big class of computationally tractable planar models reducible to a dimer model via the Belief Propagation (gauge) transformation. The Pfaffian representation can also be extended to the full Loop Series, in which case the expansion becomes a sum of Pfaffian contributions, each associated with dimer matchings on an extension to a subgraph of the original graph. Algorithmic consequences of the Pfaffian representation, as well as relations to quantum and non-planar models, are discussed

  20. Graph theory and its applications

    CERN Document Server

    Gross, Jonathan L

    2006-01-01

    Gross and Yellen take a comprehensive approach to graph theory that integrates careful exposition of classical developments with emerging methods, models, and practical needs. Their unparalleled treatment provides a text ideal for a two-semester course and a variety of one-semester classes, from an introductory one-semester course to courses slanted toward classical graph theory, operations research, data structures and algorithms, or algebra and topology.

  1. Nonschematic drawing recognition: a new approach based on attributed graph grammar with flexible embedding

    Science.gov (United States)

    Lee, Kyu J.; Kunii, T. L.; Noma, T.

    1993-01-01

    In this paper, we propose a syntactic pattern recognition method for non-schematic drawings, based on a new attributed graph grammar with flexible embedding. In our graph grammar, the embedding rule permits the nodes of a guest graph to be arbitrarily connected with the nodes of a host graph. The ambiguity caused by this flexible embedding is controlled with the evaluation of synthesized attributes and the check of context sensitivity. To integrate parsing with the synthesized attribute evaluation and the context sensitivity check, we also develop a bottom up parsing algorithm.

  2. Incidental Prophylactic Nodal Irradiation and Patterns of Nodal Relapse in Inoperable Early Stage NSCLC Patients Treated With SBRT: A Case-Matched Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lao, Louis [Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada); Department of Radiation Oncology, Auckland City Hospital, Auckland (New Zealand); Hope, Andrew J. [Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada); Maganti, Manjula [Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada); Brade, Anthony; Bezjak, Andrea; Saibishkumar, Elantholi P.; Giuliani, Meredith; Sun, Alexander [Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada); Cho, B. C. John, E-mail: john.cho@rmp.uhn.on.ca [Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada)

    2014-09-01

    Purpose: Reported rates of non-small cell lung cancer (NSCLC) nodal failure following stereotactic body radiation therapy (SBRT) are lower than those reported in the surgical series when matched for stage. We hypothesized that this effect was due to incidental prophylactic nodal irradiation. Methods and Materials: A prospectively collected group of medically inoperable early stage NSCLC patients from 2004 to 2010 was used to identify cases with nodal relapses. Controls were matched to cases, 2:1, controlling for tumor volume (ie, same or greater) and tumor location (ie, same lobe). Reference (normalized to equivalent dose for 2-Gy fractions [EQD2]) point doses at the ipsilateral hilum and carina, demographic data, and clinical outcomes were extracted from the medical records. Univariate conditional logistical regression analyses were performed with variables of interest. Results: Cases and controls were well matched except for size. The controls, as expected, had larger gross tumor volumes (P=.02). The mean ipsilateral hilar doses were 9.6 Gy and 22.4 Gy for cases and controls, respectively (P=.014). The mean carinal doses were 7.0 Gy and 9.2 Gy, respectively (P=.13). Mediastinal nodal relapses, with and without ipsilateral hilar relapse, were associated with mean ipsilateral hilar doses of 3.6 Gy and 19.8 Gy, respectively (P=.01). The conditional density plot appears to demonstrate an inverse dose-effect relationship between ipsilateral hilar normalized total dose and risk of ipsilateral hilar relapse. Conclusions: Incidental hilar dose greater than 20 Gy is significantly associated with fewer ipsilateral hilar relapses in inoperable early stage NSCLC patients treated with SBRT.

  3. Incidental Prophylactic Nodal Irradiation and Patterns of Nodal Relapse in Inoperable Early Stage NSCLC Patients Treated With SBRT: A Case-Matched Analysis

    International Nuclear Information System (INIS)

    Lao, Louis; Hope, Andrew J.; Maganti, Manjula; Brade, Anthony; Bezjak, Andrea; Saibishkumar, Elantholi P.; Giuliani, Meredith; Sun, Alexander; Cho, B. C. John

    2014-01-01

    Purpose: Reported rates of non-small cell lung cancer (NSCLC) nodal failure following stereotactic body radiation therapy (SBRT) are lower than those reported in the surgical series when matched for stage. We hypothesized that this effect was due to incidental prophylactic nodal irradiation. Methods and Materials: A prospectively collected group of medically inoperable early stage NSCLC patients from 2004 to 2010 was used to identify cases with nodal relapses. Controls were matched to cases, 2:1, controlling for tumor volume (ie, same or greater) and tumor location (ie, same lobe). Reference (normalized to equivalent dose for 2-Gy fractions [EQD2]) point doses at the ipsilateral hilum and carina, demographic data, and clinical outcomes were extracted from the medical records. Univariate conditional logistical regression analyses were performed with variables of interest. Results: Cases and controls were well matched except for size. The controls, as expected, had larger gross tumor volumes (P=.02). The mean ipsilateral hilar doses were 9.6 Gy and 22.4 Gy for cases and controls, respectively (P=.014). The mean carinal doses were 7.0 Gy and 9.2 Gy, respectively (P=.13). Mediastinal nodal relapses, with and without ipsilateral hilar relapse, were associated with mean ipsilateral hilar doses of 3.6 Gy and 19.8 Gy, respectively (P=.01). The conditional density plot appears to demonstrate an inverse dose-effect relationship between ipsilateral hilar normalized total dose and risk of ipsilateral hilar relapse. Conclusions: Incidental hilar dose greater than 20 Gy is significantly associated with fewer ipsilateral hilar relapses in inoperable early stage NSCLC patients treated with SBRT

  4. A faithful functor among algebras and graphs

    OpenAIRE

    Falcón Ganfornina, Óscar Jesús; Falcón Ganfornina, Raúl Manuel; Núñez Valdés, Juan; Pacheco Martínez, Ana María; Villar Liñán, María Trinidad; Vigo Aguiar, Jesús (Coordinador)

    2016-01-01

    The problem of identifying a functor between the categories of algebras and graphs is currently open. Based on a known algorithm that identifies isomorphisms of Latin squares with isomorphism of vertex-colored graphs, we describe here a pair of graphs that enable us to find a faithful functor between finite-dimensional algebras over finite fields and these graphs.

  5. Graphs with branchwidth at most three

    NARCIS (Netherlands)

    Bodlaender, H.L.; Thilikos, D.M.

    1997-01-01

    In this paper we investigate both the structure of graphs with branchwidth at most three, as well as algorithms to recognise such graphs. We show that a graph has branchwidth at most three, if and only if it has treewidth at most three and does not contain the three-dimensional binary cube graph

  6. A Modal-Logic Based Graph Abstraction

    NARCIS (Netherlands)

    Bauer, J.; Boneva, I.B.; Kurban, M.E.; Rensink, Arend; Ehrig, H; Heckel, R.; Rozenberg, G.; Taentzer, G.

    2008-01-01

    Infinite or very large state spaces often prohibit the successful verification of graph transformation systems. Abstract graph transformation is an approach that tackles this problem by abstracting graphs to abstract graphs of bounded size and by lifting application of productions to abstract

  7. Graphs whose complement and square are isomorphic

    DEFF Research Database (Denmark)

    Pedersen, Anders Sune

    2014-01-01

    We study square-complementary graphs, that is, graphs whose complement and square are isomorphic. We prove several necessary conditions for a graph to be square-complementary, describe ways of building new square-complementary graphs from existing ones, construct infinite families of square-compl...

  8. Acyclicity in edge-colored graphs

    DEFF Research Database (Denmark)

    Gutin, Gregory; Jones, Mark; Sheng, Bin

    2017-01-01

    A walk W in edge-colored graphs is called properly colored (PC) if every pair of consecutive edges in W is of different color. We introduce and study five types of PC acyclicity in edge-colored graphs such that graphs of PC acyclicity of type i is a proper superset of graphs of acyclicity of type...

  9. Building Scalable Knowledge Graphs for Earth Science

    Science.gov (United States)

    Ramachandran, Rahul; Maskey, Manil; Gatlin, Patrick; Zhang, Jia; Duan, Xiaoyi; Miller, J. J.; Bugbee, Kaylin; Christopher, Sundar; Freitag, Brian

    2017-01-01

    Knowledge Graphs link key entities in a specific domain with other entities via relationships. From these relationships, researchers can query knowledge graphs for probabilistic recommendations to infer new knowledge. Scientific papers are an untapped resource which knowledge graphs could leverage to accelerate research discovery. Goal: Develop an end-to-end (semi) automated methodology for constructing Knowledge Graphs for Earth Science.

  10. Port-Hamiltonian Systems on Open Graphs

    NARCIS (Netherlands)

    Schaft, A.J. van der; Maschke, B.M.

    2010-01-01

    In this talk we discuss how to define in an intrinsic manner port-Hamiltonian dynamics on open graphs. Open graphs are graphs where some of the vertices are boundary vertices (terminals), which allow interconnection with other systems. We show that a directed graph carries two natural Dirac

  11. Constructing Dense Graphs with Unique Hamiltonian Cycles

    Science.gov (United States)

    Lynch, Mark A. M.

    2012-01-01

    It is not difficult to construct dense graphs containing Hamiltonian cycles, but it is difficult to generate dense graphs that are guaranteed to contain a unique Hamiltonian cycle. This article presents an algorithm for generating arbitrarily large simple graphs containing "unique" Hamiltonian cycles. These graphs can be turned into dense graphs…

  12. Chromatic polynomials of random graphs

    International Nuclear Information System (INIS)

    Van Bussel, Frank; Fliegner, Denny; Timme, Marc; Ehrlich, Christoph; Stolzenberg, Sebastian

    2010-01-01

    Chromatic polynomials and related graph invariants are central objects in both graph theory and statistical physics. Computational difficulties, however, have so far restricted studies of such polynomials to graphs that were either very small, very sparse or highly structured. Recent algorithmic advances (Timme et al 2009 New J. Phys. 11 023001) now make it possible to compute chromatic polynomials for moderately sized graphs of arbitrary structure and number of edges. Here we present chromatic polynomials of ensembles of random graphs with up to 30 vertices, over the entire range of edge density. We specifically focus on the locations of the zeros of the polynomial in the complex plane. The results indicate that the chromatic zeros of random graphs have a very consistent layout. In particular, the crossing point, the point at which the chromatic zeros with non-zero imaginary part approach the real axis, scales linearly with the average degree over most of the density range. While the scaling laws obtained are purely empirical, if they continue to hold in general there are significant implications: the crossing points of chromatic zeros in the thermodynamic limit separate systems with zero ground state entropy from systems with positive ground state entropy, the latter an exception to the third law of thermodynamics.

  13. Commuting graphs of matrix algebras

    International Nuclear Information System (INIS)

    Akbari, S.; Bidkhori, H.; Mohammadian, A.

    2006-08-01

    The commuting graph of a ring R, denoted by Γ(R), is a graph whose vertices are all non- central elements of R and two distinct vertices x and y are adjacent if and only if xy = yx. The commuting graph of a group G, denoted by Γ(G), is similarly defined. In this paper we investigate some graph theoretic properties of Γ(M n (F)), where F is a field and n ≥ 2. Also we study the commuting graphs of some classical groups such as GL n (F) and SL n (F). We show that Γ(M n (F)) is a connected graph if and only if every field extension of F of degree n contains a proper intermediate field. We prove that apart from finitely many fields, a similar result is true for Γ(GL n (F)) and Γ(SL n (F)). Also we show that for two fields E and F and integers m, n ≥> 2, if Γ(M m (E)) ≅ Γ(M n (F)), then m = n and vertical bar E vertical bar = vertical bar F vertical bar. (author)

  14. The index-based subgraph matching algorithm (ISMA: fast subgraph enumeration in large networks using optimized search trees.

    Directory of Open Access Journals (Sweden)

    Sofie Demeyer

    Full Text Available Subgraph matching algorithms are designed to find all instances of predefined subgraphs in a large graph or network and play an important role in the discovery and analysis of so-called network motifs, subgraph patterns which occur more often than expected by chance. We present the index-based subgraph matching algorithm (ISMA, a novel tree-based algorithm. ISMA realizes a speedup compared to existing algorithms by carefully selecting the order in which the nodes of a query subgraph are investigated. In order to achieve this, we developed a number of data structures and maximally exploited symmetry characteristics of the subgraph. We compared ISMA to a naive recursive tree-based algorithm and to a number of well-known subgraph matching algorithms. Our algorithm outperforms the other algorithms, especially on large networks and with large query subgraphs. An implementation of ISMA in Java is freely available at http://sourceforge.net/projects/isma/.

  15. The Index-Based Subgraph Matching Algorithm (ISMA): Fast Subgraph Enumeration in Large Networks Using Optimized Search Trees

    Science.gov (United States)

    Demeyer, Sofie; Michoel, Tom; Fostier, Jan; Audenaert, Pieter; Pickavet, Mario; Demeester, Piet

    2013-01-01

    Subgraph matching algorithms are designed to find all instances of predefined subgraphs in a large graph or network and play an important role in the discovery and analysis of so-called network motifs, subgraph patterns which occur more often than expected by chance. We present the index-based subgraph matching algorithm (ISMA), a novel tree-based algorithm. ISMA realizes a speedup compared to existing algorithms by carefully selecting the order in which the nodes of a query subgraph are investigated. In order to achieve this, we developed a number of data structures and maximally exploited symmetry characteristics of the subgraph. We compared ISMA to a naive recursive tree-based algorithm and to a number of well-known subgraph matching algorithms. Our algorithm outperforms the other algorithms, especially on large networks and with large query subgraphs. An implementation of ISMA in Java is freely available at http://sourceforge.net/projects/isma/. PMID:23620730

  16. Graph Quasicontinuous Functions and Densely Continuous Forms

    Directory of Open Access Journals (Sweden)

    Lubica Hola

    2017-07-01

    Full Text Available Let $X, Y$ be topological spaces. A function $f: X \\to Y$ is said to be graph quasicontinuous if there is a quasicontinuous function $g: X \\to Y$ with the graph of $g$ contained in the closure of the graph of $f$. There is a close relation between the notions of graph quasicontinuous functions and minimal usco maps as well as the notions of graph quasicontinuous functions and densely continuous forms. Every function with values in a compact Hausdorff space is graph quasicontinuous; more generally every locally compact function is graph quasicontinuous.

  17. MetricForensics: A Multi-Level Approach for Mining Volatile Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, Keith [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Eliassi-Rad, Tina [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Faloutsos, Christos [Carnegie Mellon Univ., Pittsburgh, PA (United States); Akoglu, Leman [Carnegie Mellon Univ., Pittsburgh, PA (United States); Li, Lei [Carnegie Mellon Univ., Pittsburgh, PA (United States); Maruhashi, Koji [Fujitsu Laboratories Ltd., Kanagawa (Japan); Prakash, B. Aditya [Carnegie Mellon Univ., Pittsburgh, PA (United States); Tong, H [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    2010-02-08

    Advances in data collection and storage capacity have made it increasingly possible to collect highly volatile graph data for analysis. Existing graph analysis techniques are not appropriate for such data, especially in cases where streaming or near-real-time results are required. An example that has drawn significant research interest is the cyber-security domain, where internet communication traces are collected and real-time discovery of events, behaviors, patterns and anomalies is desired. We propose MetricForensics, a scalable framework for analysis of volatile graphs. MetricForensics combines a multi-level “drill down" approach, a collection of user-selected graph metrics and a collection of analysis techniques. At each successive level, more sophisticated metrics are computed and the graph is viewed at a finer temporal resolution. In this way, MetricForensics scales to highly volatile graphs by only allocating resources for computationally expensive analysis when an interesting event is discovered at a coarser resolution first. We test MetricForensics on three real-world graphs: an enterprise IP trace, a trace of legitimate and malicious network traffic from a research institution, and the MIT Reality Mining proximity sensor data. Our largest graph has »3M vertices and »32M edges, spanning 4:5 days. The results demonstrate the scalability and capability of MetricForensics in analyzing volatile graphs; and highlight four novel phenomena in such graphs: elbows, broken correlations, prolonged spikes, and strange stars.

  18. An original approach to the mathematical concept of graph from braid crafts

    Directory of Open Access Journals (Sweden)

    Albanese Veronica

    2016-01-01

    Full Text Available In previous researches we found that a community of Argentinean artisans models its own practices of braiding using graphs. Inspired by these findings, we designed an educational activity to introduce the concept of graphs. The study of graphs helps students to develop combinatorial and systematic thinking as well as skills to model reality and abstract and generalize patterns from particular situations. The tasks proposed aim to construct the concept of graphs, then identify characteristics that allow some graphs to be models of braids and finally use them to invent more graphs for new braids. The activity performed in a secondary school teachers’ educational course, had quite satisfactory results due to the number of braids invented and the small amount of mistakes made by the participants.

  19. Schur complements of matrices with acyclic bipartite graphs

    DEFF Research Database (Denmark)

    Britz, Thomas Johann; Olesky, D.D.; van den Driessche, P.

    2005-01-01

    Bipartite graphs are used to describe the generalized Schur complements of real matrices having nos quare submatrix with two or more nonzero diagonals. For any matrix A with this property, including any nearly reducible matrix, the sign pattern of each generalized Schur complement is shown to be ...

  20. Interactive Graph Layout of a Million Nodes

    OpenAIRE

    Peng Mi; Maoyuan Sun; Moeti Masiane; Yong Cao; Chris North

    2016-01-01

    Sensemaking of large graphs, specifically those with millions of nodes, is a crucial task in many fields. Automatic graph layout algorithms, augmented with real-time human-in-the-loop interaction, can potentially support sensemaking of large graphs. However, designing interactive algorithms to achieve this is challenging. In this paper, we tackle the scalability problem of interactive layout of large graphs, and contribute a new GPU-based force-directed layout algorithm that exploits graph to...

  1. Khovanov homology of graph-links

    Energy Technology Data Exchange (ETDEWEB)

    Nikonov, Igor M [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)

    2012-08-31

    Graph-links arise as the intersection graphs of turning chord diagrams of links. Speaking informally, graph-links provide a combinatorial description of links up to mutations. Many link invariants can be reformulated in the language of graph-links. Khovanov homology, a well-known and useful knot invariant, is defined for graph-links in this paper (in the case of the ground field of characteristic two). Bibliography: 14 titles.

  2. Word Similarity From Dictionaries: Inferring Fuzzy Measures From Fuzzy Graphs

    Directory of Open Access Journals (Sweden)

    Torra

    2008-01-01

    Full Text Available The computation of similarities between words is a basic element of information retrieval systems, when retrieval is not solely based on word matching. In this work we consider a measure between words based on dictionaries. This is achieved assuming that a dictionary is formalized as a fuzzy graph. We show that the approach permits to compute measures not only for pairs of words but for sets of them.

  3. Foods served in child care facilities participating in the Child and Adult Care Food Program: Menu match and agreement with the new meal patterns and best practices

    Science.gov (United States)

    Our objective was to assess the agreement of posted menus with foods served to 3- to 5-year-old children attending federal Child and Adult Care Food Program (CACFP)-enrolled facilities, and the degree to which the facilities met the new meal patterns and best practices. On-site observations and menu...

  4. PRIVATE GRAPHS – ACCESS RIGHTS ON GRAPHS FOR SEAMLESS NAVIGATION

    Directory of Open Access Journals (Sweden)

    W. Dorner

    2016-06-01

    Full Text Available After the success of GNSS (Global Navigational Satellite Systems and navigation services for public streets, indoor seems to be the next big development in navigational services, relying on RTLS – Real Time Locating Services (e.g. WIFI and allowing seamless navigation. In contrast to navigation and routing services on public streets, seamless navigation will cause an additional challenge: how to make routing data accessible to defined users or restrict access rights for defined areas or only to parts of the graph to a defined user group? The paper will present case studies and data from literature, where seamless and especially indoor navigation solutions are presented (hospitals, industrial complexes, building sites, but the problem of restricted access rights was only touched from a real world, but not a technical perspective. The analysis of case studies will show, that the objective of navigation and the different target groups for navigation solutions will demand well defined access rights and require solutions, how to make only parts of a graph to a user or application available to solve a navigational task. The paper will therefore introduce the concept of private graphs, which is defined as a graph for navigational purposes covering the street, road or floor network of an area behind a public street and suggest different approaches how to make graph data for navigational purposes available considering access rights and data protection, privacy and security issues as well.

  5. Geometric covers, graph orientations, counter games

    DEFF Research Database (Denmark)

    Berglin, Edvin

    -directed graph is dynamic (can be altered by some outside actor), some orientations may need to be reversed in order to maintain the low out-degree. We present a new algorithm that is simpler than earlier work, yet matches or outperforms the efficiency of these results with very few exceptions. Counter games...... example is Line Cover, also known as Point-Line Cover, where a set of points in a geometric space are to be covered by placing a restricted number of lines. We present new FPT algorithms for the sub-family Curve Cover (which includes Line Cover), as well as for Hyperplane Cover restricted to R 3 (i...... are a type of abstract game played over a set of counters holding values, and these values may be moved between counters according to some set of rules. Typically they are played between two players: the adversary who tries to concentrate the greatest value possible in a single counter, and the benevolent...

  6. Query Optimizations over Decentralized RDF Graphs

    KAUST Repository

    Abdelaziz, Ibrahim

    2017-05-18

    Applications in life sciences, decentralized social networks, Internet of Things, and statistical linked dataspaces integrate data from multiple decentralized RDF graphs via SPARQL queries. Several approaches have been proposed to optimize query processing over a small number of heterogeneous data sources by utilizing schema information. In the case of schema similarity and interlinks among sources, these approaches cause unnecessary data retrieval and communication, leading to poor scalability and response time. This paper addresses these limitations and presents Lusail, a system for scalable and efficient SPARQL query processing over decentralized graphs. Lusail achieves scalability and low query response time through various optimizations at compile and run times. At compile time, we use a novel locality-aware query decomposition technique that maximizes the number of query triple patterns sent together to a source based on the actual location of the instances satisfying these triple patterns. At run time, we use selectivity-awareness and parallel query execution to reduce network latency and to increase parallelism by delaying the execution of subqueries expected to return large results. We evaluate Lusail using real and synthetic benchmarks, with data sizes up to billions of triples on an in-house cluster and a public cloud. We show that Lusail outperforms state-of-the-art systems by orders of magnitude in terms of scalability and response time.

  7. Label-based routing for a family of scale-free, modular, planar and unclustered graphs

    International Nuclear Information System (INIS)

    Comellas, Francesc; Miralles, Alicia

    2011-01-01

    We give an optimal labeling and routing algorithm for a family of scale-free, modular and planar graphs with zero clustering. The relevant properties of this family match those of some networks associated with technological and biological systems with a low clustering, including some electronic circuits and protein networks. The existence of an efficient routing protocol for this graph model should help when designing communication algorithms in real networks and also in the understanding of their dynamic processes.

  8. Eigenfunction statistics on quantum graphs

    International Nuclear Information System (INIS)

    Gnutzmann, S.; Keating, J.P.; Piotet, F.

    2010-01-01

    We investigate the spatial statistics of the energy eigenfunctions on large quantum graphs. It has previously been conjectured that these should be described by a Gaussian Random Wave Model, by analogy with quantum chaotic systems, for which such a model was proposed by Berry in 1977. The autocorrelation functions we calculate for an individual quantum graph exhibit a universal component, which completely determines a Gaussian Random Wave Model, and a system-dependent deviation. This deviation depends on the graph only through its underlying classical dynamics. Classical criteria for quantum universality to be met asymptotically in the large graph limit (i.e. for the non-universal deviation to vanish) are then extracted. We use an exact field theoretic expression in terms of a variant of a supersymmetric σ model. A saddle-point analysis of this expression leads to the estimates. In particular, intensity correlations are used to discuss the possible equidistribution of the energy eigenfunctions in the large graph limit. When equidistribution is asymptotically realized, our theory predicts a rate of convergence that is a significant refinement of previous estimates. The universal and system-dependent components of intensity correlation functions are recovered by means of an exact trace formula which we analyse in the diagonal approximation, drawing in this way a parallel between the field theory and semiclassics. Our results provide the first instance where an asymptotic Gaussian Random Wave Model has been established microscopically for eigenfunctions in a system with no disorder.

  9. Box graphs and resolutions I

    Directory of Open Access Journals (Sweden)

    Andreas P. Braun

    2016-04-01

    Full Text Available Box graphs succinctly and comprehensively characterize singular fibers of elliptic fibrations in codimension two and three, as well as flop transitions connecting these, in terms of representation theoretic data. We develop a framework that provides a systematic map between a box graph and a crepant algebraic resolution of the singular elliptic fibration, thus allowing an explicit construction of the fibers from a singular Weierstrass or Tate model. The key tool is what we call a fiber face diagram, which shows the relevant information of a (partial toric triangulation and allows the inclusion of more general algebraic blowups. We shown that each such diagram defines a sequence of weighted algebraic blowups, thus providing a realization of the fiber defined by the box graph in terms of an explicit resolution. We show this correspondence explicitly for the case of SU(5 by providing a map between box graphs and fiber faces, and thereby a sequence of algebraic resolutions of the Tate model, which realizes each of the box graphs.

  10. Degree-based graph construction

    International Nuclear Information System (INIS)

    Kim, Hyunju; Toroczkai, Zoltan; Erdos, Peter L; Miklos, Istvan; Szekely, Laszlo A

    2009-01-01

    Degree-based graph construction is a ubiquitous problem in network modelling (Newman et al 2006 The Structure and Dynamics of Networks (Princeton Studies in Complexity) (Princeton, NJ: Princeton University Press), Boccaletti et al 2006 Phys. Rep. 424 175), ranging from social sciences to chemical compounds and biochemical reaction networks in the cell. This problem includes existence, enumeration, exhaustive construction and sampling questions with aspects that are still open today. Here we give necessary and sufficient conditions for a sequence of nonnegative integers to be realized as a simple graph's degree sequence, such that a given (but otherwise arbitrary) set of connections from an arbitrarily given node is avoided. We then use this result to present a swap-free algorithm that builds all simple graphs realizing a given degree sequence. In a wider context, we show that our result provides a greedy construction method to build all the f-factor subgraphs (Tutte 1952 Can. J. Math. 4 314) embedded within K n setmn S k , where K n is the complete graph and S k is a star graph centred on one of the nodes. (fast track communication)

  11. Hierarchical organisation of causal graphs

    International Nuclear Information System (INIS)

    Dziopa, P.

    1993-01-01

    This paper deals with the design of a supervision system using a hierarchy of models formed by graphs, in which the variables are the nodes and the causal relations between the variables of the arcs. To obtain a representation of the variables evolutions which contains only the relevant features of their real evolutions, the causal relations are completed with qualitative transfer functions (QTFs) which produce roughly the behaviour of the classical transfer functions. Major improvements have been made in the building of the hierarchical organization. First, the basic variables of the uppermost level and the causal relations between them are chosen. The next graph is built by adding intermediary variables to the upper graph. When the undermost graph has been built, the transfer functions parameters corresponding to its causal relations are identified. The second task consists in the upwelling of the information from the undermost graph to the uppermost one. A fusion procedure of the causal relations has been designed to compute the QFTs relevant for each level. This procedure aims to reduce the number of parameters needed to represent an evolution at a high level of abstraction. These techniques have been applied to the hierarchical modelling of nuclear process. (authors). 8 refs., 12 figs

  12. Integer Flows and Circuit Covers of Graphs and Signed Graphs

    Science.gov (United States)

    Cheng, Jian

    The work in Chapter 2 is motivated by Tutte and Jaeger's pioneering work on converting modulo flows into integer-valued flows for ordinary graphs. For a signed graphs (G, sigma), we first prove that for each k ∈ {2, 3}, if (G, sigma) is (k - 1)-edge-connected and contains an even number of negative edges when k = 2, then every modulo k-flow of (G, sigma) can be converted into an integer-valued ( k + 1)-ow with a larger or the same support. We also prove that if (G, sigma) is odd-(2p+1)-edge-connected, then (G, sigma) admits a modulo circular (2 + 1/ p)-flows if and only if it admits an integer-valued circular (2 + 1/p)-flows, which improves all previous result by Xu and Zhang (DM2005), Schubert and Steffen (EJC2015), and Zhu (JCTB2015). Shortest circuit cover conjecture is one of the major open problems in graph theory. It states that every bridgeless graph G contains a set of circuits F such that each edge is contained in at least one member of F and the length of F is at most 7/5∥E(G)∥. This concept was recently generalized to signed graphs by Macajova et al. (JGT2015). In Chapter 3, we improve their upper bound from 11∥E( G)∥ to 14/3 ∥E(G)∥, and if G is 2-edgeconnected and has even negativeness, then it can be further reduced to 11/3 ∥E(G)∥. Tutte's 3-flow conjecture has been studied by many graph theorists in the last several decades. As a new approach to this conjecture, DeVos and Thomassen considered the vectors as ow values and found that there is a close relation between vector S1-flows and integer 3-NZFs. Motivated by their observation, in Chapter 4, we prove that if a graph G admits a vector S1-flow with rank at most two, then G admits an integer 3-NZF. The concept of even factors is highly related to the famous Four Color Theorem. We conclude this dissertation in Chapter 5 with an improvement of a recent result by Chen and Fan (JCTB2016) on the upperbound of even factors. We show that if a graph G contains an even factor, then it

  13. STRUCTURAL ANNOTATION OF EM IMAGES BY GRAPH CUT

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Hang; Auer, Manfred; Parvin, Bahram

    2009-05-08

    Biological images have the potential to reveal complex signatures that may not be amenable to morphological modeling in terms of shape, location, texture, and color. An effective analytical method is to characterize the composition of a specimen based on user-defined patterns of texture and contrast formation. However, such a simple requirement demands an improved model for stability and robustness. Here, an interactive computational model is introduced for learning patterns of interest by example. The learned patterns bound an active contour model in which the traditional gradient descent optimization is replaced by the more efficient optimization of the graph cut methods. First, the energy function is defined according to the curve evolution. Next, a graph is constructed with weighted edges on the energy function and is optimized with the graph cut algorithm. As a result, the method combines the advantages of the level set method and graph cut algorithm, i.e.,"topological" invariance and computational efficiency. The technique is extended to the multi-phase segmentation problem; the method is validated on synthetic images and then applied to specimens imaged by transmission electron microscopy(TEM).

  14. Graph modeling systems and methods

    Science.gov (United States)

    Neergaard, Mike

    2015-10-13

    An apparatus and a method for vulnerability and reliability modeling are provided. The method generally includes constructing a graph model of a physical network using a computer, the graph model including a plurality of terminating vertices to represent nodes in the physical network, a plurality of edges to represent transmission paths in the physical network, and a non-terminating vertex to represent a non-nodal vulnerability along a transmission path in the physical network. The method additionally includes evaluating the vulnerability and reliability of the physical network using the constructed graph model, wherein the vulnerability and reliability evaluation includes a determination of whether each terminating and non-terminating vertex represents a critical point of failure. The method can be utilized to evaluate wide variety of networks, including power grid infrastructures, communication network topologies, and fluid distribution systems.

  15. On the graph turnpike problem

    KAUST Repository

    Feder, Tomá s; Motwani, Rajeev

    2009-01-01

    Results on graph turnpike problem without distinctness, including its NP-completeness, and an O(m+n log n) algorithm, is presented. The usual turnpike problem has all pairwise distances given, but does not specify which pair of vertices w e corresponds to. There are two other problems that can be viewed as special cases of the graph turnpike problem, including the bandwidth problem and the low-distortion graph embedding problem. The aim for the turnpike problem in the NP-complete is to orient the edges with weights w i in either direction so that when the whole cycle is transversed in the real line, it returns to a chosen starting point for the cycle. An instance of the turnpike problem with or without distinctness is uniquely mappable if there exists at most one solution up to translation and choice of orientation.

  16. On the graph turnpike problem

    KAUST Repository

    Feder, Tomás

    2009-06-01

    Results on graph turnpike problem without distinctness, including its NP-completeness, and an O(m+n log n) algorithm, is presented. The usual turnpike problem has all pairwise distances given, but does not specify which pair of vertices w e corresponds to. There are two other problems that can be viewed as special cases of the graph turnpike problem, including the bandwidth problem and the low-distortion graph embedding problem. The aim for the turnpike problem in the NP-complete is to orient the edges with weights w i in either direction so that when the whole cycle is transversed in the real line, it returns to a chosen starting point for the cycle. An instance of the turnpike problem with or without distinctness is uniquely mappable if there exists at most one solution up to translation and choice of orientation.

  17. Negation switching invariant signed graphs

    Directory of Open Access Journals (Sweden)

    Deepa Sinha

    2014-04-01

    Full Text Available A signed graph (or, $sigraph$ in short is a graph G in which each edge x carries a value $\\sigma(x \\in \\{-, +\\}$ called its sign. Given a sigraph S, the negation $\\eta(S$ of the sigraph S is a sigraph obtained from S by reversing the sign of every edge of S. Two sigraphs $S_{1}$ and $S_{2}$ on the same underlying graph are switching equivalent if it is possible to assign signs `+' (`plus' or `-' (`minus' to vertices of $S_{1}$ such that by reversing the sign of each of its edges that has received opposite signs at its ends, one obtains $S_{2}$. In this paper, we characterize sigraphs which are negation switching invariant and also see for what sigraphs, S and $\\eta (S$ are signed isomorphic.

  18. Quantum snake walk on graphs

    International Nuclear Information System (INIS)

    Rosmanis, Ansis

    2011-01-01

    I introduce a continuous-time quantum walk on graphs called the quantum snake walk, the basis states of which are fixed-length paths (snakes) in the underlying graph. First, I analyze the quantum snake walk on the line, and I show that, even though most states stay localized throughout the evolution, there are specific states that most likely move on the line as wave packets with momentum inversely proportional to the length of the snake. Next, I discuss how an algorithm based on the quantum snake walk might potentially be able to solve an extended version of the glued trees problem, which asks to find a path connecting both roots of the glued trees graph. To the best of my knowledge, no efficient quantum algorithm solving this problem is known yet.

  19. Total Domination Versus Paired-Domination in Regular Graphs

    Directory of Open Access Journals (Sweden)

    Cyman Joanna

    2018-05-01

    Full Text Available A subset S of vertices of a graph G is a dominating set of G if every vertex not in S has a neighbor in S, while S is a total dominating set of G if every vertex has a neighbor in S. If S is a dominating set with the additional property that the subgraph induced by S contains a perfect matching, then S is a paired-dominating set. The domination number, denoted γ(G, is the minimum cardinality of a dominating set of G, while the minimum cardinalities of a total dominating set and paired-dominating set are the total domination number, γt(G, and the paired-domination number, γpr(G, respectively. For k ≥ 2, let G be a connected k-regular graph. It is known [Schaudt, Total domination versus paired domination, Discuss. Math. Graph Theory 32 (2012 435–447] that γpr(G/γt(G ≤ (2k/(k+1. In the special case when k = 2, we observe that γpr(G/γt(G ≤ 4/3, with equality if and only if G ≅ C5. When k = 3, we show that γpr(G/γt(G ≤ 3/2, with equality if and only if G is the Petersen graph. More generally for k ≥ 2, if G has girth at least 5 and satisfies γpr(G/γt(G = (2k/(k + 1, then we show that G is a diameter-2 Moore graph. As a consequence of this result, we prove that for k ≥ 2 and k ≠ 57, if G has girth at least 5, then γpr(G/γt(G ≤ (2k/(k +1, with equality if and only if k = 2 and G ≅ C5 or k = 3 and G is the Petersen graph.

  20. Exploring the Role of the Food Environment on Food Shopping Patterns in Philadelphia, PA, USA: A Semiquantitative Comparison of Two Matched Neighborhood Groups

    Directory of Open Access Journals (Sweden)

    Amy Hillier

    2013-01-01

    Full Text Available Increasing research has focused on the built food environment and nutrition-related outcomes, yet what constitutes a food environment and how this environment influences individual behavior still remain unclear. This study assesses whether travel mode and distance to food shopping venues differ among individuals in varying food environments and whether individual- and household-level factors are associated with food shopping patterns. Fifty neighbors who share a traditionally defined food environment (25 in an unfavorable environment and 25 in a favorable environment were surveyed using a mix of close- and open-ended survey questions. Food shopping patterns were mapped using Geographic Information Systems (GIS. Stores visited were beyond the 0.5-mile (805 meters radius traditionally used to represent the extent of an individual’s food environment in an urban area. We found no significant difference in shopping frequency or motivating factor behind store choice between the groups. No differences existed between the two groups for big food shopping trips. For small trips, individuals in the favorable food environment traveled shorter distances and were more likely to walk than drive. Socioeconomic status, including car ownership, education, and income influenced distance traveled. These findings highlight the complexities involved in the study and measurement of food environments.

  1. Exploring the role of the food environment on food shopping patterns in Philadelphia, PA, USA: a semiquantitative comparison of two matched neighborhood groups.

    Science.gov (United States)

    Hirsch, Jana A; Hillier, Amy

    2013-01-14

    Increasing research has focused on the built food environment and nutrition-related outcomes, yet what constitutes a food environment and how this environment influences individual behavior still remain unclear. This study assesses whether travel mode and distance to food shopping venues differ among individuals in varying food environments and whether individual- and household-level factors are associated with food shopping patterns. Fifty neighbors who share a traditionally defined food environment (25 in an unfavorable environment and 25 in a favorable environment) were surveyed using a mix of close- and open-ended survey questions. Food shopping patterns were mapped using Geographic Information Systems (GIS). Stores visited were beyond the 0.5-mile (805 meters) radius traditionally used to represent the extent of an individual's food environment in an urban area. We found no significant difference in shopping frequency or motivating factor behind store choice between the groups. No differences existed between the two groups for big food shopping trips. For small trips, individuals in the favorable food environment traveled shorter distances and were more likely to walk than drive. Socioeconomic status, including car ownership, education, and income influenced distance traveled. These findings highlight the complexities involved in the study and measurement of food environments.

  2. On Graph Rewriting, Reduction and Evaluation

    DEFF Research Database (Denmark)

    Zerny, Ian

    2010-01-01

    We inter-derive two prototypical styles of graph reduction: reduction machines à la Turner and graph rewriting systems à la Barendregt et al. To this end, we adapt Danvy et al.'s mechanical program derivations from the world of terms to the world of graphs. We also outline how to inter-derive a t......We inter-derive two prototypical styles of graph reduction: reduction machines à la Turner and graph rewriting systems à la Barendregt et al. To this end, we adapt Danvy et al.'s mechanical program derivations from the world of terms to the world of graphs. We also outline how to inter...

  3. The fascinating world of graph theory

    CERN Document Server

    Benjamin, Arthur; Zhang, Ping

    2015-01-01

    Graph theory goes back several centuries and revolves around the study of graphs-mathematical structures showing relations between objects. With applications in biology, computer science, transportation science, and other areas, graph theory encompasses some of the most beautiful formulas in mathematics-and some of its most famous problems. The Fascinating World of Graph Theory explores the questions and puzzles that have been studied, and often solved, through graph theory. This book looks at graph theory's development and the vibrant individuals responsible for the field's growth. Introducin

  4. Graph-based modelling in engineering

    CERN Document Server

    Rysiński, Jacek

    2017-01-01

    This book presents versatile, modern and creative applications of graph theory in mechanical engineering, robotics and computer networks. Topics related to mechanical engineering include e.g. machine and mechanism science, mechatronics, robotics, gearing and transmissions, design theory and production processes. The graphs treated are simple graphs, weighted and mixed graphs, bond graphs, Petri nets, logical trees etc. The authors represent several countries in Europe and America, and their contributions show how different, elegant, useful and fruitful the utilization of graphs in modelling of engineering systems can be. .

  5. GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.

    Directory of Open Access Journals (Sweden)

    Rosalba Giugno

    Full Text Available Biological applications, from genomics to ecology, deal with graphs that represents the structure of interactions. Analyzing such data requires searching for subgraphs in collections of graphs. This task is computationally expensive. Even though multicore architectures, from commodity computers to more advanced symmetric multiprocessing (SMP, offer scalable computing power, currently published software implementations for indexing and graph matching are fundamentally sequential. As a consequence, such software implementations (i do not fully exploit available parallel computing power and (ii they do not scale with respect to the size of graphs in the database. We present GRAPES, software for parallel searching on databases of large biological graphs. GRAPES implements a parallel version of well-established graph searching algorithms, and introduces new strategies which naturally lead to a faster parallel searching system especially for large graphs. GRAPES decomposes graphs into subcomponents that can be efficiently searched in parallel. We show the performance of GRAPES on representative biological datasets containing antiviral chemical compounds, DNA, RNA, proteins, protein contact maps and protein interactions networks.

  6. XML Graphs in Program Analysis

    DEFF Research Database (Denmark)

    Møller, Anders; Schwartzbach, Michael Ignatieff

    2007-01-01

    XML graphs have shown to be a simple and effective formalism for representing sets of XML documents in program analysis. It has evolved through a six year period with variants tailored for a range of applications. We present a unified definition, outline the key properties including validation...... of XML graphs against different XML schema languages, and provide a software package that enables others to make use of these ideas. We also survey four very different applications: XML in Java, Java Servlets and JSP, transformations between XML and non-XML data, and XSLT....

  7. Graph topologies on closed multifunctions

    Directory of Open Access Journals (Sweden)

    Giuseppe Di Maio

    2003-10-01

    Full Text Available In this paper we study function space topologies on closed multifunctions, i.e. closed relations on X x Y using various hypertopologies. The hypertopologies are in essence, graph topologies i.e topologies on functions considered as graphs which are subsets of X x Y . We also study several topologies, including one that is derived from the Attouch-Wets filter on the range. We state embedding theorems which enable us to generalize and prove some recent results in the literature with the use of known results in the hyperspace of the range space and in the function space topologies of ordinary functions.

  8. Cyclic graphs and Apery's theorem

    International Nuclear Information System (INIS)

    Sorokin, V N

    2002-01-01

    This is a survey of results about the behaviour of Hermite-Pade approximants for graphs of Markov functions, and a survey of interpolation problems leading to Apery's result about the irrationality of the value ζ(3) of the Riemann zeta function. The first example is given of a cyclic graph for which the Hermite-Pade problem leads to Apery's theorem. Explicit formulae for solutions are obtained, namely, Rodrigues' formulae and integral representations. The asymptotic behaviour of the approximants is studied, and recurrence formulae are found

  9. Interacting particle systems on graphs

    Science.gov (United States)

    Sood, Vishal

    In this dissertation, the dynamics of socially or biologically interacting populations are investigated. The individual members of the population are treated as particles that interact via links on a social or biological network represented as a graph. The effect of the structure of the graph on the properties of the interacting particle system is studied using statistical physics techniques. In the first chapter, the central concepts of graph theory and social and biological networks are presented. Next, interacting particle systems that are drawn from physics, mathematics and biology are discussed in the second chapter. In the third chapter, the random walk on a graph is studied. The mean time for a random walk to traverse between two arbitrary sites of a random graph is evaluated. Using an effective medium approximation it is found that the mean first-passage time between pairs of sites, as well as all moments of this first-passage time, are insensitive to the density of links in the graph. The inverse of the mean-first passage time varies non-monotonically with the density of links near the percolation transition of the random graph. Much of the behavior can be understood by simple heuristic arguments. Evolutionary dynamics, by which mutants overspread an otherwise uniform population on heterogeneous graphs, are studied in the fourth chapter. Such a process underlies' epidemic propagation, emergence of fads, social cooperation or invasion of an ecological niche by a new species. The first part of this chapter is devoted to neutral dynamics, in which the mutant genotype does not have a selective advantage over the resident genotype. The time to extinction of one of the two genotypes is derived. In the second part of this chapter, selective advantage or fitness is introduced such that the mutant genotype has a higher birth rate or a lower death rate. This selective advantage leads to a dynamical competition in which selection dominates for large populations

  10. Optimal background matching camouflage.

    Science.gov (United States)

    Michalis, Constantine; Scott-Samuel, Nicholas E; Gibson, David P; Cuthill, Innes C

    2017-07-12

    Background matching is the most familiar and widespread camouflage strategy: avoiding detection by having a similar colour and pattern to the background. Optimizing background matching is straightforward in a homogeneous environment, or when the habitat has very distinct sub-types and there is divergent selection leading to polymorphism. However, most backgrounds have continuous variation in colour and texture, so what is the best solution? Not all samples of the background are likely to be equally inconspicuous, and laboratory experiments on birds and humans support this view. Theory suggests that the most probable background sample (in the statistical sense), at the size of the prey, would, on average, be the most cryptic. We present an analysis, based on realistic assumptions about low-level vision, that estimates the distribution of background colours and visual textures, and predicts the best camouflage. We present data from a field experiment that tests and supports our predictions, using artificial moth-like targets under bird predation. Additionally, we present analogous data for humans, under tightly controlled viewing conditions, searching for targets on a computer screen. These data show that, in the absence of predator learning, the best single camouflage pattern for heterogeneous backgrounds is the most probable sample. © 2017 The Authors.

  11. Techniques Used in String Matching for Network Security

    OpenAIRE

    Jamuna Bhandari

    2014-01-01

    String matching also known as pattern matching is one of primary concept for network security. In this area the effectiveness and efficiency of string matching algorithms is important for applications in network security such as network intrusion detection, virus detection, signature matching and web content filtering system. This paper presents brief review on some of string matching techniques used for network security.

  12. Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

    Science.gov (United States)

    Lin, Yi-Hsuan; Brady, Jacob P.; Forman-Kay, Julie D.; Chan, Hue Sun

    2017-11-01

    Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartments. Pertinent physics was addressed recently by applying random-phase-approximation (RPA) polymer theory to electrostatics, which is a major energetic component governing IDP phase properties. RPA accounts for charge patterns and thus has advantages over Flory-Huggins (FH) and Overbeek-Voorn mean-field theories. To make progress toward deciphering the phase behaviors of multiple IDP sequences, the RPA formulation for one IDP species plus solvent is hereby extended to treat polyampholyte solutions containing two IDP species plus solvent. The new formulation generally allows for binary coexistence of two phases, each containing a different set of volume fractions ({φ }1,{φ }2) for the two different IDP sequences. The asymmetry between the two predicted coexisting phases with regard to their {φ }1/{φ }2 ratios for the two sequences increases with increasing mismatch between their charge patterns. This finding points to a multivalent, stochastic, ‘fuzzy’ mode of molecular recognition that helps populate various IDP sequences differentially into separate phase compartments. An intuitive illustration of this trend is provided by FH models, whereby a hypothetical case of ternary coexistence is also explored. Augmentations of the present RPA theory with a relative permittivity {ɛ }{{r}}(φ ) that depends on IDP volume fraction φ ={φ }1+{φ }2 lead to higher propensities to phase separate, in line with the case with one IDP species we studied previously. Notably, the cooperative, phase-separation-enhancing effects predicted by the prescriptions for {ɛ }{{r}}(φ ) we deem physically plausible are much more prominent than that entailed by common

  13. Multiple graph regularized protein domain ranking

    KAUST Repository

    Wang, Jim Jing-Yan

    2012-11-19

    Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

  14. Multiple graph regularized protein domain ranking

    KAUST Repository

    Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

    2012-01-01

    Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

  15. Multiple graph regularized protein domain ranking.

    Science.gov (United States)

    Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

    2012-11-19

    Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

  16. Multiple graph regularized protein domain ranking

    Directory of Open Access Journals (Sweden)

    Wang Jim

    2012-11-01

    Full Text Available Abstract Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

  17. Hemithoracic Intensity Modulated Radiation Therapy After Pleurectomy/Decortication for Malignant Pleural Mesothelioma: Toxicity, Patterns of Failure, and a Matched Survival Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chance, William W. [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Rice, David C. [Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Allen, Pamela K. [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Tsao, Anne S. [Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Fontanilla, Hiral P. [Princeton Radiation Oncology, Monroe Township, New Jersey (United States); Liao, Zhongxing; Chang, Joe Y.; Tang, Chad; Pan, Hubert Y.; Welsh, James W. [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Mehran, Reza J. [Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Gomez, Daniel R., E-mail: dgomez@mdanderson.org [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States)

    2015-01-01

    Purpose: To investigate safety, efficacy, and recurrence after hemithoracic intensity modulated radiation therapy after pleurectomy/decortication (PD-IMRT) and after extrapleural pneumonectomy (EPP-IMRT). Methods and Materials: In 2009-2013, 24 patients with mesothelioma underwent PD-IMRT to the involved hemithorax to a dose of 45 Gy, with an optional integrated boost; 22 also received chemotherapy. Toxicity was scored with the Common Terminology Criteria for Adverse Events v4.0. Pulmonary function was compared at baseline, after surgery, and after IMRT. Kaplan-Meier analysis was used to calculate overall survival (OS), progression-free survival (PFS), time to locoregional failure, and time to distant metastasis. Failures were in-field, marginal, or out of field. Outcomes were compared with those of 24 patients, matched for age, nodal status, performance status, and chemotherapy, who had received EPP-IMRT. Results: Median follow-up time was 12.2 months. Grade 3 toxicity rates were 8% skin and 8% pulmonary. Pulmonary function declined from baseline to after surgery (by 21% for forced vital capacity, 16% for forced expiratory volume in 1 second, and 19% for lung diffusion of carbon monoxide [P for all = .01]) and declined still further after IMRT (by 31% for forced vital capacity [P=.02], 25% for forced expiratory volume in 1 second [P=.01], and 30% for lung diffusion of carbon monoxide [P=.01]). The OS and PFS rates were 76% and 67%, respectively, at 1 year and 56% and 34% at 2 years. Median OS (28.4 vs 14.2 months, P=.04) and median PFS (16.4 vs 8.2 months, P=.01) favored PD-IMRT versus EPP-IMRT. No differences were found in grade 4-5 toxicity (0 of 24 vs 3 of 24, P=.23), median time to locoregional failure (18.7 months vs not reached, P not calculable), or median time to distant metastasis (18.8 vs 11.8 months, P=.12). Conclusions: Hemithoracic intensity modulated radiation therapy after pleurectomy/decortication produced little high-grade toxicity but

  18. Constructing Knowledge Graphs of Depression

    NARCIS (Netherlands)

    Huang, Zhisheng; Yang, Jie; van Harmelen, Frank; Hu, Qing

    2017-01-01

    Knowledge Graphs have been shown to be useful tools for integrating multiple medical knowledge sources, and to support such tasks as medical decision making, literature retrieval, determining healthcare quality indicators, co-morbodity analysis and many others. A large number of medical knowledge

  19. Partitioning graphs into connected parts

    NARCIS (Netherlands)

    Hof, van 't P.; Paulusma, D.; Woeginger, G.J.; Frid, A.; Morozov, A.S.; Rybalchenko, A.; Wagner, K.W.

    2009-01-01

    The 2-DISJOINT CONNECTED SUBGRAPHS problem asks if a given graph has two vertex-disjoint connected subgraphs containing pre-specified sets of vertices. We show that this problem is NP-complete even if one of the sets has cardinality 2. The LONGEST PATH CONTRACTIBILITY problem asks for the largest

  20. Isoperimetric inequalities for minimal graphs

    International Nuclear Information System (INIS)

    Pacelli Bessa, G.; Montenegro, J.F.

    2007-09-01

    Based on Markvorsen and Palmer's work on mean time exit and isoperimetric inequalities we establish slightly better isoperimetric inequalities and mean time exit estimates for minimal graphs in N x R. We also prove isoperimetric inequalities for submanifolds of Hadamard spaces with tamed second fundamental form. (author)

  1. Ancestral Genres of Mathematical Graphs

    Science.gov (United States)

    Gerofsky, Susan

    2011-01-01

    Drawing from sources in gesture studies, cognitive science, the anthropology of religion and art/architecture history, this article explores cultural, bodily and cosmological resonances carried (unintentionally) by mathematical graphs on Cartesian coordinates. Concepts of asymmetric bodily spaces, grids, orthogonality, mapping and sacred spaces…

  2. Humidity Graphs for All Seasons.

    Science.gov (United States)

    Esmael, F.

    1982-01-01

    In a previous article in this journal (Vol. 17, p358, 1979), a wet-bulb depression table was recommended for two simple experiments to determine relative humidity. However, the use of a graph is suggested because it gives the relative humidity directly from the wet and dry bulb readings. (JN)

  3. Graph Model Based Indoor Tracking

    DEFF Research Database (Denmark)

    Jensen, Christian Søndergaard; Lu, Hua; Yang, Bin

    2009-01-01

    The tracking of the locations of moving objects in large indoor spaces is important, as it enables a range of applications related to, e.g., security and indoor navigation and guidance. This paper presents a graph model based approach to indoor tracking that offers a uniform data management...

  4. A graph with fractional revival

    Science.gov (United States)

    Bernard, Pierre-Antoine; Chan, Ada; Loranger, Érika; Tamon, Christino; Vinet, Luc

    2018-02-01

    An example of a graph that admits balanced fractional revival between antipodes is presented. It is obtained by establishing the correspondence between the quantum walk on a hypercube where the opposite vertices across the diagonals of each face are connected and, the coherent transport of single excitations in the extension of the Krawtchouk spin chain with next-to-nearest neighbour interactions.

  5. Fixation Time for Evolutionary Graphs

    Science.gov (United States)

    Nie, Pu-Yan; Zhang, Pei-Ai

    Evolutionary graph theory (EGT) is recently proposed by Lieberman et al. in 2005. EGT is successful for explaining biological evolution and some social phenomena. It is extremely important to consider the time of fixation for EGT in many practical problems, including evolutionary theory and the evolution of cooperation. This study characterizes the time to asymptotically reach fixation.

  6. Mathematical Minute: Rotating a Function Graph

    Science.gov (United States)

    Bravo, Daniel; Fera, Joseph

    2013-01-01

    Using calculus only, we find the angles you can rotate the graph of a differentiable function about the origin and still obtain a function graph. We then apply the solution to odd and even degree polynomials.

  7. Towards a theory of geometric graphs

    CERN Document Server

    Pach, Janos

    2004-01-01

    The early development of graph theory was heavily motivated and influenced by topological and geometric themes, such as the Konigsberg Bridge Problem, Euler's Polyhedral Formula, or Kuratowski's characterization of planar graphs. In 1936, when Denes Konig published his classical Theory of Finite and Infinite Graphs, the first book ever written on the subject, he stressed this connection by adding the subtitle Combinatorial Topology of Systems of Segments. He wanted to emphasize that the subject of his investigations was very concrete: planar figures consisting of points connected by straight-line segments. However, in the second half of the twentieth century, graph theoretical research took an interesting turn. In the most popular and most rapidly growing areas (the theory of random graphs, Ramsey theory, extremal graph theory, algebraic graph theory, etc.), graphs were considered as abstract binary relations rather than geometric objects. Many of the powerful techniques developed in these fields have been su...

  8. Bounds on Gromov hyperbolicity constant in graphs

    Indian Academy of Sciences (India)

    Infinite graphs; Cartesian product graphs; independence number; domin- ation number; geodesics ... the secure transmission of information through the internet (see [15, 16]). In particular, ..... In particular, δ(G) is an integer multiple of 1/4.

  9. Summary: beyond fault trees to fault graphs

    International Nuclear Information System (INIS)

    Alesso, H.P.; Prassinos, P.; Smith, C.F.

    1984-09-01

    Fault Graphs are the natural evolutionary step over a traditional fault-tree model. A Fault Graph is a failure-oriented directed graph with logic connectives that allows cycles. We intentionally construct the Fault Graph to trace the piping and instrumentation drawing (P and ID) of the system, but with logical AND and OR conditions added. Then we evaluate the Fault Graph with computer codes based on graph-theoretic methods. Fault Graph computer codes are based on graph concepts, such as path set (a set of nodes traveled on a path from one node to another) and reachability (the complete set of all possible paths between any two nodes). These codes are used to find the cut-sets (any minimal set of component failures that will fail the system) and to evaluate the system reliability

  10. Torsional rigidity, isospectrality and quantum graphs

    International Nuclear Information System (INIS)

    Colladay, Don; McDonald, Patrick; Kaganovskiy, Leon

    2017-01-01

    We study torsional rigidity for graph and quantum graph analogs of well-known pairs of isospectral non-isometric planar domains. We prove that such isospectral pairs are distinguished by torsional rigidity. (paper)

  11. [A retrieval method of drug molecules based on graph collapsing].

    Science.gov (United States)

    Qu, J W; Lv, X Q; Liu, Z M; Liao, Y; Sun, P H; Wang, B; Tang, Z

    2018-04-18

    To establish a compact and efficient hypergraph representation and a graph-similarity-based retrieval method of molecules to achieve effective and efficient medicine information retrieval. Chemical structural formula (CSF) was a primary search target as a unique and precise identifier for each compound at the molecular level in the research field of medicine information retrieval. To retrieve medicine information effectively and efficiently, a complete workflow of the graph-based CSF retrieval system was introduced. This system accepted the photos taken from smartphones and the sketches drawn on tablet personal computers as CSF inputs, and formalized the CSFs with the corresponding graphs. Then this paper proposed a compact and efficient hypergraph representation for molecules on the basis of analyzing factors that directly affected the efficiency of graph matching. According to the characteristics of CSFs, a hierarchical collapsing method combining graph isomorphism and frequent subgraph mining was adopted. There was yet a fundamental challenge, subgraph overlapping during the collapsing procedure, which hindered the method from establishing the correct compact hypergraph of an original CSF graph. Therefore, a graph-isomorphism-based algorithm was proposed to select dominant acyclic subgraphs on the basis of overlapping analysis. Finally, the spatial similarity among graphical CSFs was evaluated by multi-dimensional measures of similarity. To evaluate the performance of the proposed method, the proposed system was firstly compared with Wikipedia Chemical Structure Explorer (WCSE), the state-of-the-art system that allowed CSF similarity searching within Wikipedia molecules dataset, on retrieval accuracy. The system achieved higher values on mean average precision, discounted cumulative gain, rank-biased precision, and expected reciprocal rank than WCSE from the top-2 to the top-10 retrieved results. Specifically, the system achieved 10%, 1.41, 6.42%, and 1

  12. Tensor GSVD of Patient- and Platform-Matched Tumor and Normal DNA Copy-Number Profiles Uncovers Chromosome Arm-Wide Patterns of Tumor-Exclusive Platform-Consistent Alterations Encoding for Cell Transformation and Predicting Ovarian Cancer Survival

    Science.gov (United States)

    Sankaranarayanan, Preethi; Schomay, Theodore E.; Aiello, Katherine A.; Alter, Orly

    2015-01-01

    The number of large-scale high-dimensional datasets recording different aspects of a single disease is growing, accompanied by a need for frameworks that can create one coherent model from multiple tensors of matched columns, e.g., patients and platforms, but independent rows, e.g., probes. We define and prove the mathematical properties of a novel tensor generalized singular value decomposition (GSVD), which can simultaneously find the similarities and dissimilarities, i.e., patterns of varying relative significance, between any two such tensors. We demonstrate the tensor GSVD in comparative modeling of patient- and platform-matched but probe-independent ovarian serous cystadenocarcinoma (OV) tumor, mostly high-grade, and normal DNA copy-number profiles, across each chromosome arm, and combination of two arms, separately. The modeling uncovers previously unrecognized patterns of tumor-exclusive platform-consistent co-occurring copy-number alterations (CNAs). We find, first, and validate that each of the patterns across only 7p and Xq, and the combination of 6p+12p, is correlated with a patient’s prognosis, is independent of the tumor’s stage, the best predictor of OV survival to date, and together with stage makes a better predictor than stage alone. Second, these patterns include most known OV-associated CNAs that map to these chromosome arms, as well as several previously unreported, yet frequent focal CNAs. Third, differential mRNA, microRNA, and protein expression consistently map to the DNA CNAs. A coherent picture emerges for each pattern, suggesting roles for the CNAs in OV pathogenesis and personalized therapy. In 6p+12p, deletion of the p21-encoding CDKN1A and p38-encoding MAPK14 and amplification of RAD51AP1 and KRAS encode for human cell transformation, and are correlated with a cell’s immortality, and a patient’s shorter survival time. In 7p, RPA3 deletion and POLD2 amplification are correlated with DNA stability, and a longer survival. In Xq

  13. Tensor GSVD of patient- and platform-matched tumor and normal DNA copy-number profiles uncovers chromosome arm-wide patterns of tumor-exclusive platform-consistent alterations encoding for cell transformation and predicting ovarian cancer survival.

    Directory of Open Access Journals (Sweden)

    Preethi Sankaranarayanan

    Full Text Available The number of large-scale high-dimensional datasets recording different aspects of a single disease is growing, accompanied by a need for frameworks that can create one coherent model from multiple tensors of matched columns, e.g., patients and platforms, but independent rows, e.g., probes. We define and prove the mathematical properties of a novel tensor generalized singular value decomposition (GSVD, which can simultaneously find the similarities and dissimilarities, i.e., patterns of varying relative significance, between any two such tensors. We demonstrate the tensor GSVD in comparative modeling of patient- and platform-matched but probe-independent ovarian serous cystadenocarcinoma (OV tumor, mostly high-grade, and normal DNA copy-number profiles, across each chromosome arm, and combination of two arms, separately. The modeling uncovers previously unrecognized patterns of tumor-exclusive platform-consistent co-occurring copy-number alterations (CNAs. We find, first, and validate that each of the patterns across only 7p and Xq, and the combination of 6p+12p, is correlated with a patient's prognosis, is independent of the tumor's stage, the best predictor of OV survival to date, and together with stage makes a better predictor than stage alone. Second, these patterns include most known OV-associated CNAs that map to these chromosome arms, as well as several previously unreported, yet frequent focal CNAs. Third, differential mRNA, microRNA, and protein expression consistently map to the DNA CNAs. A coherent picture emerges for each pattern, suggesting roles for the CNAs in OV pathogenesis and personalized therapy. In 6p+12p, deletion of the p21-encoding CDKN1A and p38-encoding MAPK14 and amplification of RAD51AP1 and KRAS encode for human cell transformation, and are correlated with a cell's immortality, and a patient's shorter survival time. In 7p, RPA3 deletion and POLD2 amplification are correlated with DNA stability, and a longer survival

  14. Bond graph modeling of centrifugal compression systems

    OpenAIRE

    Uddin, Nur; Gravdahl, Jan Tommy

    2015-01-01

    A novel approach to model unsteady fluid dynamics in a compressor network by using a bond graph is presented. The model is intended in particular for compressor control system development. First, we develop a bond graph model of a single compression system. Bond graph modeling offers a different perspective to previous work by modeling the compression system based on energy flow instead of fluid dynamics. Analyzing the bond graph model explains the energy flow during compressor surge. Two pri...

  15. A Graph Calculus for Predicate Logic

    Directory of Open Access Journals (Sweden)

    Paulo A. S. Veloso

    2013-03-01

    Full Text Available We introduce a refutation graph calculus for classical first-order predicate logic, which is an extension of previous ones for binary relations. One reduces logical consequence to establishing that a constructed graph has empty extension, i. e. it represents bottom. Our calculus establishes that a graph has empty extension by converting it to a normal form, which is expanded to other graphs until we can recognize conflicting situations (equivalent to a formula and its negation.

  16. Sphere and dot product representations of graphs

    NARCIS (Netherlands)

    R.J. Kang (Ross); T. Müller (Tobias)

    2012-01-01

    textabstractA graph $G$ is a $k$-sphere graph if there are $k$-dimensional real vectors $v_1,\\dots,v_n$ such that $ij\\in E(G)$ if and only if the distance between $v_i$ and $v_j$ is at most $1$. A graph $G$ is a $k$-dot product graph if there are $k$-dimensional real vectors $v_1,\\dots,v_n$ such

  17. Deep Learning with Dynamic Computation Graphs

    OpenAIRE

    Looks, Moshe; Herreshoff, Marcello; Hutchins, DeLesley; Norvig, Peter

    2017-01-01

    Neural networks that compute over graph structures are a natural fit for problems in a variety of domains, including natural language (parse trees) and cheminformatics (molecular graphs). However, since the computation graph has a different shape and size for every input, such networks do not directly support batched training or inference. They are also difficult to implement in popular deep learning libraries, which are based on static data-flow graphs. We introduce a technique called dynami...

  18. VIGOR: Interactive Visual Exploration of Graph Query Results.

    Science.gov (United States)

    Pienta, Robert; Hohman, Fred; Endert, Alex; Tamersoy, Acar; Roundy, Kevin; Gates, Chris; Navathe, Shamkant; Chau, Duen Horng

    2018-01-01

    Finding patterns in graphs has become a vital challenge in many domains from biological systems, network security, to finance (e.g., finding money laundering rings of bankers and business owners). While there is significant interest in graph databases and querying techniques, less research has focused on helping analysts make sense of underlying patterns within a group of subgraph results. Visualizing graph query results is challenging, requiring effective summarization of a large number of subgraphs, each having potentially shared node-values, rich node features, and flexible structure across queries. We present VIGOR, a novel interactive visual analytics system, for exploring and making sense of query results. VIGOR uses multiple coordinated views, leveraging different data representations and organizations to streamline analysts sensemaking process. VIGOR contributes: (1) an exemplar-based interaction technique, where an analyst starts with a specific result and relaxes constraints to find other similar results or starts with only the structure (i.e., without node value constraints), and adds constraints to narrow in on specific results; and (2) a novel feature-aware subgraph result summarization. Through a collaboration with Symantec, we demonstrate how VIGOR helps tackle real-world problems through the discovery of security blindspots in a cybersecurity dataset with over 11,000 incidents. We also evaluate VIGOR with a within-subjects study, demonstrating VIGOR's ease of use over a leading graph database management system, and its ability to help analysts understand their results at higher speed and make fewer errors.

  19. On the sizes of expander graphs and minimum distances of graph codes

    DEFF Research Database (Denmark)

    Høholdt, Tom; Justesen, Jørn

    2014-01-01

    We give lower bounds for the minimum distances of graph codes based on expander graphs. The bounds depend only on the second eigenvalue of the graph and the parameters of the component codes. We also give an upper bound on the size of a degree regular graph with given second eigenvalue....

  20. My Bar Graph Tells a Story

    Science.gov (United States)

    McMillen, Sue; McMillen, Beth

    2010-01-01

    Connecting stories to qualitative coordinate graphs has been suggested as an effective instructional strategy. Even students who are able to "create" bar graphs may struggle to correctly "interpret" them. Giving children opportunities to work with qualitative graphs can help them develop the skills to interpret, describe, and compare information…

  1. The groupies of random multipartite graphs

    OpenAIRE

    Portmann, Marius; Wang, Hongyun

    2012-01-01

    If a vertex $v$ in a graph $G$ has degree larger than the average of the degrees of its neighbors, we call it a groupie in $G$. In the current work, we study the behavior of groupie in random multipartite graphs with the link probability between sets of nodes fixed. Our results extend the previous ones on random (bipartite) graphs.

  2. Modeling Software Evolution using Algebraic Graph Rewriting

    NARCIS (Netherlands)

    Ciraci, Selim; van den Broek, Pim

    We show how evolution requests can be formalized using algebraic graph rewriting. In particular, we present a way to convert the UML class diagrams to colored graphs. Since changes in software may effect the relation between the methods of classes, our colored graph representation also employs the

  3. A Type Graph Model for Java Programs

    NARCIS (Netherlands)

    Rensink, Arend; Zambon, Eduardo

    2009-01-01

    In this report we present a type graph that models all executable constructs of the Java programming language. Such a model is useful for any graph-based technique that relies on a representation of Java programs as graphs. The model can be regarded as a common representation to which all Java

  4. An intersection graph of straight lines

    DEFF Research Database (Denmark)

    Thomassen, Carsten

    2002-01-01

    G. Ehrlich, S. Even, and R.E. Tarjan conjectured that the graph obtained from a complete 3 partite graph K4,4,4 by deleting the edges of four disjoint triangles is not the intersection graph of straight line segments in the plane. We show that it is....

  5. Girth 5 graphs from relative difference sets

    DEFF Research Database (Denmark)

    Jørgensen, Leif Kjær

    2005-01-01

    We consider the problem of construction of graphs with given degree $k$ and girth 5 and as few vertices as possible. We give a construction of a family of girth 5 graphs based on relative difference sets. This family contains the smallest known graph of degree 8 and girth 5 which was constructed ...

  6. Cycles in weighted graphs and related topics

    NARCIS (Netherlands)

    Zhang, Shenggui

    2002-01-01

    This thesis contains results on paths andcycles in graphs andon a more or less relatedtopic, the vulnerability of graphs. In the first part of the thesis, Chapters 2 through 5, we concentrate on paths andcycles in weightedgraphs. A number of sufficient conditions are presentedfor graphs to contain

  7. Graph Transformation Semantics for a QVT Language

    NARCIS (Netherlands)

    Rensink, Arend; Nederpel, Ronald; Bruni, Roberto; Varró, Dániel

    It has been claimed by many in the graph transformation community that model transformation, as understood in the context of Model Driven Architecture, can be seen as an application of graph transformation. In this paper we substantiate this claim by giving a graph transformation-based semantics to

  8. Girth 5 graphs from relative difference sets

    DEFF Research Database (Denmark)

    Jørgensen, Leif Kjær

    We consider the problem of construction of graphs with given degree and girth 5 and as few vertices as possible. We give a construction of a family of girth 5 graphs based on relative difference sets. This family contains the smallest known graph of degree 8 and girth 5 which was constructed by G...

  9. Improper colouring of (random) unit disk graphs

    NARCIS (Netherlands)

    Kang, R.J.; Müller, T.; Sereni, J.S.

    2008-01-01

    For any graph G, the k-improper chromatic number ¿k(G) is the smallest number of colours used in a colouring of G such that each colour class induces a subgraph of maximum degree k. We investigate ¿k for unit disk graphs and random unit disk graphs to generalise results of McDiarmid and Reed

  10. Alliances and Bisection Width for Planar Graphs

    DEFF Research Database (Denmark)

    Olsen, Martin; Revsbæk, Morten

    2013-01-01

    An alliance in a graph is a set of vertices (allies) such that each vertex in the alliance has at least as many allies (counting the vertex itself) as non-allies in its neighborhood of the graph. We show that any planar graph with minimum degree at least 4 can be split into two alliances in polyn...

  11. A Type Graph Model for Java Programs

    NARCIS (Netherlands)

    Rensink, Arend; Zambon, Eduardo; Lee, D.; Lopes, A.; Poetzsch-Heffter, A.

    2009-01-01

    In this work we present a type graph that models all executable constructs of the Java programming language. Such a model is useful for any graph-based technique that relies on a representation of Java programs as graphs. The model can be regarded as a common representation to which all Java syntax

  12. RATGRAPH: Computer Graphing of Rational Functions.

    Science.gov (United States)

    Minch, Bradley A.

    1987-01-01

    Presents an easy-to-use Applesoft BASIC program that graphs rational functions and any asymptotes that the functions might have. Discusses the nature of rational functions, graphing them manually, employing a computer to graph rational functions, and describes how the program works. (TW)

  13. A new cluster algorithm for graphs

    NARCIS (Netherlands)

    S. van Dongen

    1998-01-01

    textabstractA new cluster algorithm for graphs called the emph{Markov Cluster algorithm ($MCL$ algorithm) is introduced. The graphs may be both weighted (with nonnegative weight) and directed. Let~$G$~be such a graph. The $MCL$ algorithm simulates flow in $G$ by first identifying $G$ in a

  14. Well-covered graphs and factors

    DEFF Research Database (Denmark)

    Randerath, Bert; Vestergaard, Preben D.

    2006-01-01

    A maximum independent set of vertices in a graph is a set of pairwise nonadjacent vertices of largest cardinality α. Plummer defined a graph to be well-covered, if every independent set is contained in a maximum independent set of G. Every well-covered graph G without isolated vertices has a perf...

  15. A new characterization of trivially perfect graphs

    Directory of Open Access Journals (Sweden)

    Christian Rubio Montiel

    2015-03-01

    Full Text Available A graph $G$ is \\emph{trivially perfect} if for every induced subgraph the cardinality of the largest set of pairwise nonadjacent vertices (the stability number $\\alpha(G$ equals the number of (maximal cliques $m(G$. We characterize the trivially perfect graphs in terms of vertex-coloring and we extend some definitions to infinite graphs.

  16. 47 CFR 80.761 - Conversion graphs.

    Science.gov (United States)

    2010-10-01

    ... MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.761 Conversion graphs. The following graphs must be employed where conversion from one to the other of the indicated types of units is... 47 Telecommunication 5 2010-10-01 2010-10-01 false Conversion graphs. 80.761 Section 80.761...

  17. Towards optimal packed string matching

    DEFF Research Database (Denmark)

    Ben-Kiki, Oren; Bille, Philip; Breslauer, Dany

    2014-01-01

    -size string-matching instruction wssm is available in contemporary commodity processors. The other word-size maximum-suffix instruction wslm is only required during the pattern pre-processing. Benchmarks show that our solution can be efficiently implemented, unlike some prior theoretical packed string...

  18. On a conjecture concerning helly circle graphs

    Directory of Open Access Journals (Sweden)

    Durán Guillermo

    2003-01-01

    Full Text Available We say that G is an e-circle graph if there is a bijection between its vertices and straight lines on the cartesian plane such that two vertices are adjacent in G if and only if the corresponding lines intersect inside the circle of radius one. This definition suggests a method for deciding whether a given graph G is an e-circle graph, by constructing a convenient system S of equations and inequations which represents the structure of G, in such a way that G is an e-circle graph if and only if S has a solution. In fact, e-circle graphs are exactly the circle graphs (intersection graphs of chords in a circle, and thus this method provides an analytic way for recognizing circle graphs. A graph G is a Helly circle graph if G is a circle graph and there exists a model of G by chords such that every three pairwise intersecting chords intersect at the same point. A conjecture by Durán (2000 states that G is a Helly circle graph if and only if G is a circle graph and contains no induced diamonds (a diamond is a graph formed by four vertices and five edges. Many unsuccessful efforts - mainly based on combinatorial and geometrical approaches - have been done in order to validate this conjecture. In this work, we utilize the ideas behind the definition of e-circle graphs and restate this conjecture in terms of an equivalence between two systems of equations and inequations, providing a new, analytic tool to deal with it.

  19. Equilibrium statistical mechanics on correlated random graphs

    Science.gov (United States)

    Barra, Adriano; Agliari, Elena

    2011-02-01

    Biological and social networks have recently attracted great attention from physicists. Among several aspects, two main ones may be stressed: a non-trivial topology of the graph describing the mutual interactions between agents and, typically, imitative, weighted, interactions. Despite such aspects being widely accepted and empirically confirmed, the schemes currently exploited in order to generate the expected topology are based on a priori assumptions and, in most cases, implement constant intensities for links. Here we propose a simple shift [-1,+1]\\to [0,+1] in the definition of patterns in a Hopfield model: a straightforward effect is the conversion of frustration into dilution. In fact, we show that by varying the bias of pattern distribution, the network topology (generated by the reciprocal affinities among agents, i.e. the Hebbian rule) crosses various well-known regimes, ranging from fully connected, to an extreme dilution scenario, then to completely disconnected. These features, as well as small-world properties, are, in this context, emergent and no longer imposed a priori. The model is throughout investigated also from a thermodynamics perspective: the Ising model defined on the resulting graph is analytically solved (at a replica symmetric level) by extending the double stochastic stability technique, and presented together with its fluctuation theory for a picture of criticality. Overall, our findings show that, at least at equilibrium, dilution (of whatever kind) simply decreases the strength of the coupling felt by the spins, but leaves the paramagnetic/ferromagnetic flavors unchanged. The main difference with respect to previous investigations is that, within our approach, replicas do not appear: instead of (multi)-overlaps as order parameters, we introduce a class of magnetizations on all the possible subgraphs belonging to the main one investigated: as a consequence, for these objects a closure for a self-consistent relation is achieved.

  20. Equilibrium statistical mechanics on correlated random graphs

    International Nuclear Information System (INIS)

    Barra, Adriano; Agliari, Elena

    2011-01-01

    Biological and social networks have recently attracted great attention from physicists. Among several aspects, two main ones may be stressed: a non-trivial topology of the graph describing the mutual interactions between agents and, typically, imitative, weighted, interactions. Despite such aspects being widely accepted and empirically confirmed, the schemes currently exploited in order to generate the expected topology are based on a priori assumptions and, in most cases, implement constant intensities for links. Here we propose a simple shift [-1,+1]→[0,+1] in the definition of patterns in a Hopfield model: a straightforward effect is the conversion of frustration into dilution. In fact, we show that by varying the bias of pattern distribution, the network topology (generated by the reciprocal affinities among agents, i.e. the Hebbian rule) crosses various well-known regimes, ranging from fully connected, to an extreme dilution scenario, then to completely disconnected. These features, as well as small-world properties, are, in this context, emergent and no longer imposed a priori. The model is throughout investigated also from a thermodynamics perspective: the Ising model defined on the resulting graph is analytically solved (at a replica symmetric level) by extending the double stochastic stability technique, and presented together with its fluctuation theory for a picture of criticality. Overall, our findings show that, at least at equilibrium, dilution (of whatever kind) simply decreases the strength of the coupling felt by the spins, but leaves the paramagnetic/ferromagnetic flavors unchanged. The main difference with respect to previous investigations is that, within our approach, replicas do not appear: instead of (multi)-overlaps as order parameters, we introduce a class of magnetizations on all the possible subgraphs belonging to the main one investigated: as a consequence, for these objects a closure for a self-consistent relation is achieved

  1. Analyzing and synthesizing phylogenies using tree alignment graphs.

    Directory of Open Access Journals (Sweden)

    Stephen A Smith

    Full Text Available Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG. The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees, we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to

  2. Analyzing and synthesizing phylogenies using tree alignment graphs.

    Science.gov (United States)

    Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

    2013-01-01

    Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

  3. Centrosymmetric Graphs And A Lower Bound For Graph Energy Of Fullerenes

    Directory of Open Access Journals (Sweden)

    Katona Gyula Y.

    2014-11-01

    Full Text Available The energy of a molecular graph G is defined as the summation of the absolute values of the eigenvalues of adjacency matrix of a graph G. In this paper, an infinite class of fullerene graphs with 10n vertices, n ≥ 2, is considered. By proving centrosymmetricity of the adjacency matrix of these fullerene graphs, a lower bound for its energy is given. Our method is general and can be extended to other class of fullerene graphs.

  4. Demadroid: Object Reference Graph-Based Malware Detection in Android

    Directory of Open Access Journals (Sweden)

    Huanran Wang

    2018-01-01

    Full Text Available Smartphone usage has been continuously increasing in recent years. In addition, Android devices are widely used in our daily life, becoming the most attractive target for hackers. Therefore, malware analysis of Android platform is in urgent demand. Static analysis and dynamic analysis methods are two classical approaches. However, they also have some drawbacks. Motivated by this, we present Demadroid, a framework to implement the detection of Android malware. We obtain the dynamic information to build Object Reference Graph and propose λ-VF2 algorithm for graph matching. Extensive experiments show that Demadroid can efficiently identify the malicious features of malware. Furthermore, the system can effectively resist obfuscated attacks and the variants of known malware to meet the demand for actual use.

  5. Subsampling for graph power spectrum estimation

    KAUST Repository

    Chepuri, Sundeep Prabhakar; Leus, Geert

    2016-01-01

    In this paper we focus on subsampling stationary random signals that reside on the vertices of undirected graphs. Second-order stationary graph signals are obtained by filtering white noise and they admit a well-defined power spectrum. Estimating the graph power spectrum forms a central component of stationary graph signal processing and related inference tasks. We show that by sampling a significantly smaller subset of vertices and using simple least squares, we can reconstruct the power spectrum of the graph signal from the subsampled observations, without any spectral priors. In addition, a near-optimal greedy algorithm is developed to design the subsampling scheme.

  6. On 4-critical t-perfect graphs

    OpenAIRE

    Benchetrit, Yohann

    2016-01-01

    It is an open question whether the chromatic number of $t$-perfect graphs is bounded by a constant. The largest known value for this parameter is 4, and the only example of a 4-critical $t$-perfect graph, due to Laurent and Seymour, is the complement of the line graph of the prism $\\Pi$ (a graph is 4-critical if it has chromatic number 4 and all its proper induced subgraphs are 3-colorable). In this paper, we show a new example of a 4-critical $t$-perfect graph: the complement of the line gra...

  7. Subsampling for graph power spectrum estimation

    KAUST Repository

    Chepuri, Sundeep Prabhakar

    2016-10-06

    In this paper we focus on subsampling stationary random signals that reside on the vertices of undirected graphs. Second-order stationary graph signals are obtained by filtering white noise and they admit a well-defined power spectrum. Estimating the graph power spectrum forms a central component of stationary graph signal processing and related inference tasks. We show that by sampling a significantly smaller subset of vertices and using simple least squares, we can reconstruct the power spectrum of the graph signal from the subsampled observations, without any spectral priors. In addition, a near-optimal greedy algorithm is developed to design the subsampling scheme.

  8. Proving relations between modular graph functions

    International Nuclear Information System (INIS)

    Basu, Anirban

    2016-01-01

    We consider modular graph functions that arise in the low energy expansion of the four graviton amplitude in type II string theory. The vertices of these graphs are the positions of insertions of vertex operators on the toroidal worldsheet, while the links are the scalar Green functions connecting the vertices. Graphs with four and five links satisfy several non-trivial relations, which have been proved recently. We prove these relations by using elementary properties of Green functions and the details of the graphs. We also prove a relation between modular graph functions with six links. (paper)

  9. A graph edit dictionary for correcting errors in roof topology graphs reconstructed from point clouds

    Science.gov (United States)

    Xiong, B.; Oude Elberink, S.; Vosselman, G.

    2014-07-01

    In the task of 3D building model reconstruction from point clouds we face the problem of recovering a roof topology graph in the presence of noise, small roof faces and low point densities. Errors in roof topology graphs will seriously affect the final modelling results. The aim of this research is to automatically correct these errors. We define the graph correction as a graph-to-graph problem, similar to the spelling correction problem (also called the string-to-string problem). The graph correction is more complex than string correction, as the graphs are 2D while strings are only 1D. We design a strategy based on a dictionary of graph edit operations to automatically identify and correct the errors in the input graph. For each type of error the graph edit dictionary stores a representative erroneous subgraph as well as the corrected version. As an erroneous roof topology graph may contain several errors, a heuristic search is applied to find the optimum sequence of graph edits to correct the errors one by one. The graph edit dictionary can be expanded to include entries needed to cope with errors that were previously not encountered. Experiments show that the dictionary with only fifteen entries already properly corrects one quarter of erroneous graphs in about 4500 buildings, and even half of the erroneous graphs in one test area, achieving as high as a 95% acceptance rate of the reconstructed models.

  10. Significance evaluation in factor graphs

    DEFF Research Database (Denmark)

    Madsen, Tobias; Hobolth, Asger; Jensen, Jens Ledet

    2017-01-01

    in genomics and the multiple-testing issues accompanying them, accurate significance evaluation is of great importance. We here address the problem of evaluating statistical significance of observations from factor graph models. Results Two novel numerical approximations for evaluation of statistical...... significance are presented. First a method using importance sampling. Second a saddlepoint approximation based method. We develop algorithms to efficiently compute the approximations and compare them to naive sampling and the normal approximation. The individual merits of the methods are analysed both from....... Conclusions The applicability of saddlepoint approximation and importance sampling is demonstrated on known models in the factor graph framework. Using the two methods we can substantially improve computational cost without compromising accuracy. This contribution allows analyses of large datasets...

  11. Groups, graphs and random walks

    CERN Document Server

    Salvatori, Maura; Sava-Huss, Ecaterina

    2017-01-01

    An accessible and panoramic account of the theory of random walks on groups and graphs, stressing the strong connections of the theory with other branches of mathematics, including geometric and combinatorial group theory, potential analysis, and theoretical computer science. This volume brings together original surveys and research-expository papers from renowned and leading experts, many of whom spoke at the workshop 'Groups, Graphs and Random Walks' celebrating the sixtieth birthday of Wolfgang Woess in Cortona, Italy. Topics include: growth and amenability of groups; Schrödinger operators and symbolic dynamics; ergodic theorems; Thompson's group F; Poisson boundaries; probability theory on buildings and groups of Lie type; structure trees for edge cuts in networks; and mathematical crystallography. In what is currently a fast-growing area of mathematics, this book provides an up-to-date and valuable reference for both researchers and graduate students, from which future research activities will undoubted...

  12. Flux networks in metabolic graphs

    International Nuclear Information System (INIS)

    Warren, P B; Queiros, S M Duarte; Jones, J L

    2009-01-01

    A metabolic model can be represented as a bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a conserved metabolite property such as molecular weight. A similar flux network can be constructed by combining the primal and dual solutions to the linear programming problem that typically arises in constraint-based modelling. Such constructions may help with the visualization of flux distributions in complex metabolic networks. The analysis also explains the strong correlation observed between metabolite shadow prices (the dual linear programming variables) and conserved metabolite properties. The methods were applied to recent metabolic models for Escherichia coli, Saccharomyces cerevisiae and Methanosarcina barkeri. Detailed results are reported for E. coli; similar results were found for other organisms

  13. 3-biplacement of bipartite graphs

    Directory of Open Access Journals (Sweden)

    Lech Adamus

    2008-01-01

    Full Text Available Let \\(G=(L,R;E\\ be a bipartite graph with color classes \\(L\\ and \\(R\\ and edge set \\(E\\. A set of two bijections \\(\\{\\varphi_1 , \\varphi_2\\}\\, \\(\\varphi_1 , \\varphi_2 :L \\cup R \\to L \\cup R\\, is said to be a \\(3\\-biplacement of \\(G\\ if \\(\\varphi_1(L= \\varphi_2(L = L\\ and \\(E \\cap \\varphi_1^*(E=\\emptyset\\, \\(E \\cap \\varphi_2^*(E=\\emptyset\\, \\(\\varphi_1^*(E \\cap \\varphi_2^*(E=\\emptyset\\, where \\(\\varphi_1^*\\, \\(\\varphi_2^*\\ are the maps defined on \\(E\\, induced by \\(\\varphi_1\\, \\(\\varphi_2\\, respectively. We prove that if \\(|L| = p\\, \\(|R| = q\\, \\(3 \\leq p \\leq q\\, then every graph \\(G=(L,R;E\\ of size at most \\(p\\ has a \\(3\\-biplacement.

  14. Individual Travel Behavior Modeling of Public Transport Passenger Based on Graph Construction

    Directory of Open Access Journals (Sweden)

    Quan Liang

    2018-01-01

    Full Text Available This paper presents a novel method for mining the individual travel behavior regularity of different public transport passengers through constructing travel behavior graph based model. The individual travel behavior graph is developed to represent spatial positions, time distributions, and travel routes and further forecasts the public transport passenger’s behavior choice. The proposed travel behavior graph is composed of macronodes, arcs, and transfer probability. Each macronode corresponds to a travel association map and represents a travel behavior. A travel association map also contains its own nodes. The nodes of a travel association map are created when the processed travel chain data shows significant change. Thus, each node of three layers represents a significant change of spatial travel positions, travel time, and routes, respectively. Since a travel association map represents a travel behavior, the graph can be considered a sequence of travel behaviors. Through integrating travel association map and calculating the probabilities of the arcs, it is possible to construct a unique travel behavior graph for each passenger. The data used in this study are multimode data matched by certain rules based on the data of public transport smart card transactions and network features. The case study results show that graph based method to model the individual travel behavior of public transport passengers is effective and feasible. Travel behavior graphs support customized public transport travel characteristics analysis and demand prediction.

  15. On the centrality of some graphs

    Directory of Open Access Journals (Sweden)

    Vecdi Aytac

    2017-10-01

    Full Text Available A central issue in the analysis of complex networks is the assessment of their stability and vulnerability. A variety of measures have been proposed in the literature to quantify the stability of networks and a number of graph-theoretic parameters have been used to derive formulas for calculating network reliability. Different measures for graph vulnerability have been introduced so far to study different aspects of the graph behavior after removal of vertices or links such as connectivity, toughness, scattering number, binding number, residual closeness and integrity. In this paper, we consider betweenness centrality of a graph. Betweenness centrality of a vertex of a graph is portion of the shortest paths all pairs of vertices passing through a given vertex. In this paper, we obtain exact values for betweenness centrality for some wheel related graphs namely gear, helm, sunflower and friendship graphs.

  16. Quantum walk on a chimera graph

    Science.gov (United States)

    Xu, Shu; Sun, Xiangxiang; Wu, Jizhou; Zhang, Wei-Wei; Arshed, Nigum; Sanders, Barry C.

    2018-05-01

    We analyse a continuous-time quantum walk on a chimera graph, which is a graph of choice for designing quantum annealers, and we discover beautiful quantum walk features such as localization that starkly distinguishes classical from quantum behaviour. Motivated by technological thrusts, we study continuous-time quantum walk on enhanced variants of the chimera graph and on diminished chimera graph with a random removal of vertices. We explain the quantum walk by constructing a generating set for a suitable subgroup of graph isomorphisms and corresponding symmetry operators that commute with the quantum walk Hamiltonian; the Hamiltonian and these symmetry operators provide a complete set of labels for the spectrum and the stationary states. Our quantum walk characterization of the chimera graph and its variants yields valuable insights into graphs used for designing quantum-annealers.

  17. Fibonacci number of the tadpole graph

    Directory of Open Access Journals (Sweden)

    Joe DeMaio

    2014-10-01

    Full Text Available In 1982, Prodinger and Tichy defined the Fibonacci number of a graph G to be the number of independent sets of the graph G. They did so since the Fibonacci number of the path graph Pn is the Fibonacci number F(n+2 and the Fibonacci number of the cycle graph Cn is the Lucas number Ln. The tadpole graph Tn,k is the graph created by concatenating Cn and Pk with an edge from any vertex of Cn to a pendant of Pk for integers n=3 and k=0. This paper establishes formulae and identities for the Fibonacci number of the tadpole graph via algebraic and combinatorial methods.

  18. Software for Graph Analysis and Visualization

    Directory of Open Access Journals (Sweden)

    M. I. Kolomeychenko

    2014-01-01

    Full Text Available This paper describes the software for graph storage, analysis and visualization. The article presents a comparative analysis of existing software for analysis and visualization of graphs, describes the overall architecture of application and basic principles of construction and operation of the main modules. Furthermore, a description of the developed graph storage oriented to storage and processing of large-scale graphs is presented. The developed algorithm for finding communities and implemented algorithms of autolayouts of graphs are the main functionality of the product. The main advantage of the developed software is high speed processing of large size networks (up to millions of nodes and links. Moreover, the proposed graph storage architecture is unique and has no analogues. The developed approaches and algorithms are optimized for operating with big graphs and have high productivity.

  19. Parallel External Memory Graph Algorithms

    DEFF Research Database (Denmark)

    Arge, Lars Allan; Goodrich, Michael T.; Sitchinava, Nodari

    2010-01-01

    In this paper, we study parallel I/O efficient graph algorithms in the Parallel External Memory (PEM) model, one o f the private-cache chip multiprocessor (CMP) models. We study the fundamental problem of list ranking which leads to efficient solutions to problems on trees, such as computing lowest...... an optimal speedup of ¿(P) in parallel I/O complexity and parallel computation time, compared to the single-processor external memory counterparts....

  20. Submanifolds weakly associated with graphs

    Indian Academy of Sciences (India)

    A CARRIAZO, L M FERN ´ANDEZ and A RODRÍGUEZ-HIDALGO. Department of Geometry and Topology, ..... by means of trees (connected graphs without cycles) and forests (disjoint unions of trees, see [6]) given in [3], by extending it to weak ... CR-submanifold. In this case, every tree is a K2. Finally, Theorem 3.8 of [3] can ...

  1. Feature selection and multi-kernel learning for adaptive graph regularized nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-09-20

    Nonnegative matrix factorization (NMF), a popular part-based representation technique, does not capture the intrinsic local geometric structure of the data space. Graph regularized NMF (GNMF) was recently proposed to avoid this limitation by regularizing NMF with a nearest neighbor graph constructed from the input data set. However, GNMF has two main bottlenecks. First, using the original feature space directly to construct the graph is not necessarily optimal because of the noisy and irrelevant features and nonlinear distributions of data samples. Second, one possible way to handle the nonlinear distribution of data samples is by kernel embedding. However, it is often difficult to choose the most suitable kernel. To solve these bottlenecks, we propose two novel graph-regularized NMF methods, AGNMFFS and AGNMFMK, by introducing feature selection and multiple-kernel learning to the graph regularized NMF, respectively. Instead of using a fixed graph as in GNMF, the two proposed methods learn the nearest neighbor graph that is adaptive to the selected features and learned multiple kernels, respectively. For each method, we propose a unified objective function to conduct feature selection/multi-kernel learning, NMF and adaptive graph regularization simultaneously. We further develop two iterative algorithms to solve the two optimization problems. Experimental results on two challenging pattern classification tasks demonstrate that the proposed methods significantly outperform state-of-the-art data representation methods.

  2. Exploiting graph kernels for high performance biomedical relation extraction.

    Science.gov (United States)

    Panyam, Nagesh C; Verspoor, Karin; Cohn, Trevor; Ramamohanarao, Kotagiri

    2018-01-30

    Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineering methods, when classifying highly ordered structures such as trees and graphs obtained from syntactic parsing of a sentence. Tree kernels such as the Subset Tree Kernel and Partial Tree Kernel have been shown to be effective for classifying constituency parse trees and basic dependency parse graphs of a sentence. Graph kernels such as the All Path Graph kernel (APG) and Approximate Subgraph Matching (ASM) kernel have been shown to be suitable for classifying general graphs with cycles, such as the enhanced dependency parse graph of a sentence. In this work, we present a high performance Chemical-Induced Disease (CID) relation extraction system. We present a comparative study of kernel methods for the CID task and also extend our study to the Protein-Protein Interaction (PPI) extraction task, an important biomedical relation extraction task. We discuss novel modifications to the ASM kernel to boost its performance and a method to apply graph kernels for extracting relations expressed in multiple sentences. Our system for CID relation extraction attains an F-score of 60%, without using external knowledge sources or task specific heuristic or rules. In comparison, the state of the art Chemical-Disease Relation Extraction system achieves an F-score of 56% using an ensemble of multiple machine learning methods, which is then boosted to 61% with a rule based system employing task specific post processing rules. For the CID task, graph kernels outperform tree kernels substantially, and the best performance is obtained with APG kernel that attains an F-score of 60%, followed by the ASM kernel at 57%. The performance difference between the ASM and APG kernels for CID sentence level relation extraction is not significant. In our evaluation of ASM for the PPI task, ASM

  3. Identifying Threats Using Graph-based Anomaly Detection

    Science.gov (United States)

    Eberle, William; Holder, Lawrence; Cook, Diane

    Much of the data collected during the monitoring of cyber and other infrastructures is structural in nature, consisting of various types of entities and relationships between them. The detection of threatening anomalies in such data is crucial to protecting these infrastructures. We present an approach to detecting anomalies in a graph-based representation of such data that explicitly represents these entities and relationships. The approach consists of first finding normative patterns in the data using graph-based data mining and then searching for small, unexpected deviations to these normative patterns, assuming illicit behavior tries to mimic legitimate, normative behavior. The approach is evaluated using several synthetic and real-world datasets. Results show that the approach has high truepositive rates, low false-positive rates, and is capable of detecting complex structural anomalies in real-world domains including email communications, cellphone calls and network traffic.

  4. Topological structure of dictionary graphs

    International Nuclear Information System (INIS)

    Fuks, Henryk; Krzeminski, Mark

    2009-01-01

    We investigate the topological structure of the subgraphs of dictionary graphs constructed from WordNet and Moby thesaurus data. In the process of learning a foreign language, the learner knows only a subset of all words of the language, corresponding to a subgraph of a dictionary graph. When this subgraph grows with time, its topological properties change. We introduce the notion of the pseudocore and argue that the growth of the vocabulary roughly follows decreasing pseudocore numbers-that is, one first learns words with a high pseudocore number followed by smaller pseudocores. We also propose an alternative strategy for vocabulary growth, involving decreasing core numbers as opposed to pseudocore numbers. We find that as the core or pseudocore grows in size, the clustering coefficient first decreases, then reaches a minimum and starts increasing again. The minimum occurs when the vocabulary reaches a size between 10 3 and 10 4 . A simple model exhibiting similar behavior is proposed. The model is based on a generalized geometric random graph. Possible implications for language learning are discussed.

  5. Quantum information processing with graph states

    International Nuclear Information System (INIS)

    Schlingemann, Dirk-Michael

    2005-04-01

    Graph states are multiparticle states which are associated with graphs. Each vertex of the graph corresponds to a single system or particle. The links describe quantum correlations (entanglement) between pairs of connected particles. Graph states were initiated independently by two research groups: On the one hand, graph states were introduced by Briegel and Raussendorf as a resource for a new model of one-way quantum computing, where algorithms are implemented by a sequence of measurements at single particles. On the other hand, graph states were developed by the author of this thesis and ReinhardWerner in Braunschweig, as a tool to build quantum error correcting codes, called graph codes. The connection between the two approaches was fully realized in close cooperation of both research groups. This habilitation thesis provides a survey of the theory of graph codes, focussing mainly, but not exclusively on the author's own research work. We present the theoretical and mathematical background for the analysis of graph codes. The concept of one-way quantum computing for general graph states is discussed. We explicitly show how to realize the encoding and decoding device of a graph code on a one-way quantum computer. This kind of implementation is to be seen as a mathematical description of a quantum memory device. In addition to that, we investigate interaction processes, which enable the creation of graph states on very large systems. Particular graph states can be created, for instance, by an Ising type interaction between next neighbor particles which sits at the points of an infinitely extended cubic lattice. Based on the theory of quantum cellular automata, we give a constructive characterization of general interactions which create a translationally invariant graph state. (orig.)

  6. Degree Associated Edge Reconstruction Number of Graphs with Regular Pruned Graph

    Directory of Open Access Journals (Sweden)

    P. Anusha Devi

    2015-10-01

    Full Text Available An ecard of a graph $G$ is a subgraph formed by deleting an edge. A da-ecard specifies the degree of the deleted edge along with the ecard. The degree associated edge reconstruction number of a graph $G,~dern(G,$ is the minimum number of da-ecards that uniquely determines $G.$  The adversary degree associated edge reconstruction number of a graph $G, adern(G,$ is the minimum number $k$ such that every collection of $k$ da-ecards of $G$ uniquely determines $G.$ The maximal subgraph without end vertices of a graph $G$ which is not a tree is the pruned graph of $G.$ It is shown that $dern$ of complete multipartite graphs and some connected graphs with regular pruned graph is $1$ or $2.$ We also determine $dern$ and $adern$ of corona product of standard graphs.

  7. Encoding and analyzing aerial imagery using geospatial semantic graphs

    Energy Technology Data Exchange (ETDEWEB)

    Watson, Jean-Paul; Strip, David R.; McLendon, William Clarence,; Parekh, Ojas D.; Diegert, Carl F.; Martin, Shawn Bryan; Rintoul, Mark Daniel

    2014-02-01

    While collection capabilities have yielded an ever-increasing volume of aerial imagery, analytic techniques for identifying patterns in and extracting relevant information from this data have seriously lagged. The vast majority of imagery is never examined, due to a combination of the limited bandwidth of human analysts and limitations of existing analysis tools. In this report, we describe an alternative, novel approach to both encoding and analyzing aerial imagery, using the concept of a geospatial semantic graph. The advantages of our approach are twofold. First, intuitive templates can be easily specified in terms of the domain language in which an analyst converses. These templates can be used to automatically and efficiently search large graph databases, for specific patterns of interest. Second, unsupervised machine learning techniques can be applied to automatically identify patterns in the graph databases, exposing recurring motifs in imagery. We illustrate our approach using real-world data for Anne Arundel County, Maryland, and compare the performance of our approach to that of an expert human analyst.

  8. Multiple Kernel Learning for adaptive graph regularized nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan; AbdulJabbar, Mustafa Abdulmajeed

    2012-01-01

    Nonnegative Matrix Factorization (NMF) has been continuously evolving in several areas like pattern recognition and information retrieval methods. It factorizes a matrix into a product of 2 low-rank non-negative matrices that will define parts-based, and linear representation of non-negative data. Recently, Graph regularized NMF (GrNMF) is proposed to find a compact representation, which uncovers the hidden semantics and simultaneously respects the intrinsic geometric structure. In GNMF, an affinity graph is constructed from the original data space to encode the geometrical information. In this paper, we propose a novel idea which engages a Multiple Kernel Learning approach into refining the graph structure that reflects the factorization of the matrix and the new data space. The GrNMF is improved by utilizing the graph refined by the kernel learning, and then a novel kernel learning method is introduced under the GrNMF framework. Our approach shows encouraging results of the proposed algorithm in comparison to the state-of-the-art clustering algorithms like NMF, GrNMF, SVD etc.

  9. On Resolution Complexity of Matching Principles

    DEFF Research Database (Denmark)

    Dantchev, Stefan S.

    proof system. The results in the thesis fall in this category. We study the Resolution complexity of some Matching Principles. The three major contributions of the thesis are as follows. Firstly, we develop a general technique of proving resolution lower bounds for the perfect matchingprinciples based...... Chessboard as well as for Tseitin tautologies based on rectangular grid graph. We reduce these problems to Tiling games, a concept introduced by us, which may be of interest on its own. Secondly, we find the exact Tree-Resolution complexity of the Weak Pigeon-Hole Principle. It is the most studied...

  10. Replica methods for loopy sparse random graphs

    International Nuclear Information System (INIS)

    Coolen, ACC

    2016-01-01

    I report on the development of a novel statistical mechanical formalism for the analysis of random graphs with many short loops, and processes on such graphs. The graphs are defined via maximum entropy ensembles, in which both the degrees (via hard constraints) and the adjacency matrix spectrum (via a soft constraint) are prescribed. The sum over graphs can be done analytically, using a replica formalism with complex replica dimensions. All known results for tree-like graphs are recovered in a suitable limit. For loopy graphs, the emerging theory has an appealing and intuitive structure, suggests how message passing algorithms should be adapted, and what is the structure of theories describing spin systems on loopy architectures. However, the formalism is still largely untested, and may require further adjustment and refinement. (paper)

  11. Chemical Graph Transformation with Stereo-Information

    DEFF Research Database (Denmark)

    Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel

    2017-01-01

    Double Pushout graph transformation naturally facilitates the modelling of chemical reactions: labelled undirected graphs model molecules and direct derivations model chemical reactions. However, the most straightforward modelling approach ignores the relative placement of atoms and their neighbo......Double Pushout graph transformation naturally facilitates the modelling of chemical reactions: labelled undirected graphs model molecules and direct derivations model chemical reactions. However, the most straightforward modelling approach ignores the relative placement of atoms...... and their neighbours in space. Stereoisomers of chemical compounds thus cannot be distinguished, even though their chemical activity may differ substantially. In this contribution we propose an extended chemical graph transformation system with attributes that encode information about local geometry. The modelling...... of graph transformation, but we here propose a framework that also allows for partially specified stereoinformation. While there are several stereochemical configurations to be considered, we focus here on the tetrahedral molecular shape, and suggest general principles for how to treat all other chemically...

  12. Reconstructing Topological Graphs and Continua

    OpenAIRE

    Gartside, Paul; Pitz, Max F.; Suabedissen, Rolf

    2015-01-01

    The deck of a topological space $X$ is the set $\\mathcal{D}(X)=\\{[X \\setminus \\{x\\}] \\colon x \\in X\\}$, where $[Z]$ denotes the homeomorphism class of $Z$. A space $X$ is topologically reconstructible if whenever $\\mathcal{D}(X)=\\mathcal{D}(Y)$ then $X$ is homeomorphic to $Y$. It is shown that all metrizable compact connected spaces are reconstructible. It follows that all finite graphs, when viewed as a 1-dimensional cell-complex, are reconstructible in the topological sense, and more genera...

  13. Decomposing a graph into bistars

    DEFF Research Database (Denmark)

    Thomassen, Carsten

    2013-01-01

    Bárat and the present author conjectured that, for each tree T, there exists a natural number kT such that the following holds: If G is a kT-edge-connected graph such that |E(T)| divides |E(G)|, then G has a T-decomposition, that is, a decomposition of the edge set into trees each of which...... is isomorphic to T. The conjecture has been verified for infinitely many paths and for each star. In this paper we verify the conjecture for an infinite family of trees that are neither paths nor stars, namely all the bistars S(k,k+1)....

  14. On path hypercompositions in graphs and automata

    Directory of Open Access Journals (Sweden)

    Massouros Christos G.

    2016-01-01

    Full Text Available The paths in graphs define hypercompositions in the set of their vertices and therefore it is feasible to associate hypercompositional structures to each graph. Similarly, the strings of letters from their alphabet, define hypercompositions in the automata, which in turn define the associated hypergroups to the automata. The study of the associated hypercompositional structures gives results in both, graphs and automata theory.

  15. Attack Graph Construction for Security Events Analysis

    Directory of Open Access Journals (Sweden)

    Andrey Alexeevich Chechulin

    2014-09-01

    Full Text Available The paper is devoted to investigation of the attack graphs construction and analysis task for a network security evaluation and real-time security event processing. Main object of this research is the attack modeling process. The paper contains the description of attack graphs building, modifying and analysis technique as well as overview of implemented prototype for network security analysis based on attack graph approach.

  16. Steiner Distance in Graphs--A Survey

    OpenAIRE

    Mao, Yaping

    2017-01-01

    For a connected graph $G$ of order at least $2$ and $S\\subseteq V(G)$, the \\emph{Steiner distance} $d_G(S)$ among the vertices of $S$ is the minimum size among all connected subgraphs whose vertex sets contain $S$. In this paper, we summarize the known results on the Steiner distance parameters, including Steiner distance, Steiner diameter, Steiner center, Steiner median, Steiner interval, Steiner distance hereditary graph, Steiner distance stable graph, average Steiner distance, and Steiner ...

  17. Density conditions for triangles in multipartite graphs

    DEFF Research Database (Denmark)

    Bondy, Adrian; Shen, Jin; Thomassé, Stephan

    2006-01-01

    subgraphs in G. We investigate in particular the case where G is a complete multipartite graph. We prove that a finite tripartite graph with all edge densities greater than the golden ratio has a triangle and that this bound is best possible. Also we show that an infinite-partite graph with finite parts has...... a triangle, provided that the edge density between any two parts is greater than 1/2....

  18. Efficient Algorithmic Frameworks via Structural Graph Theory

    Science.gov (United States)

    2016-10-28

    constant. For example, they measured that, on large samples of the entire network, the Amazon graph has average degree 17.7, the Facebook graph has average...department heads’ opinions of departments, and generally lack transparency and well-defined measures . On the other hand, the National Research Council (the...Efficient and practical resource block allocation for LTE -based D2D network via graph coloring. Wireless Networks 20(4): 611-624 (2014) 50. Hossein

  19. Stinging Insect Matching Game

    Science.gov (United States)

    ... for Kids ▸ Stinging Insect Matching Game Share | Stinging Insect Matching Game Stinging insects can ruin summer fun for those who are ... the difference between the different kinds of stinging insects in order to keep your summer safe and ...

  20. EmptyHeaded: A Relational Engine for Graph Processing.

    Science.gov (United States)

    Aberger, Christopher R; Tu, Susan; Olukotun, Kunle; Ré, Christopher

    2016-01-01

    There are two types of high-performance graph processing engines: low- and high-level engines. Low-level engines (Galois, PowerGraph, Snap) provide optimized data structures and computation models but require users to write low-level imperative code, hence ensuring that efficiency is the burden of the user. In high-level engines, users write in query languages like datalog (SociaLite) or SQL (Grail). High-level engines are easier to use but are orders of magnitude slower than the low-level graph engines. We present EmptyHeaded, a high-level engine that supports a rich datalog-like query language and achieves performance comparable to that of low-level engines. At the core of EmptyHeaded's design is a new class of join algorithms that satisfy strong theoretical guarantees but have thus far not achieved performance comparable to that of specialized graph processing engines. To achieve high performance, EmptyHeaded introduces a new join engine architecture, including a novel query optimizer and data layouts that leverage single-instruction multiple data (SIMD) parallelism. With this architecture, EmptyHeaded outperforms high-level approaches by up to three orders of magnitude on graph pattern queries, PageRank, and Single-Source Shortest Paths (SSSP) and is an order of magnitude faster than many low-level baselines. We validate that EmptyHeaded competes with the best-of-breed low-level engine (Galois), achieving comparable performance on PageRank and at most 3× worse performance on SSSP.