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Sample records for improving graph partitions

  1. Graph Partitioning and Sequencing Software

    1995-09-19

    Graph partitioning is a fundemental problem in many scientific contexts. CHACO2.0 is a software package designed to partition and sequence graphs. CHACO2.0 allows for recursive application of several methods for finding small edge separators in weighted graphs. These methods include inertial, spectral, Kernighan Lin and multilevel methods in addition to several simpler strategies. Each of these approaches can be used to partition the graph into two, four, or eight pieces at each level of recursion.more » In addition, the Kernighan Lin method can be used to improve partitions generated by any of the other algorithms. CHACO2.0 can also be used to address various graph sequencing problems, with applications to scientific computing, database design, gene sequencing and other problems.« less

  2. Isoperimetric graph partitioning for image segmentation.

    PubMed

    Grady, Leo; Schwartz, Eric L

    2006-03-01

    Spectral graph partitioning provides a powerful approach to image segmentation. We introduce an alternate idea that finds partitions with a small isoperimetric constant, requiring solution to a linear system rather than an eigenvector problem. This approach produces the high quality segmentations of spectral methods, but with improved speed and stability.

  3. Multi-A Graph Patrolling and Partitioning

    NASA Astrophysics Data System (ADS)

    Elor, Y.; Bruckstein, A. M.

    2012-12-01

    We introduce a novel multi agent patrolling algorithm inspired by the behavior of gas filled balloons. Very low capability ant-like agents are considered with the task of patrolling an unknown area modeled as a graph. While executing the proposed algorithm, the agents dynamically partition the graph between them using simple local interactions, every agent assuming the responsibility for patrolling his subgraph. Balanced graph partition is an emergent behavior due to the local interactions between the agents in the swarm. Extensive simulations on various graphs (environments) showed that the average time to reach a balanced partition is linear with the graph size. The simulations yielded a convincing argument for conjecturing that if the graph being patrolled contains a balanced partition, the agents will find it. However, we could not prove this. Nevertheless, we have proved that if a balanced partition is reached, the maximum time lag between two successive visits to any vertex using the proposed strategy is at most twice the optimal so the patrol quality is at least half the optimal. In case of weighted graphs the patrol quality is at least (1)/(2){lmin}/{lmax} of the optimal where lmax (lmin) is the longest (shortest) edge in the graph.

  4. Bipartite graph partitioning and data clustering

    SciTech Connect

    Zha, Hongyuan; He, Xiaofeng; Ding, Chris; Gu, Ming; Simon, Horst D.

    2001-05-07

    Many data types arising from data mining applications can be modeled as bipartite graphs, examples include terms and documents in a text corpus, customers and purchasing items in market basket analysis and reviewers and movies in a movie recommender system. In this paper, the authors propose a new data clustering method based on partitioning the underlying biopartite graph. The partition is constructed by minimizing a normalized sum of edge weights between unmatched pairs of vertices of the bipartite graph. They show that an approximate solution to the minimization problem can be obtained by computing a partial singular value decomposition (SVD) of the associated edge weight matrix of the bipartite graph. They point out the connection of their clustering algorithm to correspondence analysis used in multivariate analysis. They also briefly discuss the issue of assigning data objects to multiple clusters. In the experimental results, they apply their clustering algorithm to the problem of document clustering to illustrate its effectiveness and efficiency.

  5. Linear Time Vertex Partitioning on Massive Graphs

    PubMed Central

    Mell, Peter; Harang, Richard; Gueye, Assane

    2016-01-01

    The problem of optimally removing a set of vertices from a graph to minimize the size of the largest resultant component is known to be NP-complete. Prior work has provided near optimal heuristics with a high time complexity that function on up to hundreds of nodes and less optimal but faster techniques that function on up to thousands of nodes. In this work, we analyze how to perform vertex partitioning on massive graphs of tens of millions of nodes. We use a previously known and very simple heuristic technique: iteratively removing the node of largest degree and all of its edges. This approach has an apparent quadratic complexity since, upon removal of a node and adjoining set of edges, the node degree calculations must be updated prior to choosing the next node. However, we describe a linear time complexity solution using an array whose indices map to node degree and whose values are hash tables indicating the presence or absence of a node at that degree value. This approach also has a linear growth with respect to memory usage which is surprising since we lowered the time complexity from quadratic to linear. We empirically demonstrate linear scalability and linear memory usage on random graphs of up to 15000 nodes. We then demonstrate tractability on massive graphs through execution on a graph with 34 million nodes representing Internet wide router connectivity. PMID:27336059

  6. RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology.

    PubMed

    Kim, Namhee; Zheng, Zhe; Elmetwaly, Shereef; Schlick, Tamar

    2014-01-01

    Graph representations have been widely used to analyze and design various economic, social, military, political, and biological networks. In systems biology, networks of cells and organs are useful for understanding disease and medical treatments and, in structural biology, structures of molecules can be described, including RNA structures. In our RNA-As-Graphs (RAG) framework, we represent RNA structures as tree graphs by translating unpaired regions into vertices and helices into edges. Here we explore the modularity of RNA structures by applying graph partitioning known in graph theory to divide an RNA graph into subgraphs. To our knowledge, this is the first application of graph partitioning to biology, and the results suggest a systematic approach for modular design in general. The graph partitioning algorithms utilize mathematical properties of the Laplacian eigenvector (µ2) corresponding to the second eigenvalues (λ2) associated with the topology matrix defining the graph: λ2 describes the overall topology, and the sum of µ2's components is zero. The three types of algorithms, termed median, sign, and gap cuts, divide a graph by determining nodes of cut by median, zero, and largest gap of µ2's components, respectively. We apply these algorithms to 45 graphs corresponding to all solved RNA structures up through 11 vertices (∼ 220 nucleotides). While we observe that the median cut divides a graph into two similar-sized subgraphs, the sign and gap cuts partition a graph into two topologically-distinct subgraphs. We find that the gap cut produces the best biologically-relevant partitioning for RNA because it divides RNAs at less stable connections while maintaining junctions intact. The iterative gap cuts suggest basic modules and assembly protocols to design large RNA structures. Our graph substructuring thus suggests a systematic approach to explore the modularity of biological networks. In our applications to RNA structures, subgraphs also suggest

  7. Partitioning sparse matrices with eigenvectors of graphs

    NASA Technical Reports Server (NTRS)

    Pothen, Alex; Simon, Horst D.; Liou, Kang-Pu

    1990-01-01

    The problem of computing a small vertex separator in a graph arises in the context of computing a good ordering for the parallel factorization of sparse, symmetric matrices. An algebraic approach for computing vertex separators is considered in this paper. It is shown that lower bounds on separator sizes can be obtained in terms of the eigenvalues of the Laplacian matrix associated with a graph. The Laplacian eigenvectors of grid graphs can be computed from Kronecker products involving the eigenvectors of path graphs, and these eigenvectors can be used to compute good separators in grid graphs. A heuristic algorithm is designed to compute a vertex separator in a general graph by first computing an edge separator in the graph from an eigenvector of the Laplacian matrix, and then using a maximum matching in a subgraph to compute the vertex separator. Results on the quality of the separators computed by the spectral algorithm are presented, and these are compared with separators obtained from other algorithms for computing separators. Finally, the time required to compute the Laplacian eigenvector is reported, and the accuracy with which the eigenvector must be computed to obtain good separators is considered. The spectral algorithm has the advantage that it can be implemented on a medium-size multiprocessor in a straightforward manner.

  8. Graph Partitioning for Parallel Applications in Heterogeneous Grid Environments

    NASA Technical Reports Server (NTRS)

    Bisws, Rupak; Kumar, Shailendra; Das, Sajal K.; Biegel, Bryan (Technical Monitor)

    2002-01-01

    The problem of partitioning irregular graphs and meshes for parallel computations on homogeneous systems has been extensively studied. However, these partitioning schemes fail when the target system architecture exhibits heterogeneity in resource characteristics. With the emergence of technologies such as the Grid, it is imperative to study the partitioning problem taking into consideration the differing capabilities of such distributed heterogeneous systems. In our model, the heterogeneous system consists of processors with varying processing power and an underlying non-uniform communication network. We present in this paper a novel multilevel partitioning scheme for irregular graphs and meshes, that takes into account issues pertinent to Grid computing environments. Our partitioning algorithm, called MiniMax, generates and maps partitions onto a heterogeneous system with the objective of minimizing the maximum execution time of the parallel distributed application. For experimental performance study, we have considered both a realistic mesh problem from NASA as well as synthetic workloads. Simulation results demonstrate that MiniMax generates high quality partitions for various classes of applications targeted for parallel execution in a distributed heterogeneous environment.

  9. Graph partitions and cluster synchronization in networks of oscillators

    NASA Astrophysics Data System (ADS)

    Schaub, Michael T.; O'Clery, Neave; Billeh, Yazan N.; Delvenne, Jean-Charles; Lambiotte, Renaud; Barahona, Mauricio

    2016-09-01

    Synchronization over networks depends strongly on the structure of the coupling between the oscillators. When the coupling presents certain regularities, the dynamics can be coarse-grained into clusters by means of External Equitable Partitions of the network graph and their associated quotient graphs. We exploit this graph-theoretical concept to study the phenomenon of cluster synchronization, in which different groups of nodes converge to distinct behaviors. We derive conditions and properties of networks in which such clustered behavior emerges and show that the ensuing dynamics is the result of the localization of the eigenvectors of the associated graph Laplacians linked to the existence of invariant subspaces. The framework is applied to both linear and non-linear models, first for the standard case of networks with positive edges, before being generalized to the case of signed networks with both positive and negative interactions. We illustrate our results with examples of both signed and unsigned graphs for consensus dynamics and for partial synchronization of oscillator networks under the master stability function as well as Kuramoto oscillators.

  10. Region Graph Partition Function Expansion and Approximate Free Energy Landscapes: Theory and Some Numerical Results

    NASA Astrophysics Data System (ADS)

    Zhou, Haijun; Wang, Chuang

    2012-08-01

    Graphical models for finite-dimensional spin glasses and real-world combinatorial optimization and satisfaction problems usually have an abundant number of short loops. The cluster variation method and its extension, the region graph method, are theoretical approaches for treating the complicated short-loop-induced local correlations. For graphical models represented by non-redundant or redundant region graphs, approximate free energy landscapes are constructed in this paper through the mathematical framework of region graph partition function expansion. Several free energy functionals are obtained, each of which use a set of probability distribution functions or functionals as order parameters. These probability distribution function/functionals are required to satisfy the region graph belief-propagation equation or the region graph survey-propagation equation to ensure vanishing correction contributions of region subgraphs with dangling edges. As a simple application of the general theory, we perform region graph belief-propagation simulations on the square-lattice ferromagnetic Ising model and the Edwards-Anderson model. Considerable improvements over the conventional Bethe-Peierls approximation are achieved. Collective domains of different sizes in the disordered and frustrated square lattice are identified by the message-passing procedure. Such collective domains and the frustrations among them are responsible for the low-temperature glass-like dynamical behaviors of the system.

  11. Betweenness-based algorithm for a partition scale-free graph

    NASA Astrophysics Data System (ADS)

    Zhang, Bai-Da; Wu, Jun-Jie; Tang, Yu-Hua; Zhou, Jing

    2011-11-01

    Many real-world networks are found to be scale-free. However, graph partition technology, as a technology capable of parallel computing, performs poorly when scale-free graphs are provided. The reason for this is that traditional partitioning algorithms are designed for random networks and regular networks, rather than for scale-free networks. Multilevel graph-partitioning algorithms are currently considered to be the state of the art and are used extensively. In this paper, we analyse the reasons why traditional multilevel graph-partitioning algorithms perform poorly and present a new multilevel graph-partitioning paradigm, top down partitioning, which derives its name from the comparison with the traditional bottom—up partitioning. A new multilevel partitioning algorithm, named betweenness-based partitioning algorithm, is also presented as an implementation of top—down partitioning paradigm. An experimental evaluation of seven different real-world scale-free networks shows that the betweenness-based partitioning algorithm significantly outperforms the existing state-of-the-art approaches.

  12. A Weakly Robust PTAS for Minimum Clique Partition in Unit Disk Graphs

    NASA Astrophysics Data System (ADS)

    Pirwani, Imran A.; Salavatipour, Mohammad R.

    We consider the problem of partitioning the set of vertices of a given unit disk graph (UDG) into a minimum number of cliques. The problem is NP-hard and various constant factor approximations are known, with the best known ratio of 3. Our main result is a weakly robust polynomial time approximation scheme (PTAS) for UDGs expressed with edge-lengths and ɛ> 0 that either (i) computes a clique partition, or (ii) produces a certificate proving that the graph is not a UDG; if the graph is a UDG, then our partition is guaranteed to be within (1 + ɛ) ratio of the optimum; however, if the graph is not a UDG, it either computes a clique partition, or detects that the graph is not a UDG. Noting that recognition of UDG's is NP-hard even with edge lengths, this is a significant weakening of the input model.

  13. Semiclassical limits of quantum partition functions on infinite graphs

    SciTech Connect

    Güneysu, Batu

    2015-02-15

    We prove that if H denotes the operator corresponding to the canonical Dirichlet form on a possibly locally infinite weighted graph (X, b, m), and if v : X → ℝ is such that H + v/ħ is well-defined as a form sum for all ħ > 0, then the quantum partition function tr(e{sup −βħ(H+v/ħ)}) converges to ∑{sub x∈X}e{sup −βv(x)} as ħ → 0 +, for all β > 0, regardless of the fact whether e{sup −βv} is a priori summable or not. This fact can be interpreted as a semiclassical limit, and it allows geometric Weyl-type convergence results. We also prove natural generalizations of this semiclassical limit to a large class of covariant Schrödinger operators that act on sections in Hermitian vector bundle over (X, m, b), a result that particularly applies to magnetic Schrödinger operators that are defined on (X, m, b)

  14. Integrating graph partitioning and matching for trajectory analysis in video surveillance.

    PubMed

    Lin, Liang; Lu, Yongyi; Pan, Yan; Chen, Xiaowu

    2012-12-01

    In order to track moving objects in long range against occlusion, interruption, and background clutter, this paper proposes a unified approach for global trajectory analysis. Instead of the traditional frame-by-frame tracking, our method recovers target trajectories based on a short sequence of video frames, e.g., 15 frames. We initially calculate a foreground map at each frame obtained from a state-of-the-art background model. An attribute graph is then extracted from the foreground map, where the graph vertices are image primitives represented by the composite features. With this graph representation, we pose trajectory analysis as a joint task of spatial graph partitioning and temporal graph matching. The task can be formulated by maximizing a posteriori under the Bayesian framework, in which we integrate the spatio-temporal contexts and the appearance models. The probabilistic inference is achieved by a data-driven Markov chain Monte Carlo algorithm. Given a period of observed frames, the algorithm simulates an ergodic and aperiodic Markov chain, and it visits a sequence of solution states in the joint space of spatial graph partitioning and temporal graph matching. In the experiments, our method is tested on several challenging videos from the public datasets of visual surveillance, and it outperforms the state-of-the-art methods. PMID:22875250

  15. Accurate Segmentation of Cervical Cytoplasm and Nuclei Based on Multiscale Convolutional Network and Graph Partitioning.

    PubMed

    Song, Youyi; Zhang, Ling; Chen, Siping; Ni, Dong; Lei, Baiying; Wang, Tianfu

    2015-10-01

    In this paper, a multiscale convolutional network (MSCN) and graph-partitioning-based method is proposed for accurate segmentation of cervical cytoplasm and nuclei. Specifically, deep learning via the MSCN is explored to extract scale invariant features, and then, segment regions centered at each pixel. The coarse segmentation is refined by an automated graph partitioning method based on the pretrained feature. The texture, shape, and contextual information of the target objects are learned to localize the appearance of distinctive boundary, which is also explored to generate markers to split the touching nuclei. For further refinement of the segmentation, a coarse-to-fine nucleus segmentation framework is developed. The computational complexity of the segmentation is reduced by using superpixel instead of raw pixels. Extensive experimental results demonstrate that the proposed cervical nucleus cell segmentation delivers promising results and outperforms existing methods.

  16. Partitioning a chordal graph into transitive subgraphs for parallel sparse triangular solution

    SciTech Connect

    Peyton, B.W. ); Pothen, A. . Dept. of Computer Science); Yuan, Xiaoqing )

    1992-12-01

    A recent approach for solving sparse triangular systems of equations on massively parallel computers employs a factorization of the triangular coefficient matrix to obtain a representation of its inverse in product form. The number of general communication steps required by this approach is proportional to the number of factors in the factorization. The triangular matrix can be symmetrically permuted to minimize the number of factors over suitable classes of permutations, and thereby the complexity of the parallel algorithm can be minimized. Algorithms for minimizing the number of factors over several classes of permutations have been considered in earlier work. Let F = L+L[sup T] denote the symmetric filled matrix corresponding to a Cholesky factor L, and let G[sub F] denote the adjacency graph of F. In this paper we consider the problem of minirriizing the number of factors over all permutations which preserve the structure of G[sub F]. The graph model of this problem is to partition the vertices G[sub F] into the fewest transitively closed subgraphs over all perfect elimination orderings while satisfying a certain precedence relationship. The solution to this chordal graph partitioning problem can be described by a greedy scheme which eliminates a largest permissible subgraph at each step. Further, the subgraph eliminated at each step can be characterized in terms of lengths of chordless paths in the current elimination graph. This solution relies on several results concerning transitive perfect elimination orderings introduced in this paper. We describe a partitioning algorithm with [Omicron]([vert bar]V[vert bar] + [vert bar]E[vert bar]) time and space complexity.

  17. Partitioning a chordal graph into transitive subgraphs for parallel sparse triangular solution

    SciTech Connect

    Peyton, B.W.; Pothen, A.; Yuan, Xiaoqing

    1992-12-01

    A recent approach for solving sparse triangular systems of equations on massively parallel computers employs a factorization of the triangular coefficient matrix to obtain a representation of its inverse in product form. The number of general communication steps required by this approach is proportional to the number of factors in the factorization. The triangular matrix can be symmetrically permuted to minimize the number of factors over suitable classes of permutations, and thereby the complexity of the parallel algorithm can be minimized. Algorithms for minimizing the number of factors over several classes of permutations have been considered in earlier work. Let F = L+L{sup T} denote the symmetric filled matrix corresponding to a Cholesky factor L, and let G{sub F} denote the adjacency graph of F. In this paper we consider the problem of minirriizing the number of factors over all permutations which preserve the structure of G{sub F}. The graph model of this problem is to partition the vertices G{sub F} into the fewest transitively closed subgraphs over all perfect elimination orderings while satisfying a certain precedence relationship. The solution to this chordal graph partitioning problem can be described by a greedy scheme which eliminates a largest permissible subgraph at each step. Further, the subgraph eliminated at each step can be characterized in terms of lengths of chordless paths in the current elimination graph. This solution relies on several results concerning transitive perfect elimination orderings introduced in this paper. We describe a partitioning algorithm with {Omicron}({vert_bar}V{vert_bar} + {vert_bar}E{vert_bar}) time and space complexity.

  18. Segmentation and classification of PolSAR data using spectral graph partitioning

    NASA Astrophysics Data System (ADS)

    Zhao, Lei; Chen, Erxue

    2013-10-01

    Polar metric synthetic aperture radar (PolSAR) image classification is an important technique in the remote sensing area, has been deeply studied for a couple of decades. This paper proposes a new approach for segmentation and classification of PolSAR datain two steps. First, segmentation is performed based on spectral graph partitioning using edge information. Graph partitioning process is completed using the normalized cut criterion. Then, classification is performed based on the object level. We use Cloude and Pottier‟s method to initially classify the PolSAR image. The initial classification map defines training sets for classification based on the Wishart distribution. The advantages of this method are the automated classification, and the interpretation of each class based on the region‟s scattering mechanism. We tested this object-based analysis on our study area. It showed that this result well overcome the pepper-sault phenomenon appearing in the one using traditional pixel-based method, providing robust performance and the results more understandable and easier for further analyses

  19. On the validity of a front-oriented approach to partitioning large sparse graphs with a connectivity constraint

    NASA Astrophysics Data System (ADS)

    Ciarlet, P.; Lamour, F.

    1996-03-01

    In this paper we consider the problem of partitioning large sparse graphs, such as finite element meshes. The heuristic which is proposed allows to partition into connected and quasi-balanced subgraphs in a reasonable amount of time, while attempting to minimize the number of edge cuts. Here the goal is to build partitions for graphs containing large numbers of nodes and edges, in practice at least 104. Basically, the algorithm relies on the iterative construction of connected subgraphs. This construction is achieved by successively exploring clusters of nodes called fronts. Indeed, a judicious use of fronts ensures the connectivity of the subsets at low cost: it is shown that locally, i.e. for a given subgraph, the complexity of such operations grows at most linearly with the number of edges. Moreover, a few examples are given to illustrate the quality and speed of the heuristic.

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

    SciTech Connect

    Kuhlemann, Verena; Vassilevski, Panayot S.

    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.

  1. Improving Attack Graph Visualization through Data Reduction and Attack Grouping

    SciTech Connect

    John Homer; Ashok Varikuti; Xinming Ou; Miles A. McQueen

    2008-09-01

    Various tools exist to analyze enterprise network systems and to produce attack graphs detailing how attackers might penetrate into the system. These attack graphs, however, are often complex and difficult to comprehend fully, and a human user may find it problematic to reach appropriate configuration decisions. This paper presents methodologies that can 1) automatically identify portions of an attack graph that do not help a user to understand the core security problems and so can be trimmed, and 2) automatically group similar attack steps as virtual nodes in a model of the network topology, to immediately increase the understandability of the data. We believe both methods are important steps toward improving visualization of attack graphs to make them more useful in configuration management for large enterprise networks. We implemented our methods using one of the existing attack-graph toolkits. Initial experimentation shows that the proposed approaches can 1) significantly reduce the complexity of attack graphs by trimming a large portion of the graph that is not needed for a user to understand the security problem, and 2) significantly increase the accessibility and understandability of the data presented in the attack graph by clearly showing, within a generated visualization of the network topology, the number and type of potential attacks to which each host is exposed.

  2. An improved approach of register allocation via graph coloring

    NASA Astrophysics Data System (ADS)

    Gao, Lei; Shi, Ce

    2005-03-01

    Register allocation is an important part of optimizing compiler. The algorithm of register allocation via graph coloring is implemented by Chaitin and his colleagues firstly and improved by Briggs and others. By abstracting register allocation to graph coloring, the allocation process is simplified. As the physical register number is limited, coloring of the interference graph can"t succeed for every node. The uncolored nodes must be spilled. There is an assumption that almost all the allocation method obeys: when a register is allocated to a variable v, it can"t be used by others before v quit even if v is not used for a long time. This may causes a waste of register resource. The authors relax this restriction under certain conditions and make some improvement. In this method, one register can be mapped to two or more interfered "living" live ranges at the same time if they satisfy some requirements. An operation named merge is defined which can arrange two interfered nodes occupy the same register with some cost. Thus, the resource of register can be used more effectively and the cost of memory access can be reduced greatly.

  3. Improved biological network reconstruction using graph Laplacian regularization.

    PubMed

    Freschi, Valerio

    2011-08-01

    Biological networks reconstruction is a crucial step towards the functional characterization and elucidation of living cells. Computational methods for inferring the structure of these networks are of paramount importance since they provide valuable information regarding organization and behavior of the cell at a system level and also enable careful design of wet-lab experiments. Despite many recent advances, according to the scientific literature, there is room for improvements from both the efficiency and the accuracy point of view in link prediction algorithms. In this article, we propose a new method for the inference of biological networks that makes use of a notion of similarity between graph vertices within the framework of graph regularization for ranking the links to be predicted. The proposed approach results in more accurate classification rates in a wide range of experiments, while the computational complexity is reduced by two orders of magnitude with respect to many current state-of-the-art algorithms.

  4. Co-Clustering by Bipartite Spectral Graph Partitioning for Out-of-Tutor Prediction

    ERIC Educational Resources Information Center

    Trivedi, Shubhendu; Pardos, Zachary A.; Sarkozy, Gabor N.; Heffernan, Neil T.

    2012-01-01

    Learning a more distributed representation of the input feature space is a powerful method to boost the performance of a given predictor. Often this is accomplished by partitioning the data into homogeneous groups by clustering so that separate models could be trained on each cluster. Intuitively each such predictor is a better representative of…

  5. Cascading Failures in Bi-partite Graphs: Model for Systemic Risk Propagation

    PubMed Central

    Huang, Xuqing; Vodenska, Irena; Havlin, Shlomo; Stanley, H. Eugene

    2013-01-01

    As economic entities become increasingly interconnected, a shock in a financial network can provoke significant cascading failures throughout the system. To study the systemic risk of financial systems, we create a bi-partite banking network model composed of banks and bank assets and propose a cascading failure model to describe the risk propagation process during crises. We empirically test the model with 2007 US commercial banks balance sheet data and compare the model prediction of the failed banks with the real failed banks after 2007. We find that our model efficiently identifies a significant portion of the actual failed banks reported by Federal Deposit Insurance Corporation. The results suggest that this model could be useful for systemic risk stress testing for financial systems. The model also identifies that commercial rather than residential real estate assets are major culprits for the failure of over 350 US commercial banks during 2008–2011. PMID:23386974

  6. Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates

    PubMed Central

    Hinne, Max; Janssen, Ronald J.; Heskes, Tom; van Gerven, Marcel A.J.

    2015-01-01

    Functional connectivity concerns the correlated activity between neuronal populations in spatially segregated regions of the brain, which may be studied using functional magnetic resonance imaging (fMRI). This coupled activity is conveniently expressed using covariance, but this measure fails to distinguish between direct and indirect effects. A popular alternative that addresses this issue is partial correlation, which regresses out the signal of potentially confounding variables, resulting in a measure that reveals only direct connections. Importantly, provided the data are normally distributed, if two variables are conditionally independent given all other variables, their respective partial correlation is zero. In this paper, we propose a probabilistic generative model that allows us to estimate functional connectivity in terms of both partial correlations and a graph representing conditional independencies. Simulation results show that this methodology is able to outperform the graphical LASSO, which is the de facto standard for estimating partial correlations. Furthermore, we apply the model to estimate functional connectivity for twenty subjects using resting-state fMRI data. Results show that our model provides a richer representation of functional connectivity as compared to considering partial correlations alone. Finally, we demonstrate how our approach can be extended in several ways, for instance to achieve data fusion by informing the conditional independence graph with data from probabilistic tractography. As our Bayesian formulation of functional connectivity provides access to the posterior distribution instead of only to point estimates, we are able to quantify the uncertainty associated with our results. This reveals that while we are able to infer a clear backbone of connectivity in our empirical results, the data are not accurately described by simply looking at the mode of the distribution over connectivity. The implication of this is that

  7. Improved visibility graph fractality with application for the diagnosis of Autism Spectrum Disorder

    NASA Astrophysics Data System (ADS)

    Ahmadlou, Mehran; Adeli, Hojjat; Adeli, Amir

    2012-10-01

    Recently, the visibility graph (VG) algorithm was proposed for mapping a time series to a graph to study complexity and fractality of the time series through investigation of the complexity of its graph. The visibility graph algorithm converts a fractal time series to a scale-free graph. VG has been used for the investigation of fractality in the dynamic behavior of both artificial and natural complex systems. However, robustness and performance of the power of scale-freeness of VG (PSVG) as an effective method for measuring fractality has not been investigated. Since noise is unavoidable in real life time series, the robustness of a fractality measure is of paramount importance. To improve the accuracy and robustness of PSVG to noise for measurement of fractality of time series in biological time-series, an improved PSVG is presented in this paper. The proposed method is evaluated using two examples: a synthetic benchmark time series and a complicated real life Electroencephalograms (EEG)-based diagnostic problem, that is distinguishing autistic children from non-autistic children. It is shown that the proposed improved PSVG is less sensitive to noise and therefore more robust compared with PSVG. Further, it is shown that using improved PSVG in the wavelet-chaos neural network model of Adeli and c-workers in place of the Katz fractality dimension results in a more accurate diagnosis of autism, a complicated neurological and psychiatric disorder.

  8. Application and improvement of Raupach's shear stress partitioning model

    NASA Astrophysics Data System (ADS)

    Walter, B. A.; Lehning, M.; Gromke, C.

    2012-12-01

    Aeolian processes such as the entrainment, transport and redeposition of sand, soil or snow are able to significantly reshape the earth's surface. In times of increasing desertification and land degradation, often driven by wind erosion, investigations of aeolian processes become more and more important in environmental sciences. The reliable prediction of the sheltering effect of vegetation canopies against sediment erosion, for instance, is a clear practical application of such investigations to identify suitable and sustainable counteractive measures against wind erosion. This study presents an application and improvement of a theoretical model presented by Raupach (Boundary-Layer Meteorology, 1992, Vol.60, 375-395 and Journal of Geophysical Research, 1993, Vol.98, 3023-3029) which allows for quantifying the sheltering effect of vegetation against sediment erosion. The model predicts the shear stress ratios τS'/τ and τS''/τ. Here, τS is the part of the total shear stress τ that acts on the ground beneath the plants. The spatial peak τS'' of the surface shear stress is responsible for the onset of particle entrainment whereas the spatial mean τS' can be used to quantify particle mass fluxes. The precise and accurate prediction of these quantities is essential when modeling wind erosion. Measurements of the surface shear stress distributions τS(x,y) on the ground beneath live vegetation canopies (plant species: lolium perenne) were performed in a controlled wind tunnel environment to determine the model parameters and to evaluate the model performance. Rigid, non-porous wooden blocks instead of the plants were additionally tested for the purpose of comparison, since previous wind tunnel studies used exclusively artificial plant imitations for their experiments on shear stress partitioning. The model constant c, which is needed to determine the total stress τ for a canopy of interest and which remained rather unspecified to date, was found to be c ≈ 0

  9. A graph-based method for improving GSAT

    SciTech Connect

    Kask, K.; Dechter, R.

    1996-12-31

    GSAT is a randomized greedy local repair procedure that was introduced for solving propositional satisfiability and constraint satisfaction problems. We present an improvement to GSAT that is sensitive to the problem`s structure. When the problem has a tree structure the algorithm is guaranteed to find a solution in linear time. For non-tree networks, the algorithm designates a subset of nodes, called cutset, and executes a regular GSAT algorithm on this set of variables. On all the rest of the variables it executes a specialized local search algorithm for trees. This algorithm finds an assignment that, like GSAT, locally minimizes the sum of unsatisfied constraints and also globally minimizes the number of conflicts in every tree-like sub-network. We will present results of experiments showing that this new algorithm outperforms regular GSAT on sparse networks whose cycle-cutset size is bounded by 30% of the nodes.

  10. Improved segmentation of abnormal cervical nuclei using a graph-search based approach

    NASA Astrophysics Data System (ADS)

    Zhang, Ling; Liu, Shaoxiong; Wang, Tianfu; Chen, Siping; Sonka, Milan

    2015-03-01

    Reliable segmentation of abnormal nuclei in cervical cytology is of paramount importance in automation-assisted screening techniques. This paper presents a general method for improving the segmentation of abnormal nuclei using a graph-search based approach. More specifically, the proposed method focuses on the improvement of coarse (initial) segmentation. The improvement relies on a transform that maps round-like border in the Cartesian coordinate system into lines in the polar coordinate system. The costs consisting of nucleus-specific edge and region information are assigned to the nodes. The globally optimal path in the constructed graph is then identified by dynamic programming. We have tested the proposed method on abnormal nuclei from two cervical cell image datasets, Herlev and H and E stained liquid-based cytology (HELBC), and the comparative experiments with recent state-of-the-art approaches demonstrate the superior performance of the proposed method.

  11. Improved measurements of partition coefficients for polybrominated diphenyl ethers.

    PubMed

    Wang, Wei; Delgado-Moreno, Laura; Ye, Qingfu; Gan, Jay

    2011-02-15

    Polybrominated diphenyl ethers (PBDEs) are a class of widely used brominated flame retardants with strong hydrophobicity. Due to their strong affinity for organic matter, accurate measurement of adsorption coefficients for PBDEs using conventional batch methods can be confounded by biases caused by their sorption to dissolved organic carbon (DOC). In this study, sorption isotherms were constructed for BDE-47 and BDE-99 in sediments by using different methods to measure the aqueous phase concentration Cw. Upon centrifugation, Cw measured by automated solid-phase microextraction (Cw-SPME) was consistently smaller than by liquid-liquid extraction (Cw-LLE), suggesting substantial association of PBDEs with DOC. Significant underestimations (1.2-106-fold) of sediment-water partition coefficient Kd occurred when Cw was measured by LLE. The log KDOC values derived from the SPME measurements ranged from 5.10 to 8.02 for eight congeners from BDE-28 to BDE-183, suggesting a strong tendency for PBDEs to complex with DOC. This study showed that PBDE congeners have larger sorption coefficients than would be measured by the conventional method. The high affinity to DOC also means a potential for DOC-facilitated transport, thus enhancing the environmental mobility of PBDEs. PMID:21210679

  12. Clique graphs and overlapping communities

    NASA Astrophysics Data System (ADS)

    Evans, T. S.

    2010-12-01

    It is shown how to construct a clique graph in which properties of cliques of a fixed order in a given graph are represented by vertices in a weighted graph. Various definitions and motivations for these weights are given. The detection of communities or clusters is used to illustrate how a clique graph may be exploited. In particular a benchmark network is shown where clique graphs find the overlapping communities accurately while vertex partition methods fail.

  13. Improved genome inference in the MHC using a population reference graph

    PubMed Central

    Dilthey, Alexander; Cox, Charles; Iqbal, Zamin; Nelson, Matthew R.; McVean, Gil

    2015-01-01

    While much is known about human genetic variation, such information is typically ignored in assembling novel genomes. Instead, reads are mapped to a single reference, which can lead to poor characterization of regions of high sequence or structural diversity. We introduce a population reference graph, which combines multiple reference sequences and catalogues of variation. The genomes of novel samples are reconstructed as paths through the graph using an efficient hidden Markov model, allowing for recombination between different haplotypes and additional variants. By applying the method to the 4.5Mb extended MHC region on human chromosome 6, combining eight assembled haplotypes, sequences of known classical HLA alleles and 87,640 SNP variants from the 1000 Genomes Project, we demonstrate, using simulations, SNP genotyping, short-read and long-read data, how the method improves the accuracy of genome inference and reveals regions where the current set of reference sequences is substantially incomplete. PMID:25915597

  14. Partition dataset according to amino acid type improves the prediction of deleterious non-synonymous SNPs

    SciTech Connect

    Yang, Jing; Li, Yuan-Yuan; Li, Yi-Xue; Ye, Zhi-Qiang

    2012-03-02

    Highlights: Black-Right-Pointing-Pointer Proper dataset partition can improve the prediction of deleterious nsSNPs. Black-Right-Pointing-Pointer Partition according to original residue type at nsSNP is a good criterion. Black-Right-Pointing-Pointer Similar strategy is supposed promising in other machine learning problems. -- Abstract: Many non-synonymous SNPs (nsSNPs) are associated with diseases, and numerous machine learning methods have been applied to train classifiers for sorting disease-associated nsSNPs from neutral ones. The continuously accumulated nsSNP data allows us to further explore better prediction approaches. In this work, we partitioned the training data into 20 subsets according to either original or substituted amino acid type at the nsSNP site. Using support vector machine (SVM), training classification models on each subset resulted in an overall accuracy of 76.3% or 74.9% depending on the two different partition criteria, while training on the whole dataset obtained an accuracy of only 72.6%. Moreover, the dataset was also randomly divided into 20 subsets, but the corresponding accuracy was only 73.2%. Our results demonstrated that partitioning the whole training dataset into subsets properly, i.e., according to the residue type at the nsSNP site, will improve the performance of the trained classifiers significantly, which should be valuable in developing better tools for predicting the disease-association of nsSNPs.

  15. High dimensional data clustering by partitioning the hypergraphs using dense subgraph partition

    NASA Astrophysics Data System (ADS)

    Sun, Xili; Tian, Shoucai; Lu, Yonggang

    2015-12-01

    Due to the curse of dimensionality, traditional clustering methods usually fail to produce meaningful results for the high dimensional data. Hypergraph partition is believed to be a promising method for dealing with this challenge. In this paper, we first construct a graph G from the data by defining an adjacency relationship between the data points using Shared Reverse k Nearest Neighbors (SRNN). Then a hypergraph is created from the graph G by defining the hyperedges to be all the maximal cliques in the graph G. After the hypergraph is produced, a powerful hypergraph partitioning method called dense subgraph partition (DSP) combined with the k-medoids method is used to produce the final clustering results. The proposed method is evaluated on several real high-dimensional datasets, and the experimental results show that the proposed method can improve the clustering results of the high dimensional data compared with applying k-medoids method directly on the original data.

  16. An improved bi-level algorithm for partitioning dynamic grid hierarchies.

    SciTech Connect

    Deiterding, Ralf (California Institute of Technology, Pasadena, CA); Johansson, Henrik (Uppsala University, Uppsala, Sweden); Steensland, Johan; Ray, Jaideep

    2006-05-01

    Structured adaptive mesh refinement methods are being widely used for computer simulations of various physical phenomena. Parallel implementations potentially offer realistic simulations of complex three-dimensional applications. But achieving good scalability for large-scale applications is non-trivial. Performance is limited by the partitioner's ability to efficiently use the underlying parallel computer's resources. Designed on sound SAMR principles, Nature+Fable is a hybrid, dedicated SAMR partitioning tool that brings together the advantages of both domain-based and patch-based techniques while avoiding their drawbacks. But the original bi-level partitioning approach in Nature+Fable is insufficient as it for realistic applications regards frequently occurring bi-levels as ''impossible'' and fails. This document describes an improved bi-level partitioning algorithm that successfully copes with all possible bi-levels. The improved algorithm uses the original approach side-by-side with a new, complementing approach. By using a new, customized classification method, the improved algorithm switches automatically between the two approaches. This document describes the algorithms, discusses implementation issues, and presents experimental results. The improved version of Nature+Fable was found to be able to handle realistic applications and also to generate less imbalances, similar box count, but more communication as compared to the native, domain-based partitioner in the SAMR framework AMROC.

  17. Partition search

    SciTech Connect

    Ginsberg, M.L.

    1996-12-31

    We introduce a new form of game search called partition search that incorporates dependency analysis, allowing substantial reductions in the portion of the tree that needs to be expanded. Both theoretical results and experimental data are presented. For the game of bridge, partition search provides approximately as much of an improvement over existing methods as {alpha}-{beta} pruning provides over minimax.

  18. Using the SWAT model to improve process descriptions and define hydrologic partitioning in South Korea

    NASA Astrophysics Data System (ADS)

    Shope, C. L.; Maharjan, G. R.; Tenhunen, J.; Seo, B.; Kim, K.; Riley, J.; Arnhold, S.; Koellner, T.; Ok, Y. S.; Peiffer, S.; Kim, B.; Park, J.-H.; Huwe, B.

    2014-02-01

    Watershed-scale modeling can be a valuable tool to aid in quantification of water quality and yield; however, several challenges remain. In many watersheds, it is difficult to adequately quantify hydrologic partitioning. Data scarcity is prevalent, accuracy of spatially distributed meteorology is difficult to quantify, forest encroachment and land use issues are common, and surface water and groundwater abstractions substantially modify watershed-based processes. Our objective is to assess the capability of the Soil and Water Assessment Tool (SWAT) model to capture event-based and long-term monsoonal rainfall-runoff processes in complex mountainous terrain. To accomplish this, we developed a unique quality-control, gap-filling algorithm for interpolation of high-frequency meteorological data. We used a novel multi-location, multi-optimization calibration technique to improve estimations of catchment-wide hydrologic partitioning. The interdisciplinary model was calibrated to a unique combination of statistical, hydrologic, and plant growth metrics. Our results indicate scale-dependent sensitivity of hydrologic partitioning and substantial influence of engineered features. The addition of hydrologic and plant growth objective functions identified the importance of culverts in catchment-wide flow distribution. While this study shows the challenges of applying the SWAT model to complex terrain and extreme environments; by incorporating anthropogenic features into modeling scenarios, we can enhance our understanding of the hydroecological impact.

  19. Improving Students' Understanding of Waves by Plotting a Displacement-Time Graph in Class

    NASA Astrophysics Data System (ADS)

    Wei, Yajun

    2012-04-01

    The topic of waves is one that many high school physics students find difficult to understand. This is especially true when using some A-level textbooks1,2used in the U.K., where the concept of waves is introduced prior to the concept of simple harmonic oscillations. One of the challenges my students encounter is understanding the difference between displacement-time graphs and displacement-position graphs. Many students wonder why these two graphs have the same sinusoidal shape. Having the students use multimedia simulations allows them to see, in a hands-on fashion, the relationship between the two graphs.

  20. Area law for random graph states

    NASA Astrophysics Data System (ADS)

    Collins, Benoît; Nechita, Ion; Życzkowski, Karol

    2013-08-01

    Random pure states of multi-partite quantum systems, associated with arbitrary graphs, are investigated. Each vertex of the graph represents a generic interaction between subsystems, described by a random unitary matrix distributed according to the Haar measure, while each edge of the graph represents a bipartite, maximally entangled state. For any splitting of the graph into two parts we consider the corresponding partition of the quantum system and compute the average entropy of entanglement. First, in the special case where the partition does not cross any vertex of the graph, we show that the area law is satisfied exactly. In the general case, we show that the entropy of entanglement obeys an area law on average, this time with a correction term that depends on the topologies of the graph and of the partition. The results obtained are applied to the problem of distribution of quantum entanglement in a quantum network with prescribed topology.

  1. In-gel β-elimination and aqueous-organic partition for improved O- and sulfoglycomics

    PubMed Central

    Kumagai, Tadahiro; Katoh, Toshihiko; Nix, David B.; Tiemeyer, Michael; Aoki, Kazuhiro

    2014-01-01

    SDS-PAGE is a widely used technique for protein separation and in-gel tryptic digestion of resolved protein bands has enhanced the resolution of protoeomic analysis. To augment this technology and expand its usefulness for glycoproteomics, we have developed and improved methods to release and recover O-linked glycans from proteins resolved in SDS-PAGE gels for subsequent analysis by mass spectrometry (MS). Gel pieces containing target proteins are washed to remove contaminants. O-linked glycans are released through reductive β-elimination by hydrating gel pieces in base and adding reductant. Following straightforward sample cleanup, this simple treatment of glycoprotein gel pieces produces material suitable for MS analysis. We have applied this method to the analysis of mucin-type glycoproteins that are expected to carry high densities of sialylated and sulfated O-linked glycans. However, the strongly acidic nature of the sulfate moiety suppresses MS signal intensities, hampering detection and quantitative analysis. To enhance detection, we present an improved method for sulfoglycomics. A mixture of sulflo-, sialo-, and neutral glycans were permethylated and partitioned into a water-dichloromethane (DCM) solvent mixture. Sulfated glycans were selectively recovered from the aqueous phase, while neutral and sialylated glycans remained in the DCM phase. When applied to the analysis of human mucin salivary glycans, this partition method generated material of sufficient quality to identify more than sixty glycan structures by NSI-MS (LTQ-Orbitrap) in positive and negative ion modes. Also, nearly 100% of the sulfated O-linked glycans were recovered in the aqueous phase, demonstrating the feasibility of in-depth sulfoglycomic analysis using SDS-PAGE resolved proteins. PMID:23937624

  2. Graph ensemble boosting for imbalanced noisy graph stream classification.

    PubMed

    Pan, Shirui; Wu, Jia; Zhu, Xingquan; Zhang, Chengqi

    2015-05-01

    Many applications involve stream data with structural dependency, graph representations, and continuously increasing volumes. For these applications, it is very common that their class distributions are imbalanced with minority (or positive) samples being only a small portion of the population, which imposes significant challenges for learning models to accurately identify minority samples. This problem is further complicated with the presence of noise, because they are similar to minority samples and any treatment for the class imbalance may falsely focus on the noise and result in deterioration of accuracy. In this paper, we propose a classification model to tackle imbalanced graph streams with noise. Our method, graph ensemble boosting, employs an ensemble-based framework to partition graph stream into chunks each containing a number of noisy graphs with imbalanced class distributions. For each individual chunk, we propose a boosting algorithm to combine discriminative subgraph pattern selection and model learning as a unified framework for graph classification. To tackle concept drifting in graph streams, an instance level weighting mechanism is used to dynamically adjust the instance weight, through which the boosting framework can emphasize on difficult graph samples. The classifiers built from different graph chunks form an ensemble for graph stream classification. Experiments on real-life imbalanced graph streams demonstrate clear benefits of our boosting design for handling imbalanced noisy graph stream.

  3. Graph-based sampling for approximating global helical topologies of RNA.

    PubMed

    Kim, Namhee; Laing, Christian; Elmetwaly, Shereef; Jung, Segun; Curuksu, Jeremy; Schlick, Tamar

    2014-03-18

    A current challenge in RNA structure prediction is the description of global helical arrangements compatible with a given secondary structure. Here we address this problem by developing a hierarchical graph sampling/data mining approach to reduce conformational space and accelerate global sampling of candidate topologies. Starting from a 2D structure, we construct an initial graph from size measures deduced from solved RNAs and junction topologies predicted by our data-mining algorithm RNAJAG trained on known RNAs. We sample these graphs in 3D space guided by knowledge-based statistical potentials derived from bending and torsion measures of internal loops as well as radii of gyration for known RNAs. Graph sampling results for 30 representative RNAs are analyzed and compared with reference graphs from both solved structures and predicted structures by available programs. This comparison indicates promise for our graph-based sampling approach for characterizing global helical arrangements in large RNAs: graph rmsds range from 2.52 to 28.24 Å for RNAs of size 25-158 nucleotides, and more than half of our graph predictions improve upon other programs. The efficiency in graph sampling, however, implies an additional step of translating candidate graphs into atomic models. Such models can be built with the same idea of graph partitioning and build-up procedures we used for RNA design.

  4. The use of acoustically tuned resonators to improve the sound transmission loss of double-panel partitions

    NASA Astrophysics Data System (ADS)

    Mason, J. M.; Fahy, F. J.

    1988-07-01

    Double-leaf partitions are often utilized in situations requiring low weight structures with high transmission loss, an example of current interest being the fuselage walls of propeller-driven aircraft. In this case, acoustic excitation is periodic and, if one of the frequencies of excitation lies in the region of the fundamental mass-air-mass frequency of the partition, insulation performance is considerably less than desired. The potential effectiveness of tuned Helmholtz resonators connected to the partition cavity is investigated as a method of improving transmission loss. This is demonstrated by a simple theoretical model and then experimentally verified. Results show that substantial improvements may be obtained at and around the mass-air-mass frequency for a total resonator volume 15 percent of the cavity volume.

  5. Anatomically-adapted graph wavelets for improved group-level fMRI activation mapping.

    PubMed

    Behjat, Hamid; Leonardi, Nora; Sörnmo, Leif; Van De Ville, Dimitri

    2015-12-01

    A graph based framework for fMRI brain activation mapping is presented. The approach exploits the spectral graph wavelet transform (SGWT) for the purpose of defining an advanced multi-resolutional spatial transformation for fMRI data. The framework extends wavelet based SPM (WSPM), which is an alternative to the conventional approach of statistical parametric mapping (SPM), and is developed specifically for group-level analysis. We present a novel procedure for constructing brain graphs, with subgraphs that separately encode the structural connectivity of the cerebral and cerebellar gray matter (GM), and address the inter-subject GM variability by the use of template GM representations. Graph wavelets tailored to the convoluted boundaries of GM are then constructed as a means to implement a GM-based spatial transformation on fMRI data. The proposed approach is evaluated using real as well as semi-synthetic multi-subject data. Compared to SPM and WSPM using classical wavelets, the proposed approach shows superior type-I error control. The results on real data suggest a higher detection sensitivity as well as the capability to capture subtle, connected patterns of brain activity.

  6. Quantitative synteny scoring improves homology inference and partitioning of gene families

    PubMed Central

    2013-01-01

    Background Clustering sequences into families has long been an important step in characterization of genes and proteins. There are many algorithms developed for this purpose, most of which are based on either direct similarity between gene pairs or some sort of network structure, where weights on edges of constructed graphs are based on similarity. However, conserved synteny is an important signal that can help distinguish homology and it has not been utilized to its fullest potential. Results Here, we present GenFamClust, a pipeline that combines the network properties of sequence similarity and synteny to assess homology relationship and merge known homologs into groups of gene families. GenFamClust identifies homologs in a more informed and accurate manner as compared to similarity based approaches. We tested our method against the Neighborhood Correlation method on two diverse datasets consisting of fully sequenced genomes of eukaryotes and synthetic data. Conclusions The results obtained from both datasets confirm that synteny helps determine homology and GenFamClust improves on Neighborhood Correlation method. The accuracy as well as the definition of synteny scores is the most valuable contribution of GenFamClust. PMID:24564516

  7. On some trees having partition dimension four

    NASA Astrophysics Data System (ADS)

    Ida Bagus Kade Puja Arimbawa, K.; Baskoro, Edy Tri

    2016-02-01

    In 1998, G. Chartrand, E. Salehi and P. Zhang introduced the notion of partition dimension of a graph. Since then, the study of this graph parameter has received much attention. A number of results have been obtained to know the values of partition dimensions of various classes of graphs. However, for some particular classes of graphs, finding of their partition dimensions is still not completely solved, for instances a class of general tree. In this paper, we study the properties of trees having partition dimension 4. In particular, we show that, for olive trees O(n), its partition dimension is equal to 4 if and only if 8 ≤ n ≤ 17. We also characterize all centipede trees having partition dimension 4.

  8. Graph Library

    2007-06-12

    GraphLib is a support library used by other tools to create, manipulate, store, and export graphs. It provides a simple interface to specifS’ arbitrary directed and undirected graphs by adding nodes and edges. Each node and edge can be associated with a set of attributes describing size, color, and shape. Once created, graphs can be manipulated using a set of graph analysis algorithms, including merge, prune, and path coloring operations. GraphLib also has the abilitymore » to export graphs into various open formats such as DOT and GML.« less

  9. "Improved Geometric Network Model" (IGNM): a novel approach for deriving Connectivity Graphs for Indoor Navigation

    NASA Astrophysics Data System (ADS)

    Mortari, F.; Zlatanova, S.; Liu, L.; Clementini, E.

    2014-04-01

    Over the past few years Personal Navigation Systems have become an established tool for route planning, but they are mainly designed for outdoor environments. Indoor navigation is still a challenging research area for several reasons: positioning is not very accurate, users can freely move between the interior boundaries of buildings, path network construction process may not be easy and straightforward due to complexity of indoor space configurations. Therefore the creation of a good network is essential for deriving overall connectivity of a building and for representing position of objects within the environment. This paper reviews current approaches to automatic derivation of route graphs for indoor navigation and discusses some of their limitations. Then, it introduces a novel algorithmic strategy for extracting a 3D connectivity graph for indoor navigation based on 2D floor plans.

  10. Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer

    PubMed Central

    2011-01-01

    Background One of the main goals in cancer studies including high-throughput microRNA (miRNA) and mRNA data is to find and assess prognostic signatures capable of predicting clinical outcome. Both mRNA and miRNA expression changes in cancer diseases are described to reflect clinical characteristics like staging and prognosis. Furthermore, miRNA abundance can directly affect target transcripts and translation in tumor cells. Prediction models are trained to identify either mRNA or miRNA signatures for patient stratification. With the increasing number of microarray studies collecting mRNA and miRNA from the same patient cohort there is a need for statistical methods to integrate or fuse both kinds of data into one prediction model in order to find a combined signature that improves the prediction. Results Here, we propose a new method to fuse miRNA and mRNA data into one prediction model. Since miRNAs are known regulators of mRNAs we used the correlations between them as well as the target prediction information to build a bipartite graph representing the relations between miRNAs and mRNAs. This graph was used to guide the feature selection in order to improve the prediction. The method is illustrated on a prostate cancer data set comprising 98 patient samples with miRNA and mRNA expression data. The biochemical relapse was used as clinical endpoint. It could be shown that the bipartite graph in combination with both data sets could improve prediction performance as well as the stability of the feature selection. Conclusions Fusion of mRNA and miRNA expression data into one prediction model improves clinical outcome prediction in terms of prediction error and stable feature selection. The R source code of the proposed method is available in the supplement. PMID:22188670

  11. Improved initialisation of model-based clustering using Gaussian hierarchical partitions

    PubMed Central

    Scrucca, Luca; Raftery, Adrian E.

    2015-01-01

    Initialisation of the EM algorithm in model-based clustering is often crucial. Various starting points in the parameter space often lead to different local maxima of the likelihood function and, so to different clustering partitions. Among the several approaches available in the literature, model-based agglomerative hierarchical clustering is used to provide initial partitions in the popular mclust R package. This choice is computationally convenient and often yields good clustering partitions. However, in certain circumstances, poor initial partitions may cause the EM algorithm to converge to a local maximum of the likelihood function. We propose several simple and fast refinements based on data transformations and illustrate them through data examples. PMID:26949421

  12. Application of annular centrifugal contactors in the hot test of the improved total partitioning process for high level liquid waste.

    PubMed

    Duan, Wuhua; Chen, Jing; Wang, Jianchen; Wang, Shuwei; Feng, Xiaogui; Wang, Xinghai; Li, Shaowei; Xu, Chao

    2014-08-15

    High level liquid waste (HLLW) produced from the reprocessing of the spent nuclear fuel still contains moderate amounts of uranium, transuranium (TRU) actinides, (90)Sr, (137)Cs, etc., and thus constitutes a permanent hazard to the environment. The partitioning and transmutation (P&T) strategy has increasingly attracted interest for the safe treatment and disposal of HLLW, in which the partitioning of HLLW is one of the critical technical issues. An improved total partitioning process, including a TRPO (tri-alkylphosphine oxide) process for the removal of actinides, a CESE (crown ether strontium extraction) process for the removal of Sr, and a CECE (calixcrown ether cesium extraction) process for the removal of Cs, has been developed to treat Chinese HLLW. A 160-hour hot test of the improved total partitioning process was carried out using 72-stage 10-mm-dia annular centrifugal contactors (ACCs) and genuine HLLW. The hot test results showed that the average DFs of total α activity, Sr and Cs were 3.57 × 10(3), 2.25 × 10(4) and 1.68 × 10(4) after the hot test reached equilibrium, respectively. During the hot test, 72-stage 10-mm-dia ACCs worked stable, continuously with no stage failing or interruption of the operation.

  13. Subgraph-Based Filterbanks for Graph Signals

    NASA Astrophysics Data System (ADS)

    Tremblay, Nicolas; Borgnat, Pierre

    2016-08-01

    We design a critically-sampled compact-support biorthogonal transform for graph signals, via graph filterbanks. Instead of partitioning the nodes in two sets so as to remove one every two nodes in the filterbank downsampling operations, the design is based on a partition of the graph in connected subgraphs. Coarsening is achieved by defining one "supernode" for each subgraph and the edges for this coarsened graph derives from the connectivity between the subgraphs. Unlike the "one every two nodes" downsampling on bipartite graphs, this coarsening operation does not have an exact formulation in the graph Fourier domain. Instead, we rely on the local Fourier bases of each subgraph to define filtering operations. We apply successfully this method to decompose graph signals, and show promising performance on compression and denoising.

  14. Subdominant pseudoultrametric on graphs

    SciTech Connect

    Dovgoshei, A A; Petrov, E A

    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.

  15. Partitioning technique for discrete quantum systems

    SciTech Connect

    Jin, L.; Song, Z.

    2011-06-15

    We develop the partitioning technique for quantum discrete systems. The graph consists of several subgraphs: a central graph and several branch graphs, with each branch graph being rooted by an individual node on the central one. We show that the effective Hamiltonian on the central graph can be constructed by adding additional potentials on the branch-root nodes, which generates the same result as does the the original Hamiltonian on the entire graph. Exactly solvable models are presented to demonstrate the main points of this paper.

  16. A partitioned shift-without-invert algorithm to improve parallel eigensolution efficiency in real-space electronic transport

    NASA Astrophysics Data System (ADS)

    Feldman, Baruch; Zhou, Yunkai

    2016-10-01

    We present an eigenspectrum partitioning scheme without inversion for the recently described real-space electronic transport code, TRANSEC. The primary advantage of TRANSEC is its highly parallel algorithm, which enables studying conductance in large systems. The present scheme adds a new source of parallelization, significantly enhancing TRANSEC's parallel scalability, especially for systems with many electrons. In principle, partitioning could enable super-linear parallel speedup, as we demonstrate in calculations within TRANSEC. In practical cases, we report better than five-fold improvement in CPU time and similar improvements in wall time, compared to previously-published large calculations. Importantly, the suggested scheme is relatively simple to implement. It can be useful for general large Hermitian or weakly non-Hermitian eigenvalue problems, whenever relatively accurate inversion via direct or iterative linear solvers is impractical.

  17. Detecting alternative graph clusterings.

    PubMed

    Mandala, Supreet; Kumara, Soundar; Yao, Tao

    2012-07-01

    The problem of graph clustering or community detection has enjoyed a lot of attention in complex networks literature. A quality function, modularity, quantifies the strength of clustering and on maximization yields sensible partitions. However, in most real world networks, there are an exponentially large number of near-optimal partitions with some being very different from each other. Therefore, picking an optimal clustering among the alternatives does not provide complete information about network topology. To tackle this problem, we propose a graph perturbation scheme which can be used to identify an ensemble of near-optimal and diverse clusterings. We establish analytical properties of modularity function under the perturbation which ensures diversity. Our approach is algorithm independent and therefore can leverage any of the existing modularity maximizing algorithms. We numerically show that our methodology can systematically identify very different partitions on several existing data sets. The knowledge of diverse partitions sheds more light into the topological organization and helps gain a more complete understanding of the underlying complex network.

  18. Some trees with partition dimension three

    NASA Astrophysics Data System (ADS)

    Fredlina, Ketut Queena; Baskoro, Edy Tri

    2016-02-01

    The concept of partition dimension of a graph was introduced by Chartrand, E. Salehi and P. Zhang (1998) [2]. Let G(V, E) be a connected graph. For S ⊆ V (G) and v ∈ V (G), define the distance d(v, S) from v to S is min{d(v, x)|x ∈ S}. Let Π be an ordered partition of V (G) and Π = {S1, S2, ..., Sk }. The representation r(v|Π) of vertex v with respect to Π is (d(v, S1), d(v, S2), ..., d(v, Sk)). If the representations of all vertices are distinct, then the partition Π is called a resolving partition of G. The partition dimension of G is the minimum k such that G has a resolving partition with k partition classes. In this paper, we characterize some classes of trees with partition dimension three, namely olive trees, weeds, and centipedes.

  19. Path similarity skeleton graph matching.

    PubMed

    Bai, Xiang; Latecki, Longin Jan

    2008-07-01

    This paper presents a novel framework to for shape recognition based on object silhouettes. The main idea is to match skeleton graphs by comparing the shortest paths between skeleton endpoints. In contrast to typical tree or graph matching methods, we completely ignore the topological graph structure. Our approach is motivated by the fact that visually similar skeleton graphs may have completely different topological structures. The proposed comparison of shortest paths between endpoints of skeleton graphs yields correct matching results in such cases. The skeletons are pruned by contour partitioning with Discrete Curve Evolution, which implies that the endpoints of skeleton branches correspond to visual parts of the objects. The experimental results demonstrate that our method is able to produce correct results in the presence of articulations, stretching, and occlusion.

  20. The peculiar phase structure of random graph bisection

    SciTech Connect

    Percus, Allon G; Istrate, Gabriel; Goncalves, Bruno T; Sumi, Robert Z

    2008-01-01

    The mincut graph bisection problem involves partitioning the n vertices of a graph into disjoint subsets, each containing exactly n/2 vertices, while minimizing the number of 'cut' edges with an endpoint in each subset. When considered over sparse random graphs, the phase structure of the graph bisection problem displays certain familiar properties, but also some surprises. It is known that when the mean degree is below the critical value of 2 log 2, the cutsize is zero with high probability. We study how the minimum cutsize increases with mean degree above this critical threshold, finding a new analytical upper bound that improves considerably upon previous bounds. Combined with recent results on expander graphs, our bound suggests the unusual scenario that random graph bisection is replica symmetric up to and beyond the critical threshold, with a replica symmetry breaking transition possibly taking place above the threshold. An intriguing algorithmic consequence is that although the problem is NP-hard, we can find near-optimal cutsizes (whose ratio to the optimal value approaches 1 asymptotically) in polynomial time for typical instances near the phase transition.

  1. Graph-based modeling of tandem repeats improves global multiple sequence alignment.

    PubMed

    Szalkowski, Adam M; Anisimova, Maria

    2013-09-01

    Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein family.

  2. Light Competition and Carbon Partitioning-Allocation in an improved Forest Ecosystem Model

    NASA Astrophysics Data System (ADS)

    Collalti, Alessio; Santini, Monia; Valentini Valentini, Riccardo

    2010-05-01

    In Italy about 100.000 km2 are covered by forests. This surface is the 30% of the whole national land and this shows how the forests are important both for socio-economic and for environmental aspects. Forests changes affect a delicate balance that involve not only vegetation components but also bio-geochemical cycles and global climate. The knowledge of the amount of Carbon sequestered by forests represents a precious information for their sustainable management in the framework of climate changes. Primary studies in terms of model about this important issue, has been done through Forest Ecosystem Model (FEM), well known and validated as 3PG (Landsberg et Waring, 1997; Sands 2004). It is based on light use efficiency approach at the canopy level. The present study started from the original model 3PG, producing an improved version that uses many of explicit formulations of all relevant ecophysiological processes but makes it able to be applied for natural forests. The mutual interaction of forest growth and light conditions causes vertical and horizontal differentiation in the natural forest mosaic. Only ecophysiological parameters which can be either directly measured or estimates with reasonable certainty are used. The model has been written in C language and has been created considering a tri-dimensional cell structure with different vertical layers depending on the forest type that has to be simulated. This 3PG 'improved' version enable to work on multi-layer and multi-species forests type with cell resolution of one hectare for the typical Italian forest species. The multi-layer version is the result of the implementation and development of Lambert-Beer law for the estimation of intercepted, absorbed and transmitted light through different storeys of the forest. It is possible estimates, for each storey, a Par value (Photosynthetic Active Radiation) through Leaf Area Index (LAI), Light Extinction Coefficient and cell Canopy Cover using a "Big Leaf" approach

  3. Dense Subgraph Partition of Positive Hypergraphs.

    PubMed

    Liu, Hairong; Latecki, Longin Jan; Yan, Shuicheng

    2015-03-01

    In this paper, we present a novel partition framework, called dense subgraph partition (DSP), to automatically, precisely and efficiently decompose a positive hypergraph into dense subgraphs. A positive hypergraph is a graph or hypergraph whose edges, except self-loops, have positive weights. We first define the concepts of core subgraph, conditional core subgraph, and disjoint partition of a conditional core subgraph, then define DSP based on them. The result of DSP is an ordered list of dense subgraphs with decreasing densities, which uncovers all underlying clusters, as well as outliers. A divide-and-conquer algorithm, called min-partition evolution, is proposed to efficiently compute the partition. DSP has many appealing properties. First, it is a nonparametric partition and it reveals all meaningful clusters in a bottom-up way. Second, it has an exact and efficient solution, called min-partition evolution algorithm. The min-partition evolution algorithm is a divide-and-conquer algorithm, thus time-efficient and memory-friendly, and suitable for parallel processing. Third, it is a unified partition framework for a broad range of graphs and hypergraphs. We also establish its relationship with the densest k-subgraph problem (DkS), an NP-hard but fundamental problem in graph theory, and prove that DSP gives precise solutions to DkS for all kin a graph-dependent set, called critical k-set. To our best knowledge, this is a strong result which has not been reported before. Moreover, as our experimental results show, for sparse graphs, especially web graphs, the size of critical k-set is close to the number of vertices in the graph. We test the proposed partition framework on various tasks, and the experimental results clearly illustrate its advantages.

  4. Campaign graphs

    SciTech Connect

    Simmons, G.J.

    1988-01-01

    We define a class of geometrical constructions in the plane in which each (unextended) line lies on (precisely) k points, and every point is an endpoint of (precisely) one line. We will refer to any construction satisfying these conditions as a campaign graph, or as a k-campaign graph if the value of k isn't clear from the context. A k-campaign graph, G, is said to be critical if no subgraph of G is also a k-campaign graph. 11 figs.

  5. Isorropia Partitioning and Load Balancing Package

    2006-09-01

    Isorropia is a partitioning and load balancing package which interfaces with the Zoltan library. Isorropia can accept input objects such as matrices and matrix-graphs, and repartition/redistribute them into a better data distribution on parallel computers. Isorropia is primarily an interface package, utilizing graph and hypergraph partitioning algorithms that are in the Zoltan library which is a third-party library to Tilinos.

  6. Topic Model for Graph Mining.

    PubMed

    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.

  7. Graphing Predictions

    ERIC Educational Resources Information Center

    Connery, Keely Flynn

    2007-01-01

    Graphing predictions is especially important in classes where relationships between variables need to be explored and derived. In this article, the author describes how his students sketch the graphs of their predictions before they begin their investigations on two laboratory activities: Distance Versus Time Cart Race Lab and Resistance; and…

  8. Development of a floating photobioreactor with internal partitions for efficient utilization of ocean wave into improved mass transfer and algal culture mixing.

    PubMed

    Kim, Z-Hun; Park, Hanwool; Hong, Seong-Joo; Lim, Sang-Min; Lee, Choul-Gyun

    2016-05-01

    Culturing microalgae in the ocean has potentials that may reduce the production cost and provide an option for an economic biofuel production from microalgae. The ocean holds great potentials for mass microalgal cultivation with its high specific heat, mixing energy from waves, and large cultivable area. Suitable photobioreactors (PBRs) that are capable of integrating marine energy into the culture systems need to be developed for the successful ocean cultivation. In this study, prototype floating PBRs were designed and constructed using transparent low-density polyethylene film for microalgal culture in the ocean. To improve the mixing efficiency, various types of internal partitions were introduced within PBRs. Three different types of internal partitions were evaluated for their effects on the mixing efficiency in terms of mass transfer (k(L)a) and mixing time in the PBRs. The partition type with the best mixing efficiency was selected, and the number of partitions was varied from one to three for investigation of its effect on mixing efficiency. When the number of partitions is increased, mass transfer increased in proportion to the number of partitions. However, mixing time was not directly related to the number of partitions. When a green microalga, Tetraselmis sp. was cultivated using PBRs with the selected partition under semi-continuous mode in the ocean, biomass and fatty acid productivities in the PBRs were increased by up to 50 % and 44% at high initial cell density, respectively, compared to non-partitioned ones. The results of internally partitioned PBRs demonstrated potentials for culturing microalgae by efficiently utilizing ocean wave energy into culture mixing in the ocean.

  9. Development of a floating photobioreactor with internal partitions for efficient utilization of ocean wave into improved mass transfer and algal culture mixing.

    PubMed

    Kim, Z-Hun; Park, Hanwool; Hong, Seong-Joo; Lim, Sang-Min; Lee, Choul-Gyun

    2016-05-01

    Culturing microalgae in the ocean has potentials that may reduce the production cost and provide an option for an economic biofuel production from microalgae. The ocean holds great potentials for mass microalgal cultivation with its high specific heat, mixing energy from waves, and large cultivable area. Suitable photobioreactors (PBRs) that are capable of integrating marine energy into the culture systems need to be developed for the successful ocean cultivation. In this study, prototype floating PBRs were designed and constructed using transparent low-density polyethylene film for microalgal culture in the ocean. To improve the mixing efficiency, various types of internal partitions were introduced within PBRs. Three different types of internal partitions were evaluated for their effects on the mixing efficiency in terms of mass transfer (k(L)a) and mixing time in the PBRs. The partition type with the best mixing efficiency was selected, and the number of partitions was varied from one to three for investigation of its effect on mixing efficiency. When the number of partitions is increased, mass transfer increased in proportion to the number of partitions. However, mixing time was not directly related to the number of partitions. When a green microalga, Tetraselmis sp. was cultivated using PBRs with the selected partition under semi-continuous mode in the ocean, biomass and fatty acid productivities in the PBRs were increased by up to 50 % and 44% at high initial cell density, respectively, compared to non-partitioned ones. The results of internally partitioned PBRs demonstrated potentials for culturing microalgae by efficiently utilizing ocean wave energy into culture mixing in the ocean. PMID:26857371

  10. Quantum field theory of partitions

    SciTech Connect

    Bender, C.M.; Brody, D.C.; Meister, B.K.

    1999-07-01

    Given a sequence of numbers {l_brace}a{sub n}{r_brace}, it is always possible to find a set of Feynman rules that reproduce that sequence. For the special case of the partitions of the integers, the appropriate Feynman rules give rise to graphs that represent the partitions in a clear pictorial fashion. These Feynman rules can be used to generate the Bell numbers B(n) and the Stirling numbers S(n,k) that are associated with the partitions of the integers. {copyright} {ital 1999 American Institute of Physics.}

  11. Graph Theory

    SciTech Connect

    Sanfilippo, Antonio P.

    2005-12-27

    Graph theory is a branch of discrete combinatorial mathematics that studies the properties of graphs. The theory was pioneered by the Swiss mathematician Leonhard Euler in the 18th century, commenced its formal development during the second half of the 19th century, and has witnessed substantial growth during the last seventy years, with applications in areas as diverse as engineering, computer science, physics, sociology, chemistry and biology. Graph theory has also had a strong impact in computational linguistics by providing the foundations for the theory of features structures that has emerged as one of the most widely used frameworks for the representation of grammar formalisms.

  12. A Novel Technique to Improve Photometry in Confused Images Using Graphs and Bayesian Priors

    NASA Astrophysics Data System (ADS)

    Safarzadeh, Mohammadtaher; Ferguson, Henry C.; Lu, Yu; Inami, Hanae; Somerville, Rachel S.

    2015-01-01

    We present a new technique for overcoming confusion noise in deep far-infrared Herschel space telescope images making use of prior information from shorter λ < 2 μm wavelengths. For the deepest images obtained by Herschel, the flux limit due to source confusion is about a factor of three brighter than the flux limit due to instrumental noise and (smooth) sky background. We have investigated the possibility of de-confusing simulated Herschel PACS 160 μm images by using strong Bayesian priors on the positions and weak priors on the flux of sources. We find the blended sources and group them together and simultaneously fit their fluxes. We derive the posterior probability distribution function of fluxes subject to these priors through Monte Carlo Markov Chain (MCMC) sampling by fitting the image. Assuming we can predict the FIR flux of sources based on the ultraviolet-optical part of their SEDs to within an order of magnitude, the simulations show that we can obtain reliable fluxes and uncertainties at least a factor of three fainter than the confusion noise limit of 3σ c = 2.7 mJy in our simulated PACS-160 image. This technique could in principle be used to mitigate the effects of source confusion in any situation where one has prior information of positions and plausible fluxes of blended sources. For Herschel, application of this technique will improve our ability to constrain the dust content in normal galaxies at high redshift.

  13. A NOVEL TECHNIQUE TO IMPROVE PHOTOMETRY IN CONFUSED IMAGES USING GRAPHS AND BAYESIAN PRIORS

    SciTech Connect

    Safarzadeh, Mohammadtaher; Ferguson, Henry C.; Lu, Yu; Inami, Hanae; Somerville, Rachel S.

    2015-01-10

    We present a new technique for overcoming confusion noise in deep far-infrared Herschel space telescope images making use of prior information from shorter λ < 2 μm wavelengths. For the deepest images obtained by Herschel, the flux limit due to source confusion is about a factor of three brighter than the flux limit due to instrumental noise and (smooth) sky background. We have investigated the possibility of de-confusing simulated Herschel PACS 160 μm images by using strong Bayesian priors on the positions and weak priors on the flux of sources. We find the blended sources and group them together and simultaneously fit their fluxes. We derive the posterior probability distribution function of fluxes subject to these priors through Monte Carlo Markov Chain (MCMC) sampling by fitting the image. Assuming we can predict the FIR flux of sources based on the ultraviolet-optical part of their SEDs to within an order of magnitude, the simulations show that we can obtain reliable fluxes and uncertainties at least a factor of three fainter than the confusion noise limit of 3σ {sub c} = 2.7 mJy in our simulated PACS-160 image. This technique could in principle be used to mitigate the effects of source confusion in any situation where one has prior information of positions and plausible fluxes of blended sources. For Herschel, application of this technique will improve our ability to constrain the dust content in normal galaxies at high redshift.

  14. Transgenic approaches to altering carbon and nitrogen partitioning in whole plants: assessing the potential to improve crop yields and nutritional quality

    SciTech Connect

    Yadav, Umesh P.; Ayre, Brian G.; Bush, Daniel R.

    2015-04-22

    The principal components of plant productivity and nutritional value, from the standpoint of modern agriculture, are the acquisition and partitioning of organic carbon (C) and nitrogen (N) compounds among the various organs of the plant. The flow of essential organic nutrients among the plant organ systems is mediated by its complex vascular system, and is driven by a series of transport steps including export from sites of primary assimilation, transport into and out of the phloem and xylem, and transport into the various import-dependent organs. Manipulating C and N partitioning to enhance yield of harvested organs is evident in the earliest crop domestication events and continues to be a goal for modern plant biology. Research on the biochemistry, molecular and cellular biology, and physiology of C and N partitioning has now matured to an extent that strategic manipulation of these transport systems through biotechnology are being attempted to improve movement from source to sink tissues in general, but also to target partitioning to specific organs. These nascent efforts are demonstrating the potential of applied biomass targeting but are also identifying interactions between essential nutrients that require further basic research. In this review, we summarize the key transport steps involved in C and N partitioning, and discuss various transgenic approaches for directly manipulating key C and N transporters involved. In addition, we propose several experiments that could enhance biomass accumulation in targeted organs while simultaneously testing current partitioning models.

  15. Transgenic approaches to altering carbon and nitrogen partitioning in whole plants: assessing the potential to improve crop yields and nutritional quality.

    PubMed

    Yadav, Umesh P; Ayre, Brian G; Bush, Daniel R

    2015-01-01

    The principal components of plant productivity and nutritional value, from the standpoint of modern agriculture, are the acquisition and partitioning of organic carbon (C) and nitrogen (N) compounds among the various organs of the plant. The flow of essential organic nutrients among the plant organ systems is mediated by its complex vascular system, and is driven by a series of transport steps including export from sites of primary assimilation, transport into and out of the phloem and xylem, and transport into the various import-dependent organs. Manipulating C and N partitioning to enhance yield of harvested organs is evident in the earliest crop domestication events and continues to be a goal for modern plant biology. Research on the biochemistry, molecular and cellular biology, and physiology of C and N partitioning has now matured to an extent that strategic manipulation of these transport systems through biotechnology are being attempted to improve movement from source to sink tissues in general, but also to target partitioning to specific organs. These nascent efforts are demonstrating the potential of applied biomass targeting but are also identifying interactions between essential nutrients that require further basic research. In this review, we summarize the key transport steps involved in C and N partitioning, and discuss various transgenic approaches for directly manipulating key C and N transporters involved. In addition, we propose several experiments that could enhance biomass accumulation in targeted organs while simultaneously testing current partitioning models. PMID:25954297

  16. Transgenic approaches to altering carbon and nitrogen partitioning in whole plants: assessing the potential to improve crop yields and nutritional quality

    DOE PAGES

    Yadav, Umesh P.; Ayre, Brian G.; Bush, Daniel R.

    2015-04-22

    The principal components of plant productivity and nutritional value, from the standpoint of modern agriculture, are the acquisition and partitioning of organic carbon (C) and nitrogen (N) compounds among the various organs of the plant. The flow of essential organic nutrients among the plant organ systems is mediated by its complex vascular system, and is driven by a series of transport steps including export from sites of primary assimilation, transport into and out of the phloem and xylem, and transport into the various import-dependent organs. Manipulating C and N partitioning to enhance yield of harvested organs is evident in themore » earliest crop domestication events and continues to be a goal for modern plant biology. Research on the biochemistry, molecular and cellular biology, and physiology of C and N partitioning has now matured to an extent that strategic manipulation of these transport systems through biotechnology are being attempted to improve movement from source to sink tissues in general, but also to target partitioning to specific organs. These nascent efforts are demonstrating the potential of applied biomass targeting but are also identifying interactions between essential nutrients that require further basic research. In this review, we summarize the key transport steps involved in C and N partitioning, and discuss various transgenic approaches for directly manipulating key C and N transporters involved. In addition, we propose several experiments that could enhance biomass accumulation in targeted organs while simultaneously testing current partitioning models.« less

  17. Partitioning in trees and soil (PiTS) - a experimental approach to improve knowledge of forest carbon dynamics

    SciTech Connect

    Warren, Jeffrey; Garten Jr, Charles T; Iversen, Colleen M; Norby, Richard J; Thornton, Peter E; Weston, David; Gu, Lianhong; Brice, Deanne Jane; Childs, Joanne; Evans, R

    2012-01-01

    Summary The dynamics of rapid changes in carbon (C) partitioning within forest ecosystems are not well understood, which limits improvement of mechanistic models of C cycling. Our objective was to inform model processes by describing relationships between C partitioning and accessible environmental or physiological measurements, with a special emphasis on belowground C flux. We exposed eight 7-year-old loblolly pine trees to air enriched with 13CO2 and then implemented adjacent light shade (LS) and heavy shade (HS) treatments in order to manipulate C uptake and flux. A soil pit was dug adjacent to the trees to provide greater access belowground. The impacts of shading on photosynthesis, plant water potential, sap flow, basal area growth, root growth, and soil C exchange rate (CER) were assessed for each tree over a three-week period. The progression of the 13C label was concurrently tracked from the atmosphere through foliage, phloem, roots, and soil CO2 efflux. The HS treatment significantly reduced C uptake, sap flow, stem growth and root standing crop, and resulted in greater residual soil water content to 1 m depth. Sap flow was strongly correlated with CER on the previous day, but not the current day, with no apparent treatment effect on the relationship. The 13C label was immediately detected in foliage on label day (half-life = 0.5 d), progressed through phloem by day 2 (half-life = 4.7 d), roots by day 2-4, and subsequently was evident as respiratory release from soil which peaked between days 3-6. The 13C of soil CO2 efflux was strongly correlated with phloem 13C on the previous day, or two days earlier. These data detail the timing and relative magnitude of C flux through a young pine stand in relation to environmental conditions. Refinement of belowground sampling will be necessary to adequately separate and quantify the flux of recently fixed C into roots, and fate of that new C as respiratory, mycorrhizal or exudative release, storage or partitioning

  18. Graphing Reality

    NASA Astrophysics Data System (ADS)

    Beeken, Paul

    2014-11-01

    Graphing is an essential skill that forms the foundation of any physical science.1 Understanding the relationships between measurements ultimately determines which modeling equations are successful in predicting observations.2 Over the years, science and math teachers have approached teaching this skill with a variety of techniques. For secondary school instruction, the job of graphing skills falls heavily on physics teachers. By virtue of the nature of the topics we cover, it is our mission to develop this skill to the fine art that it is.

  19. Accelerating semantic graph databases on commodity clusters

    SciTech Connect

    Morari, Alessandro; Castellana, Vito G.; Haglin, David J.; Feo, John T.; Weaver, Jesse R.; Tumeo, Antonino; Villa, Oreste

    2013-10-06

    We are developing a full software system for accelerating semantic graph databases on commodity cluster that scales to hundreds of nodes while maintaining constant query throughput. Our framework comprises a SPARQL to C++ compiler, a library of parallel graph methods and a custom multithreaded runtime layer, which provides a Partitioned Global Address Space (PGAS) programming model with fork/join parallelism and automatic load balancing over a commodity clusters. We present preliminary results for the compiler and for the runtime.

  20. Graphing Reality

    ERIC Educational Resources Information Center

    Beeken, Paul

    2014-01-01

    Graphing is an essential skill that forms the foundation of any physical science. Understanding the relationships between measurements ultimately determines which modeling equations are successful in predicting observations. Over the years, science and math teachers have approached teaching this skill with a variety of techniques. For secondary…

  1. Effects of Constituent Properties on Performance Improvement of a Quenching and Partitioning Steel

    SciTech Connect

    Choi, Kyoo Sil; Hu, Xiaohua; Sun, Xin; Taylor, Mark D.; De Moor, Emmanuel; Speer, John; Matlock, David K.

    2014-04-01

    In this paper, a two-dimensional microstructure-based finite element modeling method is adopted to investigate the effects of material parameters of the constituent phases on the macroscopic tensile behavior of Q&P steel and then to do a computational materials design approach for its performance improvement. For this purpose, a model Q&P steel is first produced and various experiments are then performed to characterize the steel. Actual microstructure-based model is generated based on the information from EBSD, SEM and nano-indentation test, and the material properties for the constituent phases are determined based on the initial constituents’ properties from HEXRD test and the subsequent calibration of model prediction to tensile test results. Influence of various material parameters of the constituents on the macroscopic behaviors is then investigated by separately adjusting them by small amount. Based on the observation on the respective influence of constituents’ material parameters, a new set of material parameters are devised, which results in better performance in ductility. The results indicate that various material parameters may need to be concurrently adjusted in a cohesive way in order to improve the performance of Q&P steel. In summary, higher austenite stability, less strength difference between the phases, higher hardening exponents of the phases are generally beneficial for the performance improvement. The information from this study can be used to devise new Q&P heat-treating parameters to produce the Q&P steels with better performance.

  2. Graphing Calculator Mini Course

    NASA Technical Reports Server (NTRS)

    Karnawat, Sunil R.

    1996-01-01

    The "Graphing Calculator Mini Course" project provided a mathematically-intensive technologically-based summer enrichment workshop for teachers of American Indian students on the Turtle Mountain Indian Reservation. Eleven such teachers participated in the six-day workshop in summer of 1996 and three Sunday workshops in the academic year. The project aimed to improve science and mathematics education on the reservation by showing teachers effective ways to use high-end graphing calculators as teaching and learning tools in science and mathematics courses at all levels. In particular, the workshop concentrated on applying TI-82's user-friendly features to understand the various mathematical and scientific concepts.

  3. An Efficient Data Partitioning to Improve Classification Performance While Keeping Parameters Interpretable

    PubMed Central

    Korjus, Kristjan; Hebart, Martin N.; Vicente, Raul

    2016-01-01

    Supervised machine learning methods typically require splitting data into multiple chunks for training, validating, and finally testing classifiers. For finding the best parameters of a classifier, training and validation are usually carried out with cross-validation. This is followed by application of the classifier with optimized parameters to a separate test set for estimating the classifier’s generalization performance. With limited data, this separation of test data creates a difficult trade-off between having more statistical power in estimating generalization performance versus choosing better parameters and fitting a better model. We propose a novel approach that we term “Cross-validation and cross-testing” improving this trade-off by re-using test data without biasing classifier performance. The novel approach is validated using simulated data and electrophysiological recordings in humans and rodents. The results demonstrate that the approach has a higher probability of discovering significant results than the standard approach of cross-validation and testing, while maintaining the nominal alpha level. In contrast to nested cross-validation, which is maximally efficient in re-using data, the proposed approach additionally maintains the interpretability of individual parameters. Taken together, we suggest an addition to currently used machine learning approaches which may be particularly useful in cases where model weights do not require interpretation, but parameters do. PMID:27564393

  4. An Efficient Data Partitioning to Improve Classification Performance While Keeping Parameters Interpretable.

    PubMed

    Korjus, Kristjan; Hebart, Martin N; Vicente, Raul

    2016-01-01

    Supervised machine learning methods typically require splitting data into multiple chunks for training, validating, and finally testing classifiers. For finding the best parameters of a classifier, training and validation are usually carried out with cross-validation. This is followed by application of the classifier with optimized parameters to a separate test set for estimating the classifier's generalization performance. With limited data, this separation of test data creates a difficult trade-off between having more statistical power in estimating generalization performance versus choosing better parameters and fitting a better model. We propose a novel approach that we term "Cross-validation and cross-testing" improving this trade-off by re-using test data without biasing classifier performance. The novel approach is validated using simulated data and electrophysiological recordings in humans and rodents. The results demonstrate that the approach has a higher probability of discovering significant results than the standard approach of cross-validation and testing, while maintaining the nominal alpha level. In contrast to nested cross-validation, which is maximally efficient in re-using data, the proposed approach additionally maintains the interpretability of individual parameters. Taken together, we suggest an addition to currently used machine learning approaches which may be particularly useful in cases where model weights do not require interpretation, but parameters do. PMID:27564393

  5. Extended sorption partitioning models for pesticide leaching risk assessments: Can we improve upon the koc concept?

    PubMed

    Jarvis, Nicholas

    2016-01-01

    Models used to assess leaching of pesticides to groundwater still rely on the sorption koc value, even though its limitations have been known for several decades, especially for soils of low organic carbon content (i.e. subsoils). This is mainly because the general applicability of any improved model approach that is also simple enough to use for regulatory purposes has not been demonstrated. The objective of this study was to test and compare alternative models of sorption that could be useful in pesticide risk assessment and management. To this end, a database containing the results of batch sorption experiments for pesticides was compiled from published studies in the literature, which placed at least as much emphasis on measurements in subsoil horizons as in topsoil. The database includes 785 data entries from 34 different published studies and for 21 different active substances. Overall, the apparent koc value, koc(app), roughly doubled as the soil organic carbon content decreased by a factor of ten. Nevertheless, in nearly half of the individual datasets, a constant koc value proved to be an adequate model. Further analysis showed that significant increases in koc(app) in subsoil were found primarily for the more weakly adsorbing compounds (koc values

  6. Optimal Clustering in Graphs with Weighted Edges: A Unified Approach to the Threshold Problem.

    ERIC Educational Resources Information Center

    Goetschel, Roy; Voxman, William

    1987-01-01

    Relations on a finite set V are viewed as weighted graphs. Using the language of graph theory, two methods of partitioning V are examined: selecting threshold values and applying them to a maximal weighted spanning forest, and using a parametric linear program to obtain a most adhesive partition. (Author/EM)

  7. Carbon partitioning in photosynthesis.

    PubMed

    Melis, Anastasios

    2013-06-01

    The work seeks to raise awareness of a fundamental problem that impacts the renewable generation of fuels and chemicals via (photo)synthetic biology. At issue is regulation of the endogenous cellular carbon partitioning between different biosynthetic pathways, over which the living cell exerts stringent control. The regulation of carbon partitioning in photosynthesis is not understood. In plants, microalgae and cyanobacteria, methods need be devised to alter photosynthetic carbon partitioning between the sugar, terpenoid, and fatty acid biosynthetic pathways, to lower the prevalence of sugar biosynthesis and correspondingly upregulate terpenoid and fatty acid hydrocarbons production in the cell. Insight from unusual but naturally occurring carbon-partitioning processes can help in the design of blueprints for improved photosynthetic fuels and chemicals production.

  8. A Hybrid Parallel Strategy Based on String Graph Theory to Improve De Novo DNA Assembly on the TianHe-2 Supercomputer.

    PubMed

    Zhang, Feng; Liao, Xiangke; Peng, Shaoliang; Cui, Yingbo; Wang, Bingqiang; Zhu, Xiaoqian; Liu, Jie

    2016-06-01

    ' The de novo assembly of DNA sequences is increasingly important for biological researches in the genomic era. After more than one decade since the Human Genome Project, some challenges still exist and new solutions are being explored to improve de novo assembly of genomes. String graph assembler (SGA), based on the string graph theory, is a new method/tool developed to address the challenges. In this paper, based on an in-depth analysis of SGA we prove that the SGA-based sequence de novo assembly is an NP-complete problem. According to our analysis, SGA outperforms other similar methods/tools in memory consumption, but costs much more time, of which 60-70 % is spent on the index construction. Upon this analysis, we introduce a hybrid parallel optimization algorithm and implement this algorithm in the TianHe-2's parallel framework. Simulations are performed with different datasets. For data of small size the optimized solution is 3.06 times faster than before, and for data of middle size it's 1.60 times. The results demonstrate an evident performance improvement, with the linear scalability for parallel FM-index construction. This results thus contribute significantly to improving the efficiency of de novo assembly of DNA sequences. PMID:26403255

  9. A Hybrid Parallel Strategy Based on String Graph Theory to Improve De Novo DNA Assembly on the TianHe-2 Supercomputer.

    PubMed

    Zhang, Feng; Liao, Xiangke; Peng, Shaoliang; Cui, Yingbo; Wang, Bingqiang; Zhu, Xiaoqian; Liu, Jie

    2016-06-01

    ' The de novo assembly of DNA sequences is increasingly important for biological researches in the genomic era. After more than one decade since the Human Genome Project, some challenges still exist and new solutions are being explored to improve de novo assembly of genomes. String graph assembler (SGA), based on the string graph theory, is a new method/tool developed to address the challenges. In this paper, based on an in-depth analysis of SGA we prove that the SGA-based sequence de novo assembly is an NP-complete problem. According to our analysis, SGA outperforms other similar methods/tools in memory consumption, but costs much more time, of which 60-70 % is spent on the index construction. Upon this analysis, we introduce a hybrid parallel optimization algorithm and implement this algorithm in the TianHe-2's parallel framework. Simulations are performed with different datasets. For data of small size the optimized solution is 3.06 times faster than before, and for data of middle size it's 1.60 times. The results demonstrate an evident performance improvement, with the linear scalability for parallel FM-index construction. This results thus contribute significantly to improving the efficiency of de novo assembly of DNA sequences.

  10. Improving Budyko curve-based estimates of long-term water partitioning using hydrologic signatures from GRACE

    NASA Astrophysics Data System (ADS)

    Fang, Kuai; Shen, Chaopeng; Fisher, Joshua B.; Niu, Jie

    2016-07-01

    The Budyko hypothesis provides a first-order estimate of water partitioning into runoff (Q) and evapotranspiration (E). Observations, however, often show significant departures from the Budyko curve; moreover, past improvements to Budyko curve tend to lose predictive power when migrated between regions or to small scales. Here to estimate departures from the Budyko curve, we use hydrologic signatures extracted from Gravity Recovery And Climate Experiment (GRACE) terrestrial water storage anomalies. The signatures include GRACE amplitude as a fraction of precipitation (A/P), interannual variability, and 1-month lag autocorrelation. We created a group of linear models embodying two alternate hypotheses that departures can be predicted by (a) Taylor series expansion based on the deviation of physical characteristics (seasonality, snow fraction, and vegetation index) from reference conditions and (b) surrogate indicators covarying with E, e.g., A/P. These models are fitted using a mesoscale USA data set (HUC4) and then evaluated using world data sets and USA basins <1 × 105 km2. The model with A/P could reduce error by 50% compared to Budyko itself. We found that seasonality and fraction of precipitation as snow account for a major portion of the predictive power of A/P, while the remainder is attributed to unexplained basin characteristics. When migrated to a global data set, type b models performed better than type a. This contrast in transferability is argued to be due to data set limitations and catchment coevolution. The GRACE-based correction performs well for USA basins >1000 km2 and, according to comparison with other global data sets, is suitable for data fusion purposes, with GRACE error as estimates of uncertainty.

  11. Understanding Graphs & Charts.

    ERIC Educational Resources Information Center

    Cleary, John J.; Gravely, Mary Liles

    Developed by educators from the Emily Griffith Opportunity School, this teacher's guide was developed for a 4-hour workshop to teach employees how to read the charts and graphs they need in the workplace. The unit covers four types of graphs: pictographs, bar graphs, line graphs, and circle graphs. The guide is divided into four sections: reading…

  12. Bipartite Graphs for Visualization Analysis of Microbiome Data

    PubMed Central

    Sedlar, Karel; Videnska, Petra; Skutkova, Helena; Rychlik, Ivan; Provaznik, Ivo

    2016-01-01

    Visualization analysis plays an important role in metagenomics research. Proper and clear visualization can help researchers get their first insights into data and by selecting different features, also revealing and highlighting hidden relationships and drawing conclusions. To prevent the resulting presentations from becoming chaotic, visualization techniques have to properly tackle the high dimensionality of microbiome data. Although a number of different methods based on dimensionality reduction, correlations, Venn diagrams, and network representations have already been published, there is still room for further improvement, especially in the techniques that allow visual comparison of several environments or developmental stages in one environment. In this article, we represent microbiome data by bipartite graphs, where one partition stands for taxa and the other stands for samples. We demonstrated that community detection is independent of taxonomical level. Moreover, focusing on higher taxonomical levels and the appropriate merging of samples greatly helps improving graph organization and makes our presentations clearer than other graph and network visualizations. Capturing labels in the vertices also brings the possibility of clearly comparing two or more microbial communities by showing their common and unique parts. PMID:27279729

  13. Ezekiel graphs

    SciTech Connect

    Simmons, G.J.

    1991-01-01

    In spite of the old adage that No finite sequence of symbols is random,'' there are many instances in which it is desirable to quantify how random'' a finite sequence is. Pseudorandom number generators and cryptographic key generators typically expand a short, randomly chosen, seed sequence into a much longer sequence which should appear random to anyone ignorant of the seed. Unique initiating signals chosen to minimize the likelihood of an accidental initiation of an important action should be random'' to lessen the chance of their natural occurrence, etc. Consequently, numerous tests for the randomness of finite sequences have been proposed. John Milnor argued that if a binary sequence is random then the fraction of 1's, r{sub 1}, should be very nearly 1/2 in it and in all of what he called its derivatives. Since every sequence has a unique derivative this defines a natural family of digraphs, G{sub n}, on 2{sup n} vertices in which vertices are labeled with n-bit binary sequences and an edge is directed from the vertex labeled with the sequence A to the vertex labeled with the sequence B if B is the derivative of A. Each component of G{sub n} is eventually cyclic. This paper is concerned with a special case in which the sequences in a cycle are all cyclic shifts of a single sequence -- hence the name of Ezekiel graphs. Surprising, there are Ezekiel graphs for which r{sub 1} is as close to 1/2 as is numerically possible, i.e., that satisfy Milnor's test for randomness as closely as it can be satisfied, even though the sequence of sequences are about as far from random as is conceivable. In this paper the existence and properties of Ezekiel sequences are investigated from an algebraic standpoint.

  14. Molecular graph convolutions: moving beyond fingerprints.

    PubMed

    Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

    2016-08-01

    Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph-atoms, bonds, distances, etc.-which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement. PMID:27558503

  15. Molecular graph convolutions: moving beyond fingerprints.

    PubMed

    Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

    2016-08-01

    Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph-atoms, bonds, distances, etc.-which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

  16. Molecular graph convolutions: moving beyond fingerprints

    NASA Astrophysics Data System (ADS)

    Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

    2016-08-01

    Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular "graph convolutions", a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph---atoms, bonds, distances, etc.---which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

  17. Parallel hypergraph partitioning for scientific computing.

    SciTech Connect

    Heaphy, Robert; Devine, Karen Dragon; Catalyurek, Umit; Bisseling, Robert; Hendrickson, Bruce Alan; Boman, Erik Gunnar

    2005-07-01

    Graph partitioning is often used for load balancing in parallel computing, but it is known that hypergraph partitioning has several advantages. First, hypergraphs more accurately model communication volume, and second, they are more expressive and can better represent nonsymmetric problems. Hypergraph partitioning is particularly suited to parallel sparse matrix-vector multiplication, a common kernel in scientific computing. We present a parallel software package for hypergraph (and sparse matrix) partitioning developed at Sandia National Labs. The algorithm is a variation on multilevel partitioning. Our parallel implementation is novel in that it uses a two-dimensional data distribution among processors. We present empirical results that show our parallel implementation achieves good speedup on several large problems (up to 33 million nonzeros) with up to 64 processors on a Linux cluster.

  18. Improved prediction of octanol-water partition coefficients from liquid-solute water solubilities and molar volumes

    USGS Publications Warehouse

    Chiou, C.T.; Schmedding, D.W.; Manes, M.

    2005-01-01

    A volume-fraction-based solvent-water partition model for dilute solutes, in which the partition coefficient shows a dependence on solute molar volume (V??), is adapted to predict the octanol-water partition coefficient (K ow) from the liquid or supercooled-liquid solute water solubility (Sw), or vice versa. The established correlation is tested for a wide range of industrial compounds and pesticides (e.g., halogenated aliphatic hydrocarbons, alkylbenzenes, halogenated benzenes, ethers, esters, PAHs, PCBs, organochlorines, organophosphates, carbamates, and amidesureas-triazines), which comprise a total of 215 test compounds spanning about 10 orders of magnitude in Sw and 8.5 orders of magnitude in Kow. Except for phenols and alcohols, which require special considerations of the Kow data, the correlation predicts the Kow within 0.1 log units for most compounds, much independent of the compound type or the magnitude in K ow. With reliable Sw and V data for compounds of interest, the correlation provides an effective means for either predicting the unavailable log Kow values or verifying the reliability of the reported log Kow data. ?? 2005 American Chemical Society.

  19. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational–rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane

    SciTech Connect

    Mielke, Steven L. E-mail: truhlar@umn.edu; Truhlar, Donald G. E-mail: truhlar@umn.edu

    2015-01-28

    We present an improved version of our “path-by-path” enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P{sup −6}) to O(P{sup −12}), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational–rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan–Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300–3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.

  20. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational-rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane.

    PubMed

    Mielke, Steven L; Truhlar, Donald G

    2015-01-28

    We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P(-6)) to O(P(-12)), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.

  1. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational-rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane.

    PubMed

    Mielke, Steven L; Truhlar, Donald G

    2015-01-28

    We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P(-6)) to O(P(-12)), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities. PMID:25637967

  2. Graphing Polar Curves

    ERIC Educational Resources Information Center

    Lawes, Jonathan F.

    2013-01-01

    Graphing polar curves typically involves a combination of three traditional techniques, all of which can be time-consuming and tedious. However, an alternative method--graphing the polar function on a rectangular plane--simplifies graphing, increases student understanding of the polar coordinate system, and reinforces graphing techniques learned…

  3. Graphing for Any Grade.

    ERIC Educational Resources Information Center

    Nibbelink, William

    1982-01-01

    An instructional sequence for teaching graphing that has been extensively field tested in kindergarten through grade six is detailed. The material begins with point graphs, employs a movable y-axis to begin with minimal clutter, and has graphs constructed before reading graphs is required. (MP)

  4. Rectilinear partitioning of irregular data parallel computations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1991-01-01

    New mapping algorithms for domain oriented data-parallel computations, where the workload is distributed irregularly throughout the domain, but exhibits localized communication patterns are described. Researchers consider the problem of partitioning the domain for parallel processing in such a way that the workload on the most heavily loaded processor is minimized, subject to the constraint that the partition be perfectly rectilinear. Rectilinear partitions are useful on architectures that have a fast local mesh network. Discussed here is an improved algorithm for finding the optimal partitioning in one dimension, new algorithms for partitioning in two dimensions, and optimal partitioning in three dimensions. The application of these algorithms to real problems are discussed.

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

    PubMed

    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.

  6. Computing the isoperimetric number of a graph

    SciTech Connect

    Golovach, P.A.

    1995-01-01

    Let G be a finite graph. Denote by {partial_derivative}X, where X {contained_in} VG, the set of edges of the graph G with one end in X and the other end in the set VG{backslash}X. The ratio i(G) = min {vert_bar}{vert_bar}X{vert_bar}/{vert_bar}X{vert_bar}, where the minimum is over all nonempty subsets X of the set VG such that {vert_bar}X{vert_bar} {le} {vert_bar} VG {vert_bar}/2, is called the isoperimetric number of the graph G. It is easy to see that the isoperimetric number may be used as a {open_quotes}measure of connectivity{close_quotes} of the graph. The problem of determining the isoperimetric number is clearly linked with graph partition problems, which often arise in various applications. The isoperimetric number is also important for studying Riemann surfaces. These and other applications of the isoperimetric number justify the analysis of graphs of this kind. The properties of the isoperimetric number are presented in more detail elsewhere. It is shown elsewhere that the computation of the isoperimetric number is an NP-hard problem for graphs with multiple edges. We will show that the decision problem {open_quotes}given the graph G and two integers s and t decide if i(G) {le} s/t{close_quotes} is NP-complete even for simple graphs with vertex degrees not exceeding 3. Note that the isoperimetric number of a tree can be computed by a known polynomial-time algorithm.

  7. Improvements in Heat Transfer for Anti-Icing of Gas-Heated Airfoils with Internal Fins and Partitions

    NASA Technical Reports Server (NTRS)

    Gray, Vernon H.

    1950-01-01

    The effect of modifying the gas passage of hollow metal airfoils by the additIon of internal fins and partitions was experimentally investigated and comparisons were made among a basic unfinned airfoil section and two airfoil designs having metal fins attached at the leading edge of the internal gas passage. An analysis considering the effects of heat conduction in the airfoil metal was made to determine the internal modification effectiveness that may be obtained in gas-heated components, such as turbojet-inlet guide vanes, support struts, hollow propeller blades, arid. thin wings. Over a wide range of heated-gas flow and tunnel-air velocity, the increase In surface-heating rates with internal finning was marked (up to 3.5 times), with the greatest increase occurring at the leading edge where anti-icing heat requirements are most critical. Variations in the amount and the location of internal finning and. partitioning provided. control over the local rates of surface heat transfer and permitted efficient anti-icing utilization of the gas-stream heat content.

  8. Effective Use of Water and Increased Dry Matter Partitioned to Grain Contribute to Yield of Common Bean Improved for Drought Resistance

    PubMed Central

    Polania, Jose A.; Poschenrieder, Charlotte; Beebe, Stephen; Rao, Idupulapati M.

    2016-01-01

    Common bean (Phaseolus vulgaris L.) is the most important food legume in the diet of poor people in the tropics. Drought causes severe yield loss in this crop. Identification of traits associated with drought resistance contributes to improving the process of generating bean genotypes adapted to these conditions. Field studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia, to determine the relationship between grain yield and different parameters such as effective use of water (EUW), canopy biomass, and dry partitioning indices (pod partitioning index, harvest index, and pod harvest index) in elite lines selected for drought resistance over the past decade. Carbon isotope discrimination (CID) was used for estimation of water use efficiency (WUE). The main objectives were: (i) to identify specific morpho-physiological traits that contribute to improved resistance to drought in lines developed over several cycles of breeding and that could be useful as selection criteria in breeding; and (ii) to identify genotypes with desirable traits that could serve as parents in the corresponding breeding programs. A set of 36 bean genotypes belonging to the Middle American gene pool were evaluated under field conditions with two levels of water supply (irrigated and drought) over two seasons. Eight bean lines (NCB 280, NCB 226, SEN 56, SCR 2, SCR 16, SMC 141, RCB 593, and BFS 67) were identified as resistant to drought stress. Resistance to terminal drought stress was positively associated with EUW combined with increased dry matter partitioned to pod and seed production and negatively associated with days to flowering and days to physiological maturity. Differences in genotypic response were observed between grain CID and grain yield under irrigated and drought stress. Based on phenotypic differences in CID, leaf stomatal conductance, canopy biomass, and grain yield under drought stress, the lines tested were classified into two

  9. Effective Use of Water and Increased Dry Matter Partitioned to Grain Contribute to Yield of Common Bean Improved for Drought Resistance.

    PubMed

    Polania, Jose A; Poschenrieder, Charlotte; Beebe, Stephen; Rao, Idupulapati M

    2016-01-01

    Common bean (Phaseolus vulgaris L.) is the most important food legume in the diet of poor people in the tropics. Drought causes severe yield loss in this crop. Identification of traits associated with drought resistance contributes to improving the process of generating bean genotypes adapted to these conditions. Field studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia, to determine the relationship between grain yield and different parameters such as effective use of water (EUW), canopy biomass, and dry partitioning indices (pod partitioning index, harvest index, and pod harvest index) in elite lines selected for drought resistance over the past decade. Carbon isotope discrimination (CID) was used for estimation of water use efficiency (WUE). The main objectives were: (i) to identify specific morpho-physiological traits that contribute to improved resistance to drought in lines developed over several cycles of breeding and that could be useful as selection criteria in breeding; and (ii) to identify genotypes with desirable traits that could serve as parents in the corresponding breeding programs. A set of 36 bean genotypes belonging to the Middle American gene pool were evaluated under field conditions with two levels of water supply (irrigated and drought) over two seasons. Eight bean lines (NCB 280, NCB 226, SEN 56, SCR 2, SCR 16, SMC 141, RCB 593, and BFS 67) were identified as resistant to drought stress. Resistance to terminal drought stress was positively associated with EUW combined with increased dry matter partitioned to pod and seed production and negatively associated with days to flowering and days to physiological maturity. Differences in genotypic response were observed between grain CID and grain yield under irrigated and drought stress. Based on phenotypic differences in CID, leaf stomatal conductance, canopy biomass, and grain yield under drought stress, the lines tested were classified into two

  10. Effective Use of Water and Increased Dry Matter Partitioned to Grain Contribute to Yield of Common Bean Improved for Drought Resistance.

    PubMed

    Polania, Jose A; Poschenrieder, Charlotte; Beebe, Stephen; Rao, Idupulapati M

    2016-01-01

    Common bean (Phaseolus vulgaris L.) is the most important food legume in the diet of poor people in the tropics. Drought causes severe yield loss in this crop. Identification of traits associated with drought resistance contributes to improving the process of generating bean genotypes adapted to these conditions. Field studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia, to determine the relationship between grain yield and different parameters such as effective use of water (EUW), canopy biomass, and dry partitioning indices (pod partitioning index, harvest index, and pod harvest index) in elite lines selected for drought resistance over the past decade. Carbon isotope discrimination (CID) was used for estimation of water use efficiency (WUE). The main objectives were: (i) to identify specific morpho-physiological traits that contribute to improved resistance to drought in lines developed over several cycles of breeding and that could be useful as selection criteria in breeding; and (ii) to identify genotypes with desirable traits that could serve as parents in the corresponding breeding programs. A set of 36 bean genotypes belonging to the Middle American gene pool were evaluated under field conditions with two levels of water supply (irrigated and drought) over two seasons. Eight bean lines (NCB 280, NCB 226, SEN 56, SCR 2, SCR 16, SMC 141, RCB 593, and BFS 67) were identified as resistant to drought stress. Resistance to terminal drought stress was positively associated with EUW combined with increased dry matter partitioned to pod and seed production and negatively associated with days to flowering and days to physiological maturity. Differences in genotypic response were observed between grain CID and grain yield under irrigated and drought stress. Based on phenotypic differences in CID, leaf stomatal conductance, canopy biomass, and grain yield under drought stress, the lines tested were classified into two

  11. Cognitive Aids for Guiding Graph Comprehension

    ERIC Educational Resources Information Center

    Mautone, Patricia D.; Mayer, Richard E.

    2007-01-01

    This study sought to improve students' comprehension of scientific graphs by adapting scaffolding techniques used to aid text comprehension. In 3 experiments involving 121 female and 88 male college students, some students were shown cognitive aids prior to viewing 4 geography graphs whereas others were not; all students were then asked to write a…

  12. Subvoxel accurate graph search using non-Euclidean graph space.

    PubMed

    Abràmoff, Michael D; Wu, Xiaodong; Lee, Kyungmoo; Tang, Li

    2014-01-01

    Graph search is attractive for the quantitative analysis of volumetric medical images, and especially for layered tissues, because it allows globally optimal solutions in low-order polynomial time. However, because nodes of graphs typically encode evenly distributed voxels of the volume with arcs connecting orthogonally sampled voxels in Euclidean space, segmentation cannot achieve greater precision than a single unit, i.e. the distance between two adjoining nodes, and partial volume effects are ignored. We generalize the graph to non-Euclidean space by allowing non-equidistant spacing between nodes, so that subvoxel accurate segmentation is achievable. Because the number of nodes and edges in the graph remains the same, running time and memory use are similar, while all the advantages of graph search, including global optimality and computational efficiency, are retained. A deformation field calculated from the volume data adaptively changes regional node density so that node density varies with the inverse of the expected cost. We validated our approach using optical coherence tomography (OCT) images of the retina and 3-D MR of the arterial wall, and achieved statistically significant increased accuracy. Our approach allows improved accuracy in volume data acquired with the same hardware, and also, preserved accuracy with lower resolution, more cost-effective, image acquisition equipment. The method is not limited to any specific imaging modality and readily extensible to higher dimensions.

  13. Methods for fine registration of cadastre graphs to images.

    PubMed

    Trias-Sanz, Roger; Pierrot-Deseilligny, Marc; Louchet, Jean; Stamon, Georges

    2007-11-01

    We propose two algorithms to match edges in a geometrically-imprecise graph to geometrically-precise strong boundaries in an image, where the graph is meant to give an a priori partition of the image into objects. This can be used to partition an image into objects described by imprecise external data, and thus to simplify the segmentation problem. We apply them to the problem of registering cadastre data to georeferenced aerial images, thus correcting the lack of geometrical detail of the cadastre data, and the fact that cadastre data gives information of a different nature than that found in images (fiscal information as opposed to actual land use). PMID:17848779

  14. Using Flashcard Drill Methods and Self-Graphing Procedures to Improve the Reading Performance of English Language Learners

    ERIC Educational Resources Information Center

    Albers, Craig A.; Hoffman, Alicia

    2012-01-01

    The increasing numbers of English language learners who are enrolled in schools across the nation, combined with the escalating academic demands placed on all students, warrant the evaluation of instructional strategies designed to improve English language learners' reading performance. In this study, the authors used a multiple baseline design…

  15. Graphing Inequalities, Connecting Meaning

    ERIC Educational Resources Information Center

    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…

  16. Graph-Plotting Routine

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.

    1987-01-01

    Plotter routine for IBM PC (AKPLOT) designed for engineers and scientists who use graphs as integral parts of their documentation. Allows user to generate graph and edit its appearance on cathode-ray tube. Graph may undergo many interactive alterations before finally dumped from screen to be plotted by printer. Written in BASIC.

  17. Graphing Important People

    ERIC Educational Resources Information Center

    Reading Teacher, 2012

    2012-01-01

    The "Toolbox" column features content adapted from ReadWriteThink.org lesson plans and provides practical tools for classroom teachers. This issue's column features a lesson plan adapted from "Graphing Plot and Character in a Novel" by Lisa Storm Fink and "Bio-graph: Graphing Life Events" by Susan Spangler. Students retell biographic events…

  18. Universal Quantum Graphs

    NASA Astrophysics Data System (ADS)

    Pluhař, Z.; Weidenmüller, H. A.

    2014-04-01

    For time-reversal invariant graphs we prove the Bohigas-Giannoni-Schmit conjecture in its most general form: For graphs that are mixing in the classical limit, all spectral correlation functions coincide with those of the Gaussian orthogonal ensemble of random matrices. For open graphs, we derive the analogous identities for all S-matrix correlation functions.

  19. Graphing with "LogoWriter."

    ERIC Educational Resources Information Center

    Yoder, Sharon K.

    This book discusses four kinds of graphs that are taught in mathematics at the middle school level: pictographs, bar graphs, line graphs, and circle graphs. The chapters on each of these types of graphs contain information such as starting, scaling, drawing, labeling, and finishing the graphs using "LogoWriter." The final chapter of the book…

  20. Methods of visualizing graphs

    SciTech Connect

    Wong, Pak C.; Mackey, Patrick S.; Perrine, Kenneth A.; Foote, Harlan P.; Thomas, James J.

    2008-12-23

    Methods for visualizing a graph by automatically drawing elements of the graph as labels are disclosed. In one embodiment, the method comprises receiving node information and edge information from an input device and/or communication interface, constructing a graph layout based at least in part on that information, wherein the edges are automatically drawn as labels, and displaying the graph on a display device according to the graph layout. In some embodiments, the nodes are automatically drawn as labels instead of, or in addition to, the label-edges.

  1. Multipartite entanglement in four-qubit graph states

    NASA Astrophysics Data System (ADS)

    Jafarpour, Mojtaba; Assadi, Leila

    2016-03-01

    We consider a compendium of the non-trivial four-qubit graphs, derive their corresponding quantum states and classify them into equivalent classes. We use Meyer-Wallach measure and its generalizations to study block-partition and global entanglement in these states. We obtain several entanglement quantities for each graph state, which present a comprehensive characterization of the entanglement properties of the latter. As a result, a number of correlations between the graph structure and multipartite entanglement quantities have also been established.

  2. Can Comparison of Contrastive Examples Facilitate Graph Understanding?

    ERIC Educational Resources Information Center

    Smith, Linsey A.; Gentner, Dedre

    2011-01-01

    The authors explore the role of comparison in improving graph fluency. The ability to use graphs fluently is crucial for STEM achievement, but graphs are challenging to interpret and produce because they often involve integration of multiple variables, continuous change in variables over time, and omission of certain details in order to highlight…

  3. Weights and topology: a study of the effects of graph construction on 3D image segmentation.

    PubMed

    Grady, Leo; Jolly, Marie-Pierre

    2008-01-01

    Graph-based algorithms have become increasingly popular for medical image segmentation. The fundamental process for each of these algorithms is to use the image content to generate a set of weights for the graph and then set conditions for an optimal partition of the graph with respect to these weights. To date, the heuristics used for generating the weighted graphs from image intensities have largely been ignored, while the primary focus of attention has been on the details of providing the partitioning conditions. In this paper we empirically study the effects of graph connectivity and weighting function on the quality of the segmentation results. To control for algorithm-specific effects, we employ both the Graph Cuts and Random Walker algorithms in our experiments.

  4. A Pfaffian Formula for Monomer-Dimer Partition Functions

    NASA Astrophysics Data System (ADS)

    Giuliani, Alessandro; Jauslin, Ian; Lieb, Elliott H.

    2016-04-01

    We consider the monomer-dimer partition function on arbitrary finite planar graphs and arbitrary monomer and dimer weights, with the restriction that the only non-zero monomer weights are those on the boundary. We prove a Pfaffian formula for the corresponding partition function. As a consequence of this result, multipoint boundary monomer correlation functions at close packing are shown to satisfy fermionic statistics. Our proof is based on the celebrated Kasteleyn theorem, combined with a theorem on Pfaffians proved by one of the authors, and a careful labeling and directing procedure of the vertices and edges of the graph.

  5. Supporting Fourth Graders' Ability to Interpret Graphs through Real-Time Graphing Technology: A Preliminary Study

    ERIC Educational Resources Information Center

    Deniz, Hasan; Dulger, Mehmet F.

    2012-01-01

    This study examined to what extent inquiry-based instruction supported with real-time graphing technology improves fourth grader's ability to interpret graphs as representations of physical science concepts such as motion and temperature. This study also examined whether there is any difference between inquiry-based instruction supported with…

  6. Reflections on High School Students' Graphing Skills and Their Conceptual Understanding of Drawing Chemistry Graphs

    ERIC Educational Resources Information Center

    Gültepe, Nejla

    2016-01-01

    Graphing subjects in chemistry has been used to provide alternatives to verbal and algorithmic descriptions of a subject by handing students another way of improving their manipulation of concepts. Teachers should therefore know the level of students' graphing skills. Studies have identified that students have difficulty making connections with…

  7. Partitioning Rectangular and Structurally Nonsymmetric Sparse Matrices for Parallel Processing

    SciTech Connect

    B. Hendrickson; T.G. Kolda

    1998-09-01

    A common operation in scientific computing is the multiplication of a sparse, rectangular or structurally nonsymmetric matrix and a vector. In many applications the matrix- transpose-vector product is also required. This paper addresses the efficient parallelization of these operations. We show that the problem can be expressed in terms of partitioning bipartite graphs. We then introduce several algorithms for this partitioning problem and compare their performance on a set of test matrices.

  8. Topologies on directed graphs

    NASA Technical Reports Server (NTRS)

    Lieberman, R. N.

    1972-01-01

    Given a directed graph, a natural topology is defined and relationships between standard topological properties and graph theoretical concepts are studied. In particular, the properties of connectivity and separatedness are investigated. A metric is introduced which is shown to be related to separatedness. The topological notions of continuity and homeomorphism. A class of maps is studied which preserve both graph and topological properties. Applications involving strong maps and contractions are also presented.

  9. Young Children's Partitioning Strategies.

    ERIC Educational Resources Information Center

    Charles, Kathy; Nason, Rod

    2000-01-01

    Studies knowledge of young children's partitioning strategies by setting out not only to identify new partitioning strategies, but also to develop taxonomy for classifying young children's partitioning strategies in terms of their abilities. Provides taxonomy utilizing children's informal partitioning strategies as the foundation upon which to…

  10. Graph Generator Survey

    SciTech Connect

    Lothian, Josh; Powers, Sarah S; Sullivan, Blair D; Baker, Matthew B; Schrock, Jonathan; Poole, Stephen W

    2013-12-01

    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 dierent 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.

  11. mpiGraph

    2007-05-22

    MpiGraph consists of an MPI application called mpiGraph written in C to measure message bandwidth and an associated crunch_mpiGraph script written in Perl to process the application output into an HTMO report. The mpiGraph application is designed to inspect the health and scalability of a high-performance interconnect while under heavy load. This is useful to detect hardware and software problems in a system, such as slow nodes, links, switches, or contention in switch routing. Itmore » is also useful to characterize how interconnect performance changes with different settings or how one interconnect type compares to another.« less

  12. Exercise and Weight Loss Improve Muscle Mitochondrial Respiration, Lipid Partitioning, and Insulin Sensitivity After Gastric Bypass Surgery

    PubMed Central

    Coen, Paul M.; Menshikova, Elizabeth V.; Distefano, Giovanna; Zheng, Donghai; Tanner, Charles J.; Standley, Robert A.; Helbling, Nicole L.; Dubis, Gabriel S.; Ritov, Vladimir B.; Xie, Hui; Desimone, Marisa E.; Smith, Steven R.; Stefanovic-Racic, Maja; Toledo, Frederico G.S.; Houmard, Joseph A.

    2015-01-01

    Both Roux-en-Y gastric bypass (RYGB) surgery and exercise can improve insulin sensitivity in individuals with severe obesity. However, the impact of RYGB with or without exercise on skeletal muscle mitochondria, intramyocellular lipids, and insulin sensitivity index (SI) is unknown. We conducted a randomized exercise trial in patients (n = 101) who underwent RYGB surgery and completed either a 6-month moderate exercise (EX) or a health education control (CON) intervention. SI was determined by intravenous glucose tolerance test. Mitochondrial respiration and intramyocellular triglyceride, sphingolipid, and diacylglycerol content were measured in vastus lateralis biopsy specimens. We found that EX provided additional improvements in SI and that only EX improved cardiorespiratory fitness, mitochondrial respiration and enzyme activities, and cardiolipin profile with no change in mitochondrial content. Muscle triglycerides were reduced in type I fibers in CON, and sphingolipids decreased in both groups, with EX showing a further reduction in a number of ceramide species. In conclusion, exercise superimposed on bariatric surgery–induced weight loss enhances mitochondrial respiration, induces cardiolipin remodeling, reduces specific sphingolipids, and provides additional improvements in insulin sensitivity. PMID:26293505

  13. Exercise and Weight Loss Improve Muscle Mitochondrial Respiration, Lipid Partitioning, and Insulin Sensitivity After Gastric Bypass Surgery.

    PubMed

    Coen, Paul M; Menshikova, Elizabeth V; Distefano, Giovanna; Zheng, Donghai; Tanner, Charles J; Standley, Robert A; Helbling, Nicole L; Dubis, Gabriel S; Ritov, Vladimir B; Xie, Hui; Desimone, Marisa E; Smith, Steven R; Stefanovic-Racic, Maja; Toledo, Frederico G S; Houmard, Joseph A; Goodpaster, Bret H

    2015-11-01

    Both Roux-en-Y gastric bypass (RYGB) surgery and exercise can improve insulin sensitivity in individuals with severe obesity. However, the impact of RYGB with or without exercise on skeletal muscle mitochondria, intramyocellular lipids, and insulin sensitivity index (SI) is unknown. We conducted a randomized exercise trial in patients (n = 101) who underwent RYGB surgery and completed either a 6-month moderate exercise (EX) or a health education control (CON) intervention. SI was determined by intravenous glucose tolerance test. Mitochondrial respiration and intramyocellular triglyceride, sphingolipid, and diacylglycerol content were measured in vastus lateralis biopsy specimens. We found that EX provided additional improvements in SI and that only EX improved cardiorespiratory fitness, mitochondrial respiration and enzyme activities, and cardiolipin profile with no change in mitochondrial content. Muscle triglycerides were reduced in type I fibers in CON, and sphingolipids decreased in both groups, with EX showing a further reduction in a number of ceramide species. In conclusion, exercise superimposed on bariatric surgery-induced weight loss enhances mitochondrial respiration, induces cardiolipin remodeling, reduces specific sphingolipids, and provides additional improvements in insulin sensitivity.

  14. Improved reactor performance and operability in the biotransformation of carveol to carvone using a solid-liquid two-phase partitioning bioreactor.

    PubMed

    Morrish, Jenna L E; Daugulis, Andrew J

    2008-12-01

    In an effort to improve reactor performance and process operability, the microbial biotransformation of (-)-trans-carveol to (R)-(-)-carvone by hydrophobic Rhodococcus erythropolis DCL14 was carried out in a two phase partitioning bioreactor (TPPB) with solid polymer beads acting as the partitioning phase. Previous work had demonstrated that the substrate and product become inhibitory to the organism at elevated aqueous concentrations and the use of an immiscible second phase in the bioreactor was intended to provide a reservoir for substrates to be delivered to the aqueous phase based on the metabolic rate of the cells, while also acting as a sink to uptake the product as it is produced. The biotransformation was previously undertaken in a two liquid phase TPPB with 1-dodecene and with silicone oil as the immiscible second phase and, although improvement in the reactor performance was obtained relative to a single phase system, the hydrophobic nature of the organism caused the formation of severe emulsions leading to significant operational challenges. In the present work, eight types of polymer beads were screened for their suitability for use in a solid-liquid TPPB for this biotransformation. The use of selected solid polymer beads as the second phase completely prevented emulsion formation and therefore improved overall operability of the reactor. Three modes of solid-liquid TPPB operation were considered: the use of a single polymer bead type (styrene/butadiene copolymer) in the reactor, the use of a mixture of polymer beads in the reactor (styrene/butadiene copolymer plus Hytrel(R) 8206), and the use of one type of polymer beads in the reactor (styrene/butadiene copolymer), and another bead type (Hytrel(R) 8206) in an external column through which fermentation medium was recirculated. This last configuration achieved the best reactor performance with 7 times more substrate being added throughout the biotransformation relative to a single aqueous phase

  15. Graphs, matrices, and the GraphBLAS: Seven good reasons

    DOE PAGES

    Kepner, Jeremy; Bader, David; Buluç, Aydın; Gilbert, John; Mattson, Timothy; Meyerhenke, Henning

    2015-01-01

    The analysis of graphs has become increasingly important to a wide range of applications. Graph analysis presents a number of unique challenges in the areas of (1) software complexity, (2) data complexity, (3) security, (4) mathematical complexity, (5) theoretical analysis, (6) serial performance, and (7) parallel performance. Implementing graph algorithms using matrix-based approaches provides a number of promising solutions to these challenges. The GraphBLAS standard (istcbigdata.org/GraphBlas) is being developed to bring the potential of matrix based graph algorithms to the broadest possible audience. The GraphBLAS mathematically defines a core set of matrix-based graph operations that can be used to implementmore » a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the GraphBLAS and describes how the GraphBLAS can be used to address many of the challenges associated with analysis of graphs.« less

  16. Graphs, matrices, and the GraphBLAS: Seven good reasons

    SciTech Connect

    Kepner, Jeremy; Bader, David; Buluç, Aydın; Gilbert, John; Mattson, Timothy; Meyerhenke, Henning

    2015-01-01

    The analysis of graphs has become increasingly important to a wide range of applications. Graph analysis presents a number of unique challenges in the areas of (1) software complexity, (2) data complexity, (3) security, (4) mathematical complexity, (5) theoretical analysis, (6) serial performance, and (7) parallel performance. Implementing graph algorithms using matrix-based approaches provides a number of promising solutions to these challenges. The GraphBLAS standard (istcbigdata.org/GraphBlas) is being developed to bring the potential of matrix based graph algorithms to the broadest possible audience. The GraphBLAS mathematically defines a core set of matrix-based graph operations that can be used to implement a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the GraphBLAS and describes how the GraphBLAS can be used to address many of the challenges associated with analysis of graphs.

  17. Information-theoretic indices usage for the prediction and calculation of octanol-water partition coefficient.

    PubMed

    Persona, Marek; Kutarov, Vladimir V; Kats, Boris M; Persona, Andrzej; Marczewska, Barbara

    2007-01-01

    The paper describes the new prediction method of octanol-water partition coefficient, which is based on molecular graph theory. The results obtained using the new method are well correlated with experimental values. These results were compared with the ones obtained by use of ten other structure correlated methods. The comparison shows that graph theory can be very useful in structure correlation research.

  18. Hirshfeld-E Partitioning: AIM Charges with an Improved Trade-off between Robustness and Accurate Electrostatics.

    PubMed

    Verstraelen, T; Ayers, P W; Van Speybroeck, V; Waroquier, M

    2013-05-14

    For the development of ab initio derived force fields, atomic charges must be computed from electronic structure computations, such that (i) they accurately describe the molecular electrostatic potential (ESP) and (ii) they are transferable to the force-field application of interest. The Iterative Hirshfeld (Hirshfeld-I or HI) scheme meets both requirements for organic molecules. For inorganic oxide clusters, however, Hirshfeld-I becomes ambiguous because electron densities of nonexistent isolated anions are needed as input. Herein, we propose a simple Extended Hirshfeld (Hirshfeld-E or HE) scheme to overcome this limitation. The performance of the new HE scheme is compared to four popular atoms-in-molecules schemes, using two tests involving a set of 248 silica clusters. These tests show that the new HE scheme provides an improved trade-off between the ESP accuracy and the transferability of the charges. The new scheme is a generalization of the Hirshfeld-I scheme, and it is expected that its improvements are to a large extent applicable to molecular systems containing elements from the entire periodic table.

  19. Real World Graph Connectivity

    ERIC Educational Resources Information Center

    Lind, Joy; Narayan, Darren

    2009-01-01

    We present the topic of graph connectivity along with a famous theorem of Menger in the real-world setting of the national computer network infrastructure of "National LambdaRail". We include a set of exercises where students reinforce their understanding of graph connectivity by analysing the "National LambdaRail" network. Finally, we give…

  20. Walking Out Graphs

    ERIC Educational Resources Information Center

    Shen, Ji

    2009-01-01

    In the Walking Out Graphs Lesson described here, students experience several types of representations used to describe motion, including words, sentences, equations, graphs, data tables, and actions. The most important theme of this lesson is that students have to understand the consistency among these representations and form the habit of…

  1. Reflections on "The Graph"

    ERIC Educational Resources Information Center

    Petrosino, Anthony

    2012-01-01

    This article responds to arguments by Skidmore and Thompson (this issue of "Educational Researcher") that a graph published more than 10 years ago was erroneously reproduced and "gratuitously damaged" perceptions of the quality of education research. After describing the purpose of the original graph, the author counters assertions that the graph…

  2. Exploring Graphs: WYSIWYG.

    ERIC Educational Resources Information Center

    Johnson, Millie

    1997-01-01

    Graphs from media sources and questions developed from them can be used in the middle school mathematics classroom. Graphs depict storage temperature on a milk carton; air pressure measurements on a package of shock absorbers; sleep-wake patterns of an infant; a dog's breathing patterns; and the angle, velocity, and radius of a leaning bicyclist…

  3. Making "Photo" Graphs

    ERIC Educational Resources Information Center

    Doto, Julianne; Golbeck, Susan

    2007-01-01

    Collecting data and analyzing the results of experiments is difficult for children. The authors found a surprising way to help their third graders make graphs and draw conclusions from their data: digital photographs. The pictures bridged the gap between an abstract graph and the plants it represented. With the support of the photos, students…

  4. ACTIVITIES: Graphs and Games

    ERIC Educational Resources Information Center

    Hirsch, Christian R.

    1975-01-01

    Using a set of worksheets, students will discover and apply Euler's formula regarding connected planar graphs and play and analyze the game of Sprouts. One sheet leads to the discovery of Euler's formula; another concerns traversability of a graph; another gives an example and a game involving these ideas. (Author/KM)

  5. Using Specialized Graph Paper.

    ERIC Educational Resources Information Center

    James, C.

    1988-01-01

    Discusses the use of logarithm and reciprocal graphs in the college physics classroom. Provides examples, such as electrical conductivity, reliability function in the Weibull model, and the Clausius-Clapeyron equation for latent heat of vaporation. Shows graphs with weighting of points. (YP)

  6. Equitable random graphs

    NASA Astrophysics Data System (ADS)

    Newman, M. E. J.; Martin, Travis

    2014-11-01

    Random graph models have played a dominant role in the theoretical study of networked systems. The Poisson random graph of Erdős and Rényi, in particular, as well as the so-called configuration model, have served as the starting point for numerous calculations. In this paper we describe another large class of random graph models, which we call equitable random graphs and which are flexible enough to represent networks with diverse degree distributions and many nontrivial types of structure, including community structure, bipartite structure, degree correlations, stratification, and others, yet are exactly solvable for a wide range of properties in the limit of large graph size, including percolation properties, complete spectral density, and the behavior of homogeneous dynamical systems, such as coupled oscillators or epidemic models.

  7. Random graph states, maximal flow and Fuss-Catalan distributions

    NASA Astrophysics Data System (ADS)

    Collins, Benoît; Nechita, Ion; Życzkowski, Karol

    2010-07-01

    For any graph consisting of k vertices and m edges we construct an ensemble of random pure quantum states which describe a system composed of 2m subsystems. Each edge of the graph represents a bipartite, maximally entangled state. Each vertex represents a random unitary matrix generated according to the Haar measure, which describes the coupling between subsystems. Dividing all subsystems into two parts, one may study entanglement with respect to this partition. A general technique to derive an expression for the average entanglement entropy of random pure states associated with a given graph is presented. Our technique relies on Weingarten calculus and flow problems. We analyze the statistical properties of spectra of such random density matrices and show for which cases they are described by the free Poissonian (Marchenko-Pastur) distribution. We derive a discrete family of generalized, Fuss-Catalan distributions and explicitly construct graphs which lead to ensembles of random states characterized by these novel distributions of eigenvalues.

  8. Implementing Graph Pattern Queries on a Relational Database

    SciTech Connect

    Kaplan, I L; Abdulla, G M; Brugger, S T; Kohn, S R

    2007-12-26

    When a graph database is implemented on top of a relational database, queries in the graph query language are translated into relational SQL queries. Graph pattern queries are an important feature of a graph query language. Translating graph pattern queries into single SQL statements results in very poor query performance. By taking into account the pattern query structure and generating multiple SQL statements, pattern query performance can be dramatically improved. The performance problems encountered with the single SQL statements generated for pattern queries reflects a problem in the SQL query planner and optimizer. Addressing this problem would allow relational databases to better support semantic graph databases. Relational database systems that provide good support for graph databases may also be more flexible platforms for data warehouses.

  9. An Iterated Tabu Search Approach for the Clique Partitioning Problem

    PubMed Central

    2014-01-01

    Given an edge-weighted undirected graph with weights specifying dissimilarities between pairs of objects, represented by the vertices of the graph, the clique partitioning problem (CPP) is to partition the vertex set of the graph into mutually disjoint subsets such that the sum of the edge weights over all cliques induced by the subsets is as small as possible. We develop an iterated tabu search (ITS) algorithm for solving this problem. The proposed algorithm incorporates tabu search, local search, and solution perturbation procedures. We report computational results on CPP instances of size up to 2000 vertices. Performance comparisons of ITS against state-of-the-art methods from the literature demonstrate the competitiveness of our approach. PMID:24737968

  10. Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

    PubMed Central

    Pell, Jason; Hintze, Arend; Canino-Koning, Rosangela; Howe, Adina; Tiedje, James M.; Brown, C. Titus

    2012-01-01

    Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for de novo assembly of short-read shotgun sequencing data from these complex populations are an increasingly large practical barrier. Here we introduce a memory-efficient graph representation with which we can analyze the k-mer connectivity of metagenomic samples. The graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k-mer, albeit inexactly. We show that this data structure accurately represents DNA assembly graphs in low memory. We apply this data structure to the problem of partitioning assembly graphs into components as a prelude to assembly, and show that this reduces the overall memory requirements for de novo assembly of metagenomes. On one soil metagenome assembly, this approach achieves a nearly 40-fold decrease in the maximum memory requirements for assembly. This probabilistic graph representation is a significant theoretical advance in storing assembly graphs and also yields immediate leverage on metagenomic assembly. PMID:22847406

  11. Reaction spreading on graphs

    NASA Astrophysics Data System (ADS)

    Burioni, Raffaella; Chibbaro, Sergio; Vergni, Davide; Vulpiani, Angelo

    2012-11-01

    We study reaction-diffusion processes on graphs through an extension of the standard reaction-diffusion equation starting from first principles. We focus on reaction spreading, i.e., on the time evolution of the reaction product M(t). At variance with pure diffusive processes, characterized by the spectral dimension ds, the important quantity for reaction spreading is found to be the connectivity dimension dl. Numerical data, in agreement with analytical estimates based on the features of n independent random walkers on the graph, show that M(t)˜tdl. In the case of Erdös-Renyi random graphs, the reaction product is characterized by an exponential growth M(t)˜eαt with α proportional to ln, where is the average degree of the graph.

  12. Diagnostic performance and partition values of exercise electrocardiographic variables in the detection of coronary artery disease--improved accuracy by using ST/HR hysteresis.

    PubMed

    Kronander, Håkan; Fischer-Colbrie, Werner; Nowak, Jacek; Brodin, Lars-Ake; Elmqvist, Håkan

    2010-03-01

    Exercise electrocardiography is widely used for initial identification of patients with coronary artery disease (CAD). This study compares the measurements of ST-segment changes during exercise and during early postexercise recovery in terms of diagnostic discrimination capacity and optimal partition values. Data from 1876 patients undergoing a routine bicycle exercise test were analysed. CAD was angiographically verified in 668 patients, and excluded by angiography (n = 119), myocardial scintigraphy (n = 250), and on clinical grounds (n = 839) in 1208 patients. Postexercise ST/HR hysteresis was calculated as normalized for heart rate (HR) ST/HR loop area during the first 3 min of recovery. ST/HR index was obtained by dividing the overall ST amplitude change during exercise by exercise-induced HR change, and ST/HR slope was calculated using linear regression analysis of ST/HR data pairs during exercise. ST-segment depression was measured during, and for 3 min after the exercise. Discriminating capacity of the methods was evaluated in terms of receiver operating characteristic areas and optimal partition values providing the combination of the best sensitivity and specificity were established. The best diagnostic discrimination was provided by ST/HR hysteresis at optimal partition value of -15 microV, followed by postexercise ST amplitude measurements at gender-specific partition values of -10 to -90 microV, ST/HR slope [partition value 2.4 microV (beats/min)(-1)], ST/HR index [partition value 1.6 microV (beats/min)(-1)], and ST-segment depression during exercise (partition value 70 microV in men and 90 microV in women). The results demonstrate that analysis of postexercise ST/HR hysteresis offers the most accurate and gender indifferent identification of patients with CAD.

  13. A study on vague graphs.

    PubMed

    Rashmanlou, Hossein; Samanta, Sovan; Pal, Madhumangal; Borzooei, R A

    2016-01-01

    The main purpose of this paper is to introduce the notion of vague h-morphism on vague graphs and regular vague graphs. The action of vague h-morphism on vague strong regular graphs are studied. Some elegant results on weak and co weak isomorphism are derived. Also, [Formula: see text]-complement of highly irregular vague graphs are defined. PMID:27536517

  14. A Semantic Graph Query Language

    SciTech Connect

    Kaplan, I L

    2006-10-16

    Semantic graphs can be used to organize large amounts of information from a number of sources into one unified structure. A semantic query language provides a foundation for extracting information from the semantic graph. The graph query language described here provides a simple, powerful method for querying semantic graphs.

  15. Commuting projections on graphs

    SciTech Connect

    Vassilevski, Panayot S.; Zikatanov, Ludmil T.

    2013-02-19

    For a given (connected) graph, we consider vector spaces of (discrete) functions defined on its vertices and its edges. These two spaces are related by a discrete gradient operator, Grad and its adjoint, ₋Div, referred to as (negative) discrete divergence. We also consider a coarse graph obtained by aggregation of vertices of the original one. Then a coarse vertex space is identified with the subspace of piecewise constant functions over the aggregates. We consider the ℓ2-projection QH onto the space of these piecewise constants. In the present paper, our main result is the construction of a projection π H from the original edge-space onto a properly constructed coarse edge-space associated with the edges of the coarse graph. The projections π H and QH commute with the discrete divergence operator, i.e., we have div π H = QH div. The respective pair of coarse edge-space and coarse vertexspace offer the potential to construct two-level, and by recursion, multilevel methods for the mixed formulation of the graph Laplacian which utilizes the discrete divergence operator. The performance of one two-level method with overlapping Schwarz smoothing and correction based on the constructed coarse spaces for solving such mixed graph Laplacian systems is illustrated on a number of graph examples.

  16. Improving energy partitioning and the nighttime energy balance by implementation of a multi-layer energy budget in ORCHIDEE-CAN

    NASA Astrophysics Data System (ADS)

    Chen, Yiying; Ryder, James; Naudts, Kim; McGrath, Matthew J.; Otto, Juliane; Bastriko, Vladislav; Valade, Aude; Launiainen, Samuli; Ogée, Jérôme; Elbers, Jan A.; Foken, Thomas; Tiedemann, Frank; Heinesch, Bernard; Black, Andrew; Haverd, Vanessa; Loustau, Denis; Ottlé, Catherine; Peylin, Philippe; Polcher, Jan; Luyssaert, Sebastiaan

    2015-04-01

    Canopy structure is one of the most important vegetation characteristics for land-atmosphere interactions as it determines the energy and scalar exchanges between land surface and overlay air mass. In this study we evaluated the performance of a newly developed multi-layer energy budget (Ryder et al., 2014) in a land surface model, ORCHIDEE-CAN (Naudts et al., 2014), which simulates canopy structure and can be coupled to an atmospheric model using an implicit procedure. Furthermore, a vertical discrete drag parametrization scheme was also incorporated into this model, in order to obtain a better description of the sub-canopy wind profile simulation. Site level datasets, including the top-of-the-canopy and sub-canopy observations made available from eight flux observation sites, were collected in order to conduct this evaluation. The geo-location of the collected observation sites crossed climate zones from temperate to boreal and the vegetation types included deciduous, evergreen broad leaved and evergreen needle leaved forest with maximum LAI ranging from 2.1 to 7.0. First, we used long-term top-of-the-canopy measurements to analyze the performance of the current one-layer energy budget in ORCHIDEE-CAN. Three major processes were identified for improvement through the implementation of a multi-layer energy budget: 1) night time radiation balance, 2) energy partitioning during winter and 3) prediction of the ground heat flux. Short-term sub-canopy observations were used to calibrate the parameters in sub-canopy radiation, turbulence and resistances modules with an automatic tuning process following the maximum gradient of the user-defined objective function. The multi-layer model is able to capture the dynamic of sub-canopy turbulence, temperature and energy fluxes with imposed LAI profile and optimized parameter set at a site level calibration. The simulation result shows the improvement both on the nighttime energy balance and energy partitioning during winter

  17. A Negative Partition Relation

    PubMed Central

    Hajnal, A.

    1971-01-01

    If the continuum hypothesis is assumed, there is a graph G whose vertices form an ordered set of type ω12; G does not contain triangles or complete even graphs of form [[unk]0,[unk]0], and there is no independent subset of vertices of type ω12. PMID:16591893

  18. Further improved stability criteria for uncertain T-S fuzzy systems with time-varying delay by (m,N)-delay-partitioning approach.

    PubMed

    Yang, Jun; Luo, Wen-Pin; Wang, Yong-Hu; Cheng, Jun

    2015-11-01

    This paper mainly focuses on the robust stability criteria for uncertain T-S fuzzy systems with time-varying delay by (m,N)-delay-partitioning approach. A modified augmented LKF is established by partitioning the delay in all integral terms. Via taking into account of (i) the relationship between each subinterval and time-varying delay and (ii) the independent upper bounds of the delay derivative in the various delay intervals, some new results on tighter bounding inequalities such as Peng-Park׳s integral inequality and Free-Matrix-based integral inequality are introduced to effectively reduce the enlargement in bounding the derivative of LKF as much as possible, therefore, significant less conservative results can be expected in terms of es and LMIs, which can be solved efficiently with the Matlab LMI toolbox. Furthermore, it is worth mentioning that, when the delay-partitioning number m is fixed, the conservatism is gradually reduced with the increase of another delay-partitioning number N, but without increasing any computing burden. Finally, two numerical examples are included to show that the proposed method is less conservative than existing ones. PMID:26365365

  19. Key-Node-Separated Graph Clustering and Layouts for Human Relationship Graph Visualization.

    PubMed

    Itoh, Takayuki; Klein, Karsten

    2015-01-01

    Many graph-drawing methods apply node-clustering techniques based on the density of edges to find tightly connected subgraphs and then hierarchically visualize the clustered graphs. However, users may want to focus on important nodes and their connections to groups of other nodes for some applications. For this purpose, it is effective to separately visualize the key nodes detected based on adjacency and attributes of the nodes. This article presents a graph visualization technique for attribute-embedded graphs that applies a graph-clustering algorithm that accounts for the combination of connections and attributes. The graph clustering step divides the nodes according to the commonality of connected nodes and similarity of feature value vectors. It then calculates the distances between arbitrary pairs of clusters according to the number of connecting edges and the similarity of feature value vectors and finally places the clusters based on the distances. Consequently, the technique separates important nodes that have connections to multiple large clusters and improves the visibility of such nodes' connections. To test this technique, this article presents examples with human relationship graph datasets, including a coauthorship and Twitter communication network dataset.

  20. Tensor Spectral Clustering for Partitioning Higher-order Network Structures

    PubMed Central

    Benson, Austin R.; Gleich, David F.; Leskovec, Jure

    2016-01-01

    Spectral graph theory-based methods represent an important class of tools for studying the structure of networks. Spectral methods are based on a first-order Markov chain derived from a random walk on the graph and thus they cannot take advantage of important higher-order network substructures such as triangles, cycles, and feed-forward loops. Here we propose a Tensor Spectral Clustering (TSC) algorithm that allows for modeling higher-order network structures in a graph partitioning framework. Our TSC algorithm allows the user to specify which higher-order network structures (cycles, feed-forward loops, etc.) should be preserved by the network clustering. Higher-order network structures of interest are represented using a tensor, which we then partition by developing a multilinear spectral method. Our framework can be applied to discovering layered flows in networks as well as graph anomaly detection, which we illustrate on synthetic networks. In directed networks, a higher-order structure of particular interest is the directed 3-cycle, which captures feedback loops in networks. We demonstrate that our TSC algorithm produces large partitions that cut fewer directed 3-cycles than standard spectral clustering algorithms.

  1. Optimized Graph Search Using Multi-Level Graph Clustering

    NASA Astrophysics Data System (ADS)

    Kala, Rahul; Shukla, Anupam; Tiwari, Ritu

    Graphs find a variety of use in numerous domains especially because of their capability to model common problems. The social networking graphs that are used for social networking analysis, a feature given by various social networking sites are an example of this. Graphs can also be visualized in the search engines to carry search operations and provide results. Various searching algorithms have been developed for searching in graphs. In this paper we propose that the entire network graph be clustered. The larger graphs are clustered to make smaller graphs. These smaller graphs can again be clustered to further reduce the size of graph. The search is performed on the smallest graph to identify the general path, which may be further build up to actual nodes by working on the individual clusters involved. Since many searches are carried out on the same graph, clustering may be done once and the data may be used for multiple searches over the time. If the graph changes considerably, only then we may re-cluster the graph.

  2. Algebraic distance on graphs.

    SciTech Connect

    Chen, J.; Safro, I.

    2011-01-01

    Measuring the connection strength between a pair of vertices in a graph is one of the most important concerns in many graph applications. Simple measures such as edge weights may not be sufficient for capturing the effects associated with short paths of lengths greater than one. In this paper, we consider an iterative process that smooths an associated value for nearby vertices, and we present a measure of the local connection strength (called the algebraic distance; see [D. Ron, I. Safro, and A. Brandt, Multiscale Model. Simul., 9 (2011), pp. 407-423]) based on this process. The proposed measure is attractive in that the process is simple, linear, and easily parallelized. An analysis of the convergence property of the process reveals that the local neighborhoods play an important role in determining the connectivity between vertices. We demonstrate the practical effectiveness of the proposed measure through several combinatorial optimization problems on graphs and hypergraphs.

  3. A Graph Search Heuristic for Shortest Distance Paths

    SciTech Connect

    Chow, E

    2005-03-24

    This paper presents a heuristic for guiding A* search for finding the shortest distance path between two vertices in a connected, undirected, and explicitly stored graph. The heuristic requires a small amount of data to be stored at each vertex. The heuristic has application to quickly detecting relationships between two vertices in a large information or knowledge network. We compare the performance of this heuristic with breadth-first search on graphs with various topological properties. The results show that one or more orders of magnitude improvement in the number of vertices expanded is possible for large graphs, including Poisson random graphs.

  4. Exploiting graph properties of game trees

    SciTech Connect

    Plaat, A.; Pijls, W.; Bruin, A. de; Schaeffer, J.

    1996-12-31

    The state space of most adversary games is a directed graph. However, due to the success of simple recursive algorithms based on alpha-beta, theoreticians and practitioners have concentrated on the traversal of trees, giving the field the name {open_quotes}game-tree search,{close_quotes} This paper shows that the focus on trees has obscured some important properties of the underlying graphs. One of the hallmarks of the field of game-tree search has been the notion of the minimal tree, the smallest tree that has to be searched by any algorithm to find the minimax value. In fact, for most games it is a directed graph. As demonstrated in chess and checkers, we show that the minimal graph is significantly smaller than previously thought, proving that there is more room for improvement of current algorithms. We exploit the graph properties of the search space to reduce the size of trees built in practice by at least 25%. For over a decade, fixed-depth alpha-beta searching has been considered a closed subject, with research moving on to more application-dependent techniques. This work opens up new avenues of research for further application-independent improvements.

  5. Robustness of random graphs based on graph spectra

    NASA Astrophysics Data System (ADS)

    Wu, Jun; Barahona, Mauricio; Tan, Yue-jin; Deng, Hong-zhong

    2012-12-01

    It has been recently proposed that the robustness of complex networks can be efficiently characterized through the natural connectivity, a spectral property of the graph which corresponds to the average Estrada index. The natural connectivity corresponds to an average eigenvalue calculated from the graph spectrum and can also be interpreted as the Helmholtz free energy of the network. In this article, we explore the use of this index to characterize the robustness of Erdős-Rényi (ER) random graphs, random regular graphs, and regular ring lattices. We show both analytically and numerically that the natural connectivity of ER random graphs increases linearly with the average degree. It is also shown that ER random graphs are more robust than the corresponding random regular graphs with the same number of vertices and edges. However, the relative robustness of ER random graphs and regular ring lattices depends on the average degree and graph size: there is a critical graph size above which regular ring lattices are more robust than random graphs. We use our analytical results to derive this critical graph size as a function of the average degree.

  6. Integration of Building Knowledge Into Binary Space Partitioning for the Reconstruction of Regularized Building Models

    NASA Astrophysics Data System (ADS)

    Wichmann, A.; Jung, J.; Sohn, G.; Kada, M.; Ehlers, M.

    2015-09-01

    Recent approaches for the automatic reconstruction of 3D building models from airborne point cloud data integrate prior knowledge of roof shapes with the intention to improve the regularization of the resulting models without lessening the flexibility to generate all real-world occurring roof shapes. In this paper, we present a method to integrate building knowledge into the data-driven approach that uses binary space partitioning (BSP) for modeling the 3D building geometry. A retrospective regularization of polygons that emerge from the BSP tree is not without difficulty because it has to deal with the 2D BSP subdivision itself and the plane definitions of the resulting partition regions to ensure topological correctness. This is aggravated by the use of hyperplanes during the binary subdivision that often splits planar roof regions into several parts that are stored in different subtrees of the BSP tree. We therefore introduce the use of hyperpolylines in the generation of the BSP tree to avoid unnecessary spatial subdivisions, so that the spatial integrity of planar roof regions is better maintained. The hyperpolylines are shown to result from basic building roof knowledge that is extracted based on roof topology graphs. An adjustment of the underlying point segments ensures that the positions of the extracted hyperpolylines result in regularized 2D partitions as well as topologically correct 3D building models. The validity and limitations of the approach are demonstrated on real-world examples.

  7. Graph for locked rotor current

    NASA Technical Reports Server (NTRS)

    Peck, R. R.

    1972-01-01

    Graph determines effect of stalled motor on a distribution system and eliminates hand calculation of amperage in emergencies. Graph is useful to any manufacturer, contractor, or maintenance department involved in electrical technology.

  8. "K"-Balance Partitioning: An Exact Method with Applications to Generalized Structural Balance and Other Psychological Contexts

    ERIC Educational Resources Information Center

    Brusco, Michael; Steinley, Douglas

    2010-01-01

    Structural balance theory (SBT) has maintained a venerable status in the psychological literature for more than 5 decades. One important problem pertaining to SBT is the approximation of structural or generalized balance via the partitioning of the vertices of a signed graph into "K" clusters. This "K"-balance partitioning problem also has more…

  9. GraphLib

    2013-02-19

    This library is used in several LLNL projects, including STAT (the Stack Trace Analysis Tool for scalable debugging) and some modules in P^nMPI (a tool MPI tool infrastructure). It can also be used standalone for creating and manipulationg graphs, but its API is primarily tuned to support these other projects

  10. Line Graph Learning

    ERIC Educational Resources Information Center

    Pitts Bannister, Vanessa R.; Jamar, Idorenyin; Mutegi, Jomo W.

    2007-01-01

    In this article, the learning progress of one fifth-grade student is examined with regard to the development of her graph interpretation skills as she participated in the Junior Science Institute (JSI), a two-week, science intensive summer camp in which participants engaged in microbiology research and application. By showcasing the student's…

  11. Straight Line Graphs

    ERIC Educational Resources Information Center

    Krueger, Tom

    2010-01-01

    In this article, the author shares one effective lesson idea on straight line graphs that he applied in his lower ability Y9 class. The author wanted something interesting for his class to do, something that was fun and engaging with direct feedback, and something that worked because someone else had tried it before. In a word, the author admits…

  12. Introduction to Graphing.

    ERIC Educational Resources Information Center

    Sokol, William

    In this autoinstructional packet, the student is given an experimental situation which introduces him to the process of graphing. The lesson is presented for secondary school students in chemistry. Algebra I and a Del Mod System program (indicated as SE 018 020) are suggested prerequisites for the use of this program. Behavioral objectives are…

  13. Cookies and Graphs

    ERIC Educational Resources Information Center

    Cooper, Carol

    1975-01-01

    Teachers of an integrated elementary classroom used cookie-sharing time as a learning experience for students. Responsible for dividing varying amounts of cookies daily, the students learned to translate their experiences to graphs of differing sophistication and analyses. Further interpretation and application were done by individual students…

  14. Physics on Graphs

    NASA Astrophysics Data System (ADS)

    Schrader, Robert

    This is an extended version of the talk given at the Nato Advanced Research Workshop: New Challenges in Complex System Physics, May 20-24, 2013 in Samarkand (Uzbekistan). We report on results on three topics in joint work with V. Kostrykin (Mainz, Germany) and J. Potthoff (Mannheim, Germany): Propagation of waves on graphs,

  15. Graph-theoretical exorcism

    SciTech Connect

    Simmons, G.J.

    1985-01-01

    Given a graph G and an ordering phi of the vertices, V(G), we define a parsimonious proper coloring (PPC) of V(G) under phi to be a proper coloring of V(G) in the order phi, where a new color is introduced only when a vertex cannot be properly colored in its order with any of the colors already used.

  16. Coloring geographical threshold graphs

    SciTech Connect

    Bradonjic, Milan; Percus, Allon; Muller, Tobias

    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.

  17. New Conic Graph Paper

    ERIC Educational Resources Information Center

    Rose, Kenneth

    1974-01-01

    Two new types of graph paper are described; focus-focus conic paper and focus-directrix paper. Both types make it easier to draw families of conics. Suggestions for further work are given as is a method for establishing a connection with other ways of looking at the conic sections. (LS)

  18. Temporal Representation in Semantic Graphs

    SciTech Connect

    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.

  19. Quantum walks on quotient graphs

    SciTech Connect

    Krovi, Hari; Brun, Todd A.

    2007-06-15

    A discrete-time quantum walk on a graph {gamma} 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.

  20. A Clustering Graph Generator

    SciTech Connect

    Winlaw, Manda; De Sterck, Hans; Sanders, Geoffrey

    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.

  1. Mining and Indexing Graph Databases

    ERIC Educational Resources Information Center

    Yuan, Dayu

    2013-01-01

    Graphs are widely used to model structures and relationships of objects in various scientific and commercial fields. Chemical molecules, proteins, malware system-call dependencies and three-dimensional mechanical parts are all modeled as graphs. In this dissertation, we propose to mine and index those graph data to enable fast and scalable search.…

  2. Recursive Feature Extraction in Graphs

    SciTech Connect

    2014-08-14

    ReFeX extracts recursive topological features from graph data. The input is a graph as a csv file and the output is a csv file containing feature values for each node in the graph. The features are based on topological counts in the neighborhoods of each nodes, as well as recursive summaries of neighbors' features.

  3. Editing graphs for maximum effect

    SciTech Connect

    Murphy, P.W.; Rhiner, R.W.

    1991-01-08

    The paper contains over eighty rules for editing graphs, arranged under nine major headings in a logical sequence for editing all the graphs in a manuscript. It is excerpted from a monograph used at the Lawrence Livermore National Laboratory to train beginning technical editors in editing graphs; a corresponding Hypercard stack is also used in this training. 6 refs., 4 figs.

  4. A Note on Hamiltonian Graphs

    ERIC Educational Resources Information Center

    Skurnick, Ronald; Davi, Charles; Skurnick, Mia

    2005-01-01

    Since 1952, several well-known graph theorists have proven numerous results regarding Hamiltonian graphs. In fact, many elementary graph theory textbooks contain the theorems of Ore, Bondy and Chvatal, Chvatal and Erdos, Posa, and Dirac, to name a few. In this note, the authors state and prove some propositions of their own concerning Hamiltonian…

  5. Improving Design Efficiency for Large-Scale Heterogeneous Circuits

    NASA Astrophysics Data System (ADS)

    Gregerson, Anthony

    Despite increases in logic density, many Big Data applications must still be partitioned across multiple computing devices in order to meet their strict performance requirements. Among the most demanding of these applications is high-energy physics (HEP), which uses complex computing systems consisting of thousands of FPGAs and ASICs to process the sensor data created by experiments at particles accelerators such as the Large Hadron Collider (LHC). Designing such computing systems is challenging due to the scale of the systems, the exceptionally high-throughput and low-latency performance constraints that necessitate application-specific hardware implementations, the requirement that algorithms are efficiently partitioned across many devices, and the possible need to update the implemented algorithms during the lifetime of the system. In this work, we describe our research to develop flexible architectures for implementing such large-scale circuits on FPGAs. In particular, this work is motivated by (but not limited in scope to) high-energy physics algorithms for the Compact Muon Solenoid (CMS) experiment at the LHC. To make efficient use of logic resources in multi-FPGA systems, we introduce Multi-Personality Partitioning, a novel form of the graph partitioning problem, and present partitioning algorithms that can significantly improve resource utilization on heterogeneous devices while also reducing inter-chip connections. To reduce the high communication costs of Big Data applications, we also introduce Information-Aware Partitioning, a partitioning method that analyzes the data content of application-specific circuits, characterizes their entropy, and selects circuit partitions that enable efficient compression of data between chips. We employ our information-aware partitioning method to improve the performance of the hardware validation platform for evaluating new algorithms for the CMS experiment. Together, these research efforts help to improve the efficiency

  6. A Visual Analytics Paradigm Enabling Trillion-Edge Graph Exploration

    SciTech Connect

    Wong, Pak C.; Haglin, David J.; Gillen, David S.; Chavarría-Miranda, Daniel; Castellana, Vito G.; Joslyn, Cliff A.; Chappell, Alan R.; Zhang, Song

    2015-07-06

    We present a visual analytics paradigm and a system prototype for exploring web-scale graphs. A web-scale graph is described as a graph with ~one trillion edges and ~50 billion vertices. While there is an aggressive R&D effort in processing and exploring web-scale graphs among internet vendors such as Facebook and Google, visualizing a graph of that scale still remains an underexplored R&D area. The paper describes a nontraditional peek-and-filter strategy that facilitates the exploration of a graph database of unprecedented size for visualization and analytics. We demonstrate that our system prototype can 1) preprocess a graph with ~25 billion edges in less than two hours and 2) support database query and visualization on the processed graph database afterward. Based on our computational performance results, we argue that we most likely will achieve the one trillion edge mark (a computational performance improvement of 40 times) for graph visual analytics in the near future.

  7. Extending a Role Graph for Role-Based Access Control

    NASA Astrophysics Data System (ADS)

    Asakura, Yoshiharu; Nakamoto, Yukikazu

    Role-based access control (RBAC) is widely used as an access control mechanism in various computer systems. Since an organization's lines of authority influence the authorized privileges of jobs, roles also form a hierarchical structure. A role graph is a model that represents role hierarchies and is suitable for the runtime phase of RBAC deployment. Since a role graph cannot take various forms for given roles and cannot handle abstraction of roles well, however, it is not suitable for the design phase of RBAC deployment. Hence, an extended role graph, which can take a more flexible form than that of a role graph, is proposed. The extended role graph improves diversity and clarifies abstraction of roles, making it suitable for the design phase. An equivalent transformation algorithm (ETA), for transforming an extended role graph into an equivalent role graph, is also proposed. Using the ETA, system administrators can deploy efficiently RBAC by using an extended role graph in the design phase and a standard role graph in the runtime phase.

  8. Towards Scalable Graph Computation on Mobile Devices

    PubMed Central

    Chen, Yiqi; Lin, Zhiyuan; Pienta, Robert; Kahng, Minsuk; Chau, Duen Horng

    2015-01-01

    Mobile devices have become increasingly central to our everyday activities, due to their portability, multi-touch capabilities, and ever-improving computational power. Such attractive features have spurred research interest in leveraging mobile devices for computation. We explore a novel approach that aims to use a single mobile device to perform scalable graph computation on large graphs that do not fit in the device's limited main memory, opening up the possibility of performing on-device analysis of large datasets, without relying on the cloud. Based on the familiar memory mapping capability provided by today's mobile operating systems, our approach to scale up computation is powerful and intentionally kept simple to maximize its applicability across the iOS and Android platforms. Our experiments demonstrate that an iPad mini can perform fast computation on large real graphs with as many as 272 million edges (Google+ social graph), at a speed that is only a few times slower than a 13″ Macbook Pro. Through creating a real world iOS app with this technique, we demonstrate the strong potential application for scalable graph computation on a single mobile device using our approach. PMID:25859564

  9. Deformed graph laplacian for semisupervised learning.

    PubMed

    Gong, Chen; Liu, Tongliang; Tao, Dacheng; Fu, Keren; Tu, Enmei; Yang, Jie

    2015-10-01

    Graph Laplacian has been widely exploited in traditional graph-based semisupervised learning (SSL) algorithms to regulate the labels of examples that vary smoothly on the graph. Although it achieves a promising performance in both transductive and inductive learning, it is not effective for handling ambiguous examples (shown in Fig. 1). This paper introduces deformed graph Laplacian (DGL) and presents label prediction via DGL (LPDGL) for SSL. The local smoothness term used in LPDGL, which regularizes examples and their neighbors locally, is able to improve classification accuracy by properly dealing with ambiguous examples. Theoretical studies reveal that LPDGL obtains the globally optimal decision function, and the free parameters are easy to tune. The generalization bound is derived based on the robustness analysis. Experiments on a variety of real-world data sets demonstrate that LPDGL achieves top-level performance on both transductive and inductive settings by comparing it with popular SSL algorithms, such as harmonic functions, AnchorGraph regularization, linear neighborhood propagation, Laplacian regularized least square, and Laplacian support vector machine.

  10. A graph based algorithm for adaptable dynamic airspace configuration for NextGen

    NASA Astrophysics Data System (ADS)

    Savai, Mehernaz P.

    The National Airspace System (NAS) is a complicated large-scale aviation network, consisting of many static sectors wherein each sector is controlled by one or more controllers. The main purpose of the NAS is to enable safe and prompt air travel in the U.S. However, such static configuration of sectors will not be able to handle the continued growth of air travel which is projected to be more than double the current traffic by 2025. Under the initiative of the Next Generation of Air Transportation system (NextGen), the main objective of Adaptable Dynamic Airspace Configuration (ADAC) is that the sectors should change to the changing traffic so as to reduce the controller workload variance with time while increasing the throughput. Change in the resectorization should be such that there is a minimal increase in exchange of air traffic among controllers. The benefit of a new design (improvement in workload balance, etc.) should sufficiently exceed the transition cost, in order to deserve a change. This leads to the analysis of the concept of transition workload which is the cost associated with a transition from one sectorization to another. Given two airspace configurations, a transition workload metric which considers the air traffic as well as the geometry of the airspace is proposed. A solution to reduce this transition workload is also discussed. The algorithm is specifically designed to be implemented for the Dynamic Airspace Configuration (DAC) Algorithm. A graph model which accurately represents the air route structure and air traffic in the NAS is used to formulate the airspace configuration problem. In addition, a multilevel graph partitioning algorithm is developed for Dynamic Airspace Configuration which partitions the graph model of airspace with given user defined constraints and hence provides the user more flexibility and control over various partitions. In terms of air traffic management, vertices represent airports and waypoints. Some of the major

  11. What is a complex graph?

    NASA Astrophysics Data System (ADS)

    Kim, Jongkwang; Wilhelm, Thomas

    2008-04-01

    Many papers published in recent years show that real-world graphs G(n,m) ( n nodes, m edges) are more or less “complex” in the sense that different topological features deviate from random graphs. Here we narrow the definition of graph complexity and argue that a complex graph contains many different subgraphs. We present different measures that quantify this complexity, for instance C1e, the relative number of non-isomorphic one-edge-deleted subgraphs (i.e. DECK size). However, because these different subgraph measures are computationally demanding, we also study simpler complexity measures focussing on slightly different aspects of graph complexity. We consider heuristically defined “product measures”, the products of two quantities which are zero in the extreme cases of a path and clique, and “entropy measures” quantifying the diversity of different topological features. The previously defined network/graph complexity measures Medium Articulation and Offdiagonal complexity ( OdC) belong to these two classes. We study OdC measures in some detail and compare it with our new measures. For all measures, the most complex graph G has a medium number of edges, between the edge numbers of the minimum and the maximum connected graph n-1graph complexity measures are characterized with the help of different example graphs. For all measures the corresponding time complexity is given. Finally, we discuss the complexity of 33 real-world graphs of different biological, social and economic systems with the six computationally most simple measures (including OdC). The complexities of the real graphs are compared with average complexities of two different random graph versions: complete random graphs (just fixed n,m) and rewired graphs with fixed node degrees.

  12. Spectral fluctuations of quantum graphs

    NASA Astrophysics Data System (ADS)

    Pluhař, Z.; Weidenmüller, H. A.

    2014-10-01

    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.

  13. Spectral fluctuations of quantum graphs

    SciTech Connect

    Pluhař, Z.; Weidenmüller, H. A.

    2014-10-15

    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.

  14. Graph characterization via Ihara coefficients.

    PubMed

    Ren, Peng; Wilson, Richard C; Hancock, Edwin R

    2011-02-01

    The novel contributions of this paper are twofold. First, we demonstrate how to characterize unweighted graphs in a permutation-invariant manner using the polynomial coefficients from the Ihara zeta function, i.e., the Ihara coefficients. Second, we generalize the definition of the Ihara coefficients to edge-weighted graphs. For an unweighted graph, the Ihara zeta function is the reciprocal of a quasi characteristic polynomial of the adjacency matrix of the associated oriented line graph. Since the Ihara zeta function has poles that give rise to infinities, the most convenient numerically stable representation is to work with the coefficients of the quasi characteristic polynomial. Moreover, the polynomial coefficients are invariant to vertex order permutations and also convey information concerning the cycle structure of the graph. To generalize the representation to edge-weighted graphs, we make use of the reduced Bartholdi zeta function. We prove that the computation of the Ihara coefficients for unweighted graphs is a special case of our proposed method for unit edge weights. We also present a spectral analysis of the Ihara coefficients and indicate their advantages over other graph spectral methods. We apply the proposed graph characterization method to capturing graph-class structure and clustering graphs. Experimental results reveal that the Ihara coefficients are more effective than methods based on Laplacian spectra.

  15. An Unusual Exponential Graph

    ERIC Educational Resources Information Center

    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…

  16. A New Graph Drawing Scheme for Social Network

    PubMed Central

    Wang, Eric Ke; Zou, Futai

    2014-01-01

    With the development of social networks, people have started to use social network tools to record their life and work more and more frequently. How to analyze social networks to explore potential characteristics and trend of social events has been a hot research topic. In order to analyze it effectively, a kind of techniques called information visualization is employed to extract the potential information from the large scale of social network data and present the information briefly as visualized graphs. In the process of information visualization, graph drawing is a crucial part. In this paper, we study the graph layout algorithms and propose a new graph drawing scheme combining multilevel and single-level drawing approaches, including the graph division method based on communities and refining approach based on partitioning strategy. Besides, we compare the effectiveness of our scheme and FM3 in experiments. The experiment results show that our scheme can achieve a clearer diagram and effectively extract the community structure of the social network to be applied to drawing schemes. PMID:25157378

  17. Locating-chromatic number for a graph of two components

    NASA Astrophysics Data System (ADS)

    Welyyanti, Des; Simanjuntak, Rinovia; Uttunggadewa, Saladin; Baskoro, Edy Tri

    2016-02-01

    The study of locating-chromatic number of a graph initiated by Chartrand et al. [5] is only limited for connected graphs. In 2014, Welyyanti et al. extended this notion so that the locating-chromatic number can also be applied to disconnected graphs. Let c be a k-coloring of a disconnected graph H(V, E) and ∏ = {C1,C2, …, Ck} be the partition of V (H) induced by c, where Ci is the set of all vertices receiving color i. The color code c∏(v) of a vertex v ∈ H is the ordered k-tuple (d(v,C1), d(v,C2), …, d(v,Ck)), where d(v,Ci) = min{d(v, x)|x ∈ Ci} and d(v,Ci) < ∞ for all i ∈ [1, k]. If all vertices of H have distinct color codes, then c is called a locating-coloring of H. The locating-chromatic number of H, denoted by χ'L(H ) , is the smallest k such that H admits a locating-coloring with k colors, otherwise we say that χ'L(H )=∞ . In this paper, we determine locating-chromatic number of a graph with two components where each component has the locating-chromatic number 3.

  18. Exact Algorithms for Coloring Graphs While Avoiding Monochromatic Cycles

    NASA Astrophysics Data System (ADS)

    Talla Nobibon, Fabrice; Hurkens, Cor; Leus, Roel; Spieksma, Frits C. R.

    We consider the problem of deciding whether a given directed graph can be vertex partitioned into two acyclic subgraphs. Applications of this problem include testing rationality of collective consumption behavior, a subject in micro-economics. We identify classes of directed graphs for which the problem is easy and prove that the existence of a constant factor approximation algorithm is unlikely for an optimization version which maximizes the number of vertices that can be colored using two colors while avoiding monochromatic cycles. We present three exact algorithms, namely an integer-programming algorithm based on cycle identification, a backtracking algorithm, and a branch-and-check algorithm. We compare these three algorithms both on real-life instances and on randomly generated graphs. We find that for the latter set of graphs, every algorithm solves instances of considerable size within few seconds; however, the CPU time of the integer-programming algorithm increases with the number of vertices in the graph while that of the two other procedures does not. For every algorithm, we also study empirically the transition from a high to a low probability of YES answer as function of a parameter of the problem. For real-life instances, the integer-programming algorithm fails to solve the largest instance after one hour while the other two algorithms solve it in about ten minutes.

  19. Improved 3D-QSPR analysis of the predictive octanol-air partition coefficients of hydroxylated and methoxylated polybrominated diphenyl ethers

    NASA Astrophysics Data System (ADS)

    Liu, Hongxia; Shi, Jiaqi; Liu, Hui; Wang, Zunyao

    2013-10-01

    The octanol/air partition coefficient (KOA) is a key physicochemical parameter for describing the partition of organic pollutants between air and environment organic phase. The development of appropriate method to estimate KOA is of great importance. In the present study, the steric, electrostatic, hydrophobic, hydrogen bond donor and acceptor descriptors were computed by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). On the basis of these parameters, the statistically quantitative structure-property relationship (QSPR) models for logKOA of hydroxylated polybrominated diphenyl ethers (OH-PBDEs) and methoxylated polybrominated diphenyl ethers (MeO-PBDEs) congeners were developed using partial least-squares (PLS) analysis, of which the R2 is about 0.980, 0.952 respectively. The electrostatic field was found to be main factors governing the logKOA. The results of validation indicate the models of this study exhibit optimum stability, and thus it is feasible to predict logKOA.

  20. Fuzzy Partition Models for Fitting a Set of Partitions.

    ERIC Educational Resources Information Center

    Gordon, A. D.; Vichi, M.

    2001-01-01

    Describes methods for fitting a fuzzy consensus partition to a set of partitions of the same set of objects. Describes and illustrates three models defining median partitions and compares these methods to an alternative approach to obtaining a consensus fuzzy partition. Discusses interesting differences in the results. (SLD)

  1. Reducing variance in batch partitioning measurements

    SciTech Connect

    Mariner, Paul E.

    2010-08-11

    The partitioning experiment is commonly performed with little or no attention to reducing measurement variance. Batch test procedures such as those used to measure K{sub d} values (e.g., ASTM D 4646 and EPA402 -R-99-004A) do not explain how to evaluate measurement uncertainty nor how to minimize measurement variance. In fact, ASTM D 4646 prescribes a sorbent:water ratio that prevents variance minimization. Consequently, the variance of a set of partitioning measurements can be extreme and even absurd. Such data sets, which are commonplace, hamper probabilistic modeling efforts. An error-savvy design requires adjustment of the solution:sorbent ratio so that approximately half of the sorbate partitions to the sorbent. Results of Monte Carlo simulations indicate that this simple step can markedly improve the precision and statistical characterization of partitioning uncertainty.

  2. A brief history of partitions of numbers, partition functions and their modern applications

    NASA Astrophysics Data System (ADS)

    Debnath, Lokenath

    2016-04-01

    'Number rules the universe.' The Pythagoras 'If you wish to forsee the future of mathematics our course is to study the history and present conditions of the science.' Henri Poincaré 'The primary source (Urqell) of all mathematics are integers.' Hermann Minkowski This paper is written to commemorate the centennial anniversary of the Mathematical Association of America. It deals with a short history of different kinds of natural numbers including triangular, square, pentagonal, hexagonal and k-gonal numbers, and their simple properties and their geometrical representations. Included are Euclid's and Pythagorean's main contributions to elementary number theory with the main contents of the Euclid Elements of the 13-volume masterpiece of mathematical work. This is followed by Euler's new discovery of the additive number theory based on partitions of numbers. Special attention is given to many examples, Euler's theorems on partitions of numbers with geometrical representations of Ferrers' graphs, Young's diagrams, Lagrange's four-square theorem and the celebrated Waring problem. Included are Euler's generating functions for the partitions of numbers, Euler's pentagonal number theorem, Gauss' triangular and square number theorems and the Jacobi triple product identity. Applications of the theory of partitions of numbers to different statistics such as the Bose- Einstein, Fermi- Dirac, Gentile, and Maxwell- Boltzmann statistics are briefly discussed. Special attention is given to pedagogical information through historical approach to number theory so that students and teachers at the school, college and university levels can become familiar with the basic concepts of partitions of numbers, partition functions and their modern applications, and can pursue advanced study and research in analytical and computational number theory.

  3. Fast clique minor generation in Chimera qubit connectivity graphs

    NASA Astrophysics Data System (ADS)

    Boothby, Tomas; King, Andrew D.; Roy, Aidan

    2016-01-01

    The current generation of D-Wave quantum annealing processor is designed to minimize the energy of an Ising spin configuration whose pairwise interactions lie on the edges of a Chimera graph C_{M,N,L}. In order to solve an Ising spin problem with arbitrary pairwise interaction structure, the corresponding graph must be minor-embedded into a Chimera graph. We define a combinatorial class of native clique minors in Chimera graphs with vertex images of uniform, near minimal size and provide a polynomial-time algorithm that finds a maximum native clique minor in a given induced subgraph of a Chimera graph. These minors allow improvement over recent work and have immediate practical applications in the field of quantum annealing.

  4. Evaluation of Graph Pattern Matching Workloads in Graph Analysis Systems

    SciTech Connect

    Hong, Seokyong; Sukumar, Sreenivas Rangan; Vatsavai, Raju

    2016-01-01

    Graph analysis has emerged as a powerful method for data scientists to represent, integrate, query, and explore heterogeneous data sources. As a result, graph data management and mining became a popular area of research, and led to the development of plethora of systems in recent years. Unfortunately, the number of emerging graph analysis systems and the wide range of applications, coupled with a lack of apples-to-apples comparisons, make it difficult to understand the trade-offs between different systems and the graph operations for which they are designed. A fair comparison of these systems is a challenging task for the following reasons: multiple data models, non-standardized serialization formats, various query interfaces to users, and diverse environments they operate in. To address these key challenges, in this paper we present a new benchmark suite by extending the Lehigh University Benchmark (LUBM) to cover the most common capabilities of various graph analysis systems. We provide the design process of the benchmark, which generalizes the workflow for data scientists to conduct the desired graph analysis on different graph analysis systems. Equipped with this extended benchmark suite, we present performance comparison for nine subgraph pattern retrieval operations over six graph analysis systems, namely NetworkX, Neo4j, Jena, Titan, GraphX, and uRiKA. Through the proposed benchmark suite, this study reveals both quantitative and qualitative findings in (1) implications in loading data into each system; (2) challenges in describing graph patterns for each query interface; and (3) different sensitivity of each system to query selectivity. We envision that this study will pave the road for: (i) data scientists to select the suitable graph analysis systems, and (ii) data management system designers to advance graph analysis systems.

  5. Thermodynamic characterization of networks using graph polynomials

    NASA Astrophysics Data System (ADS)

    Ye, Cheng; Comin, César H.; Peron, Thomas K. DM.; Silva, Filipi N.; Rodrigues, Francisco A.; Costa, Luciano da F.; Torsello, Andrea; Hancock, Edwin R.

    2015-09-01

    In this paper, we present a method for characterizing the evolution of time-varying complex networks by adopting a thermodynamic representation of network structure computed from a polynomial (or algebraic) characterization of graph structure. Commencing from a representation of graph structure based on a characteristic polynomial computed from the normalized Laplacian matrix, we show how the polynomial is linked to the Boltzmann partition function of a network. This allows us to compute a number of thermodynamic quantities for the network, including the average energy and entropy. Assuming that the system does not change volume, we can also compute the temperature, defined as the rate of change of entropy with energy. All three thermodynamic variables can be approximated using low-order Taylor series that can be computed using the traces of powers of the Laplacian matrix, avoiding explicit computation of the normalized Laplacian spectrum. These polynomial approximations allow a smoothed representation of the evolution of networks to be constructed in the thermodynamic space spanned by entropy, energy, and temperature. We show how these thermodynamic variables can be computed in terms of simple network characteristics, e.g., the total number of nodes and node degree statistics for nodes connected by edges. We apply the resulting thermodynamic characterization to real-world time-varying networks representing complex systems in the financial and biological domains. The study demonstrates that the method provides an efficient tool for detecting abrupt changes and characterizing different stages in network evolution.

  6. Graph Coarsening for Path Finding in Cybersecurity Graphs

    SciTech Connect

    Hogan, Emilie A.; Johnson, John R.; Halappanavar, Mahantesh

    2013-01-01

    n the pass-the-hash attack, hackers repeatedly steal password hashes and move through a computer network with the goal of reaching a computer with high level administrative privileges. In this paper we apply graph coarsening in network graphs for the purpose of detecting hackers using this attack or assessing the risk level of the network's current state. We repeatedly take graph minors, which preserve the existence of paths in the graph, and take powers of the adjacency matrix to count the paths. This allows us to detect the existence of paths as well as find paths that have high risk of being used by adversaries.

  7. A significance test for graph-constrained estimation.

    PubMed

    Zhao, Sen; Shojaie, Ali

    2016-06-01

    Graph-constrained estimation methods encourage similarities among neighboring covariates presented as nodes of a graph, and can result in more accurate estimates, especially in high-dimensional settings. Variable selection approaches can then be utilized to select a subset of variables that are associated with the response. However, existing procedures do not provide measures of uncertainty of estimates. Further, the vast majority of existing approaches assume that available graph accurately captures the association among covariates; violations to this assumption could severely hurt the reliability of the resulting estimates. In this article, we present a new inference framework, called the Grace test, which produces coefficient estimates and corresponding p-values by incorporating the external graph information. We show, both theoretically and via numerical studies, that the proposed method asymptotically controls the type-I error rate regardless of the choice of the graph. We also show that when the underlying graph is informative, the Grace test is asymptotically more powerful than similar tests that ignore the external information. We study the power properties of the proposed test when the graph is not fully informative and develop a more powerful Grace-ridge test for such settings. Our numerical studies show that as long as the graph is reasonably informative, the proposed inference procedures deliver improved statistical power over existing methods that ignore external information.

  8. Robust deformable and occluded object tracking with dynamic graph.

    PubMed

    Cai, Zhaowei; Wen, Longyin; Lei, Zhen; Vasconcelos, Nuno; Li, Stan Z

    2014-12-01

    While some efforts have been paid to handle deformation and occlusion in visual tracking, they are still great challenges. In this paper, a dynamic graph-based tracker (DGT) is proposed to address these two challenges in a unified framework. In the dynamic target graph, nodes are the target local parts encoding appearance information, and edges are the interactions between nodes encoding inner geometric structure information. This graph representation provides much more information for tracking in the presence of deformation and occlusion. The target tracking is then formulated as tracking this dynamic undirected graph, which is also a matching problem between the target graph and the candidate graph. The local parts within the candidate graph are separated from the background with Markov random field, and spectral clustering is used to solve the graph matching. The final target state is determined through a weighted voting procedure according to the reliability of part correspondence, and refined with recourse to a foreground/background segmentation. An effective online updating mechanism is proposed to update the model, allowing DGT to robustly adapt to variations of target structure. Experimental results show improved performance over several state-of-the-art trackers, in various challenging scenarios.

  9. Fuel for the Fire: Improved Understanding of Fire Behavior in Africa Based on Partitioned Herbaceous and Woody LAI from MODIS Satellite Data

    NASA Astrophysics Data System (ADS)

    Kahiu, M. N.; Hanan, N. P.

    2014-12-01

    Fire is an important recurrent phenomenon that determines the distribution of global savanna biomes and tree cover in savanna ecosystems. Tropical savanna fires are almost exclusively ground fires, fueled by senescent herbaceous material, with crown fires being rare. Analyses of satellite-based fire activity and burned area (active fires and burn-scars) in tropical savannas reveal a close correlation with satellite-based estimates of total net primary productivity (NPP) in drier savannas, and apparent limitation by rainfall (fuel moisture) in wetter systems. However, these analyses of fire frequency and extent at continental scales ignore the different roles played by the herbaceous and woody vegetation components in promoting and/or suppressing fire ignition and spread. In this research we hypothesized that, since herbaceous vegetation provides the primary fuel, fire frequency and burn areas in African savannas and seasonal woodlands should correlate more closely with measurements of herbaceous NPP or end of season leaf area index (LAI), than with the NPP or LAI of the tree layer. Similarly, while fire patterns may correlate with patterns of total LAI and total NPP across Africa, the relationship will be confounded by variations in tree cover. Our objective is to understand how fire frequency and intensity vary with changes in herbaceous cover. To test our hypotheses we will use estimates of herbaceous and woody LAI that we have developed recently by partitioning MODIS LAI. We will explore how seasonal maximum herbaceous LAI and leaf area duration (LAD) (both potential proxies for accumulated fuel load) correlate with fire frequency in African savannas. We will demonstrate the MODIS LAI partitioning methodology, and present results on the divergent relationships between African savanna fires and total LAI, herbaceous LAI and herbaceous LAD.

  10. Program partitioning for NUMA multiprocessor computer systems. [Nonuniform memory access

    SciTech Connect

    Wolski, R.M.; Feo, J.T. )

    1993-11-01

    Program partitioning and scheduling are essential steps in programming non-shared-memory computer systems. Partitioning is the separation of program operations into sequential tasks, and scheduling is the assignment of tasks to processors. To be effective, automatic methods require an accurate representation of the model of computation and the target architecture. Current partitioning methods assume today's most prevalent models -- macro dataflow and a homogeneous/two-level multicomputer system. Based on communication channels, neither model represents well the emerging class of NUMA multiprocessor computer systems consisting of hierarchical read/write memories. Consequently, the partitions generated by extant methods do not execute well on these systems. In this paper, the authors extend the conventional graph representation of the macro-dataflow model to enable mapping heuristics to consider the complex communication options supported by NUMA architectures. They describe two such heuristics. Simulated execution times of program graphs show that the model and heuristics generate higher quality program mappings than current methods for NUMA architectures.

  11. New methods for analyzing semantic graph based assessments in science education

    NASA Astrophysics Data System (ADS)

    Vikaros, Lance Steven

    This research investigated how the scoring of semantic graphs (known by many as concept maps) could be improved and automated in order to address issues of inter-rater reliability and scalability. As part of the NSF funded SENSE-IT project to introduce secondary school science students to sensor networks (NSF Grant No. 0833440), semantic graphs illustrating how temperature change affects water ecology were collected from 221 students across 16 schools. The graphing task did not constrain students' use of terms, as is often done with semantic graph based assessment due to coding and scoring concerns. The graphing software used provided real-time feedback to help students learn how to construct graphs, stay on topic and effectively communicate ideas. The collected graphs were scored by human raters using assessment methods expected to boost reliability, which included adaptations of traditional holistic and propositional scoring methods, use of expert raters, topical rubrics, and criterion graphs. High levels of inter-rater reliability were achieved, demonstrating that vocabulary constraints may not be necessary after all. To investigate a new approach to automating the scoring of graphs, thirty-two different graph features characterizing graphs' structure, semantics, configuration and process of construction were then used to predict human raters' scoring of graphs in order to identify feature patterns correlated to raters' evaluations of graphs' topical accuracy and complexity. Results led to the development of a regression model able to predict raters' scoring with 77% accuracy, with 46% accuracy expected when used to score new sets of graphs, as estimated via cross-validation tests. Although such performance is comparable to other graph and essay based scoring systems, cross-context testing of the model and methods used to develop it would be needed before it could be recommended for widespread use. Still, the findings suggest techniques for improving the

  12. Contact Graph Routing

    NASA Technical Reports Server (NTRS)

    Burleigh, Scott C.

    2011-01-01

    Contact Graph Routing (CGR) is a dynamic routing system that computes routes through a time-varying topology of scheduled communication contacts in a network based on the DTN (Delay-Tolerant Networking) architecture. It is designed to enable dynamic selection of data transmission routes in a space network based on DTN. This dynamic responsiveness in route computation should be significantly more effective and less expensive than static routing, increasing total data return while at the same time reducing mission operations cost and risk. The basic strategy of CGR is to take advantage of the fact that, since flight mission communication operations are planned in detail, the communication routes between any pair of bundle agents in a population of nodes that have all been informed of one another's plans can be inferred from those plans rather than discovered via dialogue (which is impractical over long one-way-light-time space links). Messages that convey this planning information are used to construct contact graphs (time-varying models of network connectivity) from which CGR automatically computes efficient routes for bundles. Automatic route selection increases the flexibility and resilience of the space network, simplifying cross-support and reducing mission management costs. Note that there are no routing tables in Contact Graph Routing. The best route for a bundle destined for a given node may routinely be different from the best route for a different bundle destined for the same node, depending on bundle priority, bundle expiration time, and changes in the current lengths of transmission queues for neighboring nodes; routes must be computed individually for each bundle, from the Bundle Protocol agent's current network connectivity model for the bundle s destination node (the contact graph). Clearly this places a premium on optimizing the implementation of the route computation algorithm. The scalability of CGR to very large networks remains a research topic

  13. Quantum Graph Analysis

    SciTech Connect

    Maunz, Peter Lukas Wilhelm; Sterk, Jonathan David; Lobser, Daniel; Parekh, Ojas D.; Ryan-Anderson, Ciaran

    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%.

  14. Graph Visualization for RDF Graphs with SPARQL-EndPoints

    SciTech Connect

    Sukumar, Sreenivas R; Bond, Nathaniel

    2014-07-11

    RDF graphs are hard to visualize as triples. This software module is a web interface that connects to a SPARQL endpoint and retrieves graph data that the user can explore interactively and seamlessly. The software written in python and JavaScript has been tested to work on screens as little as the smart phones to large screens such as EVEREST.

  15. Quantization of gauge fields, graph polynomials and graph homology

    SciTech Connect

    Kreimer, Dirk; Sars, Matthias; Suijlekom, Walter D. van

    2013-09-15

    We review quantization of gauge fields using algebraic properties of 3-regular graphs. We derive the Feynman integrand at n loops for a non-abelian gauge theory quantized in a covariant gauge from scalar integrands for connected 3-regular graphs, obtained from the two Symanzik polynomials. The transition to the full gauge theory amplitude is obtained by the use of a third, new, graph polynomial, the corolla polynomial. This implies effectively a covariant quantization without ghosts, where all the relevant signs of the ghost sector are incorporated in a double complex furnished by the corolla polynomial–we call it cycle homology–and by graph homology. -- Highlights: •We derive gauge theory Feynman from scalar field theory with 3-valent vertices. •We clarify the role of graph homology and cycle homology. •We use parametric renormalization and the new corolla polynomial.

  16. Partition density functional theory

    NASA Astrophysics Data System (ADS)

    Nafziger, Jonathan

    Partition density functional theory (PDFT) is a method for dividing a molecular electronic structure calculation into fragment calculations. The molecular density and energy corresponding to Kohn Sham density-functional theory (KS-DFT) may be exactly recovered from these fragments. Each fragment acts as an isolated system except for the influence of a global one-body 'partition' potential which deforms the fragment densities. In this work, the developments of PDFT are put into the context of other fragment-based density functional methods. We developed three numerical implementations of PDFT: One within the NWChem computational chemistry package using basis sets, and the other two developed from scratch using real-space grids. It is shown that all three of these programs can exactly reproduce a KS-DFT calculation via fragment calculations. The first of our in-house codes handles non-interacting electrons in arbitrary one-dimensional potentials with any number of fragments. This code is used to explore how the exact partition potential changes for different partitionings of the same system and also to study features which determine which systems yield non-integer PDFT occupations and which systems are locked into integer PDFT occupations. The second in-house code, CADMium, performs real-space calculations of diatomic molecules. Features of the exact partition potential are studied for a variety of cases and an analytical formula determining singularities in the partition potential is derived. We introduce an approximation for the non-additive kinetic energy and show how this quantity can be computed exactly. Finally a PDFT functional is developed to address the issues of static correlation and delocalization errors in approximations within DFT. The functional is applied to the dissociation of H2 + and H2.

  17. FNAS phase partitions

    NASA Technical Reports Server (NTRS)

    Vanalstine, James M.

    1993-01-01

    Project NAS8-36955 D.O. #100 initially involved the following tasks: (1) evaluation of various coatings' ability to control wall wetting and surface zeta potential expression; (2) testing various methods to mix and control the demixing of phase systems; and (3) videomicroscopic investigation of cell partition. Three complementary areas were identified for modification and extension of the original contract. They were: (1) identification of new supports for column cell partition; (2) electrokinetic detection of protein adsorption; and (3) emulsion studies related to bioseparations.

  18. Graphs and Zero-Divisors

    ERIC Educational Resources Information Center

    Axtell, M.; Stickles, J.

    2010-01-01

    The last ten years have seen an explosion of research in the zero-divisor graphs of commutative rings--by professional mathematicians "and" undergraduates. The objective is to find algebraic information within the geometry of these graphs. This topic is approachable by anyone with one or two semesters of abstract algebra. This article gives the…

  19. A PVS Graph Theory Library

    NASA Technical Reports Server (NTRS)

    Butler, Ricky W.; Sjogren, Jon A.

    1998-01-01

    This paper documents the NASA Langley PVS graph theory library. The library provides fundamental definitions for graphs, subgraphs, walks, paths, subgraphs generated by walks, trees, cycles, degree, separating sets, and four notions of connectedness. Theorems provided include Ramsey's and Menger's and the equivalence of all four notions of connectedness.

  20. Graphs as Statements of Belief.

    ERIC Educational Resources Information Center

    Lake, David

    2002-01-01

    Identifies points where beliefs are important when making decisions about how graphs are drawn. Describes a simple case of the reaction between 'bicarb soda' and orange or lemon juice and discusses how drawing a graph becomes a statement of belief. (KHR)

  1. A Collection of Features for Semantic Graphs

    SciTech Connect

    Eliassi-Rad, T; Fodor, I K; Gallagher, B

    2007-05-02

    Semantic graphs are commonly used to represent data from one or more data sources. Such graphs extend traditional graphs by imposing types on both nodes and links. This type information defines permissible links among specified nodes and can be represented as a graph commonly referred to as an ontology or schema graph. Figure 1 depicts an ontology graph for data from National Association of Securities Dealers. Each node type and link type may also have a list of attributes. To capture the increased complexity of semantic graphs, concepts derived for standard graphs have to be extended. This document explains briefly features commonly used to characterize graphs, and their extensions to semantic graphs. This document is divided into two sections. Section 2 contains the feature descriptions for static graphs. Section 3 extends the features for semantic graphs that vary over time.

  2. Semi-Markov Graph Dynamics

    PubMed Central

    Raberto, Marco; Rapallo, Fabio; Scalas, Enrico

    2011-01-01

    In this paper, we outline a model of graph (or network) dynamics based on two ingredients. The first ingredient is a Markov chain on the space of possible graphs. The second ingredient is a semi-Markov counting process of renewal type. The model consists in subordinating the Markov chain to the semi-Markov counting process. In simple words, this means that the chain transitions occur at random time instants called epochs. The model is quite rich and its possible connections with algebraic geometry are briefly discussed. Moreover, for the sake of simplicity, we focus on the space of undirected graphs with a fixed number of nodes. However, in an example, we present an interbank market model where it is meaningful to use directed graphs or even weighted graphs. PMID:21887245

  3. Experimental quantum annealing: case study involving the graph isomorphism problem

    PubMed Central

    Zick, Kenneth M.; Shehab, Omar; French, Matthew

    2015-01-01

    Quantum annealing is a proposed combinatorial optimization technique meant to exploit quantum mechanical effects such as tunneling and entanglement. Real-world quantum annealing-based solvers require a combination of annealing and classical pre- and post-processing; at this early stage, little is known about how to partition and optimize the processing. This article presents an experimental case study of quantum annealing and some of the factors involved in real-world solvers, using a 504-qubit D-Wave Two machine and the graph isomorphism problem. To illustrate the role of classical pre-processing, a compact Hamiltonian is presented that enables a reduced Ising model for each problem instance. On random N-vertex graphs, the median number of variables is reduced from N2 to fewer than N log2 N and solvable graph sizes increase from N = 5 to N = 13. Additionally, error correction via classical post-processing majority voting is evaluated. While the solution times are not competitive with classical approaches to graph isomorphism, the enhanced solver ultimately classified correctly every problem that was mapped to the processor and demonstrated clear advantages over the baseline approach. The results shed some light on the nature of real-world quantum annealing and the associated hybrid classical-quantum solvers. PMID:26053973

  4. Inexact Matching of Ontology Graphs Using Expectation-Maximization

    PubMed Central

    Doshi, Prashant; Kolli, Ravikanth; Thomas, Christopher

    2009-01-01

    We present a new method for mapping ontology schemas that address similar domains. The problem of ontology matching is crucial since we are witnessing a decentralized development and publication of ontological data. We formulate the problem of inferring a match between two ontologies as a maximum likelihood problem, and solve it using the technique of expectation-maximization (EM). Specifically, we adopt directed graphs as our model for ontology schemas and use a generalized version of EM to arrive at a map between the nodes of the graphs. We exploit the structural, lexical and instance similarity between the graphs, and differ from the previous approaches in the way we utilize them to arrive at, a possibly inexact, match. Inexact matching is the process of finding a best possible match between the two graphs when exact matching is not possible or is computationally difficult. In order to scale the method to large ontologies, we identify the computational bottlenecks and adapt the generalized EM by using a memory bounded partitioning scheme. We provide comparative experimental results in support of our method on two well-known ontology alignment benchmarks and discuss their implications. PMID:20160892

  5. In-Memory Graph Databases for Web-Scale Data

    SciTech Connect

    Castellana, Vito G.; Morari, Alessandro; Weaver, Jesse R.; Tumeo, Antonino; Haglin, David J.; Villa, Oreste; Feo, John

    2015-03-01

    RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++ compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.

  6. Clustering Qualitative Data Based on Binary Equivalence Relations: Neighborhood Search Heuristics for the Clique Partitioning Problem

    ERIC Educational Resources Information Center

    Brusco, Michael J.; Kohn, Hans-Friedrich

    2009-01-01

    The clique partitioning problem (CPP) requires the establishment of an equivalence relation for the vertices of a graph such that the sum of the edge costs associated with the relation is minimized. The CPP has important applications for the social sciences because it provides a framework for clustering objects measured on a collection of nominal…

  7. An Efficient Algorithm for Partitioning and Authenticating Problem-Solutions of eLeaming Contents

    ERIC Educational Resources Information Center

    Dewan, Jahangir; Chowdhury, Morshed; Batten, Lynn

    2013-01-01

    Content authenticity and correctness is one of the important challenges in eLearning as there can be many solutions to one specific problem in cyber space. Therefore, the authors feel it is necessary to map problems to solutions using graph partition and weighted bipartite matching. This article proposes an efficient algorithm to partition…

  8. TIFF Image Writer patch for OpenSceneGraph

    SciTech Connect

    Eldridge, Bryce

    2012-01-05

    This software consists of code modifications to the open-source OpenSceneGraph software package to enable the creation of TlFF images containing 16 bit unsigned data. They also allow the user to disable compression and set the DPI tags in the resulting TIFF Images. Some image analysis programs require uncompressed, 16 bit unsigned input data. These code modifications allow programs based on OpenSceneGraph to write out such images, improving connectivity between applications.

  9. Partitioning structural VHDL circuits for parallel execution on hypercubes

    NASA Astrophysics Data System (ADS)

    Kapp, Kevin L.

    1993-12-01

    Distributing simulations among multiple processors is one approach to reducing VHDL simulation time for large VLSI circuit designs. However, parallel simulation introduces the problem of how to partition the logic gates and system behaviors among the available processors in order to obtain maximum speedup. This research investigates deliberate partitioning algorithms that account for the complex inter-dependency structure of the circuit behaviors. Once an initial partition has been obtained, a border annealing algorithm is used to iteratively improve the partition. In addition, methods of measuring the cost of a partition and relating it to the resulting simulation performance are investigated. Structural circuits ranging from one thousand to over four thousand behaviors are simulated. The deliberate partitions consistently provided superior speedup to a random distribution of the circuit behaviors.

  10. Graph states of prime-power dimension from generalized CNOT quantum circuit.

    PubMed

    Chen, Lin; Zhou, D L

    2016-01-01

    We construct multipartite graph states whose dimension is the power of a prime number. This is realized by the finite field, as well as the generalized controlled-NOT quantum circuit acting on two qudits. We propose the standard form of graph states up to local unitary transformations and particle permutations. The form greatly simplifies the classification of graph states as we illustrate up to five qudits. We also show that some graph states are multipartite maximally entangled states in the sense that any bipartition of the system produces a bipartite maximally entangled state. We further prove that 4-partite maximally entangled states exist when the dimension is an odd number at least three or a multiple of four. PMID:27272401

  11. Graph states of prime-power dimension from generalized CNOT quantum circuit

    PubMed Central

    Chen, Lin; Zhou, D. L.

    2016-01-01

    We construct multipartite graph states whose dimension is the power of a prime number. This is realized by the finite field, as well as the generalized controlled-NOT quantum circuit acting on two qudits. We propose the standard form of graph states up to local unitary transformations and particle permutations. The form greatly simplifies the classification of graph states as we illustrate up to five qudits. We also show that some graph states are multipartite maximally entangled states in the sense that any bipartition of the system produces a bipartite maximally entangled state. We further prove that 4-partite maximally entangled states exist when the dimension is an odd number at least three or a multiple of four. PMID:27272401

  12. Graph states of prime-power dimension from generalized CNOT quantum circuit.

    PubMed

    Chen, Lin; Zhou, D L

    2016-06-07

    We construct multipartite graph states whose dimension is the power of a prime number. This is realized by the finite field, as well as the generalized controlled-NOT quantum circuit acting on two qudits. We propose the standard form of graph states up to local unitary transformations and particle permutations. The form greatly simplifies the classification of graph states as we illustrate up to five qudits. We also show that some graph states are multipartite maximally entangled states in the sense that any bipartition of the system produces a bipartite maximally entangled state. We further prove that 4-partite maximally entangled states exist when the dimension is an odd number at least three or a multiple of four.

  13. Identifying Cognitive States Using Regularity Partitions

    PubMed Central

    2015-01-01

    Functional Magnetic Resonance (fMRI) data can be used to depict functional connectivity of the brain. Standard techniques have been developed to construct brain networks from this data; typically nodes are considered as voxels or sets of voxels with weighted edges between them representing measures of correlation. Identifying cognitive states based on fMRI data is connected with recording voxel activity over a certain time interval. Using this information, network and machine learning techniques can be applied to discriminate the cognitive states of the subjects by exploring different features of data. In this work we wish to describe and understand the organization of brain connectivity networks under cognitive tasks. In particular, we use a regularity partitioning algorithm that finds clusters of vertices such that they all behave with each other almost like random bipartite graphs. Based on the random approximation of the graph, we calculate a lower bound on the number of triangles as well as the expectation of the distribution of the edges in each subject and state. We investigate the results by comparing them to the state of the art algorithms for exploring connectivity and we argue that during epochs that the subject is exposed to stimulus, the inspected part of the brain is organized in an efficient way that enables enhanced functionality. PMID:26317983

  14. MTC: A Fast and Robust Graph-Based Transductive Learning Method.

    PubMed

    Zhang, Yan-Ming; Huang, Kaizhu; Geng, Guang-Gang; Liu, Cheng-Lin

    2015-09-01

    Despite the great success of graph-based transductive learning methods, most of them have serious problems in scalability and robustness. In this paper, we propose an efficient and robust graph-based transductive classification method, called minimum tree cut (MTC), which is suitable for large-scale data. Motivated from the sparse representation of graph, we approximate a graph by a spanning tree. Exploiting the simple structure, we develop a linear-time algorithm to label the tree such that the cut size of the tree is minimized. This significantly improves graph-based methods, which typically have a polynomial time complexity. Moreover, we theoretically and empirically show that the performance of MTC is robust to the graph construction, overcoming another big problem of traditional graph-based methods. Extensive experiments on public data sets and applications on web-spam detection and interactive image segmentation demonstrate our method's advantages in aspect of accuracy, speed, and robustness.

  15. Semantic graphs and associative memories.

    PubMed

    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.

  16. Semantic graphs and associative memories

    NASA Astrophysics Data System (ADS)

    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.

  17. Multigraph: Reusable Interactive Data Graphs

    NASA Astrophysics Data System (ADS)

    Phillips, M. B.

    2010-12-01

    There are surprisingly few good software tools available for presenting time series data on the internet. The most common practice is to use a desktop program such as Excel or Matlab to save a graph as an image which can be included in a web page like any other image. This disconnects the graph from the data in a way that makes updating a graph with new data a cumbersome manual process, and it limits the user to one particular view of the data. The Multigraph project defines an XML format for describing interactive data graphs, and software tools for creating and rendering those graphs in web pages and other internet connected applications. Viewing a Multigraph graph is extremely simple and intuitive, and requires no instructions; the user can pan and zoom by clicking and dragging, in a familiar "Google Maps" kind of way. Creating a new graph for inclusion in a web page involves writing a simple XML configuration file. Multigraph can read data in a variety of formats, and can display data from a web service, allowing users to "surf" through large data sets, downloading only those the parts of the data that are needed for display. The Multigraph XML format, or "MUGL" for short, provides a concise description of the visual properties of a graph, such as axes, plot styles, data sources, labels, etc, as well as interactivity properties such as how and whether the user can pan or zoom along each axis. Multigraph reads a file in this format, draws the described graph, and allows the user to interact with it. Multigraph software currently includes a Flash application for embedding graphs in web pages, a Flex component for embedding graphs in larger Flex/Flash applications, and a plugin for creating graphs in the WordPress content management system. Plans for the future include a Java version for desktop viewing and editing, a command line version for batch and server side rendering, and possibly Android and iPhone versions. Multigraph is currently in use on several web

  18. A Graph Based Backtracking Algorithm for Solving General CSPs

    NASA Technical Reports Server (NTRS)

    Pang, Wanlin; Goodwin, Scott D.

    2003-01-01

    Many AI tasks can be formalized as constraint satisfaction problems (CSPs), which involve finding values for variables subject to constraints. While solving a CSP is an NP-complete task in general, tractable classes of CSPs have been identified based on the structure of the underlying constraint graphs. Much effort has been spent on exploiting structural properties of the constraint graph to improve the efficiency of finding a solution. These efforts contributed to development of a class of CSP solving algorithms called decomposition algorithms. The strength of CSP decomposition is that its worst-case complexity depends on the structural properties of the constraint graph and is usually better than the worst-case complexity of search methods. Its practical application is limited, however, since it cannot be applied if the CSP is not decomposable. In this paper, we propose a graph based backtracking algorithm called omega-CDBT, which shares merits and overcomes the weaknesses of both decomposition and search approaches.

  19. Multimedia partitioning of dioxin

    SciTech Connect

    Travis, C.C.; Hattemer-Frey, H.A.

    1988-01-01

    The general population is continuously being exposed to trace amounts of dioxin as exemplified by the fact that virtually all human adipose tissue samples contain dioxin levels of three parts per trillion (ppT) or greater. The purpose of this study is to investigate how 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is partitioned in the environment and to identify the major pathways of human exposure. 61 refs., 6 tabs.

  20. Graph anomalies in cyber communications

    SciTech Connect

    Vander Wiel, Scott A; Storlie, Curtis B; Sandine, Gary; Hagberg, Aric A; Fisk, Michael

    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.

  1. Constructing Dense Graphs with Unique Hamiltonian Cycles

    ERIC Educational Resources Information Center

    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…

  2. Yamabe type equations on graphs

    NASA Astrophysics Data System (ADS)

    Grigor'yan, Alexander; Lin, Yong; Yang, Yunyan

    2016-11-01

    Let G = (V , E) be a locally finite graph, Ω ⊂ V be a bounded domain, Δ be the usual graph Laplacian, and λ1 (Ω) be the first eigenvalue of -Δ with respect to Dirichlet boundary condition. Using the mountain pass theorem due to Ambrosetti-Rabinowitz, we prove that if α <λ1 (Ω), then for any p > 2, there exists a positive solution to

  3. Maximizing run time performance of deployed data flow graphs on a multiprocessor architecture

    NASA Astrophysics Data System (ADS)

    Tobias, Richard J.; Hunt, Peter D.

    1993-10-01

    This paper discusses a practical solution for supporting the deployment of data flow graphs onto the Loral/Rolm Computer Systems, Inc. vector processing multi-processor architecture. It outlines the support software (both workstation hosted and target system hosted) that is required to design, debug, and maximize deployed data flow graph performance on the multiprocessor architecture. The deployment process guarantees real-time deadlines, minimizes run time scheduling overhead, and minimizes designer partitioning input. It is known that determining effective run time data flow graph node schedules for multi-processor architectures is an NP-complete class of problem not well suited to real-time systems. Loral/Rolm Computer Systems, Inc.'s vector processing toolset recognizes this problem and this paper discusses a prescheduling and pre-assignment approach for partitioning data flow graphs to available hardware resources. In particular the toolset components (which are based upon an enhanced data flow graph language) of workstation pre-assignment, prescheduling, run time gross allocation and local compute element dispatching are discussed in detail.

  4. Estimates of general Mayer graphs. I: Construction of upper bounds for a given graph by means of sets of subgraphs

    NASA Astrophysics Data System (ADS)

    Lavaud, Michel

    1982-03-01

    A large number of physical quantities (thermodynamic and correlation functions, scattering amplitudes, intermolecular potentials, etc. ...) can be expressed as sums of an infinite number of multiple integrals of the following type: Γ ( {x_1 ,. . . , x_n } ) = int {prod {f_L ( {x_{i,} x_j } )dx_{n + 1} . . . dx_{n + k} } } These are called Mayer graphs in statistical mechanics, Feynman graphs in quantum field theory, and multicenter integrals in quantum chemistry. We call them n-graphs here. In a preceding note [ Physics Letters 62A:295 (1977)], we have proposed a new estimation method which provides upper bounds for arbitrary n-graphs. This article is devoted to developing in detail the foundations of this method. As a first application, we prove that all virial coefficients of polar systems are finite. More generally, we show on some examples that our estimation method can give finite upper bounds for n-graphs occurring in the perturbative developments of thermodynamic functions of neutral, polar, and ionized gases and of Green's functions of Euclidean quantum field theories (thus improving Weinberg's theorem), as also in variational approximations of intermolecular potentials. Our estimation method is based on the Hölder inequality which is an improvement over the mean value estimation method, employed by Riddell, Uhlenbeck, and Groeneveld, except for the hard-sphere gas, where both methods coincide. The method is applied so far only to individual graphs and not to thermodynamic functions.

  5. Graph signatures for visual analytics.

    PubMed

    Wong, Pak Chung; Foote, Harlan; Chin, George; Mackey, Patrick; Perrine, Ken

    2006-01-01

    We present a visual analytics technique to explore graphs using the concept of a data signature. A data signature, in our context, is a multidimensional vector that captures the local topology information surrounding each graph node. Signature vectors extracted from a graph are projected onto a low-dimensional scatterplot through the use of scaling. The resultant scatterplot, which reflects the similarities of the vectors, allows analysts to examine the graph structures and their corresponding real-life interpretations through repeated use of brushing and linking between the two visualizations. The interpretation of the graph structures is based on the outcomes of multiple participatory analysis sessions with intelligence analysts conducted by the authors at the Pacific Northwest National Laboratory. The paper first uses three public domain data sets with either well-known or obvious features to explain the rationale of our design and illustrate its results. More advanced examples are then used in a customized usability study to evaluate the effectiveness and efficiency of our approach. The study results reveal not only the limitations and weaknesses of the traditional approach based solely on graph visualization, but also the advantages and strengths of our signature-guided approach presented in the paper.

  6. A Ranking Approach on Large-Scale Graph With Multidimensional Heterogeneous Information.

    PubMed

    Wei, Wei; Gao, Bin; Liu, Tie-Yan; Wang, Taifeng; Li, Guohui; Li, Hang

    2016-04-01

    Graph-based ranking has been extensively studied and frequently applied in many applications, such as webpage ranking. It aims at mining potentially valuable information from the raw graph-structured data. Recently, with the proliferation of rich heterogeneous information (e.g., node/edge features and prior knowledge) available in many real-world graphs, how to effectively and efficiently leverage all information to improve the ranking performance becomes a new challenging problem. Previous methods only utilize part of such information and attempt to rank graph nodes according to link-based methods, of which the ranking performances are severely affected by several well-known issues, e.g., over-fitting or high computational complexity, especially when the scale of graph is very large. In this paper, we address the large-scale graph-based ranking problem and focus on how to effectively exploit rich heterogeneous information of the graph to improve the ranking performance. Specifically, we propose an innovative and effective semi-supervised PageRank (SSP) approach to parameterize the derived information within a unified semi-supervised learning framework (SSLF-GR), then simultaneously optimize the parameters and the ranking scores of graph nodes. Experiments on the real-world large-scale graphs demonstrate that our method significantly outperforms the algorithms that consider such graph information only partially.

  7. Graph Matching: Relax at Your Own Risk.

    PubMed

    Lyzinski, Vince; Fishkind, Donniell E; Fiori, Marcelo; Vogelstein, Joshua T; Priebe, Carey E; Sapiro, Guillermo

    2016-01-01

    Graph matching-aligning a pair of graphs to minimize their edge disagreements-has received wide-spread attention from both theoretical and applied communities over the past several decades, including combinatorics, computer vision, and connectomics. Its attention can be partially attributed to its computational difficulty. Although many heuristics have previously been proposed in the literature to approximately solve graph matching, very few have any theoretical support for their performance. A common technique is to relax the discrete problem to a continuous problem, therefore enabling practitioners to bring gradient-descent-type algorithms to bear. We prove that an indefinite relaxation (when solved exactly) almost always discovers the optimal permutation, while a common convex relaxation almost always fails to discover the optimal permutation. These theoretical results suggest that initializing the indefinite algorithm with the convex optimum might yield improved practical performance. Indeed, experimental results illuminate and corroborate these theoretical findings, demonstrating that excellent results are achieved in both benchmark and real data problems by amalgamating the two approaches.

  8. Graph Matching: Relax at Your Own Risk.

    PubMed

    Lyzinski, Vince; Fishkind, Donniell E; Fiori, Marcelo; Vogelstein, Joshua T; Priebe, Carey E; Sapiro, Guillermo

    2016-01-01

    Graph matching-aligning a pair of graphs to minimize their edge disagreements-has received wide-spread attention from both theoretical and applied communities over the past several decades, including combinatorics, computer vision, and connectomics. Its attention can be partially attributed to its computational difficulty. Although many heuristics have previously been proposed in the literature to approximately solve graph matching, very few have any theoretical support for their performance. A common technique is to relax the discrete problem to a continuous problem, therefore enabling practitioners to bring gradient-descent-type algorithms to bear. We prove that an indefinite relaxation (when solved exactly) almost always discovers the optimal permutation, while a common convex relaxation almost always fails to discover the optimal permutation. These theoretical results suggest that initializing the indefinite algorithm with the convex optimum might yield improved practical performance. Indeed, experimental results illuminate and corroborate these theoretical findings, demonstrating that excellent results are achieved in both benchmark and real data problems by amalgamating the two approaches. PMID:26656578

  9. Khovanov homology of graph-links

    SciTech Connect

    Nikonov, Igor M

    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.

  10. Private Graphs - Access Rights on Graphs for Seamless Navigation

    NASA Astrophysics Data System (ADS)

    Dorner, W.; Hau, F.; Pagany, R.

    2016-06-01

    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.

  11. Using Correlation to Compute Better Probability Estimates in Plan Graphs

    NASA Technical Reports Server (NTRS)

    Bryce, Daniel; Smith, David E.

    2006-01-01

    Plan graphs are commonly used in planning to help compute heuristic "distance" estimates between states and goals. A few authors have also attempted to use plan graphs in probabilistic planning to compute estimates of the probability that propositions can be achieved and actions can be performed. This is done by propagating probability information forward through the plan graph from the initial conditions through each possible action to the action effects, and hence to the propositions at the next layer of the plan graph. The problem with these calculations is that they make very strong independence assumptions - in particular, they usually assume that the preconditions for each action are independent of each other. This can lead to gross overestimates in probability when the plans for those preconditions interfere with each other. It can also lead to gross underestimates of probability when there is synergy between the plans for two or more preconditions. In this paper we introduce a notion of the binary correlation between two propositions and actions within a plan graph, show how to propagate this information within a plan graph, and show how this improves probability estimates for planning. This notion of correlation can be thought of as a continuous generalization of the notion of mutual exclusion (mutex) often used in plan graphs. At one extreme (correlation=0) two propositions or actions are completely mutex. With correlation = 1, two propositions or actions are independent, and with correlation > 1, two propositions or actions are synergistic. Intermediate values can and do occur indicating different degrees to which propositions and action interfere or are synergistic. We compare this approach with another recent approach by Bryce that computes probability estimates using Monte Carlo simulation of possible worlds in plan graphs.

  12. Sharing Teaching Ideas: Graphing Families of Curves Using Transformations of Reference Graphs

    ERIC Educational Resources Information Center

    Kukla, David

    2007-01-01

    This article provides for a fast extremely accurate approach to graphing functions that is based on learning function reference graphs and then applying algebraic transformations to these reference graphs.

  13. Box graphs and resolutions I

    NASA Astrophysics Data System (ADS)

    Braun, Andreas P.; Schäfer-Nameki, Sakura

    2016-04-01

    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.

  14. Chemical amplification based on fluid partitioning

    SciTech Connect

    Anderson, Brian L.; Colston, Jr., Billy W.; Elkin, Chris

    2006-05-09

    A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

  15. Partitioning the Quaternary

    NASA Astrophysics Data System (ADS)

    Gibbard, Philip L.; Lewin, John

    2016-11-01

    We review the historical purposes and procedures for stratigraphical division and naming within the Quaternary, and summarize the current requirements for formal partitioning through the International Commission on Stratigraphy (ICS). A raft of new data and evidence has impacted traditional approaches: quasi-continuous records from ocean sediments and ice cores, new numerical dating techniques, and alternative macro-models, such as those provided through Sequence Stratigraphy and Earth-System Science. The practical usefulness of division remains, but there is now greater appreciation of complex Quaternary detail and the modelling of time continua, the latter also extending into the future. There are problems both of commission (what is done, but could be done better) and of omission (what gets left out) in partitioning the Quaternary. These include the challenge set by the use of unconformities as stage boundaries, how to deal with multiphase records in ocean and terrestrial sediments, what happened at the 'Early-Mid- (Middle) Pleistocene Transition', dealing with trends that cross phase boundaries, and the current controversial focus on how to subdivide the Holocene and formally define an 'Anthropocene'.

  16. Unsupervised segmentation of MRI knees using image partition forests

    NASA Astrophysics Data System (ADS)

    Marčan, Marija; Voiculescu, Irina

    2016-03-01

    Nowadays many people are affected by arthritis, a condition of the joints with limited prevention measures, but with various options of treatment the most radical of which is surgical. In order for surgery to be successful, it can make use of careful analysis of patient-based models generated from medical images, usually by manual segmentation. In this work we show how to automate the segmentation of a crucial and complex joint -- the knee. To achieve this goal we rely on our novel way of representing a 3D voxel volume as a hierarchical structure of partitions which we have named Image Partition Forest (IPF). The IPF contains several partition layers of increasing coarseness, with partitions nested across layers in the form of adjacency graphs. On the basis of a set of properties (size, mean intensity, coordinates) of each node in the IPF we classify nodes into different features. Values indicating whether or not any particular node belongs to the femur or tibia are assigned through node filtering and node-based region growing. So far we have evaluated our method on 15 MRI knee images. Our unsupervised segmentation compared against a hand-segmented gold standard has achieved an average Dice similarity coefficient of 0.95 for femur and 0.93 for tibia, and an average symmetric surface distance of 0.98 mm for femur and 0.73 mm for tibia. The paper also discusses ways to introduce stricter morphological and spatial conditioning in the bone labelling process.

  17. Sequential visibility-graph motifs

    NASA Astrophysics Data System (ADS)

    Iacovacci, Jacopo; Lacasa, Lucas

    2016-04-01

    Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of sequential visibility-graph motifs, smaller substructures of n consecutive nodes that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated with general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable of distinguishing among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification and description of physical, biological, and financial time series.

  18. Algebraic connectivity and graph robustness.

    SciTech Connect

    Feddema, John Todd; Byrne, Raymond Harry; Abdallah, Chaouki T.

    2009-07-01

    Recent papers have used Fiedler's definition of algebraic connectivity to show that network robustness, as measured by node-connectivity and edge-connectivity, can be increased by increasing the algebraic connectivity of the network. By the definition of algebraic connectivity, the second smallest eigenvalue of the graph Laplacian is a lower bound on the node-connectivity. In this paper we show that for circular random lattice graphs and mesh graphs algebraic connectivity is a conservative lower bound, and that increases in algebraic connectivity actually correspond to a decrease in node-connectivity. This means that the networks are actually less robust with respect to node-connectivity as the algebraic connectivity increases. However, an increase in algebraic connectivity seems to correlate well with a decrease in the characteristic path length of these networks - which would result in quicker communication through the network. Applications of these results are then discussed for perimeter security.

  19. The fragment assembly string graph.

    PubMed

    Myers, Eugene W

    2005-09-01

    We present a concept and formalism, the string graph, which represents all that is inferable about a DNA sequence from a collection of shotgun sequencing reads collected from it. We give time and space efficient algorithms for constructing a string graph given the collection of overlaps between the reads and, in particular, present a novel linear expected time algorithm for transitive reduction in this context. The result demonstrates that the decomposition of reads into kmers employed in the de Bruijn graph approach described earlier is not essential, and exposes its close connection to the unitig approach we developed at Celera. This paper is a preliminary piece giving the basic algorithm and results that demonstrate the efficiency and scalability of the method. These ideas are being used to build a next-generation whole genome assembler called BOA (Berkeley Open Assembler) that will easily scale to mammalian genomes.

  20. Graph Analytics for Signature Discovery

    SciTech Connect

    Hogan, Emilie A.; Johnson, John R.; Halappanavar, Mahantesh; Lo, Chaomei

    2013-06-01

    Within large amounts of seemingly unstructured data it can be diffcult to find signatures of events. In our work we transform unstructured data into a graph representation. By doing this we expose underlying structure in the data and can take advantage of existing graph analytics capabilities, as well as develop new capabilities. Currently we focus on applications in cybersecurity and communication domains. Within cybersecurity we aim to find signatures for perpetrators using the pass-the-hash attack, and in communications we look for emails or phone calls going up or down a chain of command. In both of these areas, and in many others, the signature we look for is a path with certain temporal properties. In this paper we discuss our methodology for finding these temporal paths within large graphs.

  1. Graph modeling systems and methods

    DOEpatents

    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.

  2. Quantum snake walk on graphs

    SciTech Connect

    Rosmanis, Ansis

    2011-02-15

    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.

  3. Use of graph theory measures to identify errors in record linkage.

    PubMed

    Randall, Sean M; Boyd, James H; Ferrante, Anna M; Bauer, Jacqueline K; Semmens, James B

    2014-07-01

    Ensuring high linkage quality is important in many record linkage applications. Current methods for ensuring quality are manual and resource intensive. This paper seeks to determine the effectiveness of graph theory techniques in identifying record linkage errors. A range of graph theory techniques was applied to two linked datasets, with known truth sets. The ability of graph theory techniques to identify groups containing errors was compared to a widely used threshold setting technique. This methodology shows promise; however, further investigations into graph theory techniques are required. The development of more efficient and effective methods of improving linkage quality will result in higher quality datasets that can be delivered to researchers in shorter timeframes.

  4. Morphological algorithms based on Voronoi and Delaunay graphs: microscopic and medical applications

    NASA Astrophysics Data System (ADS)

    Bertin, Etienne; Marcelpoil, Raphael; Chassery, Jean-Marc

    1992-06-01

    We illustrate a cooperation between Voronoi diagram and Mathematical Morphology in 2-D and 3-D. Domains of application are multiple: 2-D image segmentation, and 3-D image representation, cellular sociology in 2-D and 3-D. The principal tool that we use is the algorithm of research of connected components in a graph abiding by constraints. The originality takes place in the choice of the constraint parameters. Other tools are used: binary dilation, labeling, and influence zone on graphs. The graph support of our work is the Voronoi diagram, well known for its power of modelling for natural reality. The dual graph of this space partition is the Delaunay graph containing all the neighboring information. The first developed application concerns a method for 2-D and 3-D images segmentation. We have elaborated tools to measure intra-graph structures distance, search of connected component under constraints to extract a 3-d object included in a volume data. The second application we developed concerns the theory of cellular sociology where the set of points identified the location of cells. Our method makes it possible to determine for a given set of cells, a model including its nearest homogeneous set, and the intrinsic disorder to which it refers. In this paper, our methods will be discussed and illustrated in the biological domain.

  5. A tillering inhibition gene influences root–shoot carbon partitioning and pattern of water use to improve wheat productivity in rainfed environments

    PubMed Central

    Hendriks, P.W.; Kirkegaard, J.A.; Lilley, J.M.; Gregory, P.J.; Rebetzke, G.J.

    2016-01-01

    Genetic modification of shoot and root morphology has potential to improve water and nutrient uptake of wheat crops in rainfed environments. Near-isogenic lines (NILs) varying for a tillering inhibition (tin) gene and representing multiple genetic backgrounds were phenotyped in contrasting, controlled environments for shoot and root growth. Leaf area, shoot and root biomass were similar until tillering, whereupon reduced tillering in tin-containing NILs produced reductions of up to 60% in total leaf area and biomass, and increases in total root length of up to 120% and root biomass to 145%. Together, the root-to-shoot ratio increased two-fold with the tin gene. The influence of tin on shoot and root growth was greatest in the cv. Banks genetic background, particularly in the biculm-selected NIL, and was typically strongest in cooler environments. A separate de-tillering study confirmed greater root-to-shoot ratios with regular tiller removal in non-tin-containing genotypes. In validating these observations in a rainfed field study, the tin allele had a negligible effect on seedling growth but was associated with significantly (P<0.05) reduced tiller number (–37%), leaf area index (–26%), and spike number (–35%) to reduce plant biomass (–19%) at anthesis. Root biomass, root-to-shoot ratio at early stem elongation, and root depth at maturity were all increased in tin-containing NILs. Soil water use was slowed in tin-containing NILs, resulting in greater water availability, greater stomatal conductance, cooler canopy temperatures, and maintenance of green leaf area during grain-filling. Together these effects contributed to increases in harvest index and grain yield. In both the controlled and field environments, the tin gene was commonly associated with increased root length and biomass, but the significant influence of genetic background and environment suggests careful assessment of tin-containing progeny in selection for genotypic increases in root growth

  6. Synchronizability of random rectangular graphs

    SciTech Connect

    Estrada, Ernesto Chen, Guanrong

    2015-08-15

    Random rectangular graphs (RRGs) represent a generalization of the random geometric graphs in which the nodes are embedded into hyperrectangles instead of on hypercubes. The synchronizability of RRG model is studied. Both upper and lower bounds of the eigenratio of the network Laplacian matrix are determined analytically. It is proven that as the rectangular network is more elongated, the network becomes harder to synchronize. The synchronization processing behavior of a RRG network of chaotic Lorenz system nodes is numerically investigated, showing complete consistence with the theoretical results.

  7. Midlet Navigation Graphs in JML

    NASA Astrophysics Data System (ADS)

    Mostowski, Wojciech; Poll, Erik

    In the context of the EU project Mobius on Proof Carrying Code for Java programs (midlets) on mobile devices, we present a way to express midlet navigation graphs in JML. Such navigation graphs express certain security policies for a midlet. The resulting JML specifications can be automatically checked with the static checker ESC/Java2. Our work was guided by a realistically sized case study developed as demonstrator in the project. We discuss practical difficulties with creating efficient and meaningful JML specifications for automatic verification with a lightweight verification tool such as ESC/Java2, and the potential use of these specifications for PCC.

  8. Detecting labor using graph theory on connectivity matrices of uterine EMG.

    PubMed

    Al-Omar, S; Diab, A; Nader, N; Khalil, M; Karlsson, B; Marque, C

    2015-08-01

    Premature labor is one of the most serious health problems in the developed world. One of the main reasons for this is that no good way exists to distinguish true labor from normal pregnancy contractions. The aim of this paper is to investigate if the application of graph theory techniques to multi-electrode uterine EMG signals can improve the discrimination between pregnancy contractions and labor. To test our methods we first applied them to synthetic graphs where we detected some differences in the parameters results and changes in the graph model from pregnancy-like graphs to labor-like graphs. Then, we applied the same methods to real signals. We obtained the best differentiation between pregnancy and labor through the same parameters. Major improvements in differentiating between pregnancy and labor were obtained using a low pass windowing preprocessing step. Results show that real graphs generally became more organized when moving from pregnancy, where the graph showed random characteristics, to labor where the graph became a more small-world like graph.

  9. An Integer Programming Formulation of the Minimum Common String Partition Problem.

    PubMed

    Ferdous, S M; Rahman, M Sohel

    2015-01-01

    We consider the problem of finding a minimum common string partition (MCSP) of two strings, which is an NP-hard problem. The MCSP problem is closely related to genome comparison and rearrangement, an important field in Computational Biology. In this paper, we map the MCSP problem into a graph applying a prior technique and using this graph, we develop an Integer Linear Programming (ILP) formulation for the problem. We implement the ILP formulation and compare the results with the state-of-the-art algorithms from the literature. The experimental results are found to be promising.

  10. Boosting for multi-graph classification.

    PubMed

    Wu, Jia; Pan, Shirui; Zhu, Xingquan; Cai, Zhihua

    2015-03-01

    In this paper, we formulate a novel graph-based learning problem, multi-graph classification (MGC), which aims to learn a classifier from a set of labeled bags each containing a number of graphs inside the bag. A bag is labeled positive, if at least one graph in the bag is positive, and negative otherwise. Such a multi-graph representation can be used for many real-world applications, such as webpage classification, where a webpage can be regarded as a bag with texts and images inside the webpage being represented as graphs. This problem is a generalization of multi-instance learning (MIL) but with vital differences, mainly because instances in MIL share a common feature space whereas no feature is available to represent graphs in a multi-graph bag. To solve the problem, we propose a boosting based multi-graph classification framework (bMGC). Given a set of labeled multi-graph bags, bMGC employs dynamic weight adjustment at both bag- and graph-levels to select one subgraph in each iteration as a weak classifier. In each iteration, bag and graph weights are adjusted such that an incorrectly classified bag will receive a higher weight because its predicted bag label conflicts to the genuine label, whereas an incorrectly classified graph will receive a lower weight value if the graph is in a positive bag (or a higher weight if the graph is in a negative bag). Accordingly, bMGC is able to differentiate graphs in positive and negative bags to derive effective classifiers to form a boosting model for MGC. Experiments and comparisons on real-world multi-graph learning tasks demonstrate the algorithm performance.

  11. Graphs for Early Elementary Social Studies.

    ERIC Educational Resources Information Center

    Freeland, Kent; Brewer, Samrie

    1989-01-01

    Describes a lesson plan that instructs third graders to use graphs. Explains learning objectives, motivating students, conducting a class activity that includes graph construction, and concluding and evaluating the lesson. Lists materials needed. (GG)

  12. Standard Distributions: One Graph Fits All

    ERIC Educational Resources Information Center

    Wagner, Clifford H.

    2007-01-01

    Standard distributions are ubiquitous but not unique. With suitable scaling, the graph of a standard distribution serves as the graph for every distribution in the family. The standard exponential can easily be taught in elementary statistics courses.

  13. Understanding Conic Sections Using Alternate Graph Paper

    ERIC Educational Resources Information Center

    Brown, Elizabeth M.; Jones, Elizabeth

    2006-01-01

    This article describes two alternative coordinate systems and their use in graphing conic sections. This alternative graph paper helps students explore the idea of eccentricity using the definitions of the conic sections.

  14. Graphing and Social Studies: An Interdisciplinary Activity.

    ERIC Educational Resources Information Center

    Brehm, Julia L.

    1996-01-01

    Describes a graphing activity that promotes mathematical connections with social studies lessons. Students should be familiar with graphing on the Cartesian coordinate system to play this variation of the game Battleship on maps of various regions of the world. (AIM)

  15. Comparison Graph of Sea Ice Minimum - 2010

    NASA Video Gallery

    This animated graph tracks the retreat of sea ice, measured in millions of square kilometers, averaged from the start of the satellite record in 1979 through 2000 (white). Next, the graph follows t...

  16. Mathematical Minute: Rotating a Function Graph

    ERIC Educational Resources Information Center

    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.

  17. Dr.L: Distributed Recursive (Graph) Layout

    2007-11-19

    Dr. L provides two-dimensional visualizations of very large abstract graph structures. it can be used for data mining applications including biology, scientific literature, and social network analysis. Dr. L is a graph layout program that uses a multilevel force-directed algorithm. A graph is input and drawn using a force-directed algorithm based on simulated annealing. The resulting layout is clustered using a single link algorithm. This clustering is used to produce a coarsened graph (fewer nodes)more » which is then re-drawn. this process is repeated until a sufficiently small graph is produced. The smallest graph is drawn and then used as a basis for drawing the original graph by refining the series of coarsened graphs that were produced. The layout engine can be run in serial or in parallel.« less

  18. Designing a Good Graph.

    ERIC Educational Resources Information Center

    Vinberg, Anders

    Although computer graphics professionals usually consider only technical graphic design issues, recent improvements may make the only limiting design factors the user's purpose, imagination, style, and taste rather than computer hardware or software technology. Computer graphics designers can be helped to avoid pitfalls by understanding the visual…

  19. Microcomputer Unit: Graphing Straight Lines.

    ERIC Educational Resources Information Center

    Hastings, Ellen H.; Yates, Daniel S.

    1983-01-01

    The material is designed to help pupils investigate how the value for slope in the equation of a line affects the inclination for the graph of an equation. A program written in BASIC designed to run on an Apple microcomputer is included. Worksheet masters for duplication are provided. (MP)

  20. Situating Graphs as Workplace Knowledge

    ERIC Educational Resources Information Center

    Noss, Richard; Bakker, Arthur; Hoyles, Celia; Kent, Phillip

    2007-01-01

    We investigate the use and knowledge of graphs in the context of a large industrial factory. We are particularly interested in the question of "transparency", a question that has been extensively considered in the general literature on tool use and, more recently, by Michael Roth and his colleagues in the context of scientific work. Roth uses the…

  1. Fibonacci Identities, Matrices, and Graphs

    ERIC Educational Resources Information Center

    Huang, Danrun

    2005-01-01

    General strategies used to help discover, prove, and generalize identities for Fibonacci numbers are described along with some properties about the determinants of square matrices. A matrix proof for identity (2) that has received immense attention from many branches of mathematics, like linear algebra, dynamical systems, graph theory and others…

  2. Box graphs and singular fibers

    NASA Astrophysics Data System (ADS)

    Hayashi, Hirotaka; Lawrie, Craig; Morrison, David R.; Schafer-Nameki, Sakura

    2014-05-01

    We determine the higher codimension fibers of elliptically fibered Calabi-Yau fourfolds with section by studying the three-dimensional = 2 supersymmetric gauge theory with matter which describes the low energy effective theory of M-theory compactified on the associated Weierstrass model, a singular model of the fourfold. Each phase of the Coulomb branch of this theory corresponds to a particular resolution of the Weierstrass model, and we show that these have a concise description in terms of decorated box graphs based on the representation graph of the matter multiplets, or alternatively by a class of convex paths on said graph. Transitions between phases have a simple interpretation as "flopping" of the path, and in the geometry correspond to actual flop transitions. This description of the phases enables us to enumerate and determine the entire network between them, with various matter representations for all reductive Lie groups. Furthermore, we observe that each network of phases carries the structure of a (quasi-)minuscule representation of a specific Lie algebra. Interpreted from a geometric point of view, this analysis determines the generators of the cone of effective curves as well as the network of flop transitions between crepant resolutions of singular elliptic Calabi-Yau fourfolds. From the box graphs we determine all fiber types in codimensions two and three, and we find new, non-Kodaira, fiber types for E 6, E7 and E 8.

  3. Affect and Graphing Calculator Use

    ERIC Educational Resources Information Center

    McCulloch, Allison W.

    2011-01-01

    This article reports on a qualitative study of six high school calculus students designed to build an understanding about the affect associated with graphing calculator use in independent situations. DeBellis and Goldin's (2006) framework for affect as a representational system was used as a lens through which to understand the ways in which…

  4. Ancestral Genres of Mathematical Graphs

    ERIC Educational Resources Information Center

    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…

  5. Humidity Graphs for All Seasons.

    ERIC Educational Resources Information Center

    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)

  6. Graphs and Enhancing Maple Multiplication.

    ERIC Educational Resources Information Center

    Cecil, David R.; Wang, Rongdong

    2002-01-01

    Description of a technique in Maple programming language that automatically prints all paths of any desired length along with the name of each vertex, proceeding in order from the beginning vertex to the ending vertex for a given graph. (Author/MM)

  7. Characterizing brain anatomical connections using diffusion weighted MRI and graph theory.

    PubMed

    Iturria-Medina, Y; Canales-Rodríguez, E J; Melie-García, L; Valdés-Hernández, P A; Martínez-Montes, E; Alemán-Gómez, Y; Sánchez-Bornot, J M

    2007-07-01

    A new methodology based on Diffusion Weighted Magnetic Resonance Imaging (DW-MRI) and Graph Theory is presented for characterizing the anatomical connections between brain gray matter areas. In a first step, brain voxels are modeled as nodes of a non-directed graph in which the weight of an arc linking two neighbor nodes is assumed to be proportional to the probability of being connected by nervous fibers. This probability is estimated by means of probabilistic tissue segmentation and intravoxel white matter orientational distribution function, obtained from anatomical MRI and DW-MRI, respectively. A new tractography algorithm for finding white matter routes is also introduced. This algorithm solves the most probable path problem between any two nodes, leading to the assessment of probabilistic brain anatomical connection maps. In a second step, for assessing anatomical connectivity between K gray matter structures, the previous graph is redefined as a K+1 partite graph by partitioning the initial nodes set in K non-overlapped gray matter subsets and one subset clustering the remaining nodes. Three different measures are proposed for quantifying anatomical connections between any pair of gray matter subsets: Anatomical Connection Strength (ACS), Anatomical Connection Density (ACD) and Anatomical Connection Probability (ACP). This methodology was applied to both artificial and actual human data. Results show that nervous fiber pathways between some regions of interest were reconstructed correctly. Additionally, mean connectivity maps of ACS, ACD and ACP between 71 gray matter structures for five healthy subjects are presented.

  8. Control by quantum dynamics on graphs

    SciTech Connect

    Godsil, Chris; Severini, Simone

    2010-05-15

    We address the study of controllability of a closed quantum system whose dynamical Lie algebra is generated by adjacency matrices of graphs. We characterize a large family of graphs that renders a system controllable. The key property is a graph-theoretic feature consisting of a particularly disordered cycle structure. Disregarding efficiency of control functions, but choosing subfamilies of sparse graphs, the results translate into continuous-time quantum walks for universal computation.

  9. Chemical Applications of Graph Theory: Part II. Isomer Enumeration.

    ERIC Educational Resources Information Center

    Hansen, Peter J.; Jurs, Peter C.

    1988-01-01

    Discusses the use of graph theory to aid in the depiction of organic molecular structures. Gives a historical perspective of graph theory and explains graph theory terminology with organic examples. Lists applications of graph theory to current research projects. (ML)

  10. My Bar Graph Tells a Story

    ERIC Educational Resources Information Center

    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…

  11. So Many Graphs, So Little Time

    ERIC Educational Resources Information Center

    Wall, Jennifer J.; Benson, Christine C.

    2009-01-01

    Interpreting graphs found in various content areas is an important skill for students, especially in light of high-stakes testing. In addition, reading and understanding graphs is an important part of numeracy, or numeric literacy, a skill necessary for informed citizenry. This article explores the different categories of graphs, provides…

  12. Collaborative Robotic Instruction: A Graph Teaching Experience

    ERIC Educational Resources Information Center

    Mitnik, Ruben; Recabarren, Matias; Nussbaum, Miguel; Soto, Alvaro

    2009-01-01

    Graphing is a key skill in the study of Physics. Drawing and interpreting graphs play a key role in the understanding of science, while the lack of these has proved to be a handicap and a limiting factor in the learning of scientific concepts. It has been observed that despite the amount of previous graph-working experience, students of all ages…

  13. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Conversion graphs. 80.761 Section 80.761... 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...

  14. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 5 2011-10-01 2011-10-01 false Conversion graphs. 80.761 Section 80.761... 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...

  15. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 5 2013-10-01 2013-10-01 false Conversion graphs. 80.761 Section 80.761... 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...

  16. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 5 2012-10-01 2012-10-01 false Conversion graphs. 80.761 Section 80.761... 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...

  17. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 5 2014-10-01 2014-10-01 false Conversion graphs. 80.761 Section 80.761... 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...

  18. Multiple directed graph large-class multi-spectral processor

    NASA Technical Reports Server (NTRS)

    Casasent, David; Liu, Shiaw-Dong; Yoneyama, Hideyuki

    1988-01-01

    Numerical analysis techniques for the interpretation of high-resolution imaging-spectrometer data are described and demonstrated. The method proposed involves the use of (1) a hierarchical classifier with a tree structure generated automatically by a Fisher linear-discriminant-function algorithm and (2) a novel multiple-directed-graph scheme which reduces the local maxima and the number of perturbations required. Results for a 500-class test problem involving simulated imaging-spectrometer data are presented in tables and graphs; 100-percent-correct classification is achieved with an improvement factor of 5.

  19. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance. PMID:23701000

  20. Visual exploratory search of relationship graphs on smartphones.

    PubMed

    Ouyang, Jianquan; Zheng, Hao; Kong, Fanbin; Liu, Tianming

    2013-01-01

    This paper presents a novel framework for Visual Exploratory Search of Relationship Graphs on Smartphones (VESRGS) that is composed of three major components: inference and representation of semantic relationship graphs on the Web via meta-search, visual exploratory search of relationship graphs through both querying and browsing strategies, and human-computer interactions via the multi-touch interface and mobile Internet on smartphones. In comparison with traditional lookup search methodologies, the proposed VESRGS system is characterized with the following perceived advantages. 1) It infers rich semantic relationships between the querying keywords and other related concepts from large-scale meta-search results from Google, Yahoo! and Bing search engines, and represents semantic relationships via graphs; 2) the exploratory search approach empowers users to naturally and effectively explore, adventure and discover knowledge in a rich information world of interlinked relationship graphs in a personalized fashion; 3) it effectively takes the advantages of smartphones' user-friendly interfaces and ubiquitous Internet connection and portability. Our extensive experimental results have demonstrated that the VESRGS framework can significantly improve the users' capability of seeking the most relevant relationship information to their own specific needs. We envision that the VESRGS framework can be a starting point for future exploration of novel, effective search strategies in the mobile Internet era.

  1. Plan-graph Based Heuristics for Conformant Probabilistic Planning

    NASA Technical Reports Server (NTRS)

    Ramakrishnan, Salesh; Pollack, Martha E.; Smith, David E.

    2004-01-01

    In this paper, we introduce plan-graph based heuristics to solve a variation of the conformant probabilistic planning (CPP) problem. In many real-world problems, it is the case that the sensors are unreliable or take too many resources to provide knowledge about the environment. These domains are better modeled as conformant planning problems. POMDP based techniques are currently the most successful approach for solving CPP but have the limitation of state- space explosion. Recent advances in deterministic and conformant planning have shown that plan-graphs can be used to enhance the performance significantly. We show that this enhancement can also be translated to CPP. We describe our process for developing the plan-graph heuristics and estimating the probability of a partial plan. We compare the performance of our planner PVHPOP when used with different heuristics. We also perform a comparison with a POMDP solver to show over a order of magnitude improvement in performance.

  2. Efficient solution for finding Hamilton cycles in undirected graphs.

    PubMed

    Alhalabi, Wadee; Kitanneh, Omar; Alharbi, Amira; Balfakih, Zain; Sarirete, Akila

    2016-01-01

    The Hamilton cycle problem is closely related to a series of famous problems and puzzles (traveling salesman problem, Icosian game) and, due to the fact that it is NP-complete, it was extensively studied with different algorithms to solve it. The most efficient algorithm is not known. In this paper, a necessary condition for an arbitrary un-directed graph to have Hamilton cycle is proposed. Based on this condition, a mathematical solution for this problem is developed and several proofs and an algorithmic approach are introduced. The algorithm is successfully implemented on many Hamiltonian and non-Hamiltonian graphs. This provides a new effective approach to solve a problem that is fundamental in graph theory and can influence the manner in which the existing applications are used and improved. PMID:27516930

  3. Fast graph operations in quantum computation

    NASA Astrophysics Data System (ADS)

    Zhao, Liming; Pérez-Delgado, Carlos A.; Fitzsimons, Joseph F.

    2016-03-01

    The connection between certain entangled states and graphs has been heavily studied in the context of measurement-based quantum computation as a tool for understanding entanglement. Here we show that this correspondence can be harnessed in the reverse direction to yield a graph data structure, which allows for more efficient manipulation and comparison of graphs than any possible classical structure. We introduce efficient algorithms for many transformation and comparison operations on graphs represented as graph states, and prove that no classical data structure can have similar performance for the full set of operations studied.

  4. Temporal stability of network partitions.

    PubMed

    Petri, Giovanni; Expert, Paul

    2014-08-01

    We present a method to find the best temporal partition at any time scale and rank the relevance of partitions found at different time scales. This method is based on random walkers coevolving with the network and as such constitutes a generalization of partition stability to the case of temporal networks. We show that, when applied to a toy model and real data sets, temporal stability uncovers structures that are persistent over meaningful time scales as well as important isolated events, making it an effective tool to study both abrupt changes and gradual evolution of a network mesoscopic structures.

  5. Temporal stability of network partitions.

    PubMed

    Petri, Giovanni; Expert, Paul

    2014-08-01

    We present a method to find the best temporal partition at any time scale and rank the relevance of partitions found at different time scales. This method is based on random walkers coevolving with the network and as such constitutes a generalization of partition stability to the case of temporal networks. We show that, when applied to a toy model and real data sets, temporal stability uncovers structures that are persistent over meaningful time scales as well as important isolated events, making it an effective tool to study both abrupt changes and gradual evolution of a network mesoscopic structures. PMID:25215787

  6. Partitioning ecosystems for sustainability.

    PubMed

    Murray, Martyn G

    2016-03-01

    Decline in the abundance of renewable natural resources (RNRs) coupled with increasing demands of an expanding human population will greatly intensify competition for Earth's natural resources during this century, yet curiously, analytical approaches to the management of productive ecosystems (ecological theory of wildlife harvesting, tragedy of the commons, green economics, and bioeconomics) give only peripheral attention to the driving influence of competition on resource exploitation. Here, I apply resource competition theory (RCT) to the exploitation of RNRs and derive four general policies in support of their sustainable and equitable use: (1) regulate resource extraction technology to avoid damage to the resource base; (2) increase efficiency of resource use and reduce waste at every step in the resource supply chain and distribution network; (3) partition ecosystems with the harvesting niche as the basic organizing principle for sustainable management of natural resources by multiple users; and (4) increase negative feedback between consumer and resource to bring about long-term sustainable use. A simple policy framework demonstrates how RCT integrates with other elements of sustainability science to better manage productive ecosystems. Several problem areas of RNR management are discussed in the light of RCT, including tragedy of the commons, overharvesting, resource collapse, bycatch, single species quotas, and simplification of ecosystems.

  7. Partitioning ecosystems for sustainability.

    PubMed

    Murray, Martyn G

    2016-03-01

    Decline in the abundance of renewable natural resources (RNRs) coupled with increasing demands of an expanding human population will greatly intensify competition for Earth's natural resources during this century, yet curiously, analytical approaches to the management of productive ecosystems (ecological theory of wildlife harvesting, tragedy of the commons, green economics, and bioeconomics) give only peripheral attention to the driving influence of competition on resource exploitation. Here, I apply resource competition theory (RCT) to the exploitation of RNRs and derive four general policies in support of their sustainable and equitable use: (1) regulate resource extraction technology to avoid damage to the resource base; (2) increase efficiency of resource use and reduce waste at every step in the resource supply chain and distribution network; (3) partition ecosystems with the harvesting niche as the basic organizing principle for sustainable management of natural resources by multiple users; and (4) increase negative feedback between consumer and resource to bring about long-term sustainable use. A simple policy framework demonstrates how RCT integrates with other elements of sustainability science to better manage productive ecosystems. Several problem areas of RNR management are discussed in the light of RCT, including tragedy of the commons, overharvesting, resource collapse, bycatch, single species quotas, and simplification of ecosystems. PMID:27209800

  8. Hierarchical image feature extraction by an irregular pyramid of polygonal partitions

    SciTech Connect

    Skurikhin, Alexei N

    2008-01-01

    We present an algorithmic framework for hierarchical image segmentation and feature extraction. We build a successive fine-to-coarse hierarchy of irregular polygonal partitions of the original image. This multiscale hierarchy forms the basis for object-oriented image analysis. The framework incorporates the Gestalt principles of visual perception, such as proximity and closure, and exploits spectral and textural similarities of polygonal partitions, while iteratively grouping them until dissimilarity criteria are exceeded. Seed polygons are built upon a triangular mesh composed of irregular sized triangles, whose spatial arrangement is adapted to the image content. This is achieved by building the triangular mesh on the top of detected spectral discontinuities (such as edges), which form a network of constraints for the Delaunay triangulation. The image is then represented as a spatial network in the form of a graph with vertices corresponding to the polygonal partitions and edges reflecting their relations. The iterative agglomeration of partitions into object-oriented segments is formulated as Minimum Spanning Tree (MST) construction. An important characteristic of the approach is that the agglomeration of polygonal partitions is constrained by the detected edges; thus the shapes of agglomerated partitions are more likely to correspond to the outlines of real-world objects. The constructed partitions and their spatial relations are characterized using spectral, textural and structural features based on proximity graphs. The framework allows searching for object-oriented features of interest across multiple levels of details of the built hierarchy and can be generalized to the multi-criteria MST to account for multiple criteria important for an application.

  9. Multiresolution analysis over simple graphs for brain computer interfaces

    NASA Astrophysics Data System (ADS)

    Asensio-Cubero, J.; Gan, J. Q.; Palaniappan, R.

    2013-08-01

    Objective. Multiresolution analysis (MRA) offers a useful framework for signal analysis in the temporal and spectral domains, although commonly employed MRA methods may not be the best approach for brain computer interface (BCI) applications. This study aims to develop a new MRA system for extracting tempo-spatial-spectral features for BCI applications based on wavelet lifting over graphs. Approach. This paper proposes a new graph-based transform for wavelet lifting and a tailored simple graph representation for electroencephalography (EEG) data, which results in an MRA system where temporal, spectral and spatial characteristics are used to extract motor imagery features from EEG data. The transformed data is processed within a simple experimental framework to test the classification performance of the new method. Main Results. The proposed method can significantly improve the classification results obtained by various wavelet families using the same methodology. Preliminary results using common spatial patterns as feature extraction method show that we can achieve comparable classification accuracy to more sophisticated methodologies. From the analysis of the results we can obtain insights into the pattern development in the EEG data, which provide useful information for feature basis selection and thus for improving classification performance. Significance. Applying wavelet lifting over graphs is a new approach for handling BCI data. The inherent flexibility of the lifting scheme could lead to new approaches based on the hereby proposed method for further classification performance improvement.

  10. Constrained Graph Optimization: Interdiction and Preservation Problems

    SciTech Connect

    Schild, Aaron V

    2012-07-30

    The maximum flow, shortest path, and maximum matching problems are a set of basic graph problems that are critical in theoretical computer science and applications. Constrained graph optimization, a variation of these basic graph problems involving modification of the underlying graph, is equally important but sometimes significantly harder. In particular, one can explore these optimization problems with additional cost constraints. In the preservation case, the optimizer has a budget to preserve vertices or edges of a graph, preventing them from being deleted. The optimizer wants to find the best set of preserved edges/vertices in which the cost constraints are satisfied and the basic graph problems are optimized. For example, in shortest path preservation, the optimizer wants to find a set of edges/vertices within which the shortest path between two predetermined points is smallest. In interdiction problems, one deletes vertices or edges from the graph with a particular cost in order to impede the basic graph problems as much as possible (for example, delete edges/vertices to maximize the shortest path between two predetermined vertices). Applications of preservation problems include optimal road maintenance, power grid maintenance, and job scheduling, while interdiction problems are related to drug trafficking prevention, network stability assessment, and counterterrorism. Computational hardness results are presented, along with heuristic methods for approximating solutions to the matching interdiction problem. Also, efficient algorithms are presented for special cases of graphs, including on planar graphs. The graphs in many of the listed applications are planar, so these algorithms have important practical implications.

  11. Generalized graph states based on Hadamard matrices

    SciTech Connect

    Cui, Shawn X.; Yu, Nengkun; Zeng, Bei

    2015-07-15

    Graph states are widely used in quantum information theory, including entanglement theory, quantum error correction, and one-way quantum computing. Graph states have a nice structure related to a certain graph, which is given by either a stabilizer group or an encoding circuit, both can be directly given by the graph. To generalize graph states, whose stabilizer groups are abelian subgroups of the Pauli group, one approach taken is to study non-abelian stabilizers. In this work, we propose to generalize graph states based on the encoding circuit, which is completely determined by the graph and a Hadamard matrix. We study the entanglement structures of these generalized graph states and show that they are all maximally mixed locally. We also explore the relationship between the equivalence of Hadamard matrices and local equivalence of the corresponding generalized graph states. This leads to a natural generalization of the Pauli (X, Z) pairs, which characterizes the local symmetries of these generalized graph states. Our approach is also naturally generalized to construct graph quantum codes which are beyond stabilizer codes.

  12. GRAPHIE: graph based histology image explorer

    PubMed Central

    2015-01-01

    Background Histology images comprise one of the important sources of knowledge for phenotyping studies in systems biology. However, the annotation and analyses of histological data have remained a manual, subjective and relatively low-throughput process. Results We introduce Graph based Histology Image Explorer (GRAPHIE)-a visual analytics tool to explore, annotate and discover potential relationships in histology image collections within a biologically relevant context. The design of GRAPHIE is guided by domain experts' requirements and well-known InfoVis mantras. By representing each image with informative features and then subsequently visualizing the image collection with a graph, GRAPHIE allows users to effectively explore the image collection. The features were designed to capture localized morphological properties in the given tissue specimen. More importantly, users can perform feature selection in an interactive way to improve the visualization of the image collection and the overall annotation process. Finally, the annotation allows for a better prospective examination of datasets as demonstrated in the users study. Thus, our design of GRAPHIE allows for the users to navigate and explore large collections of histology image datasets. Conclusions We demonstrated the usefulness of our visual analytics approach through two case studies. Both of the cases showed efficient annotation and analysis of histology image collection. PMID:26330277

  13. Hierarchical structure of the logical Internet graph

    NASA Astrophysics Data System (ADS)

    Ge, Zihui; Figueiredo, Daniel R.; Jaiswal, Sharad; Gao, Lixin

    2001-07-01

    The study of the Internet topology has recently received much attention from the research community. In particular, the observation that the network graph has interesting properties, such as power laws, that might be explored in a myriad of ways. Most of the work in characterizing the Internet graph is based on the physical network graph, i.e., the connectivity graph. In this paper we investigate how logical relationships between nodes of the AS graph can be used to gain insight to its structure. We characterize the logical graph using various metrics and identify the presence of power laws in the number of customers that a provider has. Using these logical relationships we define a structural model of the AS graph. The model highlights the hierarchical nature of logical relationships and the preferential connection to larger providers. We also investigate the consistency of this model over time and observe interesting properties of the hierarchical structure.

  14. The Feynman Identity for Planar Graphs

    NASA Astrophysics Data System (ADS)

    da Costa, G. A. T. F.

    2016-08-01

    The Feynman identity (FI) of a planar graph relates the Euler polynomial of the graph to an infinite product over the equivalence classes of closed nonperiodic signed cycles in the graph. The main objectives of this paper are to compute the number of equivalence classes of nonperiodic cycles of given length and sign in a planar graph and to interpret the data encoded by the FI in the context of free Lie superalgebras. This solves in the case of planar graphs a problem first raised by Sherman and sets the FI as the denominator identity of a free Lie superalgebra generated from a graph. Other results are obtained. For instance, in connection with zeta functions of graphs.

  15. Fast Approximate Quadratic Programming for Graph Matching

    PubMed Central

    Vogelstein, Joshua T.; Conroy, John M.; Lyzinski, Vince; Podrazik, Louis J.; Kratzer, Steven G.; Harley, Eric T.; Fishkind, Donniell E.; Vogelstein, R. Jacob; Priebe, Carey E.

    2015-01-01

    Quadratic assignment problems arise in a wide variety of domains, spanning operations research, graph theory, computer vision, and neuroscience, to name a few. The graph matching problem is a special case of the quadratic assignment problem, and graph matching is increasingly important as graph-valued data is becoming more prominent. With the aim of efficiently and accurately matching the large graphs common in big data, we present our graph matching algorithm, the Fast Approximate Quadratic assignment algorithm. We empirically demonstrate that our algorithm is faster and achieves a lower objective value on over 80% of the QAPLIB benchmark library, compared with the previous state-of-the-art. Applying our algorithm to our motivating example, matching C. elegans connectomes (brain-graphs), we find that it efficiently achieves performance. PMID:25886624

  16. On a programming language for graph algorithms

    NASA Technical Reports Server (NTRS)

    Rheinboldt, W. C.; Basili, V. R.; Mesztenyi, C. K.

    1971-01-01

    An algorithmic language, GRAAL, is presented for describing and implementing graph algorithms of the type primarily arising in applications. The language is based on a set algebraic model of graph theory which defines the graph structure in terms of morphisms between certain set algebraic structures over the node set and arc set. GRAAL is modular in the sense that the user specifies which of these mappings are available with any graph. This allows flexibility in the selection of the storage representation for different graph structures. In line with its set theoretic foundation, the language introduces sets as a basic data type and provides for the efficient execution of all set and graph operators. At present, GRAAL is defined as an extension of ALGOL 60 (revised) and its formal description is given as a supplement to the syntactic and semantic definition of ALGOL. Several typical graph algorithms are written in GRAAL to illustrate various features of the language and to show its applicability.

  17. Line graphs as social networks

    NASA Astrophysics Data System (ADS)

    Krawczyk, M. J.; Muchnik, L.; Mańka-Krasoń, A.; Kułakowski, K.

    2011-07-01

    It was demonstrated recently that the line graphs are clustered and assortative. These topological features are known to characterize some social networks [M.E.J. Newman, Y. Park, Why social networks are different from other types of networks, Phys. Rev. E 68 (2003) 036122]; it was argued that this similarity reveals their cliquey character. In the model proposed here, a social network is the line graph of an initial network of families, communities, interest groups, school classes and small companies. These groups play the role of nodes, and individuals are represented by links between these nodes. The picture is supported by the data on the LiveJournal network of about 8×10 6 people.

  18. Graph distance for complex networks

    NASA Astrophysics Data System (ADS)

    Shimada, Yutaka; Hirata, Yoshito; Ikeguchi, Tohru; Aihara, Kazuyuki

    2016-10-01

    Networks are widely used as a tool for describing diverse real complex systems and have been successfully applied to many fields. The distance between networks is one of the most fundamental concepts for properly classifying real networks, detecting temporal changes in network structures, and effectively predicting their temporal evolution. However, this distance has rarely been discussed in the theory of complex networks. Here, we propose a graph distance between networks based on a Laplacian matrix that reflects the structural and dynamical properties of networked dynamical systems. Our results indicate that the Laplacian-based graph distance effectively quantifies the structural difference between complex networks. We further show that our approach successfully elucidates the temporal properties underlying temporal networks observed in the context of face-to-face human interactions.

  19. Graph distance for complex networks

    PubMed Central

    Shimada, Yutaka; Hirata, Yoshito; Ikeguchi, Tohru; Aihara, Kazuyuki

    2016-01-01

    Networks are widely used as a tool for describing diverse real complex systems and have been successfully applied to many fields. The distance between networks is one of the most fundamental concepts for properly classifying real networks, detecting temporal changes in network structures, and effectively predicting their temporal evolution. However, this distance has rarely been discussed in the theory of complex networks. Here, we propose a graph distance between networks based on a Laplacian matrix that reflects the structural and dynamical properties of networked dynamical systems. Our results indicate that the Laplacian-based graph distance effectively quantifies the structural difference between complex networks. We further show that our approach successfully elucidates the temporal properties underlying temporal networks observed in the context of face-to-face human interactions. PMID:27725690

  20. Relativity on Rotated Graph Paper

    NASA Astrophysics Data System (ADS)

    Salgado, Roberto

    2011-11-01

    We present visual calculations in special relativity using spacetime diagrams drawn on graph paper that has been rotated by 45 degrees. The rotated lines represent lightlike directions in Minkowski spacetime, and the boxes in the grid (called light-clock diamonds) represent ticks of an inertial observer's lightclock. We show that many quantitative results can be read off a spacetime diagram by counting boxes, using a minimal amount of algebra.

  1. Topological structure of dictionary graphs

    NASA Astrophysics Data System (ADS)

    Fukś, Henryk; Krzemiński, Mark

    2009-09-01

    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 103 and 104. 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.

  2. Helping Students Make Sense of Graphs: An Experimental Trial of SmartGraphs Software

    NASA Astrophysics Data System (ADS)

    Zucker, Andrew; Kay, Rachel; Staudt, Carolyn

    2014-06-01

    Graphs are commonly used in science, mathematics, and social sciences to convey important concepts; yet students at all ages demonstrate difficulties interpreting graphs. This paper reports on an experimental study of free, Web-based software called SmartGraphs that is specifically designed to help students overcome their misconceptions regarding graphs. SmartGraphs allows students to interact with graphs and provides hints and scaffolding to help students, if they need help. SmartGraphs activities can be authored to be useful in teaching and learning a variety of topics that use graphs (such as slope, velocity, half-life, and global warming). A 2-year experimental study in physical science classrooms was conducted with dozens of teachers and thousands of students. In the first year, teachers were randomly assigned to experimental or control conditions. Data show that students of teachers who use SmartGraphs as a supplement to normal instruction make greater gains understanding graphs than control students studying the same content using the same textbooks, but without SmartGraphs. Additionally, teachers believe that the SmartGraphs activities help students meet learning goals in the physical science course, and a great majority reported they would use the activities with students again. In the second year of the study, several specific variations of SmartGraphs were researched to help determine what makes SmartGraphs effective.

  3. Computational Genomics Using Graph Theory

    NASA Astrophysics Data System (ADS)

    Schlick, Tamar

    2005-03-01

    With exciting new discoveries concerning RNA's regulatory cellular roles in gene expression, structural and functional problems associated with DNA's venerable cousin have come to the forefront. RNA folding, for example, is analogous to the well-known protein folding problem, and seeks to link RNA's primary sequence with secondary and tertiary structures. As a single-stranded polynucleotide, RNA's secondary structures are defined by a network of hydrogen bonds, which lead to a variety of stems, loops, junctions, bulges, and other motifs. Supersecondary pseudoknot structures can also occur and, together, lead to RNA's complex tertiary interactions stabilized by salt and solvent ions in the natural cellular milieu. Besides folding, challenges in RNA research include identifying locations and functions of RNA genes, discovering RNA's structural repertoire (folding motifs), designing novel RNAs, and developing new antiviral and antibiotic compounds composed of, or targeting, RNAs. In this talk, I will describe some of these new biological findings concerning RNA and present an approach using graph theory (network theory) to represent RNA secondary structures. Because the RNA motif space using graphs is vastly smaller than RNA's sequence space, many problems related to analyzing and discovering new RNAs can be simplified and studied systematically. Some preliminary applications to designing novel RNAs will also be described.Related ReadingH. H. Gan, S. Pasquali, and T. Schlick, ``A Survey of Existing RNAs using Graph Theory with Implications to RNA Analysis and Design,'' Nuc. Acids Res. 31: 2926--2943 (2003). J. Zorn, H. H. Gan, N. Shiffeldrim, and T. Schlick, ``Structural Motifs in Ribosomal RNAs: Implications for RNA Design and Genomics,'' Biopolymers 73: 340--347 (2004). H. H. Gan, D. Fera, J. Zorn, M. Tang, N. Shiffeldrim, U. Laserson, N. Kim, and T. Schlick,``RAG: RNA-As-Graphs Database -- Concepts, Analysis, and Features,'' Bioinformatics 20: 1285--1291 (2004). U

  4. Many-core graph analytics using accelerated sparse linear algebra routines

    NASA Astrophysics Data System (ADS)

    Kozacik, Stephen; Paolini, Aaron L.; Fox, Paul; Kelmelis, Eric

    2016-05-01

    Graph analytics is a key component in identifying emerging trends and threats in many real-world applications. Largescale graph analytics frameworks provide a convenient and highly-scalable platform for developing algorithms to analyze large datasets. Although conceptually scalable, these techniques exhibit poor performance on modern computational hardware. Another model of graph computation has emerged that promises improved performance and scalability by using abstract linear algebra operations as the basis for graph analysis as laid out by the GraphBLAS standard. By using sparse linear algebra as the basis, existing highly efficient algorithms can be adapted to perform computations on the graph. This approach, however, is often less intuitive to graph analytics experts, who are accustomed to vertex-centric APIs such as Giraph, GraphX, and Tinkerpop. We are developing an implementation of the high-level operations supported by these APIs in terms of linear algebra operations. This implementation is be backed by many-core implementations of the fundamental GraphBLAS operations required, and offers the advantages of both the intuitive programming model of a vertex-centric API and the performance of a sparse linear algebra implementation. This technology can reduce the number of nodes required, as well as the run-time for a graph analysis problem, enabling customers to perform more complex analysis with less hardware at lower cost. All of this can be accomplished without the requirement for the customer to make any changes to their analytics code, thanks to the compatibility with existing graph APIs.

  5. 25 CFR 152.33 - Partition.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Partition. 152.33 Section 152.33 Indians BUREAU OF INDIAN..., REMOVAL OF RESTRICTIONS, AND SALE OF CERTAIN INDIAN LANDS Partitions in Kind of Inherited Allotments § 152.33 Partition. (a) Partition without application. If the Secretary of the Interior shall find that...

  6. 25 CFR 152.33 - Partition.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Partition. 152.33 Section 152.33 Indians BUREAU OF INDIAN..., REMOVAL OF RESTRICTIONS, AND SALE OF CERTAIN INDIAN LANDS Partitions in Kind of Inherited Allotments § 152.33 Partition. (a) Partition without application. If the Secretary of the Interior shall find that...

  7. Measuring Edge Importance: A Quantitative Analysis of the Stochastic Shielding Approximation for Random Processes on Graphs

    PubMed Central

    2014-01-01

    Mathematical models of cellular physiological mechanisms often involve random walks on graphs representing transitions within networks of functional states. Schmandt and Galán recently introduced a novel stochastic shielding approximation as a fast, accurate method for generating approximate sample paths from a finite state Markov process in which only a subset of states are observable. For example, in ion-channel models, such as the Hodgkin–Huxley or other conductance-based neural models, a nerve cell has a population of ion channels whose states comprise the nodes of a graph, only some of which allow a transmembrane current to pass. The stochastic shielding approximation consists of neglecting fluctuations in the dynamics associated with edges in the graph not directly affecting the observable states. We consider the problem of finding the optimal complexity reducing mapping from a stochastic process on a graph to an approximate process on a smaller sample space, as determined by the choice of a particular linear measurement functional on the graph. The partitioning of ion-channel states into conducting versus nonconducting states provides a case in point. In addition to establishing that Schmandt and Galán’s approximation is in fact optimal in a specific sense, we use recent results from random matrix theory to provide heuristic error estimates for the accuracy of the stochastic shielding approximation for an ensemble of random graphs. Moreover, we provide a novel quantitative measure of the contribution of individual transitions within the reaction graph to the accuracy of the approximate process. PMID:24742077

  8. Computing Information Value from RDF Graph Properties

    SciTech Connect

    al-Saffar, Sinan; Heileman, Gregory

    2010-11-08

    Information value has been implicitly utilized and mostly non-subjectively computed in information retrieval (IR) systems. We explicitly define and compute the value of an information piece as a function of two parameters, the first is the potential semantic impact the target information can subjectively have on its recipient's world-knowledge, and the second parameter is trust in the information source. We model these two parameters as properties of RDF graphs. Two graphs are constructed, a target graph representing the semantics of the target body of information and a context graph representing the context of the consumer of that information. We compute information value subjectively as a function of both potential change to the context graph (impact) and the overlap between the two graphs (trust). Graph change is computed as a graph edit distance measuring the dissimilarity between the context graph before and after the learning of the target graph. A particular application of this subjective information valuation is in the construction of a personalized ranking component in Web search engines. Based on our method, we construct a Web re-ranking system that personalizes the information experience for the information-consumer.

  9. Components in time-varying graphs

    NASA Astrophysics Data System (ADS)

    Nicosia, Vincenzo; Tang, John; Musolesi, Mirco; Russo, Giovanni; Mascolo, Cecilia; Latora, Vito

    2012-06-01

    Real complex systems are inherently time-varying. Thanks to new communication systems and novel technologies, today it is possible to produce and analyze social and biological networks with detailed information on the time of occurrence and duration of each link. However, standard graph metrics introduced so far in complex network theory are mainly suited for static graphs, i.e., graphs in which the links do not change over time, or graphs built from time-varying systems by aggregating all the links as if they were concurrent in time. In this paper, we extend the notion of connectedness, and the definitions of node and graph components, to the case of time-varying graphs, which are represented as time-ordered sequences of graphs defined over a fixed set of nodes. We show that the problem of finding strongly connected components in a time-varying graph can be mapped into the problem of discovering the maximal-cliques in an opportunely constructed static graph, which we name the affine graph. It is, therefore, an NP-complete problem. As a practical example, we have performed a temporal component analysis of time-varying graphs constructed from three data sets of human interactions. The results show that taking time into account in the definition of graph components allows to capture important features of real systems. In particular, we observe a large variability in the size of node temporal in- and out-components. This is due to intrinsic fluctuations in the activity patterns of individuals, which cannot be detected by static graph analysis.

  10. Components in time-varying graphs.

    PubMed

    Nicosia, Vincenzo; Tang, John; Musolesi, Mirco; Russo, Giovanni; Mascolo, Cecilia; Latora, Vito

    2012-06-01

    Real complex systems are inherently time-varying. Thanks to new communication systems and novel technologies, today it is possible to produce and analyze social and biological networks with detailed information on the time of occurrence and duration of each link. However, standard graph metrics introduced so far in complex network theory are mainly suited for static graphs, i.e., graphs in which the links do not change over time, or graphs built from time-varying systems by aggregating all the links as if they were concurrent in time. In this paper, we extend the notion of connectedness, and the definitions of node and graph components, to the case of time-varying graphs, which are represented as time-ordered sequences of graphs defined over a fixed set of nodes. We show that the problem of finding strongly connected components in a time-varying graph can be mapped into the problem of discovering the maximal-cliques in an opportunely constructed static graph, which we name the affine graph. It is, therefore, an NP-complete problem. As a practical example, we have performed a temporal component analysis of time-varying graphs constructed from three data sets of human interactions. The results show that taking time into account in the definition of graph components allows to capture important features of real systems. In particular, we observe a large variability in the size of node temporal in- and out-components. This is due to intrinsic fluctuations in the activity patterns of individuals, which cannot be detected by static graph analysis. PMID:22757508

  11. JavaGenes: Evolving Graphs with Crossover

    NASA Technical Reports Server (NTRS)

    Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

    2000-01-01

    Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

  12. On the spectral distribution of distance-k graph of free product graphs

    NASA Astrophysics Data System (ADS)

    Arizmendi, Octavio; Gaxiola, Tulio

    2016-08-01

    We calculate the distribution with respect to the vacuum state of the distance-k graph of a d-regular tree. From this result we show that the distance-k graph of a d-regular graphs converges to the distribution of the distance-k graph of a regular tree. Finally, we prove that, properly normalized, the asymptotic distributions of distance-k graphs of the d-fold free product graph, as d tends to infinity, is given by the distribution of Pk(s), where s is a semicirlce random variable and Pk is the kth Chebychev polynomial.

  13. Expanding our understanding of students' use of graphs for learning physics

    NASA Astrophysics Data System (ADS)

    Laverty, James T.

    It is generally agreed that the ability to visualize functional dependencies or physical relationships as graphs is an important step in modeling and learning. However, several studies in Physics Education Research (PER) have shown that many students in fact do not master this form of representation and even have misconceptions about the meaning of graphs that impede learning physics concepts. Working with graphs in classroom settings has been shown to improve student abilities with graphs, particularly when the students can interact with them. We introduce a novel problem type in an online homework system, which requires students to construct the graphs themselves in free form, and requires no hand-grading by instructors. A study of pre/post-test data using the Test of Understanding Graphs in Kinematics (TUG-K) over several semesters indicates that students learn significantly more from these graph construction problems than from the usual graph interpretation problems, and that graph interpretation alone may not have any significant effect. The interpretation of graphs, as well as the representation translation between textual, mathematical, and graphical representations of physics scenarios, are frequently listed among the higher order thinking skills we wish to convey in an undergraduate course. But to what degree do we succeed? Do students indeed employ higher order thinking skills when working through graphing exercises? We investigate students working through a variety of graph problems, and, using a think-aloud protocol, aim to reconstruct the cognitive processes that the students go through. We find that to a certain degree, these problems become commoditized and do not trigger the desired higher order thinking processes; simply translating ``textbook-like'' problems into the graphical realm will not achieve any additional educational goals. Whether the students have to interpret or construct a graph makes very little difference in the methods used by the

  14. Motifs in triadic random graphs based on Steiner triple systems

    NASA Astrophysics Data System (ADS)

    Winkler, Marco; Reichardt, Jörg

    2013-08-01

    Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade, the overabundance of certain subnetwork patterns, i.e., the so-called motifs, has attracted much attention. It has been hypothesized that these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information, is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graph models (ERGMs) to define models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obstacle, we use Steiner triple systems (STSs). These are partitions of sets of nodes into pair-disjoint triads, which thus can be specified independently. Combining the concepts of ERGMs and STSs, we suggest generative models capable of generating ensembles of networks with nontrivial triadic Z-score profiles. Further, we discover inevitable correlations between the abundance of triad patterns, which occur solely for statistical reasons and need to be taken into account when discussing the functional implications of motif statistics. Moreover, we calculate the degree distributions of our triadic random graphs analytically.

  15. Fast dual graph-based hotspot detection

    NASA Astrophysics Data System (ADS)

    Kahng, Andrew B.; Park, Chul-Hong; Xu, Xu

    2006-10-01

    features or "L-shaped" features; (2) face-level detection finds the pattern-related hotspots which span several close features; and (3) merged-face-level detection finds hotspots with more complex patterns. To find the merged faces which capture the pattern-related hotspots, we propose to convert the layout into a planar graph G. We then construct its dual graph G D and sort the dual nodes according to their weights. We merge the sorted dual nodes (i.e., the faces in G) that share a given feature, in sequence. We have tested our flow on several industry testcases. The experimental results show that our method is promising: for a 90nm metal layer with 17 hotspots detected by commercial optical rule check (ORC) tools, our method can detect all of them while the overall runtime improvement is more than 287X.

  16. Replica methods for loopy sparse random graphs

    NASA Astrophysics Data System (ADS)

    Coolen, ACC

    2016-03-01

    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. This paper is dedicated to the memory of our colleague and friend Jun-Ichi Inoue, with whom the author has had the great pleasure and privilege of collaborating.

  17. Graph Frequency Analysis of Brain Signals

    NASA Astrophysics Data System (ADS)

    Huang, Weiyu; Goldsberry, Leah; Wymbs, Nicholas F.; Grafton, Scott T.; Bassett, Danielle S.; Ribeiro, Alejandro

    2016-10-01

    This paper presents methods to analyze functional brain networks and signals from graph spectral perspectives. The notion of frequency and filters traditionally defined for signals supported on regular domains such as discrete time and image grids has been recently generalized to irregular graph domains, and defines brain graph frequencies associated with different levels of spatial smoothness across the brain regions. Brain network frequency also enables the decomposition of brain signals into pieces corresponding to smooth or rapid variations. We relate graph frequency with principal component analysis when the networks of interest denote functional connectivity. The methods are utilized to analyze brain networks and signals as subjects master a simple motor skill. We observe that brain signals corresponding to different graph frequencies exhibit different levels of adaptability throughout learning. Further, we notice a strong association between graph spectral properties of brain networks and the level of exposure to tasks performed, and recognize the most contributing and important frequency signatures at different task familiarity.

  18. Fast generation of sparse random kernel graphs

    SciTech Connect

    Hagberg, Aric; Lemons, Nathan; Du, Wen -Bo

    2015-09-10

    The development of kernel-based inhomogeneous random graphs has provided models that are flexible enough to capture many observed characteristics of real networks, and that are also mathematically tractable. We specify a class of inhomogeneous random graph models, called random kernel graphs, that produces sparse graphs with tunable graph properties, and we develop an efficient generation algorithm to sample random instances from this model. As real-world networks are usually large, it is essential that the run-time of generation algorithms scales better than quadratically in the number of vertices n. We show that for many practical kernels our algorithm runs in time at most ο(n(logn)²). As an example, we show how to generate samples of power-law degree distribution graphs with tunable assortativity.

  19. Fast generation of sparse random kernel graphs

    DOE PAGES

    Hagberg, Aric; Lemons, Nathan; Du, Wen -Bo

    2015-09-10

    The development of kernel-based inhomogeneous random graphs has provided models that are flexible enough to capture many observed characteristics of real networks, and that are also mathematically tractable. We specify a class of inhomogeneous random graph models, called random kernel graphs, that produces sparse graphs with tunable graph properties, and we develop an efficient generation algorithm to sample random instances from this model. As real-world networks are usually large, it is essential that the run-time of generation algorithms scales better than quadratically in the number of vertices n. We show that for many practical kernels our algorithm runs in timemore » at most ο(n(logn)²). As an example, we show how to generate samples of power-law degree distribution graphs with tunable assortativity.« less

  20. Image clustering using fuzzy graph theory

    NASA Astrophysics Data System (ADS)

    Jafarkhani, Hamid; Tarokh, Vahid

    1999-12-01

    We propose an image clustering algorithm which uses fuzzy graph theory. First, we define a fuzzy graph and the concept of connectivity for a fuzzy graph. Then, based on our definition of connectivity we propose an algorithm which finds connected subgraphs of the original fuzzy graph. Each connected subgraph can be considered as a cluster. As an application of our algorithm, we consider a database of images. We calculate a similarity measure between any paris of images in the database and generate the corresponding fuzzy graph. The, we find the subgraphs of the resulting fuzzy graph using our algorithm. Each subgraph corresponds to a cluster. We apply our image clustering algorithm to the key frames of news programs to find the anchorperson clusters. Simulation results show that our algorithm is successful to find most of anchorperson frames from the database.

  1. Spectral correlations of individual quantum graphs.

    PubMed

    Gnutzmann, Sven; Altland, Alexander

    2005-11-01

    We investigate the spectral properties of chaotic quantum graphs. We demonstrate that the energy-average over the spectrum of individual graphs can be traded for the functional average over a supersymmetric nonlinear -model action. This proves that spectral correlations of individual quantum graphs behave according to the predictions of Wigner-Dyson random matrix theory. We explore the stability of the universal random matrix behavior with regard to perturbations, and discuss the crossover between different types of symmetries.

  2. Spectral correlations of individual quantum graphs

    SciTech Connect

    Gnutzmann, Sven; Altland, Alexander

    2005-11-01

    We investigate the spectral properties of chaotic quantum graphs. We demonstrate that the energy-average over the spectrum of individual graphs can be traded for the functional average over a supersymmetric nonlinear {sigma}-model action. This proves that spectral correlations of individual quantum graphs behave according to the predictions of Wigner-Dyson random matrix theory. We explore the stability of the universal random matrix behavior with regard to perturbations, and discuss the crossover between different types of symmetries.

  3. Separability of Generalized Graph Product States

    NASA Astrophysics Data System (ADS)

    Zhao, Hui; Fan, Jiao

    2013-09-01

    We construct two classes of generalized graph product states and study the entanglement of these states. It is first presented that the density matrices of complex edge-weighted digraphs associated with the generalized graph product in mn systems are positive partial transformation and separable states. Then we prove that the density matrices of the vertex-weighted digraphs associated with another generalized graph product are entangled states.

  4. High Pressure/Temperature Metal Silicate Partitioning of Tungsten

    NASA Technical Reports Server (NTRS)

    Shofner, G. A.; Danielson, L.; Righter, K.; Campbell, A. J.

    2010-01-01

    The behavior of chemical elements during metal/silicate segregation and their resulting distribution in Earth's mantle and core provide insight into core formation processes. Experimental determination of partition coefficients allows calculations of element distributions that can be compared to accepted values of element abundances in the silicate (mantle) and metallic (core) portions of the Earth. Tungsten (W) is a moderately siderophile element and thus preferentially partitions into metal versus silicate under many planetary conditions. The partitioning behavior has been shown to vary with temperature, silicate composition, oxygen fugacity, and pressure. Most of the previous work on W partitioning has been conducted at 1-bar conditions or at relatively low pressures, i.e. <10 GPa, and in two cases at or near 20 GPa. According to those data, the stronger influences on the distribution coefficient of W are temperature, composition, and oxygen fugacity with a relatively slight influence in pressure. Predictions based on extrapolation of existing data and parameterizations suggest an increased pressured dependence on metal/ silicate partitioning of W at higher pressures 5. However, the dependence on pressure is not as well constrained as T, fO2, and silicate composition. This poses a problem because proposed equilibration pressures for core formation range from 27 to 50 GPa, falling well outside the experimental range, therefore requiring exptrapolation of a parametereized model. Higher pressure data are needed to improve our understanding of W partitioning at these more extreme conditions.

  5. Breddin's graph for tectonic regimes

    NASA Astrophysics Data System (ADS)

    Célérier, Bernard; Séranne, Michel

    2001-05-01

    A simple graphical method is proposed to infer the tectonic regime from a fault and slip data set. An abacus is overlaid on a plot of the rake versus strike of the data. This yields the horizontal principal stress directions and a constraint on the stress tensor aspect ratio, in a manner similar to Breddin's graph for two-dimensional strain analysis. The main requirement is that one of the principal stress directions is close to the vertical. This method is illustrated on monophase synthetic and natural data, but is also expected to help sort out multiphase data sets.

  6. Naming on a Directed Graph

    NASA Astrophysics Data System (ADS)

    Gosti, Giorgio; Batchelder, William H.

    We address how the structure of a social communication system affects language coordination. The naming game is an abstraction of lexical acquisition dynamics, in which N agents try to find an agreement on the names to give to objects. Most results on naming games are specific to certain communication network topologies. We present two important results that are general to any graph topology: the first proves that under certain topologies the system always converges to a name-object agreement; the second proves that if these conditions are not met the system may end up in a state in which sub-networks with different competing object-name associations coexist.

  7. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment-distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  8. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  9. Givental Graphs and Inversion Symmetry

    NASA Astrophysics Data System (ADS)

    Dunin-Barkowski, Petr; Shadrin, Sergey; Spitz, Loek

    2013-05-01

    Inversion symmetry is a very non-trivial discrete symmetry of Frobenius manifolds. It was obtained by Dubrovin from one of the elementary Schlesinger transformations of a special ODE associated to a Frobenius manifold. In this paper, we review the Givental group action on Frobenius manifolds in terms of Feynman graphs and obtain an interpretation of the inversion symmetry in terms of the action of the Givental group. We also consider the implication of this interpretation of the inversion symmetry for the Schlesinger transformations and for the Hamiltonians of the associated principle hierarchy.

  10. Graph algorithms in the titan toolkit.

    SciTech Connect

    McLendon, William Clarence, III; Wylie, Brian Neil

    2009-10-01

    Graph algorithms are a key component in a wide variety of intelligence analysis activities. The Graph-Based Informatics for Non-Proliferation and Counter-Terrorism project addresses the critical need of making these graph algorithms accessible to Sandia analysts in a manner that is both intuitive and effective. Specifically we describe the design and implementation of an open source toolkit for doing graph analysis, informatics, and visualization that provides Sandia with novel analysis capability for non-proliferation and counter-terrorism.

  11. Evolutionary Games of Multiplayer Cooperation on Graphs.

    PubMed

    Peña, Jorge; Wu, Bin; Arranz, Jordi; Traulsen, Arne

    2016-08-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering. PMID:27513946

  12. Simple scale interpolator facilitates reading of graphs

    NASA Technical Reports Server (NTRS)

    Fetterman, D. E., Jr.

    1965-01-01

    Simple transparent overlay with interpolation scale facilitates accurate, rapid reading of graph coordinate points. This device can be used for enlarging drawings and locating points on perspective drawings.

  13. Evolutionary Games of Multiplayer Cooperation on Graphs.

    PubMed

    Peña, Jorge; Wu, Bin; Arranz, Jordi; Traulsen, Arne

    2016-08-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering.

  14. Generation of graph-state streams

    SciTech Connect

    Ballester, Daniel; Cho, Jaeyoon; Kim, M. S.

    2011-01-15

    We propose a protocol to generate a stream of mobile qubits in a graph state through a single stationary parent qubit and discuss two types of its physical implementation, namely, the generation of photonic graph states through an atomlike qubit and the generation of flying atoms through a cavity-mode photonic qubit. The generated graph states fall into an important class that can hugely reduce the resource requirement of fault-tolerant linear optics quantum computation, which was previously known to be far from realistic. In regard to the flying atoms, we also propose a heralded generation scheme, which allows for high-fidelity graph states even under the photon loss.

  15. Evolutionary Games of Multiplayer Cooperation on Graphs

    PubMed Central

    Arranz, Jordi; Traulsen, Arne

    2016-01-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering. PMID:27513946

  16. Deep graphs-A general framework to represent and analyze heterogeneous complex systems across scales.

    PubMed

    Traxl, Dominik; Boers, Niklas; Kurths, Jürgen

    2016-06-01

    Network theory has proven to be a powerful tool in describing and analyzing systems by modelling the relations between their constituent objects. Particularly in recent years, a great progress has been made by augmenting "traditional" network theory in order to account for the multiplex nature of many networks, multiple types of connections between objects, the time-evolution of networks, networks of networks and other intricacies. However, existing network representations still lack crucial features in order to serve as a general data analysis tool. These include, most importantly, an explicit association of information with possibly heterogeneous types of objects and relations, and a conclusive representation of the properties of groups of nodes as well as the interactions between such groups on different scales. In this paper, we introduce a collection of definitions resulting in a framework that, on the one hand, entails and unifies existing network representations (e.g., network of networks and multilayer networks), and on the other hand, generalizes and extends them by incorporating the above features. To implement these features, we first specify the nodes and edges of a finite graph as sets of properties (which are permitted to be arbitrary mathematical objects). Second, the mathematical concept of partition lattices is transferred to the network theory in order to demonstrate how partitioning the node and edge set of a graph into supernodes and superedges allows us to aggregate, compute, and allocate information on and between arbitrary groups of nodes. The derived partition lattice of a graph, which we denote by deep graph, constitutes a concise, yet comprehensive representation that enables the expression and analysis of heterogeneous properties, relations, and interactions on all scales of a complex system in a self-contained manner. Furthermore, to be able to utilize existing network-based methods and models, we derive different representations of

  17. STRUCTURAL ANNOTATION OF EM IMAGES BY GRAPH CUT

    SciTech Connect

    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).

  18. Aspects of Performance on Line Graph Description Tasks: Influenced by Graph Familiarity and Different Task Features

    ERIC Educational Resources Information Center

    Xi, Xiaoming

    2010-01-01

    Motivated by cognitive theories of graph comprehension, this study systematically manipulated characteristics of a line graph description task in a speaking test in ways to mitigate the influence of graph familiarity, a potential source of construct-irrelevant variance. It extends Xi (2005), which found that the differences in holistic scores on…

  19. GPD: a graph pattern diffusion kernel for accurate graph classification with applications in cheminformatics.

    PubMed

    Smalter, Aaron; Huan, Jun Luke; Jia, Yi; Lushington, Gerald

    2010-01-01

    Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogeneous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In this paper, we demonstrate a novel technique called graph pattern diffusion (GPD) kernel. Our idea is to leverage existing frequent pattern discovery methods and to explore the application of kernel classifier (e.g., support vector machine) in building highly accurate graph classification. In our method, we first identify all frequent patterns from a graph database. We then map subgraphs to graphs in the graph database and use a process we call "pattern diffusion" to label nodes in the graphs. Finally, we designed a graph alignment algorithm to compute the inner product of two graphs. We have tested our algorithm using a number of chemical structure data. The experimental results demonstrate that our method is significantly better than competing methods such as those kernel functions based on paths, cycles, and subgraphs.

  20. Helping Students Make Sense of Graphs: An Experimental Trial of SmartGraphs Software

    ERIC Educational Resources Information Center

    Zucker, Andrew; Kay, Rachel; Staudt, Carolyn

    2014-01-01

    Graphs are commonly used in science, mathematics, and social sciences to convey important concepts; yet students at all ages demonstrate difficulties interpreting graphs. This paper reports on an experimental study of free, Web-based software called SmartGraphs that is specifically designed to help students overcome their misconceptions regarding…

  1. Feature Tracking Using Reeb Graphs

    SciTech Connect

    Weber, Gunther H.; Bremer, Peer-Timo; Day, Marcus S.; Bell, John B.; Pascucci, Valerio

    2010-08-02

    Tracking features and exploring their temporal dynamics can aid scientists in identifying interesting time intervals in a simulation and serve as basis for performing quantitative analyses of temporal phenomena. In this paper, we develop a novel approach for tracking subsets of isosurfaces, such as burning regions in simulated flames, which are defined as areas of high fuel consumption on a temperature isosurface. Tracking such regions as they merge and split over time can provide important insights into the impact of turbulence on the combustion process. However, the convoluted nature of the temperature isosurface and its rapid movement make this analysis particularly challenging. Our approach tracks burning regions by extracting a temperature isovolume from the four-dimensional space-time temperature field. It then obtains isosurfaces for the original simulation time steps and labels individual connected 'burning' regions based on the local fuel consumption value. Based on this information, a boundary surface between burning and non-burning regions is constructed. The Reeb graph of this boundary surface is the tracking graph for burning regions.

  2. Clique percolation in random graphs

    NASA Astrophysics Data System (ADS)

    Li, Ming; Deng, Youjin; Wang, Bing-Hong

    2015-10-01

    As a generation of the classical percolation, clique percolation focuses on the connection of cliques in a graph, where the connection of two k cliques means that they share at least l graphs, which gives not only the exact solutions of the critical point, but also the corresponding order parameter. Based on this, we prove theoretically that the fraction ψ of cliques in the giant clique cluster always makes a continuous phase transition as the classical percolation. However, the fraction ϕ of vertices in the giant clique cluster for l >1 makes a step-function-like discontinuous phase transition in the thermodynamic limit and a continuous phase transition for l =1 . More interesting, our analysis shows that at the critical point, the order parameter ϕc for l >1 is neither 0 nor 1, but a constant depending on k and l . All these theoretical findings are in agreement with the simulation results, which give theoretical support and clarification for previous simulation studies of clique percolation.

  3. Large constraint length high speed viterbi decoder based on a modular hierarchial decomposition of the deBruijn graph

    NASA Technical Reports Server (NTRS)

    Collins, Oliver (Inventor); Dolinar, Jr., Samuel J. (Inventor); Hus, In-Shek (Inventor); Bozzola, Fabrizio P. (Inventor); Olson, Erlend M. (Inventor); Statman, Joseph I. (Inventor); Zimmerman, George A. (Inventor)

    1991-01-01

    A method of formulating and packaging decision-making elements into a long constraint length Viterbi decoder which involves formulating the decision-making processors as individual Viterbi butterfly processors that are interconnected in a deBruijn graph configuration. A fully distributed architecture, which achieves high decoding speeds, is made feasible by novel wiring and partitioning of the state diagram. This partitioning defines universal modules, which can be used to build any size decoder, such that a large number of wires is contained inside each module, and a small number of wires is needed to connect modules. The total system is modular and hierarchical, and it implements a large proportion of the required wiring internally within modules and may include some external wiring to fully complete the deBruijn graph. pg,14.

  4. Enabling Graph Appliance for Genome Assembly

    SciTech Connect

    Singh, Rina; Graves, Jeffrey A; Lee, Sangkeun; Sukumar, Sreenivas R; Shankar, Mallikarjun

    2015-01-01

    In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to store and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.

  5. Time Domain Partitioning of Electricity Production Cost Simulations

    SciTech Connect

    Barrows, C.; Hummon, M.; Jones, W.; Hale, E.

    2014-01-01

    Production cost models are often used for planning by simulating power system operations over long time horizons. The simulation of a day-ahead energy market can take several weeks to compute. Tractability improvements are often made through model simplifications, such as: reductions in transmission modeling detail, relaxation of commitment variable integrality, reductions in cost modeling detail, etc. One common simplification is to partition the simulation horizon so that weekly or monthly horizons can be simulated in parallel. However, horizon partitions are often executed with overlap periods of arbitrary and sometimes zero length. We calculate the time domain persistence of historical unit commitment decisions to inform time domain partitioning of production cost models. The results are implemented using PLEXOS production cost modeling software in an HPC environment to improve the computation time of simulations while maintaining solution integrity.

  6. Exotic equilibria of Harary graphs and a new minimum degree lower bound for synchronization

    SciTech Connect

    Canale, Eduardo A.; Monzón, Pablo

    2015-02-15

    This work is concerned with stability of equilibria in the homogeneous (equal frequencies) Kuramoto model of weakly coupled oscillators. In 2012 [R. Taylor, J. Phys. A: Math. Theor. 45, 1–15 (2012)], a sufficient condition for almost global synchronization was found in terms of the minimum degree–order ratio of the graph. In this work, a new lower bound for this ratio is given. The improvement is achieved by a concrete infinite sequence of regular graphs. Besides, non standard unstable equilibria of the graphs studied in Wiley et al. [Chaos 16, 015103 (2006)] are shown to exist as conjectured in that work.

  7. Teaching Discrete Mathematics with Graphing Calculators.

    ERIC Educational Resources Information Center

    Masat, Francis E.

    Graphing calculator use is often thought of in terms of pre-calculus or continuous topics in mathematics. This paper contains examples and activities that demonstrate useful, interesting, and easy ways to use a graphing calculator with discrete topics. Examples are given for each of the following topics: functions, mathematical induction and…

  8. Student Reasoning about Graphs in Different Contexts

    ERIC Educational Resources Information Center

    Ivanjek, Lana; Susac, Ana; Planinic, Maja; Andrasevic, Aneta; Milin-Sipus, Zeljka

    2016-01-01

    This study investigates university students' graph interpretation strategies and difficulties in mathematics, physics (kinematics), and contexts other than physics. Eight sets of parallel (isomorphic) mathematics, physics, and other context questions about graphs, which were developed by us, were administered to 385 first-year students at the…

  9. Universal spectral statistics in quantum graphs.

    PubMed

    Gnutzmann, Sven; Altland, Alexander

    2004-11-01

    We prove that the spectrum of an individual chaotic quantum graph shows universal spectral correlations, as predicted by random-matrix theory. The stability of these correlations with regard to nonuniversal corrections is analyzed in terms of the linear operator governing the classical dynamics on the graph.

  10. Graphs and Statistics: A Resource Handbook.

    ERIC Educational Resources Information Center

    New York State Education Dept., Albany. Bureau of General Education Curriculum Development.

    Graphical representation of statistical data is the focus of this resource handbook. Only graphs which present numerical information are discussed. Activities involving the making, interpreting, and use of various types of graphs and tables are included. Sections are also included which discuss statistical terms, normal distribution and…

  11. Using a Microcomputer for Graphing Practice.

    ERIC Educational Resources Information Center

    Beichner, Robert J.

    1986-01-01

    Describes a laboratory exercise that introduces physics students to graphing. Presents the program format and sample output of a computer simulation of an experiment which tests the effects of sound intensity on the crawling speed of a snail. Provides students with practice in making exponential or logarithmic graphs. (ML)

  12. Graphing Calculators: The Newest Revolution in Mathematics.

    ERIC Educational Resources Information Center

    Clutter, Martha

    1999-01-01

    Asserts that there are numerous advantages to using graphing calculators, including the teaching of higher-level thinking skills and allowing students to draw conclusions about what they are learning. However, mathematics educators face such challenges as teaching students when it is appropriate to use graphing calculators, course-content…

  13. Pattern Perception and the Comprehension of Graphs.

    ERIC Educational Resources Information Center

    Pinker, Steven

    Three experiments tested the hypothesis that graphs convey information effectively because they can display global trends as geometric patterns that visual systems encode easily. A novel type of graph was invented in which angles/lengths of line segments joined end-to-end represented variables of rainfall and temperature of a set of months. It was…

  14. Developing Data Graph Comprehension. Third Edition

    ERIC Educational Resources Information Center

    Curcio, Frances

    2010-01-01

    Since the dawn of civilization, pictorial representations and symbols have been used to communicate simple statistics. Efficient and effective, they are still used today in the form of pictures and graphs to record and present data. Who can tie their shoes? How many calories are in your favorite food? Make data and graphs relevant and interesting…

  15. A Ring Construction Using Finite Directed Graphs

    ERIC Educational Resources Information Center

    Bardzell, Michael

    2012-01-01

    In this paper we discuss an interesting class of noncommutative rings which can be constructed using finite directed graphs. This construction also creates a vector space. These structures provide undergraduate students connections between ring theory and graph theory and, among other things, allow them to see a ring unity element that looks quite…

  16. TI-83 Graphing Calculator Keystroke Guide.

    ERIC Educational Resources Information Center

    Panik, Cathy

    This document presents keystrokes for the Texas Instrument (TI-83) graphing calculator. After presenting some basic TI-83 keystrokes, activities for student practice are listed. This is followed by keystrokes for TI-83 advanced functions such as evaluating function values, finding the zero of a function, finding the intersection of two graphs,…

  17. Supplantation of Mental Operations on Graphs

    ERIC Educational Resources Information Center

    Vogel, Markus; Girwidz, Raimund; Engel, Joachim

    2007-01-01

    Research findings show the difficulties younger students have in working with graphs. Higher mental operations are necessary for a skilled interpretation of abstract representations. We suggest connecting a concrete representation of the modeled problem with the related graph. The idea is to illustrate essential mental operations externally. This…

  18. METAL PARTITIONING IN COMBUSTION PROCESSES

    EPA Science Inventory

    This article summarizes ongoing research efforts at the National Risk Management Research Laboratory of the U.S. Environmental Protection Agency examining [high temperature] metal behavior within combustion environments. The partitioning of non-volatile (Cr and Ni), semi-volatil...

  19. Graph Mining Meets the Semantic Web

    SciTech Connect

    Lee, Sangkeun; Sukumar, Sreenivas R; Lim, Seung-Hwan

    2015-01-01

    The Resource Description Framework (RDF) and SPARQL Protocol and RDF Query Language (SPARQL) were introduced about a decade ago to enable flexible schema-free data interchange on the Semantic Web. Today, data scientists use the framework as a scalable graph representation for integrating, querying, exploring and analyzing data sets hosted at different sources. With increasing adoption, the need for graph mining capabilities for the Semantic Web has emerged. We address that need through implementation of three popular iterative Graph Mining algorithms (Triangle count, Connected component analysis, and PageRank). We implement these algorithms as SPARQL queries, wrapped within Python scripts. We evaluate the performance of our implementation on 6 real world data sets and show graph mining algorithms (that have a linear-algebra formulation) can indeed be unleashed on data represented as RDF graphs using the SPARQL query interface.

  20. Vortices and superfields on a graph

    SciTech Connect

    Kan, Nahomi; Kobayashi, Koichiro; Shiraishi, Kiyoshi

    2009-08-15

    We extend the dimensional deconstruction by utilizing the knowledge of graph theory. In the dimensional deconstruction, one uses the moose diagram to exhibit the structure of the 'theory space'. We generalize the moose diagram to a general graph with oriented edges. In the present paper, we consider only the U(1) gauge symmetry. We also introduce supersymmetry into our model by use of superfields. We suppose that vector superfields reside at the vertices and chiral superfields at the edges of a given graph. Then we can consider multivector, multi-Higgs models. In our model, [U(1)]{sup p} (where p is the number of vertices) is broken to a single U(1). Therefore, for specific graphs, we get vortexlike classical solutions in our model. We show some examples of the graphs admitting the vortex solutions of simple structure as the Bogomolnyi solution.

  1. Vortices and superfields on a graph

    NASA Astrophysics Data System (ADS)

    Kan, Nahomi; Kobayashi, Koichiro; Shiraishi, Kiyoshi

    2009-08-01

    We extend the dimensional deconstruction by utilizing the knowledge of graph theory. In the dimensional deconstruction, one uses the moose diagram to exhibit the structure of the “theory space.” We generalize the moose diagram to a general graph with oriented edges. In the present paper, we consider only the U(1) gauge symmetry. We also introduce supersymmetry into our model by use of superfields. We suppose that vector superfields reside at the vertices and chiral superfields at the edges of a given graph. Then we can consider multivector, multi-Higgs models. In our model, [U(1)]p (where p is the number of vertices) is broken to a single U(1). Therefore, for specific graphs, we get vortexlike classical solutions in our model. We show some examples of the graphs admitting the vortex solutions of simple structure as the Bogomolnyi solution.

  2. On linear area embedding of planar graphs

    NASA Astrophysics Data System (ADS)

    Dolev, D.; Trickey, H.

    1981-09-01

    Planar embedding with minimal area of graphs on an integer grid is one of the major issues in VLSI. Valiant (V) gave an algorithm to construct a planar embedding for trees in linear area; he also proved that there are planar graphs that require quadratic area. An algorithm to embed outerplanar graphs in linear area is given. This algorithm is extended to work for every planar graph that has the following property: for every vertex there exists a path of length less than K to the exterior face, where K is a constant. Finally, finding a minimal embedding area is shown to be NP-complete for forests, and hence more general types of graphs.

  3. Structure and strategy in encoding simplified graphs

    NASA Technical Reports Server (NTRS)

    Schiano, Diane J.; Tversky, Barbara

    1992-01-01

    Tversky and Schiano (1989) found a systematic bias toward the 45-deg line in memory for the slopes of identical lines when embedded in graphs, but not in maps, suggesting the use of a cognitive reference frame specifically for encoding meaningful graphs. The present experiments explore this issue further using the linear configurations alone as stimuli. Experiments 1 and 2 demonstrate that perception and immediate memory for the slope of a test line within orthogonal 'axes' are predictable from purely structural considerations. In Experiments 3 and 4, subjects were instructed to use a diagonal-reference strategy in viewing the stimuli, which were described as 'graphs' only in Experiment 3. Results for both studies showed the diagonal bias previously found only for graphs. This pattern provides converging evidence for the diagonal as a cognitive reference frame in encoding linear graphs, and demonstrates that even in highly simplified displays, strategic factors can produce encoding biases not predictable solely from stimulus structure alone.

  4. Hierarchical, 4-connected Small-World Graph

    NASA Astrophysics Data System (ADS)

    Goncalves, Bruno; Boettcher, Stefan

    2008-03-01

    A new sequences of graphs are introduced that mimic small-world properties. The graphs are recursively constructed but retain a fixed, regular degree. They consist of a one-dimensional lattice backbone overlayed by a hierarchical sequence of long-distance links in a pattern reminiscent of the tower-of-hanoi sequence. These 4-regular graphs are non-planar, have a diameter growing as 2^√2N^2 (or as [2N]^α with α˜√2N^2/22N^2), and a nontrivial phase transition Tc>0, for the Ising ferromagnet. These results suggest that these graphs are similar to small-world graphs with mean-field-like properties.

  5. Quantum graphs and random-matrix theory

    NASA Astrophysics Data System (ADS)

    Pluhař, Z.; Weidenmüller, H. A.

    2015-07-01

    For simple connected graphs with incommensurate bond lengths and with unitary symmetry we prove the Bohigas-Giannoni-Schmit (BGS) conjecture in its most general form. Using supersymmetry and taking the limit of infinite graph size, we show that the generating function for every (P,Q) correlation function for both closed and open graphs coincides with the corresponding expression of random-matrix theory. We show that the classical Perron-Frobenius operator is bistochastic and possesses a single eigenvalue +1. In the quantum case that implies the existence of a zero (or massless) mode of the effective action. That mode causes universal fluctuation properties. Avoiding the saddle-point approximation we show that for graphs that are classically mixing (i.e. for which the spectrum of the classical Perron-Frobenius operator possesses a finite gap) and that do not carry a special class of bound states, the zero mode dominates in the limit of infinite graph size.

  6. GraphReduce: Large-Scale Graph Analytics on Accelerator-Based HPC Systems

    SciTech Connect

    Sengupta, Dipanjan; Agarwal, Kapil; Song, Shuaiwen; Schwan, Karsten

    2015-09-30

    Recent work on real-world graph analytics has sought to leverage the massive amount of parallelism offered by GPU devices, but challenges remain due to the inherent irregularity of graph algorithms and limitations in GPU-resident memory for storing large graphs. We present GraphReduce, a highly efficient and scalable GPU-based framework that operates on graphs that exceed the device’s internal memory capacity. GraphReduce adopts a combination of both edge- and vertex-centric implementations of the Gather-Apply-Scatter programming model and operates on multiple asynchronous GPU streams to fully exploit the high degrees of parallelism in GPUs with efficient graph data movement between the host and the device.

  7. GraphReduce: Processing Large-Scale Graphs on Accelerator-Based Systems

    SciTech Connect

    Sengupta, Dipanjan; Song, Shuaiwen; Agarwal, Kapil; Schwan, Karsten

    2015-11-15

    Recent work on real-world graph analytics has sought to leverage the massive amount of parallelism offered by GPU devices, but challenges remain due to the inherent irregularity of graph algorithms and limitations in GPU-resident memory for storing large graphs. We present GraphReduce, a highly efficient and scalable GPU-based framework that operates on graphs that exceed the device’s internal memory capacity. GraphReduce adopts a combination of edge- and vertex-centric implementations of the Gather-Apply-Scatter programming model and operates on multiple asynchronous GPU streams to fully exploit the high degrees of parallelism in GPUs with efficient graph data movement between the host and device.

  8. Balanced Paths in Colored Graphs

    NASA Astrophysics Data System (ADS)

    Bianco, Alessandro; Faella, Marco; Mogavero, Fabio; Murano, Aniello

    We consider finite graphs whose edges are labeled with elements, called colors, taken from a fixed finite alphabet. We study the problem of determining whether there is an infinite path where either (i) all colors occur with the same asymptotic frequency, or (ii) there is a constant which bounds the difference between the occurrences of any two colors for all prefixes of the path. These two notions can be viewed as refinements of the classical notion of fair path, whose simplest form checks whether all colors occur infinitely often. Our notions provide stronger criteria, particularly suitable for scheduling applications based on a coarse-grained model of the jobs involved. We show that both problems are solvable in polynomial time, by reducing them to the feasibility of a linear program.

  9. Relativity on rotated graph paper

    NASA Astrophysics Data System (ADS)

    Salgado, Roberto B.

    2016-05-01

    We demonstrate a method for constructing spacetime diagrams for special relativity on graph paper that has been rotated by 45°. The diagonal grid lines represent light-flash worldlines in Minkowski spacetime, and the boxes in the grid (called "clock diamonds") represent units of measurement corresponding to the ticks of an inertial observer's light clock. We show that many quantitative results can be read off a spacetime diagram simply by counting boxes, with very little algebra. In particular, we show that the squared interval between two events is equal to the signed area of the parallelogram on the grid (called the "causal diamond") with opposite vertices corresponding to those events. We use the Doppler effect—without explicit use of the Doppler formula—to motivate the method.

  10. Solving graph data issues using a layered architecture approach with applications to web spam detection.

    PubMed

    Scarselli, Franco; Tsoi, Ah Chung; Hagenbuchner, Markus; Noi, Lucia Di

    2013-12-01

    This paper proposes the combination of two state-of-the-art algorithms for processing graph input data, viz., the probabilistic mapping graph self organizing map, an unsupervised learning approach, and the graph neural network, a supervised learning approach. We organize these two algorithms in a cascade architecture containing a probabilistic mapping graph self organizing map, and a graph neural network. We show that this combined approach helps us to limit the long-term dependency problem that exists when training the graph neural network resulting in an overall improvement in performance. This is demonstrated in an application to a benchmark problem requiring the detection of spam in a relatively large set of web sites. It is found that the proposed method produces results which reach the state of the art when compared with some of the best results obtained by others using quite different approaches. A particular strength of our method is its applicability towards any input domain which can be represented as a graph.

  11. Support vector machine classification of major depressive disorder using diffusion-weighted neuroimaging and graph theory.

    PubMed

    Sacchet, Matthew D; Prasad, Gautam; Foland-Ross, Lara C; Thompson, Paul M; Gotlib, Ian H

    2015-01-01

    Recently, there has been considerable interest in understanding brain networks in major depressive disorder (MDD). Neural pathways can be tracked in the living brain using diffusion-weighted imaging (DWI); graph theory can then be used to study properties of the resulting fiber networks. To date, global abnormalities have not been reported in tractography-based graph metrics in MDD, so we used a machine learning approach based on "support vector machines" to differentiate depressed from healthy individuals based on multiple brain network properties. We also assessed how important specific graph metrics were for this differentiation. Finally, we conducted a local graph analysis to identify abnormal connectivity at specific nodes of the network. We were able to classify depression using whole-brain graph metrics. Small-worldness was the most useful graph metric for classification. The right pars orbitalis, right inferior parietal cortex, and left rostral anterior cingulate all showed abnormal network connectivity in MDD. This is the first use of structural global graph metrics to classify depressed individuals. These findings highlight the importance of future research to understand network properties in depression across imaging modalities, improve classification results, and relate network alterations to psychiatric symptoms, medication, and comorbidities.

  12. Terminology for trace-element partitioning

    SciTech Connect

    Beattie, P. ); Drake, M. ); Jones, J.; McKay, G. ); Leeman, W. ); Longhi, J. ); Nielsen, R. ); Palme, H. ); Shaw, D. ); Takahashi, E. ); Watson, B. )

    1993-04-01

    A self-consistent terminology for partitioning data is presented. Ratios of the concentration of a component in two phases are termed partition coefficients and given the symbol D. Ratios of partition coefficients are termed exchange coefficients and given the symbol K[sub D]. The prefix bulk implies that these coefficients are weighted according to the proportions of coexisting phases. Bulk partition and bulk exchange coefficients are denoted by [bar D] and [ovr K[sub D

  13. 25 CFR 158.56 - Partition records.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Partition records. 158.56 Section 158.56 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER OSAGE LANDS § 158.56 Partition records. Upon completion of an action in partition, a copy of the judgment roll showing schedule of costs...

  14. 25 CFR 158.56 - Partition records.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Partition records. 158.56 Section 158.56 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER OSAGE LANDS § 158.56 Partition records. Upon completion of an action in partition, a copy of the judgment roll showing schedule of costs...

  15. Massive graph visualization : LDRD final report.

    SciTech Connect

    Wylie, Brian Neil; Moreland, Kenneth D.

    2007-10-01

    Graphs are a vital way of organizing data with complex correlations. A good visualization of a graph can fundamentally change human understanding of the data. Consequently, there is a rich body of work on graph visualization. Although there are many techniques that are effective on small to medium sized graphs (tens of thousands of nodes), there is a void in the research for visualizing massive graphs containing millions of nodes. Sandia is one of the few entities in the world that has the means and motivation to handle data on such a massive scale. For example, homeland security generates graphs from prolific media sources such as television, telephone, and the Internet. The purpose of this project is to provide the groundwork for visualizing such massive graphs. The research provides for two major feature gaps: a parallel, interactive visualization framework and scalable algorithms to make the framework usable to a practical application. Both the frameworks and algorithms are designed to run on distributed parallel computers, which are already available at Sandia. Some features are integrated into the ThreatView{trademark} application and future work will integrate further parallel algorithms.

  16. Object Discovery: Soft Attributed Graph Mining.

    PubMed

    Zhang, Quanshi; Song, Xuan; Shao, Xiaowei; Zhao, Huijing; Shibasaki, Ryosuke

    2016-03-01

    We categorize this research in terms of its contribution to both graph theory and computer vision. From the theoretical perspective, this study can be considered as the first attempt to formulate the idea of mining maximal frequent subgraphs in the challenging domain of messy visual data, and as a conceptual extension to the unsupervised learning of graph matching. We define a soft attributed pattern (SAP) to represent the common subgraph pattern among a set of attributed relational graphs (ARGs), considering both their structure and attributes. Regarding the differences between ARGs with fuzzy attributes and conventional labeled graphs, we propose a new mining strategy that directly extracts the SAP with the maximal graph size without applying node enumeration. Given an initial graph template and a number of ARGs, we develop an unsupervised method to modify the graph template into the maximal-size SAP. From a practical perspective, this research develops a general platform for learning the category model (i.e., the SAP) from cluttered visual data (i.e., the ARGs) without labeling "what is where," thereby opening the possibility for a series of applications in the era of big visual data. Experiments demonstrate the superior performance of the proposed method on RGB/RGB-D images and videos.

  17. Graph isomorphism and adiabatic quantum computing

    NASA Astrophysics Data System (ADS)

    Gaitan, Frank; Clark, Lane

    2014-03-01

    In the Graph Isomorphism (GI) problem two N-vertex graphs G and G' are given and the task is to determine whether there exists a permutation of the vertices of G that preserves adjacency and maps G --> G'. If yes (no), then G and G' are said to be isomorphic (non-isomorphic). The GI problem is an important problem in computer science and is thought to be of comparable difficulty to integer factorization. We present a quantum algorithm that solves arbitrary instances of GI, and which provides a novel approach to determining all automorphisms of a graph. The algorithm converts a GI instance to a combinatorial optimization problem that can be solved using adiabatic quantum evolution. Numerical simulation of the algorithm's quantum dynamics shows that it correctly distinguishes non-isomorphic graphs; recognizes isomorphic graphs; and finds the automorphism group of a graph. We also discuss the algorithm's experimental implementation and show how it can be leveraged to solve arbitrary instances of the NP-Complete Sub-Graph Isomorphism problem.

  18. Object Discovery: Soft Attributed Graph Mining.

    PubMed

    Zhang, Quanshi; Song, Xuan; Shao, Xiaowei; Zhao, Huijing; Shibasaki, Ryosuke

    2016-03-01

    We categorize this research in terms of its contribution to both graph theory and computer vision. From the theoretical perspective, this study can be considered as the first attempt to formulate the idea of mining maximal frequent subgraphs in the challenging domain of messy visual data, and as a conceptual extension to the unsupervised learning of graph matching. We define a soft attributed pattern (SAP) to represent the common subgraph pattern among a set of attributed relational graphs (ARGs), considering both their structure and attributes. Regarding the differences between ARGs with fuzzy attributes and conventional labeled graphs, we propose a new mining strategy that directly extracts the SAP with the maximal graph size without applying node enumeration. Given an initial graph template and a number of ARGs, we develop an unsupervised method to modify the graph template into the maximal-size SAP. From a practical perspective, this research develops a general platform for learning the category model (i.e., the SAP) from cluttered visual data (i.e., the ARGs) without labeling "what is where," thereby opening the possibility for a series of applications in the era of big visual data. Experiments demonstrate the superior performance of the proposed method on RGB/RGB-D images and videos. PMID:27046496

  19. Sketch Matching on Topology Product Graph.

    PubMed

    Liang, Shuang; Luo, Jun; Liu, Wenyin; Wei, Yichen

    2015-08-01

    Sketch matching is the fundamental problem in sketch based interfaces. After years of study, it remains challenging when there exists large irregularity and variations in the hand drawn sketch shapes. While most existing works exploit topology relations and graph representations for this problem, they are usually limited by the coarse topology exploration and heuristic (thus suboptimal) similarity metrics between graphs. We present a new sketch matching method with two novel contributions. We introduce a comprehensive definition of topology relations, which results in a rich and informative graph representation of sketches. For graph matching, we propose topology product graph that retains the full correspondence for matching two graphs. Based on it, we derive an intuitive sketch similarity metric whose exact solution is easy to compute. In addition, the graph representation and new metric naturally support partial matching, an important practical problem that received less attention in the literature. Extensive experimental results on a real challenging dataset and the superior performance of our method show that it outperforms the state-of-the-art.

  20. Lamplighter groups, de Brujin graphs, spider-web graphs and their spectra

    NASA Astrophysics Data System (ADS)

    Grigorchuk, R.; Leemann, P.-H.; Nagnibeda, T.

    2016-05-01

    We study the infinite family of spider-web graphs \\{{{ S }}k,N,M\\}, k≥slant 2, N≥slant 0 and M≥slant 1, initiated in the 50s in the context of network theory. It was later shown in physical literature that these graphs have remarkable percolation and spectral properties. We provide a mathematical explanation of these properties by putting the spider-web graphs in the context of group theory and algebraic graph theory. Namely, we realize them as tensor products of the well-known de Bruijn graphs \\{{{ B }}k,N\\} with cyclic graphs \\{{C}M\\} and show that these graphs are described by the action of the lamplighter group {{ L }}k={Z}/k{Z}\\wr {Z} on the infinite binary tree. Our main result is the identification of the infinite limit of \\{{{ S }}k,N,M\\}, as N,M\\to ∞ , with the Cayley graph of the lamplighter group {{ L }}k which, in turn, is one of the famous Diestel–Leader graphs {{DL}}k,k. As an application we compute the spectra of all spider-web graphs and show their convergence to the discrete spectral distribution associated with the Laplacian on the lamplighter group.

  1. Lamplighter groups, de Brujin graphs, spider-web graphs and their spectra

    NASA Astrophysics Data System (ADS)

    Grigorchuk, R.; Leemann, P.-H.; Nagnibeda, T.

    2016-05-01

    We study the infinite family of spider-web graphs \\{{{ S }}k,N,M\\}, k≥slant 2, N≥slant 0 and M≥slant 1, initiated in the 50s in the context of network theory. It was later shown in physical literature that these graphs have remarkable percolation and spectral properties. We provide a mathematical explanation of these properties by putting the spider-web graphs in the context of group theory and algebraic graph theory. Namely, we realize them as tensor products of the well-known de Bruijn graphs \\{{{ B }}k,N\\} with cyclic graphs \\{{C}M\\} and show that these graphs are described by the action of the lamplighter group {{ L }}k={Z}/k{Z}\\wr {Z} on the infinite binary tree. Our main result is the identification of the infinite limit of \\{{{ S }}k,N,M\\}, as N,M\\to ∞ , with the Cayley graph of the lamplighter group {{ L }}k which, in turn, is one of the famous Diestel-Leader graphs {{DL}}k,k. As an application we compute the spectra of all spider-web graphs and show their convergence to the discrete spectral distribution associated with the Laplacian on the lamplighter group.

  2. BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment

    PubMed Central

    Chin, George; Chavarria, Daniel G; Nakamura, Grant C; Sofia, Heidi J

    2008-01-01

    Background Graphs and networks are common analysis representations for biological systems. Many traditional graph algorithms such as k-clique, k-coloring, and subgraph matching have great potential as analysis techniques for newly available data in biology. Yet, as the amount of genomic and bionetwork information rapidly grows, scientists need advanced new computational strategies and tools for dealing with the complexities of the bionetwork analysis and the volume of the data. Results We introduce a computational framework for graph analysis called the Biological Graph Environment (BioGraphE), which provides a general, scalable integration platform for connecting graph problems in biology to optimized computational solvers and high-performance systems. This framework enables biology researchers and computational scientists to identify and deploy network analysis applications and to easily connect them to efficient and powerful computational software and hardware that are specifically designed and tuned to solve complex graph problems. In our particular application of BioGraphE to support network analysis in genome biology, we investigate the use of a Boolean satisfiability solver known as Survey Propagation as a core computational solver executing on standard high-performance parallel systems, as well as multi-threaded architectures. Conclusion In our application of BioGraphE to conduct bionetwork analysis of homology networks, we found that BioGraphE and a custom, parallel implementation of the Survey Propagation SAT solver were capable of solving very large bionetwork problems at high rates of execution on different high-performance computing platforms. PMID:18541059

  3. Network-theoretical approach to partitioning of real power grids

    NASA Astrophysics Data System (ADS)

    Abou Hamad, Ibrahim; Israels, Brett; Poroseva, Svetlana V.; Rikvold, Per Arne

    2010-03-01

    Modern societies depend critically on their electrical power grids. It is, therefore, essential to understand the grid's large-scale behavior in order to improve its resilience against catastrophic damage. A key factor determining the grid's large-scale behavior is its topology. In particular, an important question is whether a grid topology can be efficiently partitioned into independent communities (``islands'') of densely connected vertices (generators, substations, consumers) that are more loosely connected to other communities. Such partitioning can be utilized either to strengthen the grid by introducing new connections, or to achieve ``Intentional Intelligent Islanding'' by installing control devices in a minimal number of links in order to contain cascading failures to a limited region. Here we report on the performance of several network-partitioning algorithms, both agglomerative and spectral-based divisive, in applications to real power grids, including the high-voltage grids of Florida and Italy.

  4. Enabling Graph Mining in RDF Triplestores using SPARQL for Holistic In-situ Graph Analysis

    SciTech Connect

    Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong; Lim, Seung-Hwan

    2016-01-01

    The graph analysis is now considered as a promising technique to discover useful knowledge in data with a new perspective. We envi- sion that there are two dimensions of graph analysis: OnLine Graph Analytic Processing (OLGAP) and Graph Mining (GM) where each respectively focuses on subgraph pattern matching and automatic knowledge discovery in graph. Moreover, as these two dimensions aim to complementarily solve complex problems, holistic in-situ graph analysis which covers both OLGAP and GM in a single system is critical for minimizing the burdens of operating multiple graph systems and transferring intermediate result-sets between those systems. Nevertheless, most existing graph analysis systems are only capable of one dimension of graph analysis. In this work, we take an approach to enabling GM capabilities (e.g., PageRank, connected-component analysis, node eccentricity, etc.) in RDF triplestores, which are originally developed to store RDF datasets and provide OLGAP capability. More specifically, to achieve our goal, we implemented six representative graph mining algorithms using SPARQL. The approach allows a wide range of available RDF data sets directly applicable for holistic graph analysis within a system. For validation of our approach, we evaluate performance of our implementations with nine real-world datasets and three different computing environments - a laptop computer, an Amazon EC2 instance, and a shared-memory Cray XMT2 URIKA-GD graph-processing appliance. The experimen- tal results show that our implementation can provide promising and scalable performance for real world graph analysis in all tested environments. The developed software is publicly available in an open-source project that we initiated.

  5. Enabling Graph Mining in RDF Triplestores using SPARQL for Holistic In-situ Graph Analysis

    DOE PAGES

    Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong; Lim, Seung-Hwan

    2016-01-01

    The graph analysis is now considered as a promising technique to discover useful knowledge in data with a new perspective. We envi- sion that there are two dimensions of graph analysis: OnLine Graph Analytic Processing (OLGAP) and Graph Mining (GM) where each respectively focuses on subgraph pattern matching and automatic knowledge discovery in graph. Moreover, as these two dimensions aim to complementarily solve complex problems, holistic in-situ graph analysis which covers both OLGAP and GM in a single system is critical for minimizing the burdens of operating multiple graph systems and transferring intermediate result-sets between those systems. Nevertheless, most existingmore » graph analysis systems are only capable of one dimension of graph analysis. In this work, we take an approach to enabling GM capabilities (e.g., PageRank, connected-component analysis, node eccentricity, etc.) in RDF triplestores, which are originally developed to store RDF datasets and provide OLGAP capability. More specifically, to achieve our goal, we implemented six representative graph mining algorithms using SPARQL. The approach allows a wide range of available RDF data sets directly applicable for holistic graph analysis within a system. For validation of our approach, we evaluate performance of our implementations with nine real-world datasets and three different computing environments - a laptop computer, an Amazon EC2 instance, and a shared-memory Cray XMT2 URIKA-GD graph-processing appliance. The experimen- tal results show that our implementation can provide promising and scalable performance for real world graph analysis in all tested environments. The developed software is publicly available in an open-source project that we initiated.« less

  6. Graph Laplace for occluded face completion and recognition.

    PubMed

    Deng, Yue; Dai, Qionghai; Zhang, Zengke

    2011-08-01

    This paper proposes a spectral-graph-based algorithm for face image repairing, which can improve the recognition performance on occluded faces. The face completion algorithm proposed in this paper includes three main procedures: 1) sparse representation for partially occluded face classification; 2) image-based data mining; and 3) graph Laplace (GL) for face image completion. The novel part of the proposed framework is GL, as named from graphical models and the Laplace equation, and can achieve a high-quality repairing of damaged or occluded faces. The relationship between the GL and the traditional Poisson equation is proven. We apply our face repairing algorithm to produce completed faces, and use face recognition to evaluate the performance of the algorithm. Experimental results verify the effectiveness of the GL method for occluded face completion.

  7. Poor Textural Image Matching Based on Graph Theory

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    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.

  8. Information Retrieval and Graph Analysis Approaches for Book Recommendation.

    PubMed

    Benkoussas, Chahinez; Bellot, Patrice

    2015-01-01

    A combination of multiple information retrieval approaches is proposed for the purpose of book recommendation. In this paper, book recommendation is based on complex user's query. We used different theoretical retrieval models: probabilistic as InL2 (Divergence from Randomness model) and language model and tested their interpolated combination. Graph analysis algorithms such as PageRank have been successful in Web environments. We consider the application of this algorithm in a new retrieval approach to related document network comprised of social links. We called Directed Graph of Documents (DGD) a network constructed with documents and social information provided from each one of them. Specifically, this work tackles the problem of book recommendation in the context of INEX (Initiative for the Evaluation of XML retrieval) Social Book Search track. A series of reranking experiments demonstrate that combining retrieval models yields significant improvements in terms of standard ranked retrieval metrics. These results extend the applicability of link analysis algorithms to different environments.

  9. Got Graphs? An Assessment of Data Visualization Tools

    NASA Technical Reports Server (NTRS)

    Schaefer, C. M.; Foy, M.

    2015-01-01

    Graphs are powerful tools for simplifying complex data. They are useful for quickly assessing patterns and relationships among one or more variables from a dataset. As the amount of data increases, it becomes more difficult to visualize potential associations. Lifetime Surveillance of Astronaut Health (LSAH) was charged with assessing its current visualization tools along with others on the market to determine whether new tools would be useful for supporting NASA's occupational surveillance effort. It was concluded by members of LSAH that the current tools hindered their ability to provide quick results to researchers working with the department. Due to the high volume of data requests and the many iterations of visualizations requested by researchers, software with a better ability to replicate graphs and edit quickly could improve LSAH's efficiency and lead to faster research results.

  10. Intelligent Graph Layout Using Many Users' Input.

    PubMed

    Yuan, Xiaoru; Che, Limei; Hu, Yifan; Zhang, Xin

    2012-12-01

    In this paper, we propose a new strategy for graph drawing utilizing layouts of many sub-graphs supplied by a large group of people in a crowd sourcing manner. We developed an algorithm based on Laplacian constrained distance embedding to merge subgraphs submitted by different users, while attempting to maintain the topological information of the individual input layouts. To facilitate collection of layouts from many people, a light-weight interactive system has been designed to enable convenient dynamic viewing, modification and traversing between layouts. Compared with other existing graph layout algorithms, our approach can achieve more aesthetic and meaningful layouts with high user preference.

  11. Line graphs for a multiplex network.

    PubMed

    Criado, Regino; Flores, Julio; García Del Amo, Alejandro; Romance, Miguel; Barrena, Eva; Mesa, Juan A

    2016-06-01

    It is well known that line graphs offer a good summary of the graphs properties, which make them easier to analyze and highlight the desired properties. We extend the concept of line graph to multiplex networks in order to analyze multi-plexed and multi-layered networked systems. As these structures are very rich, different approaches to this notion are required to capture a variety of situations. Some relationships between these approaches are established. Finally, by means of some simulations, the potential utility of this concept is illustrated.

  12. Searching for nodes in random graphs.

    PubMed

    Lancaster, David

    2011-11-01

    We consider the problem of searching for a node on a labeled random graph according to a greedy algorithm that selects a route to the desired node using metric information on the graph. Motivated by peer-to-peer networks two types of random graph are proposed with properties particularly amenable to this kind of algorithm. We derive equations for the probability that the search is successful and also study the number of hops required, finding both numerical and analytic evidence of a transition as the number of links is varied.

  13. Line graphs for a multiplex network.

    PubMed

    Criado, Regino; Flores, Julio; García Del Amo, Alejandro; Romance, Miguel; Barrena, Eva; Mesa, Juan A

    2016-06-01

    It is well known that line graphs offer a good summary of the graphs properties, which make them easier to analyze and highlight the desired properties. We extend the concept of line graph to multiplex networks in order to analyze multi-plexed and multi-layered networked systems. As these structures are very rich, different approaches to this notion are required to capture a variety of situations. Some relationships between these approaches are established. Finally, by means of some simulations, the potential utility of this concept is illustrated. PMID:27368798

  14. Graph states for quantum secret sharing

    NASA Astrophysics Data System (ADS)

    Markham, Damian; Sanders, Barry C.

    2008-10-01

    We consider three broad classes of quantum secret sharing with and without eavesdropping and show how a graph state formalism unifies otherwise disparate quantum secret sharing models. In addition to the elegant unification provided by graph states, our approach provides a generalization of threshold classical secret sharing via insecure quantum channels beyond the current requirement of 100% collaboration by players to just a simple majority in the case of five players. Another innovation here is the introduction of embedded protocols within a larger graph state that serves as a one-way quantum-information processing system.

  15. The MultiThreaded Graph Library (MTGL)

    SciTech Connect

    Berry, Jonathan; Leung, Vitus; McLendon, III, William; & Madduri, Kamesh

    2008-07-17

    The MultiThreaded Graph Library (MTGL) is a set of header files that implement graph algorithm in such a way that they can run on massively multithreaded architectures. It is based upon the Boost Graph Library, but doesn’t use Boost since the latter doesn’t run well on these architectures.

  16. A heterogeneous graph-based recommendation simulator

    SciTech Connect

    Yeonchan, Ahn; Sungchan, Park; Lee, Matt Sangkeun; Sang-goo, Lee

    2013-01-01

    Heterogeneous graph-based recommendation frameworks have flexibility in that they can incorporate various recommendation algorithms and various kinds of information to produce better results. In this demonstration, we present a heterogeneous graph-based recommendation simulator which enables participants to experience the flexibility of a heterogeneous graph-based recommendation method. With our system, participants can simulate various recommendation semantics by expressing the semantics via meaningful paths like User Movie User Movie. The simulator then returns the recommendation results on the fly based on the user-customized semantics using a fast Monte Carlo algorithm.

  17. Loops in Reeb Graphs of 2-Manifolds

    SciTech Connect

    Cole-McLaughlin, K; Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V

    2004-12-16

    Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function.

  18. Loops in Reeb Graphs of 2-Manifolds

    SciTech Connect

    Cole-McLaughlin, K; Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V

    2003-02-11

    Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function.

  19. Twisted sectors from plane partitions

    NASA Astrophysics Data System (ADS)

    Datta, Shouvik; Gaberdiel, Matthias R.; Li, Wei; Peng, Cheng

    2016-09-01

    Twisted sectors arise naturally in the bosonic higher spin CFTs at their free points, as well as in the associated symmetric orbifolds. We identify the coset representations of the twisted sector states using the description of W_{∞} representations in terms of plane partitions. We confirm these proposals by a microscopic null-vector analysis, and by matching the excitation spectrum of these representations with the orbifold prediction.

  20. Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm.

    PubMed

    Chen, Weiyang; Liao, Bo; Zhu, Wen; Xiang, Xuyu

    2009-10-01

    In this article, we describe a representation for the processes of multiple sequences alignment (MSA) and used it to solve the problem of MSA. By this representation, we took every possible aligning result into account by defining the representation of gap insertion, the value of heuristic information in every optional path and scoring rule. On the basis of the proposed multidimensional graph, we used the ant colony algorithm to find the better path that denotes a better aligning result. In our article, we proposed the instance of three-dimensional graph and four-dimensional graph and advanced a special ichnographic representation to analyze MSA. It is yet only an experimental software, and we gave an example for finding the best aligning result by three-dimensional graph and ant colony algorithm. Experimental results show that our method can improve the solution quality on MSA benchmarks. PMID:19130503

  1. Graphing the order of the sexes: constructing, recalling, interpreting, and putting the self in gender difference graphs.

    PubMed

    Hegarty, Peter; Lemieux, Anthony F; McQueen, Grant

    2010-03-01

    Graphs seem to connote facts more than words or tables do. Consequently, they seem unlikely places to spot implicit sexism at work. Yet, in 6 studies (N = 741), women and men constructed (Study 1) and recalled (Study 2) gender difference graphs with men's data first, and graphed powerful groups (Study 3) and individuals (Study 4) ahead of weaker ones. Participants who interpreted graph order as evidence of author "bias" inferred that the author graphed his or her own gender group first (Study 5). Women's, but not men's, preferences to graph men first were mitigated when participants graphed a difference between themselves and an opposite-sex friend prior to graphing gender differences (Study 6). Graph production and comprehension are affected by beliefs and suppositions about the groups represented in graphs to a greater degree than cognitive models of graph comprehension or realist models of scientific thinking have yet acknowledged.

  2. Weighted graph based ordering techniques for preconditioned conjugate gradient methods

    NASA Technical Reports Server (NTRS)

    Clift, Simon S.; Tang, Wei-Pai

    1994-01-01

    We describe the basis of a matrix ordering heuristic for improving the incomplete factorization used in preconditioned conjugate gradient techniques applied to anisotropic PDE's. Several new matrix ordering techniques, derived from well-known algorithms in combinatorial graph theory, which attempt to implement this heuristic, are described. These ordering techniques are tested against a number of matrices arising from linear anisotropic PDE's, and compared with other matrix ordering techniques. A variation of RCM is shown to generally improve the quality of incomplete factorization preconditioners.

  3. Experiments on parallel graph coloring and applications

    SciTech Connect

    Lewandowski, G.; Condon, A.

    1994-12-31

    The graph coloring problem is an NP-Complete problem with a wide array of applications, such as course scheduling, exam scheduling, register allocation, and parallelizing solutions for sparse systems of linear equations. Much theoretical effort has been put into designing heuristics that perform well on randomly generated graphs. The best sequential heuristics require large amounts of time and tuning of various parameters in the heuristics. We have used parallelism to combine exhaustive search with successful heuristic strategies to create a new heuristic, Hybrid, which does well on a wide variety of graphs, without any tuning of parameters. We have also gathered real application data and tested several heuristics on this data. Our study of real data points out some flaws in studying only random graphs and also suggests interesting new problems for study.

  4. Graph500 in OpenSHMEM

    SciTech Connect

    D'Azevedo, Ed F; Imam, Neena

    2015-01-01

    This document describes the effort to implement the Graph 500 benchmark using OpenSHMEM based on the MPI-2 one-side version. The Graph 500 benchmark performs a breadth-first search in parallel on a large randomly generated undirected graph and can be implemented using basic MPI-1 and MPI-2 one-sided communication. Graph 500 requires atomic bit-wise operations on unsigned long integers but neither atomic bit-wise operations nor OpenSHMEM for unsigned long are available in OpenSHEM. Such needed bit-wise atomic operations and support for unsigned long are implemented using atomic condition swap (CSWAP) on signed long integers. Preliminary results on comparing the OpenSHMEM and MPI-2 one-sided implementations on a Silicon Graphics Incorporated (SGI) cluster and the Cray XK7 are presented.

  5. An Investigation of the Coauthor Graph.

    ERIC Educational Resources Information Center

    Logan, Elisabeth L.; Shaw, W. M., Jr.

    1987-01-01

    The role of the coauthor relationship in the structure of informal communications networks within disciplines is explored, and the validity of coauthor graphs used to map these relationships is tested for both small and large databases. (CLB)

  6. The signed permutation group on Feynman graphs

    NASA Astrophysics Data System (ADS)

    Purkart, Julian

    2016-08-01

    The Feynman rules assign to every graph an integral which can be written as a function of a scaling parameter L. Assuming L for the process under consideration is very small, so that contributions to the renormalization group are small, we can expand the integral and only consider the lowest orders in the scaling. The aim of this article is to determine specific combinations of graphs in a scalar quantum field theory that lead to a remarkable simplification of the first non-trivial term in the perturbation series. It will be seen that the result is independent of the renormalization scheme and the scattering angles. To achieve that goal we will utilize the parametric representation of scalar Feynman integrals as well as the Hopf algebraic structure of the Feynman graphs under consideration. Moreover, we will present a formula which reduces the effort of determining the first-order term in the perturbation series for the specific combination of graphs to a minimum.

  7. Fault-tolerant dynamic task graph scheduling

    SciTech Connect

    Kurt, Mehmet C.; Krishnamoorthy, Sriram; Agrawal, Kunal; Agrawal, Gagan

    2014-11-16

    In this paper, we present an approach to fault tolerant execution of dynamic task graphs scheduled using work stealing. In particular, we focus on selective and localized recovery of tasks in the presence of soft faults. We elicit from the user the basic task graph structure in terms of successor and predecessor relationships. The work stealing-based algorithm to schedule such a task graph is augmented to enable recovery when the data and meta-data associated with a task get corrupted. We use this redundancy, and the knowledge of the task graph structure, to selectively recover from faults with low space and time overheads. We show that the fault tolerant design retains the essential properties of the underlying work stealing-based task scheduling algorithm, and that the fault tolerant execution is asymptotically optimal when task re-execution is taken into account. Experimental evaluation demonstrates the low cost of recovery under various fault scenarios.

  8. Teaching Waves with a Graphing Calculator.

    ERIC Educational Resources Information Center

    Raggett, Matthew

    2000-01-01

    Stresses the value of graphing and computer algebra systems calculators when teaching about waves. Discusses how to input data into these calculators. Highlights the Texas Instruments' (TI) Web site at http://www.ti.com. (YDS)

  9. Continuous Time Group Discovery in Dynamic Graphs

    SciTech Connect

    Miller, K; Eliassi-Rad, T

    2010-11-04

    With the rise in availability and importance of graphs and networks, it has become increasingly important to have good models to describe their behavior. While much work has focused on modeling static graphs, we focus on group discovery in dynamic graphs. We adapt a dynamic extension of Latent Dirichlet Allocation to this task and demonstrate good performance on two datasets. Modeling relational data has become increasingly important in recent years. Much work has focused on static graphs - that is fixed graphs at a single point in time. Here we focus on the problem of modeling dynamic (i.e. time-evolving) graphs. We propose a scalable Bayesian approach for community discovery in dynamic graphs. Our approach is based on extensions of Latent Dirichlet Allocation (LDA). LDA is a latent variable model for topic modeling in text corpora. It was extended to deal with topic changes in discrete time and later in continuous time. These models were referred to as the discrete Dynamic Topic Model (dDTM) and the continuous Dynamic Topic Model (cDTM), respectively. When adapting these models to graphs, we take our inspiration from LDA-G and SSN-LDA, applications of LDA to static graphs that have been shown to effectively factor out community structure to explain link patterns in graphs. In this paper, we demonstrate how to adapt and apply the cDTM to the task of finding communities in dynamic networks. We use link prediction to measure the quality of the discovered community structure and apply it to two different relational datasets - DBLP author-keyword and CAIDA autonomous systems relationships. We also discuss a parallel implementation of this approach using Hadoop. In Section 2, we review LDA and LDA-G. In Section 3, we review the cDTM and introduce cDTMG, its adaptation to modeling dynamic graphs. We discuss inference for the cDTM-G and details of our parallel implementation in Section 4 and present its performance on two datasets in Section 5 before concluding in

  10. Pre-Service Elementary Teachers' Understandings of Graphs

    ERIC Educational Resources Information Center

    Alacaci, Cengiz; Lewis, Scott; O'Brien, George E.; Jiang, Zhonghong

    2011-01-01

    Choosing graphs to display quantitative information is a component of "graph sense". An important aspect of pre-service elementary teachers' content knowledge; ability to choose appropriate graphs in applied contexts is investigated in this study. They were given three scenarios followed by four graphs representing the same quantitative data. They…

  11. On the Kirchhoff Index of Graphs

    NASA Astrophysics Data System (ADS)

    Das, Kinkar C.

    2013-09-01

    Let G be a connected graph of order n with Laplacian eigenvalues μ1 ≥ μ2 ≥ ... ≥ μn-1 > mn = 0. The Kirchhoff index of G is defined as [xxx] In this paper. we give lower and upper bounds on Kf of graphs in terms on n, number of edges, maximum degree, and number of spanning trees. Moreover, we present lower and upper bounds on the Nordhaus-Gaddum-type result for the Kirchhoff index.

  12. A software tool for dataflow graph scheduling

    NASA Technical Reports Server (NTRS)

    Jones, Robert L., III

    1994-01-01

    A graph-theoretic design process and software tool is presented for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described using a dataflow graph and are intended to be executed repetitively on multiple processors. The dataflow paradigm is very useful in exposing the parallelism inherent in algorithms. It provides a graphical and mathematical model which describes a partial ordering of algorithm tasks based on data precedence.

  13. Program for Generating Graphs and Charts

    NASA Technical Reports Server (NTRS)

    Ackerson, C. T.

    1986-01-01

    Office Automation Pilot (OAP) Graphics Database system offers IBM personal computer user assistance in producing wide variety of graphs and charts and convenient data-base system, called chart base, for creating and maintaining data associated with graphs and charts. Thirteen different graphics packages available. Access graphics capabilities obtained in similar manner. User chooses creation, revision, or chartbase-maintenance options from initial menu; Enters or modifies data displayed on graphic chart. OAP graphics data-base system written in Microsoft PASCAL.

  14. A Fermi golden rule for quantum graphs

    NASA Astrophysics Data System (ADS)

    Lee, Minjae; Zworski, Maciej

    2016-09-01

    We present a Fermi golden rule giving rates of decay of states obtained by perturbing embedded eigenvalues of a quantum graph. To illustrate the procedure in a notationally simpler setting, we first describe a Fermi golden rule for boundary value problems on surfaces with constant curvature cusps. We also provide a resonance existence result which is uniform on compact sets of energies and metric graphs. The results are illustrated by numerical experiments.

  15. Overlapped partitioning for ensemble classifiers of P300-based brain-computer interfaces.

    PubMed

    Onishi, Akinari; Natsume, Kiyohisa

    2014-01-01

    A P300-based brain-computer interface (BCI) enables a wide range of people to control devices that improve their quality of life. Ensemble classifiers with naive partitioning were recently applied to the P300-based BCI and these classification performances were assessed. However, they were usually trained on a large amount of training data (e.g., 15300). In this study, we evaluated ensemble linear discriminant analysis (LDA) classifiers with a newly proposed overlapped partitioning method using 900 training data. In addition, the classification performances of the ensemble classifier with naive partitioning and a single LDA classifier were compared. One of three conditions for dimension reduction was applied: the stepwise method, principal component analysis (PCA), or none. The results show that an ensemble stepwise LDA (SWLDA) classifier with overlapped partitioning achieved a better performance than the commonly used single SWLDA classifier and an ensemble SWLDA classifier with naive partitioning. This result implies that the performance of the SWLDA is improved by overlapped partitioning and the ensemble classifier with overlapped partitioning requires less training data than that with naive partitioning. This study contributes towards reducing the required amount of training data and achieving better classification performance.

  16. Overlapped Partitioning for Ensemble Classifiers of P300-Based Brain-Computer Interfaces

    PubMed Central

    Onishi, Akinari; Natsume, Kiyohisa

    2014-01-01

    A P300-based brain-computer interface (BCI) enables a wide range of people to control devices that improve their quality of life. Ensemble classifiers with naive partitioning were recently applied to the P300-based BCI and these classification performances were assessed. However, they were usually trained on a large amount of training data (e.g., 15300). In this study, we evaluated ensemble linear discriminant analysis (LDA) classifiers with a newly proposed overlapped partitioning method using 900 training data. In addition, the classification performances of the ensemble classifier with naive partitioning and a single LDA classifier were compared. One of three conditions for dimension reduction was applied: the stepwise method, principal component analysis (PCA), or none. The results show that an ensemble stepwise LDA (SWLDA) classifier with overlapped partitioning achieved a better performance than the commonly used single SWLDA classifier and an ensemble SWLDA classifier with naive partitioning. This result implies that the performance of the SWLDA is improved by overlapped partitioning and the ensemble classifier with overlapped partitioning requires less training data than that with naive partitioning. This study contributes towards reducing the required amount of training data and achieving better classification performance. PMID:24695550

  17. Graph representation of protein free energy landscape

    SciTech Connect

    Li, Minghai; Duan, Mojie; Fan, Jue; Huo, Shuanghong; Han, Li

    2013-11-14

    The thermodynamics and kinetics of protein folding and protein conformational changes are governed by the underlying free energy landscape. However, the multidimensional nature of the free energy landscape makes it difficult to describe. We propose to use a weighted-graph approach to depict the free energy landscape with the nodes on the graph representing the conformational states and the edge weights reflecting the free energy barriers between the states. Our graph is constructed from a molecular dynamics trajectory and does not involve projecting the multi-dimensional free energy landscape onto a low-dimensional space defined by a few order parameters. The calculation of free energy barriers was based on transition-path theory using the MSMBuilder2 package. We compare our graph with the widely used transition disconnectivity graph (TRDG) which is constructed from the same trajectory and show that our approach gives more accurate description of the free energy landscape than the TRDG approach even though the latter can be organized into a simple tree representation. The weighted-graph is a general approach and can be used on any complex system.

  18. Graph representation of protein free energy landscape.

    PubMed

    Li, Minghai; Duan, Mojie; Fan, Jue; Han, Li; Huo, Shuanghong

    2013-11-14

    The thermodynamics and kinetics of protein folding and protein conformational changes are governed by the underlying free energy landscape. However, the multidimensional nature of the free energy landscape makes it difficult to describe. We propose to use a weighted-graph approach to depict the free energy landscape with the nodes on the graph representing the conformational states and the edge weights reflecting the free energy barriers between the states. Our graph is constructed from a molecular dynamics trajectory and does not involve projecting the multi-dimensional free energy landscape onto a low-dimensional space defined by a few order parameters. The calculation of free energy barriers was based on transition-path theory using the MSMBuilder2 package. We compare our graph with the widely used transition disconnectivity graph (TRDG) which is constructed from the same trajectory and show that our approach gives more accurate description of the free energy landscape than the TRDG approach even though the latter can be organized into a simple tree representation. The weighted-graph is a general approach and can be used on any complex system.

  19. Student reasoning about graphs in different contexts

    NASA Astrophysics Data System (ADS)

    Ivanjek, Lana; Susac, Ana; Planinic, Maja; Andrasevic, Aneta; Milin-Sipus, Zeljka

    2016-06-01

    This study investigates university students' graph interpretation strategies and difficulties in mathematics, physics (kinematics), and contexts other than physics. Eight sets of parallel (isomorphic) mathematics, physics, and other context questions about graphs, which were developed by us, were administered to 385 first-year students at the Faculty of Science, University of Zagreb. Students were asked to provide explanations and/or mathematical procedures with their answers. Students' main strategies and difficulties identified through the analysis of those explanations and procedures are described. Student strategies of graph interpretation were found to be largely context dependent and domain specific. A small fraction of students have used the same strategy in all three domains (mathematics, physics, and other contexts) on most sets of parallel questions. Some students have shown indications of transfer of knowledge in the sense that they used techniques and strategies developed in physics for solving (or attempting to solve) other context problems. In physics, the preferred strategy was the use of formulas, which sometimes seemed to block the use of other, more productive strategies which students displayed in other domains. Students' answers indicated the presence of slope-height confusion and interval-point confusion in all three domains. Students generally better interpreted graph slope than the area under a graph, although the concept of slope still seemed to be quite vague for many. The interpretation of the concept of area under a graph needs more attention in both physics and mathematics teaching.

  20. On Ramsey (P3, P6)-minimal graphs

    NASA Astrophysics Data System (ADS)

    Rahmadani, Desi; Baskoro, Edy Tri; Assiyatun, Hilda

    2016-02-01

    Finding all Ramsey (G, H)-minimal graphs for a certain pair of graphs G and H is an interesting and difficult problem. Even though, it is just for small graphs G and H. In this paper, we determine some Ramsey (P3, P6)-minimal graphs of small order. We also characterize all such Ramsey minimal graphs of order 6 by using their degree sequences. We prove that Ramsey (P3, P6)-minimal graphs have diameter at least two. We construct an infinite class of trees [6] which provides Ramsey (P3, P6)-minimal graphs.

  1. Bipartite separability and nonlocal quantum operations on graphs

    NASA Astrophysics Data System (ADS)

    Dutta, Supriyo; Adhikari, Bibhas; Banerjee, Subhashish; Srikanth, R.

    2016-07-01

    In this paper we consider the separability problem for bipartite quantum states arising from graphs. Earlier it was proved that the degree criterion is the graph-theoretic counterpart of the familiar positive partial transpose criterion for separability, although there are entangled states with positive partial transpose for which the degree criterion fails. Here we introduce the concept of partially symmetric graphs and degree symmetric graphs by using the well-known concept of partial transposition of a graph and degree criteria, respectively. Thus, we provide classes of bipartite separable states of dimension m ×n arising from partially symmetric graphs. We identify partially asymmetric graphs that lack the property of partial symmetry. We develop a combinatorial procedure to create a partially asymmetric graph from a given partially symmetric graph. We show that this combinatorial operation can act as an entanglement generator for mixed states arising from partially symmetric graphs.

  2. A Factor Graph Approach to Automated GO Annotation.

    PubMed

    Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

  3. A Factor Graph Approach to Automated GO Annotation

    PubMed Central

    Spetale, Flavio E.; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

  4. A Factor Graph Approach to Automated GO Annotation.

    PubMed

    Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.

  5. Contact Graph Routing Enhancements Developed in ION for DTN

    NASA Technical Reports Server (NTRS)

    Segui, John S.; Burleigh, Scott

    2013-01-01

    The Interplanetary Overlay Network (ION) software suite is an open-source, flight-ready implementation of networking protocols including the Delay/Disruption Tolerant Networking (DTN) Bundle Protocol (BP), the CCSDS (Consultative Committee for Space Data Systems) File Delivery Protocol (CFDP), and many others including the Contact Graph Routing (CGR) DTN routing system. While DTN offers the capability to tolerate disruption and long signal propagation delays in transmission, without an appropriate routing protocol, no data can be delivered. CGR was built for space exploration networks with scheduled communication opportunities (typically based on trajectories and orbits), represented as a contact graph. Since CGR uses knowledge of future connectivity, the contact graph can grow rather large, and so efficient processing is desired. These enhancements allow CGR to scale to predicted NASA space network complexities and beyond. This software improves upon CGR by adopting an earliest-arrival-time cost metric and using the Dijkstra path selection algorithm. Moving to Dijkstra path selection also enables construction of an earliest- arrival-time tree for multicast routing. The enhancements have been rolled into ION 3.0 available on sourceforge.net.

  6. Partitioned-Interval Quantum Optical Communications Receiver

    NASA Technical Reports Server (NTRS)

    Vilnrotter, Victor A.

    2013-01-01

    The proposed quantum receiver in this innovation partitions each binary signal interval into two unequal segments: a short "pre-measurement" segment in the beginning of the symbol interval used to make an initial guess with better probability than 50/50 guessing, and a much longer segment used to make the high-sensitivity signal detection via field-cancellation and photon-counting detection. It was found that by assigning as little as 10% of the total signal energy to the pre-measurement segment, the initial 50/50 guess can be improved to about 70/30, using the best available measurements such as classical coherent or "optimized Kennedy" detection.

  7. Preserving Differential Privacy in Degree-Correlation based Graph Generation

    PubMed Central

    Wang, Yue; Wu, Xintao

    2014-01-01

    Enabling accurate analysis of social network data while preserving differential privacy has been challenging since graph features such as cluster coefficient often have high sensitivity, which is different from traditional aggregate functions (e.g., count and sum) on tabular data. In this paper, we study the problem of enforcing edge differential privacy in graph generation. The idea is to enforce differential privacy on graph model parameters learned from the original network and then generate the graphs for releasing using the graph model with the private parameters. In particular, we develop a differential privacy preserving graph generator based on the dK-graph generation model. We first derive from the original graph various parameters (i.e., degree correlations) used in the dK-graph model, then enforce edge differential privacy on the learned parameters, and finally use the dK-graph model with the perturbed parameters to generate graphs. For the 2K-graph model, we enforce the edge differential privacy by calibrating noise based on the smooth sensitivity, rather than the global sensitivity. By doing this, we achieve the strict differential privacy guarantee with smaller magnitude noise. We conduct experiments on four real networks and compare the performance of our private dK-graph models with the stochastic Kronecker graph generation model in terms of utility and privacy tradeoff. Empirical evaluations show the developed private dK-graph generation models significantly outperform the approach based on the stochastic Kronecker generation model. PMID:24723987

  8. Preserving Differential Privacy in Degree-Correlation based Graph Generation.

    PubMed

    Wang, Yue; Wu, Xintao

    2013-08-01

    Enabling accurate analysis of social network data while preserving differential privacy has been challenging since graph features such as cluster coefficient often have high sensitivity, which is different from traditional aggregate functions (e.g., count and sum) on tabular data. In this paper, we study the problem of enforcing edge differential privacy in graph generation. The idea is to enforce differential privacy on graph model parameters learned from the original network and then generate the graphs for releasing using the graph model with the private parameters. In particular, we develop a differential privacy preserving graph generator based on the dK-graph generation model. We first derive from the original graph various parameters (i.e., degree correlations) used in the dK-graph model, then enforce edge differential privacy on the learned parameters, and finally use the dK-graph model with the perturbed parameters to generate graphs. For the 2K-graph model, we enforce the edge differential privacy by calibrating noise based on the smooth sensitivity, rather than the global sensitivity. By doing this, we achieve the strict differential privacy guarantee with smaller magnitude noise. We conduct experiments on four real networks and compare the performance of our private dK-graph models with the stochastic Kronecker graph generation model in terms of utility and privacy tradeoff. Empirical evaluations show the developed private dK-graph generation models significantly outperform the approach based on the stochastic Kronecker generation model.

  9. Systematic Dimensionality Reduction for Quantum Walks: Optimal Spatial Search and Transport on Non-Regular Graphs

    PubMed Central

    Novo, Leonardo; Chakraborty, Shantanav; Mohseni, Masoud; Neven, Hartmut; Omar, Yasser

    2015-01-01

    Continuous time quantum walks provide an important framework for designing new algorithms and modelling quantum transport and state transfer problems. Often, the graph representing the structure of a problem contains certain symmetries that confine the dynamics to a smaller subspace of the full Hilbert space. In this work, we use invariant subspace methods, that can be computed systematically using the Lanczos algorithm, to obtain the reduced set of states that encompass the dynamics of the problem at hand without the specific knowledge of underlying symmetries. First, we apply this method to obtain new instances of graphs where the spatial quantum search algorithm is optimal: complete graphs with broken links and complete bipartite graphs, in particular, the star graph. These examples show that regularity and high-connectivity are not needed to achieve optimal spatial search. We also show that this method considerably simplifies the calculation of quantum transport efficiencies. Furthermore, we observe improved efficiencies by removing a few links from highly symmetric graphs. Finally, we show that this reduction method also allows us to obtain an upper bound for the fidelity of a single qubit transfer on an XY spin network. PMID:26330082

  10. A simple method for finding the scattering coefficients of quantum graphs

    SciTech Connect

    Cottrell, Seth S.

    2015-09-15

    Quantum walks are roughly analogous to classical random walks, and similar to classical walks they have been used to find new (quantum) algorithms. When studying the behavior of large graphs or combinations of graphs, it is useful to find the response of a subgraph to signals of different frequencies. In doing so, we can replace an entire subgraph with a single vertex with variable scattering coefficients. In this paper, a simple technique for quickly finding the scattering coefficients of any discrete-time quantum graph will be presented. These scattering coefficients can be expressed entirely in terms of the characteristic polynomial of the graph’s time step operator. This is a marked improvement over previous techniques which have traditionally required finding eigenstates for a given eigenvalue, which is far more computationally costly. With the scattering coefficients we can easily derive the “impulse response” which is the key to predicting the response of a graph to any signal. This gives us a powerful set of tools for rapidly understanding the behavior of graphs or for reducing a large graph into its constituent subgraphs regardless of how they are connected.

  11. Learning to write without writing: writing accurate descriptions of interactions after learning graph-printed description relations.

    PubMed

    Spear, Jack; Fields, Lanny

    2015-12-01

    Interpreting and describing complex information shown in graphs are essential skills to be mastered by students in many disciplines; both are skills that are difficult to learn. Thus, interventions that produce these outcomes are of great value. Previous research showed that conditional discrimination training that established stimulus control by some elements of graphs and their printed descriptions produced some improvement in the accuracy of students' written descriptions of graphs. In the present experiment, students wrote nearly perfect descriptions of the information conveyed in interaction-based graphs after the establishment of conditional relations between graphs and their printed descriptions. This outcome was achieved with the use of special conditional discrimination training procedures that required participants to attend to many of the key elements of the graphs and the phrases in the printed descriptions that corresponded to the elements in the graphs. Thus, students learned to write full descriptions of the information represented by complex graphs by an automated training procedure that did not involve the direct training of writing.

  12. Time-dependence of graph theory metrics in functional connectivity analysis.

    PubMed

    Chiang, Sharon; Cassese, Alberto; Guindani, Michele; Vannucci, Marina; Yeh, Hsiang J; Haneef, Zulfi; Stern, John M

    2016-01-15

    Brain graphs provide a useful way to computationally model the network structure of the connectome, and this has led to increasing interest in the use of graph theory to quantitate and investigate the topological characteristics of the healthy brain and brain disorders on the network level. The majority of graph theory investigations of functional connectivity have relied on the assumption of temporal stationarity. However, recent evidence increasingly suggests that functional connectivity fluctuates over the length of the scan. In this study, we investigate the stationarity of brain network topology using a Bayesian hidden Markov model (HMM) approach that estimates the dynamic structure of graph theoretical measures of whole-brain functional connectivity. In addition to extracting the stationary distribution and transition probabilities of commonly employed graph theory measures, we propose two estimators of temporal stationarity: the S-index and N-index. These indexes can be used to quantify different aspects of the temporal stationarity of graph theory measures. We apply the method and proposed estimators to resting-state functional MRI data from healthy controls and patients with temporal lobe epilepsy. Our analysis shows that several graph theory measures, including small-world index, global integration measures, and betweenness centrality, may exhibit greater stationarity over time and therefore be more robust. Additionally, we demonstrate that accounting for subject-level differences in the level of temporal stationarity of network topology may increase discriminatory power in discriminating between disease states. Our results confirm and extend findings from other studies regarding the dynamic nature of functional connectivity, and suggest that using statistical models which explicitly account for the dynamic nature of functional connectivity in graph theory analyses may improve the sensitivity of investigations and consistency across investigations.

  13. Time-dependence of graph theory metrics in functional connectivity analysis.

    PubMed

    Chiang, Sharon; Cassese, Alberto; Guindani, Michele; Vannucci, Marina; Yeh, Hsiang J; Haneef, Zulfi; Stern, John M

    2016-01-15

    Brain graphs provide a useful way to computationally model the network structure of the connectome, and this has led to increasing interest in the use of graph theory to quantitate and investigate the topological characteristics of the healthy brain and brain disorders on the network level. The majority of graph theory investigations of functional connectivity have relied on the assumption of temporal stationarity. However, recent evidence increasingly suggests that functional connectivity fluctuates over the length of the scan. In this study, we investigate the stationarity of brain network topology using a Bayesian hidden Markov model (HMM) approach that estimates the dynamic structure of graph theoretical measures of whole-brain functional connectivity. In addition to extracting the stationary distribution and transition probabilities of commonly employed graph theory measures, we propose two estimators of temporal stationarity: the S-index and N-index. These indexes can be used to quantify different aspects of the temporal stationarity of graph theory measures. We apply the method and proposed estimators to resting-state functional MRI data from healthy controls and patients with temporal lobe epilepsy. Our analysis shows that several graph theory measures, including small-world index, global integration measures, and betweenness centrality, may exhibit greater stationarity over time and therefore be more robust. Additionally, we demonstrate that accounting for subject-level differences in the level of temporal stationarity of network topology may increase discriminatory power in discriminating between disease states. Our results confirm and extend findings from other studies regarding the dynamic nature of functional connectivity, and suggest that using statistical models which explicitly account for the dynamic nature of functional connectivity in graph theory analyses may improve the sensitivity of investigations and consistency across investigations. PMID

  14. Multi-label literature classification based on the Gene Ontology graph

    PubMed Central

    Jin, Bo; Muller, Brian; Zhai, Chengxiang; Lu, Xinghua

    2008-01-01

    Background The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of text mining approaches to facilitate the process by automatically extracting the Gene Ontology annotation from literature. The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification. Results In this research, we investigated the methods of enhancing automatic multi-label classification of biomedical literature by utilizing the structure of the Gene Ontology graph. We have studied three graph-based multi-label classification algorithms, including a novel stochastic algorithm and two top-down hierarchical classification methods for multi-label literature classification. We systematically evaluated and compared these graph-based classification algorithms to a conventional flat multi-label algorithm. The results indicate that, through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods can significantly improve predictions of the Gene Ontology terms implied by the analyzed text. Furthermore, the graph-based multi-label classifiers are capable of suggesting Gene Ontology annotations (to curators) that are closely related to the true annotations even if they fail to predict the true ones directly. A software package implementing the studied algorithms is available for the research community. Conclusion Through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods have better potential than the conventional flat multi-label classification approach to facilitate protein annotation based on

  15. A graph theoretic approach to scene matching

    NASA Technical Reports Server (NTRS)

    Ranganath, Heggere S.; Chipman, Laure J.

    1991-01-01

    The ability to match two scenes is a fundamental requirement in a variety of computer vision tasks. A graph theoretic approach to inexact scene matching is presented which is useful in dealing with problems due to imperfect image segmentation. A scene is described by a set of graphs, with nodes representing objects and arcs representing relationships between objects. Each node has a set of values representing the relations between pairs of objects, such as angle, adjacency, or distance. With this method of scene representation, the task in scene matching is to match two sets of graphs. Because of segmentation errors, variations in camera angle, illumination, and other conditions, an exact match between the sets of observed and stored graphs is usually not possible. In the developed approach, the problem is represented as an association graph, in which each node represents a possible mapping of an observed region to a stored object, and each arc represents the compatibility of two mappings. Nodes and arcs have weights indicating the merit or a region-object mapping and the degree of compatibility between two mappings. A match between the two graphs corresponds to a clique, or fully connected subgraph, in the association graph. The task is to find the clique that represents the best match. Fuzzy relaxation is used to update the node weights using the contextual information contained in the arcs and neighboring nodes. This simplifies the evaluation of cliques. A method of handling oversegmentation and undersegmentation problems is also presented. The approach is tested with a set of realistic images which exhibit many types of sementation errors.

  16. Unraveling Protein Networks with Power Graph Analysis

    PubMed Central

    Royer, Loïc; Reimann, Matthias; Andreopoulos, Bill; Schroeder, Michael

    2008-01-01

    Networks play a crucial role in computational biology, yet their analysis and representation is still an open problem. Power Graph Analysis is a lossless transformation of biological networks into a compact, less redundant representation, exploiting the abundance of cliques and bicliques as elementary topological motifs. We demonstrate with five examples the advantages of Power Graph Analysis. Investigating protein-protein interaction networks, we show how the catalytic subunits of the casein kinase II complex are distinguishable from the regulatory subunits, how interaction profiles and sequence phylogeny of SH3 domains correlate, and how false positive interactions among high-throughput interactions are spotted. Additionally, we demonstrate the generality of Power Graph Analysis by applying it to two other types of networks. We show how power graphs induce a clustering of both transcription factors and target genes in bipartite transcription networks, and how the erosion of a phosphatase domain in type 22 non-receptor tyrosine phosphatases is detected. We apply Power Graph Analysis to high-throughput protein interaction networks and show that up to 85% (56% on average) of the information is redundant. Experimental networks are more compressible than rewired ones of same degree distribution, indicating that experimental networks are rich in cliques and bicliques. Power Graphs are a novel representation of networks, which reduces network complexity by explicitly representing re-occurring network motifs. Power Graphs compress up to 85% of the edges in protein interaction networks and are applicable to all types of networks such as protein interactions, regulatory networks, or homology networks. PMID:18617988

  17. Labeled Graph Kernel for Behavior Analysis.

    PubMed

    Zhao, Ruiqi; Martinez, Aleix M

    2016-08-01

    Automatic behavior analysis from video is a major topic in many areas of research, including computer vision, multimedia, robotics, biology, cognitive science, social psychology, psychiatry, and linguistics. Two major problems are of interest when analyzing behavior. First, we wish to automatically categorize observed behaviors into a discrete set of classes (i.e., classification). For example, to determine word production from video sequences in sign language. Second, we wish to understand the relevance of each behavioral feature in achieving this classification (i.e., decoding). For instance, to know which behavior variables are used to discriminate between the words apple and onion in American Sign Language (ASL). The present paper proposes to model behavior using a labeled graph, where the nodes define behavioral features and the edges are labels specifying their order (e.g., before, overlaps, start). In this approach, classification reduces to a simple labeled graph matching. Unfortunately, the complexity of labeled graph matching grows exponentially with the number of categories we wish to represent. Here, we derive a graph kernel to quickly and accurately compute this graph similarity. This approach is very general and can be plugged into any kernel-based classifier. Specifically, we derive a Labeled Graph Support Vector Machine (LGSVM) and a Labeled Graph Logistic Regressor (LGLR) that can be readily employed to discriminate between many actions (e.g., sign language concepts). The derived approach can be readily used for decoding too, yielding invaluable information for the understanding of a problem (e.g., to know how to teach a sign language). The derived algorithms allow us to achieve higher accuracy results than those of state-of-the-art algorithms in a fraction of the time. We show experimental results on a variety of problems and datasets, including multimodal data.

  18. Interpreting a Graph and Constructing Its Derivative Graph: Stability and Change in Students' Conceptions

    ERIC Educational Resources Information Center

    Ubuz, Behiye

    2007-01-01

    This present study investigated engineering students' conceptions and misconceptions related to derivative, particularly interpreting the graph of a function and constructing its derivative graph. Participants were 147 first year engineering students from four universities enrolled in first year undergraduate calculus courses with or without the…

  19. Chemical amplification based on fluid partitioning in an immiscible liquid

    DOEpatents

    Anderson, Brian L.; Colston, Bill W.; Elkin, Christopher J.

    2010-09-28

    A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.

  20. A mesh partitioning algorithm for preserving spatial locality in arbitrary geometries

    SciTech Connect

    Nivarti, Girish V. Salehi, M. Mahdi; Bushe, W. Kendal

    2015-01-15

    Highlights: •An algorithm for partitioning computational meshes is proposed. •The Morton order space-filling curve is modified to achieve improved locality. •A spatial locality metric is defined to compare results with existing approaches. •Results indicate improved performance of the algorithm in complex geometries. -- Abstract: A space-filling curve (SFC) is a proximity preserving linear mapping of any multi-dimensional space and is widely used as a clustering tool. Equi-sized partitioning of an SFC ignores the loss in clustering quality that occurs due to inaccuracies in the mapping. Often, this results in poor locality within partitions, especially for the conceptually simple, Morton order curves. We present a heuristic that improves partition locality in arbitrary geometries by slicing a Morton order curve at points where spatial locality is sacrificed. In addition, we develop algorithms that evenly distribute points to the extent possible while maintaining spatial locality. A metric is defined to estimate relative inter-partition contact as an indicator of communication in parallel computing architectures. Domain partitioning tests have been conducted on geometries relevant to turbulent reactive flow simulations. The results obtained highlight the performance of our method as an unsupervised and computationally inexpensive domain partitioning tool.

  1. Interspecific resource partitioning in sympatric ursids

    USGS Publications Warehouse

    Belant, J.L.; Kielland, K.; Follmann, E.H.; Adams, L.G.

    2006-01-01

    The fundamental niche of a species is rarely if ever realized because the presence of other species restricts it to a narrower range of ecological conditions. The effects of this narrower range of conditions define how resources are partitioned. Resource partitioning has been inferred but not demonstrated previously for sympatric ursids. We estimated assimilated diet in relation to body condition (body fat and lean and total body mass) and reproduction for sympatric brown bears (Ursus arctos) and American black bears (U. americanus) in southcentral Alaska, 1998-2000. Based on isotopic analysis of blood and keratin in claws, salmon (Oncorhynchus spp.) predominated in brown bear diets (>53% annually) whereas black bears assimilated 0-25% salmon annually. Black bears did not exploit salmon during a year with below average spawning numbers, probably because brown bears deterred black bear access to salmon. Proportion of salmon in assimilated diet was consistent across years for brown bears and represented the major portion of their diet. Body size of brown bears in the study area approached mean body size of several coastal brown bear populations, demonstrating the importance of salmon availability to body condition. Black bears occurred at a comparable density (mass:mass), but body condition varied and was related directly to the amount of salmon assimilated in their diet. Both species gained most lean body mass during spring and all body fat during summer when salmon were present. Improved body condition (i.e., increased percentage body fat) from salmon consumption reduced catabolism of lean body mass during hibernation, resulting in better body condition the following spring. Further, black bear reproduction was directly related to body condition; reproductive rates were reduced when body condition was lower. High body fat content across years for brown bears was reflected in consistently high reproductive levels. We suggest that the fundamental niche of black bears

  2. Interspecific resource partitioning in sympatric ursids.

    PubMed

    Belant, Jerrold L; Kielland, Knut; Follmann, Erich H; Adams, Layne G

    2006-12-01

    The fundamental niche of a species is rarely if ever realized because the presence of other species restricts it to a narrower range of ecological conditions. The effects of this narrower range of conditions define how resources are partitioned. Resource partitioning has been inferred but not demonstrated previously for sympatric ursids. We estimated assimilated diet in relation to body condition (body fat and lean and total body mass) and reproduction for sympatric brown bears (Ursus arctos) and American black bears (U. americanus) in south-central Alaska, 1998-2000. Based on isotopic analysis of blood and keratin in claws, salmon (Oncorhynchus spp.) predominated in brown bear diets (> 53% annually) whereas black bears assimilated 0-25% salmon annually. Black bears did not exploit salmon during a year with below average spawning numbers, probably because brown bears deterred black bear access to salmon. Proportion of salmon in assimilated diet was consistent across years for brown bears and represented the major portion of their diet. Body size of brown bears in the study area approached mean body size of several coastal brown bear populations, demonstrating the importance of salmon availability to body condition. Black bears occurred at a comparable density (mass:mass), but body condition varied and was related directly to the amount of salmon assimilated in their diet. Both species gained most lean body mass during spring and all body fat during summer when salmon were present. Improved body condition (i.e., increased percentage body fat) from salmon consumption reduced catabolism of lean body mass during hibernation, resulting in better body condition the following spring. Further, black bear reproduction was directly related to body condition; reproductive rates were reduced when body condition was lower. High body fat content across years for brown bears was reflected in consistently high reproductive levels. We suggest that the fundamental niche of black

  3. Mass partitioning effects in diffusion transport.

    PubMed

    Kojic, Milos; Milosevic, Miljan; Wu, Suhong; Blanco, Elvin; Ferrari, Mauro; Ziemys, Arturas

    2015-08-28

    Frequent mass exchange takes place in a heterogeneous environment among several phases, where mass partitioning may occur at the interface of phases. Analytical and computational methods for diffusion do not usually incorporate molecule partitioning masking the true picture of mass transport. Here we present a computational finite element methodology to calculate diffusion mass transport with a partitioning phenomenon included and the analysis of the effects of partitioning. Our numerical results showed that partitioning controls equilibrated mass distribution as expected from analytical solutions. The experimental validation of mass release from drug-loaded nanoparticles showed that partitioning might even dominate in some cases with respect to diffusion itself. The analysis of diffusion kinetics in the parameter space of partitioning and diffusivity showed that partitioning is an extremely important parameter in systems, where mass diffusivity is fast and that the concentration of nanoparticles can control payload retention inside nanoparticles. The computational and experimental results suggest that partitioning and physiochemical properties of phases play an important, if not crucial, role in diffusion transport and should be included in the studies of mass transport processes.

  4. Mass partitioning effects in diffusion transport.

    PubMed

    Kojic, Milos; Milosevic, Miljan; Wu, Suhong; Blanco, Elvin; Ferrari, Mauro; Ziemys, Arturas

    2015-08-28

    Frequent mass exchange takes place in a heterogeneous environment among several phases, where mass partitioning may occur at the interface of phases. Analytical and computational methods for diffusion do not usually incorporate molecule partitioning masking the true picture of mass transport. Here we present a computational finite element methodology to calculate diffusion mass transport with a partitioning phenomenon included and the analysis of the effects of partitioning. Our numerical results showed that partitioning controls equilibrated mass distribution as expected from analytical solutions. The experimental validation of mass release from drug-loaded nanoparticles showed that partitioning might even dominate in some cases with respect to diffusion itself. The analysis of diffusion kinetics in the parameter space of partitioning and diffusivity showed that partitioning is an extremely important parameter in systems, where mass diffusivity is fast and that the concentration of nanoparticles can control payload retention inside nanoparticles. The computational and experimental results suggest that partitioning and physiochemical properties of phases play an important, if not crucial, role in diffusion transport and should be included in the studies of mass transport processes. PMID:26204522

  5. DT-MRI segmentation using graph cuts

    NASA Astrophysics Data System (ADS)

    Weldeselassie, Yonas T.; Hamarneh, Ghassan

    2007-03-01

    An important problem in medical image analysis is the segmentation of anatomical regions of interest. Once regions of interest are segmented, one can extract shape, appearance, and structural features that can be analyzed for disease diagnosis or treatment evaluation. Diffusion tensor magnetic resonance imaging (DT-MRI) is a relatively new medical imaging modality that captures unique water diffusion properties and fiber orientation information of the imaged tissues. In this paper, we extend the interactive multidimensional graph cuts segmentation technique to operate on DT-MRI data by utilizing latest advances in tensor calculus and diffusion tensor dissimilarity metrics. The user interactively selects certain tensors as object ("obj") or background ("bkg") to provide hard constraints for the segmentation. Additional soft constraints incorporate information about both regional tissue diffusion as well as boundaries between tissues of different diffusion properties. Graph cuts are used to find globally optimal segmentation of the underlying 3D DT-MR image among all segmentations satisfying the constraints. We develop a graph structure from the underlying DT-MR image with the tensor voxels corresponding to the graph vertices and with graph edge weights computed using either Log-Euclidean or the J-divergence tensor dissimilarity metric. The topology of our segmentation is unrestricted and both obj and bkg segments may consist of several isolated parts. We test our method on synthetic DT data and apply it to real 2D and 3D MRI, providing segmentations of the corpus callosum in the brain and the ventricles of the heart.

  6. Visualizing intelligence information using correlation graphs

    NASA Astrophysics Data System (ADS)

    Verma, Vivek; Gagvani, Nikhil

    2005-03-01

    This paper presents a new information model to help intelligence analysts in organizing, querying, and visualizing the information present in large volumes of unstructured data sources such as text reports, multi-media, and human discourse. Our primary goal is to create a system that would combine the human pattern recognition abilities of intelligence analysis with the storage and processing capabilities of computers. Our system models the collective mental map of intelligence analysts in the form of the Correlation Graph, a modified graph data structure with objects and events as nodes and subjective probabilistic correlations between them as edges. Objects are entities such as people, places, and things. Events are actions that involve the objects. A taxonomy is also associated with the model to enable intelligence domain specific querying of the data. Graph drawing techniques are used to visualize the information represented by the correlation graph. Through real world examples, we demonstrate that the resulting information model can be used for efficient representation, presentation, and querying to discover novel patterns in the intelligence data via graph visualization techniques.

  7. Visibility graph network analysis of natural gas price: The case of North American market

    NASA Astrophysics Data System (ADS)

    Sun, Mei; Wang, Yaqi; Gao, Cuixia

    2016-11-01

    Fluctuations in prices of natural gas significantly affect global economy. Therefore, the research on the characteristics of natural gas price fluctuations, turning points and its influencing cycle on the subsequent price series is of great significance. Global natural gas trade concentrates on three regional markets: the North American market, the European market and the Asia-Pacific market, with North America having the most developed natural gas financial market. In addition, perfect legal supervision and coordinated regulations make the North American market more open and more competitive. This paper focuses on the North American natural gas market specifically. The Henry Hub natural gas spot price time series is converted to a visibility graph network which provides a new direction for macro analysis of time series, and several indicators are investigated: degree and degree distribution, the average shortest path length and community structure. The internal mechanisms underlying price fluctuations are explored through the indicators. The results show that the natural gas prices visibility graph network (NGP-VGN) is of small-world and scale-free properties simultaneously. After random rearrangement of original price time series, the degree distribution of network becomes exponential distribution, different from the original ones. This means that, the original price time series is of long-range negative correlation fractal characteristic. In addition, nodes with large degree correspond to significant geopolitical or economic events. Communities correspond to time cycles in visibility graph network. The cycles of time series and the impact scope of hubs can be found by community structure partition.

  8. Compact Graph Representations and Parallel Connectivity Algorithms for Massive Dynamic Network Analysis

    SciTech Connect

    Madduri, Kamesh; Bader, David A.

    2009-02-15

    Graph-theoretic abstractions are extensively used to analyze massive data sets. Temporal data streams from socioeconomic interactions, social networking web sites, communication traffic, and scientific computing can be intuitively modeled as graphs. We present the first study of novel high-performance combinatorial techniques for analyzing large-scale information networks, encapsulating dynamic interaction data in the order of billions of entities. We present new data structures to represent dynamic interaction networks, and discuss algorithms for processing parallel insertions and deletions of edges in small-world networks. With these new approaches, we achieve an average performance rate of 25 million structural updates per second and a parallel speedup of nearly28 on a 64-way Sun UltraSPARC T2 multicore processor, for insertions and deletions to a small-world network of 33.5 million vertices and 268 million edges. We also design parallel implementations of fundamental dynamic graph kernels related to connectivity and centrality queries. Our implementations are freely distributed as part of the open-source SNAP (Small-world Network Analysis and Partitioning) complex network analysis framework.

  9. Partition Theory for Periodic and Semi-Infinite Systems

    NASA Astrophysics Data System (ADS)

    Niffenegger, Kelsie; Wasserman, Adam

    Standard approximations to the exchange-correlation (XC) functional of Kohn-Sham Density-Functional Theory are insufficiently accurate to describe charge transfer at metal-atom interfaces and other systems requiring proper treatment of fractional electron charges. The root of the problem is connected to the lack of derivative discontinuities in the approximate XC functionals at integer numbers of electrons. Partition Theory (PT) is a promising, formally exact method to correct this issue. We study the simplest model for an atom adsorbed at a metal surface: A one-dimensional step potential separated a fixed distance from an attractive well that admits only one bound state when isolated. The semi-infinite metal is populated with non-interacting electrons up to the Fermi energy. We derive the PT-equations for this problem and indicate how the associated partition potential can be calculated. PT is also a promising method for improving the computational scaling of other large and/or periodic systems. We study the partition potential for periodic 1-D chains of identical attractive wells and comment on the uniqueness of the partition potential when going from finite to periodic systems.

  10. Conversion from Tree to Graph Representation of Requirements

    NASA Technical Reports Server (NTRS)

    Mayank, Vimal; Everett, David Frank; Shmunis, Natalya; Austin, Mark

    2009-01-01

    A procedure and software to implement the procedure have been devised to enable conversion from a tree representation to a graph representation of the requirements governing the development and design of an engineering system. The need for this procedure and software and for other requirements-management tools arises as follows: In systems-engineering circles, it is well known that requirements- management capability improves the likelihood of success in the team-based development of complex systems involving multiple technological disciplines. It is especially desirable to be able to visualize (in order to identify and manage) requirements early in the system- design process, when errors can be corrected most easily and inexpensively.

  11. Improving the performance of algorithms to find communities in networks.

    PubMed

    Darst, Richard K; Nussinov, Zohar; Fortunato, Santo

    2014-03-01

    Most algorithms to detect communities in networks typically work without any information on the cluster structure to be found, as one has no a priori knowledge of it, in general. Not surprisingly, knowing some features of the unknown partition could help its identification, yielding an improvement of the performance of the method. Here we show that, if the number of clusters was known beforehand, standard methods, like modularity optimization, would considerably gain in accuracy, mitigating the severe resolution bias that undermines the reliability of the results of the original unconstrained version. The number of clusters can be inferred from the spectra of the recently introduced nonbacktracking and flow matrices, even in benchmark graphs with realistic community structure. The limit of such a two-step procedure is the overhead of the computation of the spectra.

  12. A graph algebra for scalable visual analytics.

    PubMed

    Shaverdian, Anna A; Zhou, Hao; Michailidis, George; Jagadish, Hosagrahar V

    2012-01-01

    Visual analytics (VA), which combines analytical techniques with advanced visualization features, is fast becoming a standard tool for extracting information from graph data. Researchers have developed many tools for this purpose, suggesting a need for formal methods to guide these tools' creation. Increased data demands on computing requires redesigning VA tools to consider performance and reliability in the context of analysis of exascale datasets. Furthermore, visual analysts need a way to document their analyses for reuse and results justification. A VA graph framework encapsulated in a graph algebra helps address these needs. Its atomic operators include selection and aggregation. The framework employs a visual operator and supports dynamic attributes of data to enable scalable visual exploration of data. PMID:24806630

  13. Directed transport in quantum star graphs

    NASA Astrophysics Data System (ADS)

    Yusupov, Jambul; Dolgushev, Maxim; Blumen, Alexander; Mülken, Oliver

    2016-04-01

    We study the quantum dynamics of Gaussian wave packets on star graphs whose arms feature each a periodic potential and an external time-dependent field. Assuming that the potentials and the field can be manipulated separately for each arm of the star, we show that it is possible to manipulate the direction of the motion of a Gaussian wave packet through the bifurcation point by a suitable choice of the parameters of the external fields. In doing so, one can achieve a transmission of the wave packet into the desired arm with nearly 70 % while also keeping the shape of the wave packet approximately intact. Since a star graph is the simplest element of many other complex graphs, the obtained results can be considered as the first step to wave packet manipulations on complex networks.

  14. Dynamic graph system for a semantic database

    SciTech Connect

    Mizell, David

    2015-01-27

    A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

  15. Interactive Web Graphs with Fewer Restrictions

    NASA Technical Reports Server (NTRS)

    Fiedler, James

    2012-01-01

    There is growing popularity for interactive, statistical web graphs and programs to generate them. However, it seems that these programs tend to be somewhat restricted in which web browsers and statistical software are supported. For example, the software might use SVG (e.g., Protovis, gridSVG) or HTML canvas, both of which exclude most versions of Internet Explorer, or the software might be made specifically for R (gridSVG, CRanvas), thus excluding users of other stats software. There are more general tools (d3, Rapha lJS) which are compatible with most browsers, but using one of these to make statistical graphs requires more coding than is probably desired, and requires learning a new tool. This talk will present a method for making interactive web graphs, which, by design, attempts to support as many browsers and as many statistical programs as possible, while also aiming to be relatively easy to use and relatively easy to extend.

  16. Scale-invariant geometric random graphs.

    PubMed

    Xie, Zheng; Rogers, Tim

    2016-03-01

    We introduce and analyze a class of growing geometric random graphs that are invariant under rescaling of space and time. Directed connections between nodes are drawn according to influence zones that depend on node position in space and time, mimicking the heterogeneity and increased specialization found in growing networks. Through calculations and numerical simulations we explore the consequences of scale invariance for geometric random graphs generated this way. Our analysis reveals a dichotomy between scale-free and Poisson distributions of in- and out-degree, the existence of a random number of hub nodes, high clustering, and unusual percolation behavior. These properties are similar to those of empirically observed web graphs. PMID:27078369

  17. A graph algebra for scalable visual analytics.

    PubMed

    Shaverdian, Anna A; Zhou, Hao; Michailidis, George; Jagadish, Hosagrahar V

    2012-01-01

    Visual analytics (VA), which combines analytical techniques with advanced visualization features, is fast becoming a standard tool for extracting information from graph data. Researchers have developed many tools for this purpose, suggesting a need for formal methods to guide these tools' creation. Increased data demands on computing requires redesigning VA tools to consider performance and reliability in the context of analysis of exascale datasets. Furthermore, visual analysts need a way to document their analyses for reuse and results justification. A VA graph framework encapsulated in a graph algebra helps address these needs. Its atomic operators include selection and aggregation. The framework employs a visual operator and supports dynamic attributes of data to enable scalable visual exploration of data.

  18. Dynamic graph system for a semantic database

    DOEpatents

    Mizell, David

    2016-04-12

    A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

  19. The uniqueness of DMAX-matrix graph invariants.

    PubMed

    Dehmer, Matthias; Shi, Yongtang

    2014-01-01

    In this paper, we examine the uniqueness (discrimination power) of a newly proposed graph invariant based on the matrix DMAX defined by Randić et al. In order to do so, we use exhaustively generated graphs instead of special graph classes such as trees only. Using these graph classes allow us to generalize the findings towards complex networks as they usually do not possess any structural constraints. We obtain that the uniqueness of this newly proposed graph invariant is approximately as low as the uniqueness of the Balaban J index on exhaustively generated (general) graphs. PMID:24392099

  20. Graph isomorphism and adiabatic quantum computing

    NASA Astrophysics Data System (ADS)

    Gaitan, Frank; Clark, Lane

    2014-02-01

    In the graph isomorphism (GI) problem two N-vertex graphs G and G' are given and the task is to determine whether there exists a permutation of the vertices of G that preserves adjacency and transforms G →G'. If yes, then G and G' are said to be isomorphic; otherwise they are nonisomorphic. The GI problem is an important problem in computer science and is thought to be of comparable difficulty to integer factorization. In this paper we present a quantum algorithm that solves arbitrary instances of GI and which also provides an approach to determining all automorphisms of a given graph. We show how the GI problem can be converted to a combinatorial optimization problem that can be solved using adiabatic quantum evolution. We numerically simulate the algorithm's quantum dynamics and show that it correctly (i) distinguishes nonisomorphic graphs; (ii) recognizes isomorphic graphs and determines the permutation(s) that connect them; and (iii) finds the automorphism group of a given graph G. We then discuss the GI quantum algorithm's experimental implementation, and close by showing how it can be leveraged to give a quantum algorithm that solves arbitrary instances of the NP-complete subgraph isomorphism problem. The computational complexity of an adiabatic quantum algorithm is largely determined by the minimum energy gap Δ (N) separating the ground and first-excited states in the limit of large problem size N ≫1. Calculating Δ (N) in this limit is a fundamental open problem in adiabatic quantum computing, and so it is not possible to determine the computational complexity of adiabatic quantum algorithms in general, nor consequently, of the specific adiabatic quantum algorithms presented here. Adiabatic quantum computing has been shown to be equivalent to the circuit model of quantum computing, and so development of adiabatic quantum algorithms continues to be of great interest.

  1. Assimilate partitioning during reproductive growth

    SciTech Connect

    Finazzo, S.F.; Davenport, T.L.

    1987-04-01

    Leaves having various phyllotactic relationships to fruitlets were labeled for 1 hour with 10/sub r/Ci of /sup 14/CO/sub 2/. Fruitlets were also labeled. Fruitlets did fix /sup 14/CO/sub 2/. Translocation of radioactivity from the peel into the fruit occurred slowly and to a limited extent. No evidence of translocation out of the fruitlets was observed. Assimilate partitioning in avocado was strongly influenced by phyllotaxy. If a fruit and the labeled leaf had the same phyllotaxy then greater than 95% of the radiolabel was present in this fruit. When the fruit did not have the same phyllotaxy as the labeled leaf, the radiolabel distribution was skewed with 70% of the label going to a single adjacent position. Avocado fruitlets exhibit uniform labeling throughout a particular tissue. In avocado, assimilates preferentially move from leaves to fruits with the same phyllotaxy.

  2. HPAM: Hirshfeld partitioned atomic multipoles

    NASA Astrophysics Data System (ADS)

    Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.

    2012-02-01

    An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank l on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from l=0 (atomic charges) to l=4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank l are shown to exactly reproduce ab initio molecular multipole moments of rank L for L⩽l. In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only ( l=0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. Program summaryProgram title: HPAM Catalogue identifier: AEKP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v2 No. of lines in distributed program, including test data, etc.: 500 809 No. of bytes in distributed program, including test data, etc.: 13 424 494 Distribution format: tar.gz Programming language: C Computer: Any Operating system: Linux RAM: Typically, a few hundred megabytes Classification: 16.13 External routines: The program requires 'formatted checkpoint' files obtained from the Gaussian 03 or Gaussian 09 quantum chemistry program. Nature of problem: An ab initio

  3. MULTIVARIATE KERNEL PARTITION PROCESS MIXTURES

    PubMed Central

    Dunson, David B.

    2013-01-01

    Mixtures provide a useful approach for relaxing parametric assumptions. Discrete mixture models induce clusters, typically with the same cluster allocation for each parameter in multivariate cases. As a more flexible approach that facilitates sparse nonparametric modeling of multivariate random effects distributions, this article proposes a kernel partition process (KPP) in which the cluster allocation varies for different parameters. The KPP is shown to be the driving measure for a multivariate ordered Chinese restaurant process that induces a highly-flexible dependence structure in local clustering. This structure allows the relative locations of the random effects to inform the clustering process, with spatially-proximal random effects likely to be assigned the same cluster index. An exact block Gibbs sampler is developed for posterior computation, avoiding truncation of the infinite measure. The methods are applied to hormone curve data, and a dependent KPP is proposed for classification from functional predictors. PMID:24478563

  4. From cognitive maps to cognitive graphs.

    PubMed

    Chrastil, Elizabeth R; Warren, William H

    2014-01-01

    We investigate the structure of spatial knowledge that spontaneously develops during free exploration of a novel environment. We present evidence that this structure is similar to a labeled graph: a network of topological connections between places, labeled with local metric information. In contrast to route knowledge, we find that the most frequent routes and detours to target locations had not been traveled during learning. Contrary to purely topological knowledge, participants typically traveled the shortest metric distance to a target, rather than topologically equivalent but longer paths. The results are consistent with the proposal that people learn a labeled graph of their environment.

  5. PolyGraph: a Polymer Visualization system

    NASA Astrophysics Data System (ADS)

    Cutkosky, Ashok; Tarazi, Najeeb; Lieberman Aiden, Erez

    2012-02-01

    Rapid advances in computational hardware and parallelization have made complex simulations of large polymers increasingly ubiquitous. However, visualizing such simulations remains a challenge. Here we present PolyGraph, a Blender-powered visualization system for complex polymer simulations. As a specific example, we study molecular dynamics simulations of condensing polymers. We illustrate our initial simulation results, suggesting that formation of local beads is an initial step in the condensation process. (This finding is consistent with earlier conjectures about polymer condensation.) PolyGraph makes it possible to create precise and visually appealing clips of polymer simulations. *contributed equally

  6. From Cognitive Maps to Cognitive Graphs

    PubMed Central

    Chrastil, Elizabeth R.; Warren, William H.

    2014-01-01

    We investigate the structure of spatial knowledge that spontaneously develops during free exploration of a novel environment. We present evidence that this structure is similar to a labeled graph: a network of topological connections between places, labeled with local metric information. In contrast to route knowledge, we find that the most frequent routes and detours to target locations had not been traveled during learning. Contrary to purely topological knowledge, participants typically traveled the shortest metric distance to a target, rather than topologically equivalent but longer paths. The results are consistent with the proposal that people learn a labeled graph of their environment. PMID:25389769

  7. Percolation threshold on planar Euclidean Gabriel graphs

    NASA Astrophysics Data System (ADS)

    Norrenbrock, Christoph

    2016-04-01

    In the present article, numerical simulations have been performed to find the bond and site percolation thresholds on two-dimensional Gabriel graphs (GG) for Poisson point processes. GGs belong to the family of "proximity graphs" and are discussed, e.g., in context of the construction of backbones for wireless ad-hoc networks. Finite-size scaling analyses have been performed to find the critical points and critical exponents ν, β and γ. The critical exponents obtained this way verify that the associated universality class is that of standard 2D percolation.

  8. Quasiperiodic graphs at the onset of chaos.

    PubMed

    Luque, B; Cordero-Gracia, M; Gómez, M; Robledo, A

    2013-12-01

    We examine the connectivity fluctuations across networks obtained when the horizontal visibility (HV) algorithm is used on trajectories generated by nonlinear circle maps at the quasiperiodic transition to chaos. The resultant HV graph is highly anomalous as the degrees fluctuate at all scales with amplitude that increases with the size of the network. We determine families of Pesin-like identities between entropy growth rates and generalized graph-theoretical Lyapunov exponents. An irrational winding number with pure periodic continued fraction characterizes each family. We illustrate our results for the so-called golden, silver, and bronze numbers.

  9. Graphing techniques for materials laboratory using Excel

    NASA Technical Reports Server (NTRS)

    Kundu, Nikhil K.

    1994-01-01

    Engineering technology curricula stress hands on training and laboratory practices in most of the technical courses. Laboratory reports should include analytical as well as graphical evaluation of experimental data. Experience shows that many students neither have the mathematical background nor the expertise for graphing. This paper briefly describes the procedure and data obtained from a number of experiments such as spring rate, stress concentration, endurance limit, and column buckling for a variety of materials. Then with a brief introduction to Microsoft Excel the author explains the techniques used for linear regression and logarithmic graphing.

  10. Isomorphisms between Petri nets and dataflow graphs

    NASA Technical Reports Server (NTRS)

    Kavi, Krishna M.; Buckles, Billy P.; Bhat, U. Narayan

    1987-01-01

    Dataflow graphs are a generalized model of computation. Uninterpreted dataflow graphs with nondeterminism resolved via probabilities are shown to be isomorphic to a class of Petri nets known as free choice nets. Petri net analysis methods are readily available in the literature and this result makes those methods accessible to dataflow research. Nevertheless, combinatorial explosion can render Petri net analysis inoperative. Using a previously known technique for decomposing free choice nets into smaller components, it is demonstrated that, in principle, it is possible to determine aspects of the overall behavior from the particular behavior of components.

  11. Internet topology: connectivity of IP graphs

    NASA Astrophysics Data System (ADS)

    Broido, Andre; claffy, kc

    2001-07-01

    In this paper we introduce a framework for analyzing local properties of Internet connectivity. We compare BGP and probed topology data, finding that currently probed topology data yields much denser coverage of AS-level connectivity. We describe data acquisition and construction of several IP- level graphs derived from a collection of 220 M skitter traceroutes. We find that a graph consisting of IP nodes and links contains 90.5% of its 629 K nodes in the acyclic subgraph. In particular, 55% of the IP nodes are in trees. Full bidirectional connectivity is observed for a giant component containing 8.3% of IP nodes.

  12. Lattices of processes in graphs with inputs

    SciTech Connect

    Shakhbazyan, K.V.

    1995-09-01

    This article is a continuation of others work, presenting a detailed analysis of finite lattices of processes in graphs with input nodes. Lattices of processes in such graphs are studied by representing the lattices in the form of an algebra of pairs. We define the algebra of pairs somewhat generalizing the definition. Let K and D be bounded distributive lattices. A sublattice {delta} {contained_in} K x D is called an algebra of pairs if for all K {element_of} K we have (K, 1{sub D}) {element_of} {delta} and for all d {element_of} D we have (O{sub K}).

  13. A Similarity Search Using Molecular Topological Graphs

    PubMed Central

    Fukunishi, Yoshifumi; Nakamura, Haruki

    2009-01-01

    A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure. PMID:20037730

  14. Single-qubit gates by graph scattering

    NASA Astrophysics Data System (ADS)

    Underwood, Michael S.; Blumer, Benjamin A.; Feder, David L.

    2012-02-01

    Continuous-time quantum walkers with tightly peaked momenta can simulate quantum computations by scattering off finite graphs. We enumerate all single-qubit gates that can be enacted by scattering off a single graph on up to n=9 vertices at certain momentum values, and provide numerical evidence that the number of such gates grows exponentially with n. The single-qubit rotations are about axes distributed roughly uniformly on the Bloch sphere, and rotations by both rational and irrational multiples of π are found.

  15. Partition characteristics of polycyclic aromatic hydrocarbons on soils and sediments

    USGS Publications Warehouse

    Chiou, C.T.; Mcgroddy, S.E.; Kile, D.E.

    1998-01-01

    The partition behavior was determined for three polycyclic aromatic hydrocarbons (PAHs), i.e., naphthalene, phenanthrene, and pyrene, from water to a range of soil and sediment samples. The measured partition coefficients of the individual PAHs between soil/sediment organic matter (SOM) and water (i.e., K(oc) values) are relatively invariant either for the 'clean' (uncontaminated) soils or for the clean sediments; however, the mean K(oc) values on the sediments are about twice the values on the soils. This disparity is similar to the earlier observation for other nonpolar solutes and reflects the compositional differences between soil and sediment organic matters. No significant differences in K(oc) are observed between a clean coastal marine sediment and freshwater sediments. The coastal sediments that are significantly impacted by organic contaminants exhibit higher K(oc) values. At given K(ow) values (octanol-water), the PAHs exhibit much higher K(oc) values than other relatively nonpolar solutes (e.g., chlorinated hydrocarbons). This effect is shown to result from the enhanced partition of PAHs to SOM rather than from lower K(ow) values of PAHs at given supercooled liquid solute solubilities in water. The enhanced partition of PAHs over other nonpolar solutes in SOM provides an account of the markedly different correlations between log K(oc) and log K(ow) for PAHs and for other nonpolar solutes. The improved partition of PAHs in SOM stems apparently from the enhanced compatibility of their cohesive energy densities with those of the aromatic components in SOM. The approximate aromatic fraction in soil/sediment organic matter has been assessed by solid-state 13C-NMR spectroscopy.The partition behavior was determined for three polycyclic aromatic hydrocarbons (PAHs), i.e., naphthalene, phenanthrene, and pyrene, from water to a range of soil and sediment samples. The measured partition coefficients of the individual PAHs between soil/sediment organic matter (SOM

  16. Trace element partition coefficient in ionic crystals.

    PubMed

    Nagasawa, H

    1966-05-01

    Partition coefficient monovalent trace ions between liquids and either solid NaNO(2) or KCl were determined. The isotropic elastic model of ionic crystals was used for calculating the energy change caused by the ionic substitutions. The observed values of partition coefficients in KCl good agreement with calculate values.

  17. [On the partition of acupuncture academic schools].

    PubMed

    Yang, Pengyan; Luo, Xi; Xia, Youbing

    2016-05-01

    Nowadays extensive attention has been paid on the research of acupuncture academic schools, however, a widely accepted method of partition of acupuncture academic schools is still in need. In this paper, the methods of partition of acupuncture academic schools in the history have been arranged, and three typical methods of"partition of five schools" "partition of eighteen schools" and "two-stage based partition" are summarized. After adeep analysis on the disadvantages and advantages of these three methods, a new method of partition of acupuncture academic schools that is called "three-stage based partition" is proposed. In this method, after the overall acupuncture academic schools are divided into an ancient stage, a modern stage and a contemporary stage, each schoolis divided into its sub-school category. It is believed that this method of partition can remedy the weaknesses ofcurrent methods, but also explore a new model of inheritance and development under a different aspect through thedifferentiation and interaction of acupuncture academic schools at three stages.

  18. Building Ecology and Partition Design. Technical Bulletin.

    ERIC Educational Resources Information Center

    Maryland State Dept. of Education, Baltimore.

    This bulletin is intended as a resource for school system facility planners and architects who design schools. Ways in which decision makers can incorporate environmental concerns in the design of school buildings are detailed. Focus is on the design of interior partition systems. Partition systems in schools serve several purposes; they define…

  19. Exact Abjm Partition Function from Tba

    NASA Astrophysics Data System (ADS)

    Putrov, Pavel; Yamazaki, Masahito

    2012-11-01

    We report on the exact computation of the S3 partition function of U(N)k × U(N)-k ABJM theory for k = 1, N = 1, …, 19. The result is a polynomial in π-1 with rational coefficients. As an application of our results, we numerically determine the coefficient of the membrane 1-instanton correction to the partition function.

  20. A Graph Based Methodology for Temporal Signature Identification from HER.

    PubMed

    Wang, Fei; Liu, Chuanren; Wang, Yajuan; Hu, Jianying; Yu, Guoqiang

    2015-01-01

    Data driven technology is believed to be a promising technique for transforming the current status of healthcare. Electronic Health Records (EHR) is one of the main carriers for conducting the data driven healthcare research, where the goal is to derive insights from healthcare data and utilize such insights to improve the quality of care delivery. Due to the progression nature of human disease, one important aspect for analyzing healthcare data is temporality, which suggests the temporal relationships among different healthcare events and how their values evolve over time. Sequential pattern mining is a popular tool to extract time-invariant patterns from discrete sequences and has been applied in analyzing EHR before. However, due to the complexity of EHR, those approaches usually suffers from the pattern explosion problem, which means that a huge number of patterns will be detected with improper setting of the support threshold. To address this challenge, in this paper, we develop a novel representation, namely the temporal graph, for event sequences like EHR, wherein the nodes are medical events and the edges indicate the temporal relationships among those events in patient EHRs. Based on the temporal graph representation, we further develop an approach for temporal signature identification to identify the most significant and interpretable graph bases as temporal signatures, and the expressing coefficients can be treated as the embeddings of the patients in such temporal signature space. Our temporal signature identification framework is also flexible to incorporate semi-supervised/supervised information. We validate our framework on two real-world tasks. One is predicting the onset risk of heart failure. The other is predicting the risk of heart failure related hospitalization for patients with COPD pre-condition. Our results show that the prediction performance in both tasks can be improved by the proposed approaches. PMID:26958267