Perez-Benito, Joaquin F; Mulero-Raichs, Mar
2016-10-06
Many kinetic studies concerning homologous reaction series report the existence of an activation enthalpy-entropy linear correlation (compensation plot), its slope being the temperature at which all the members of the series have the same rate constant (isokinetic temperature). Unfortunately, it has been demonstrated by statistical methods that the experimental errors associated with the activation enthalpy and entropy are mutually interdependent. Therefore, the possibility that some of those correlations might be caused by accidental errors has been explored by numerical simulations. As a result of this study, a computer program has been developed to evaluate the probability that experimental errors might lead to a linear compensation plot parting from an initial randomly scattered set of activation parameters (p-test). Application of this program to kinetic data for 100 homologous reaction series extracted from bibliographic sources has allowed concluding that most of the reported compensation plots can hardly be explained by the accumulation of experimental errors, thus requiring the existence of a previously existing, physically meaningful correlation.
Case study of enthalpy-entropy noncompensation
Graziano, Giuseppe
2004-03-01
Enthalpy-entropy noncompensation characterizes the relative changes in the hydration thermodynamic functions upon "transforming" ethane into fluoromethane, chloromethane, bromomethane, and iodomethane. An analysis grounded on a simple statistical mechanical theory of hydration allows a plausible rationalization of such enthalpy-entropy noncompensation. It is shown that increasing the strength of solute-water attractive interactions modifying the chemical nature of a part of the solute molecule, but not its size, is a largely noncompensating process for the hydration of noncharged and nonhydrogen bonding species, and dominates the compensating contribution coming from the reorganization of water H bonds.
Dolomatov, M. Yu.; Aubekerov, T. M.
2018-03-01
QSPR models are proposed that satisfactorily describe the relationships between standard enthalpies/ entropies of formation and topological indices in the form of Wiener and Randić indices and the sum of the squares of the eigenvalues from the adjacency matrix of a molecular graph. The models can be recommended for use in scientific and engineering calculations of thermodynamic functions.
Enthalpy-entropy compensation: the role of solvation.
Dragan, Anatoliy I; Read, Christopher M; Crane-Robinson, Colyn
2017-05-01
Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy-entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed. We review long-established and recent cases of EEC and conclude that the large fluctuations in enthalpy and entropy observed are too great to be a result of only conformational changes and must result, to a considerable degree, from variations in the amounts of water immobilized or released on forming complexes. Two systems exhibiting EEC show a correlation between calorimetric entropies and local mobilities, interpreted to mean conformational control of the binding entropy/free energy. However, a substantial contribution from solvation gives the same effect, as a consequence of a structural link between the amount of bound water and the protein flexibility. Only by assuming substantial changes in solvation-an intrinsically compensatory process-can a more complete understanding of EEC be obtained. Faced with such large, and compensating, changes in the enthalpies and entropies of binding, the best approach to engineering elevated affinities must be through the addition of ionic links, as they generate increased entropy without affecting the enthalpy.
Enthalpy - entropy compensation effect in grain boundary phenomena
Czech Academy of Sciences Publication Activity Database
Lejček, Pavel
2005-01-01
Roč. 96, č. 10 (2005), s. 1129-1133 ISSN 0044-3093 R&D Projects: GA MPO(CZ) FF-P2/053 Institutional research plan: CEZ:AV0Z10100520 Keywords : compensation effect * enthalpy * entropy * thermodynamics * grain boundary Subject RIV: BJ - Thermodynamics Impact factor: 0.842, year: 2005
Enthalpy-entropy compensation and the isokinetic temperature in ...
Indian Academy of Sciences (India)
Enthalpy-entropy compensation supposes that differences in activation enthalpy delta-H-++ for different reactions (or, typically inbiochemistry, the same reaction catalysed by enzymes obtained from different species) may be compensated for bydifferences in activation entropy delta-S-++. At the isokinetic temperature the ...
Enthalpy?entropy compensation: the role of solvation
Dragan, Anatoliy I.; Read, Christopher M.; Crane-Robinson, Colyn
2016-01-01
Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy-entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e. a compensating conformational entropy reduct...
Enthalpy-Entropy Compensation upon Molecular Conformational Changes.
Ahmad, Mazen; Helms, Volkhard; Lengauer, Thomas; Kalinina, Olga V
2015-04-14
The change in free energy is the dominant factor in all chemical processes; it usually encompasses enthalpy-entropy compensation (EEC). Here, we use the free energy perturbation formalism to show that EEC is influenced by the molecular conformational changes (CCs) of the entire system comprising the solute and by the already known solvent reorganization. The internal changes of enthalpy and the entropy due to CCs upon modifying the interactions (perturbation) cancel each other exactly. The CCs influence the dissipation of the modified interactions and their contributions to the free energy. Using molecular simulations, we show that, for solvation of six different HIV-1 protease inhibitors, CCs in the solute cause EEC as large as 10-30 kcal/mol. Moreover, the EEC due to CCs in HIV-1 protease is shown to vary significantly upon modifying its bound ligand. These findings have important implications for understanding of EEC phenomena and for interpretation of thermodynamic measurements.
Joynt, Suzanne; Morillo, Victor; Leng, Fenfei
2009-05-20
HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)(2) is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5'-CCAAAAAAAAAAAAAAAGCCCCCGCTTTTTTTTTTTTTTTGG-3' (FL-AT-1) and 5'-CCATATATATATATATAGCCCCCGCTATATATATATATATGG-3' (FL-AT-2). Surprisingly, we observed an atypical isothermal-titration-calorimetry-binding curve at low-salt aqueous solutions whereby the apparent binding-enthalpy decreased dramatically as the titration approached the end. This unusual behavior can be attributed to the DNA-annealing coupled to the ligand DNA-binding and is eliminated by increasing the salt concentration to approximately 200 mM. At this condition, HMGA2 binding to FL-AT-1 is entropy-driven and to FL-AT-2 is enthalpy-driven. Interestingly, the DNA-binding free energies for HMGA2 binding to both hairpins are almost temperature independent; however, the enthalpy-entropy changes are dependent on temperature, which is another aspect of enthalpy-entropy compensation. The heat capacity change for HMGA2 binding to FL-AT-1 and FL-AT-2 are almost identical, indicating that the solvent displacement and charge-charge interaction in the coupled folding/binding processes for both binding reactions are similar.
Listening to PS II: enthalpy, entropy, and volume changes.
Hou, Harvey J M; Mauzerall, David
2011-01-01
Photosystem II, located in the thylakoid membranes of green plants, algae, and cyanobacteria, uses sunlight to split water into protons, electrons, and a dioxygen molecule. The mechanism of its electron transfers and oxygen evolution including the structure of the protein and rates of the S-state cycle has been extensively investigated. Substantial progress has been made; however, the thermodynamics of PS II electron transfer and of the oxygen cycle are poorly understood. Recent progress in thermodynamic measurements in photosynthesis provides novel insights on the enthalpic and entropic contribution to electron transfer in proteins. In this review the thermodynamic parameters including quantum yield, enthalpy, entropy, and volume changes of PS II photochemistry determined by photoacoustics and other laser techniques are summarized and evaluated. Light-driven volume changes via electrostriction are directly related to the photoreaction in PS II and thus can be a useful measurement of PS II activity and function. The enthalpy changes of the reactions observed can be directly measured by photoacoustics. The apparent reaction entropy can also be estimated when the free energy is known. Dissecting the free energy of a photoreaction into enthalpic and entropic components provides critical information about mechanisms of PS II function. Potential limitations and future direction of the study of the thermodynamics of PS II electron transfer and oxygen evolution are presented. Published by Elsevier B.V.
Molecular rigidity and enthalpy-entropy compensation in DNA melting.
Vargas-Lara, Fernando; Starr, Francis W; Douglas, Jack F
2017-11-15
Enthalpy-entropy compensation (EEC) is observed in diverse molecular binding processes of importance to living systems and manufacturing applications, but this widely occurring phenomenon is not sufficiently understood from a molecular physics standpoint. To gain insight into this fundamental problem, we focus on the melting of double-stranded DNA (dsDNA) since measurements exhibiting EEC are extensive for nucleic acid complexes and existing coarse-grained models of DNA allow us to explore the influence of changes in molecular parameters on the energetic parameters by using molecular dynamics simulations. Previous experimental and computational studies have indicated a correlation between EEC and changes in molecular rigidity in certain binding-unbinding processes, and, correspondingly, we estimate measures of DNA molecular rigidity under a wide range of conditions, along with resultant changes in the enthalpy and entropy of binding. In particular, we consider variations in dsDNA rigidity that arise from changes of intrinsic molecular rigidity such as varying the associative interaction strength between the DNA bases, the length of the DNA chains, and the bending stiffness of the individual DNA chains. We also consider extrinsic changes of molecular rigidity arising from the addition of polymer additives and geometrical confinement of DNA between parallel plates. All our computations confirm EEC and indicate that this phenomenon is indeed highly correlated with changes in molecular rigidity. However, two distinct patterns relating to how DNA rigidity influences the entropy of association emerge from our analysis. Increasing the intrinsic DNA rigidity increases the entropy of binding, but increases in molecular rigidity from external constraints decreases the entropy of binding. EEC arises in numerous synthetic and biological binding processes and we suggest that changes in molecular rigidity might provide a common origin of this ubiquitous phenomenon in the mutual
Hydration of lysozyme: the protein-protein interface and the enthalpy-entropy compensation.
Kocherbitov, Vitaly; Arnebrant, Thomas
2010-03-16
Water sorption isotherms of proteins are usually interpreted with such models as BET or GAB that imply the formation of multilayers at solid-gas interface. However, this approach is not applicable to globular proteins such as humid lysozyme where a solid-gas interface does not exist. Another popular approach is the D'Arcy-Watt model, where besides the formation of multilayers the heterogeneity of energies of sorption sites of proteins is taken into account. Here we present sorption calorimetric data on the hydration of lysozyme that confirms the existence of the heterogeneity. The magnitude of the heterogeneity is, however, lower than one can expect on the basis of the existence of a solid-gas interface. Moreover, the calorimetric data show a strong enthalpy-entropy compensation that leads to almost constant effective free energy of hydration in the activity range normally used for fitting the data to sorption models. This allows the use of the Langmuir equation for the fitting of the initial part of the sorption isotherm of lysozyme. Assuming the formation of a monolayer of water at the protein-protein interface, one can estimate the size of the lysozyme molecules from the sorption isotherm. The result of this estimation is in good agreement with the structural data on lysozyme, which supports the presented approach.
Enthalpy-Entropy Compensation (EEC) Effect: Decisive Role of Free Energy.
Pan, Animesh; Kar, Tanmoy; Rakshit, Animesh K; Moulik, Satya P
2016-10-03
The "enthalpy-entropy compensation" (EEC) effect has been a long-standing fascinating yet unresolved phenomenon in chemical thermodynamics. The reasons for the observation of EEC are not clear. Various views such as empirical, extrathermodynamic, error-related, solvation, and so forth as reasons for the H/S linear correlation are floating. Statistical reasons and a hidden Carnot's cycle (involving microscopic "heating and cooling" machines) have also been proposed recently for the observation of EEC. In this work, we have attempted a different line of approach to understand and explain the phenomenon. In the EEC treatment, the enthalpy (ΔH) and entropy (ΔS) values of "similar processes" are considered keeping aside the role of the other important thermodynamic parameter, that is, the free energy (ΔG). Considering ΔG along with ΔH and ΔS, it is established that the conventional EEC plot is not appropriate and mathematically sound. Consideration of ΔG may account for correlations of different kinds, linear, nonlinear, and so forth. Reports of non- or anticompensation phenomenon also prevail in the literature. A realistic account of the role of ΔG along with ΔH and ΔS in the understanding of such EEC correlations using authentic literature data is presented and discussed herein. EEC has several facets. Planned studies on similar systems with a wide range of ΔG values are required for realistic evaluation of the EEC and antienthalpy entropy compensation manifestations.
Yang, Robin C K; Huang, Jonathan T B; Chien, Shih-Chuan; Huang, Roy; Jeng, Kee-Ching G; Chen, Yen-Chung; Liao, Mokai; Wu, Jia-Rong; Hung, Wei-Kang; Hung, Chia-Chun; Chen, Yu-Ling; Waring, Michael J; Sheh, Leung
2013-01-07
This study aims to interpret the energetic basis of complex DNA-peptide interactions according to a novel allosteric interaction network approach. In common with other designed peptides, five new conjugates incorporating the XPRK or XHypRK motif (Hyp = hydroxyproline) attached to a N-methylpyrrole (Py) tract with a basic tail have been found to display cooperative binding to DNA involving multiple monodentate as well as interstrand bidentate interactions. Using quantitative DNase I footprinting it appears that allosteric communication via cooperative binding to multiple sites on complementary DNA strands corresponds to two different types of DNA-peptide interaction network. Temperature variation experiments using a dodecapeptide RY-12 show that lower temperature (25 °C) favor a circuit type of allosteric interaction network, whereas higher temperatures (31 and 37 °C) afford only a partial-circuit type of network. Circular dichroism studies show that our five peptides induce significant local conformational changes in DNA via the minor groove, with apparently dimeric binding stoichiometry. Isothermal titration calorimetry reveals that these peptides, together with another seven for comparison, are strongly exothermic upon binding to a model 13-mer DNA duplex, characterized by ΔH ranging from -14.7 to -74.4 kcal mol(-1), and also high TΔS ranging from -6.5 to -65.9 kcal mol(-1). Multiple monodentate and bidentate interactions, as well as ionic forces that mediate positive cooperativity in sequence recognition, are consistent with a dramatic decrease in entropy and a 'tightening' effect of DNA conformation. Distinctive enthalpy-entropy compensation (EEC) relationships are demonstrated for the interaction of all twelve designed peptides with DNA, affording a straight line of slope close to unity when ΔH is plotted versus TΔS, with a y-axis intercept (average ΔG) corresponding to -8.5 kcal mol(-1), while the observed ΔG ranges from -8.2 to -9.1 kcal mol(-1) for
Water networks contribute to enthalpy/entropy compensation in protein-ligand binding.
Breiten, Benjamin; Lockett, Matthew R; Sherman, Woody; Fujita, Shuji; Al-Sayah, Mohammad; Lange, Heiko; Bowers, Carleen M; Heroux, Annie; Krilov, Goran; Whitesides, George M
2013-10-16
The mechanism (or mechanisms) of enthalpy-entropy (H/S) compensation in protein-ligand binding remains controversial, and there are still no predictive models (theoretical or experimental) in which hypotheses of ligand binding can be readily tested. Here we describe a particularly well-defined system of protein and ligands--human carbonic anhydrase (HCA) and a series of benzothiazole sulfonamide ligands with different patterns of fluorination--that we use to define enthalpy/entropy (H/S) compensation in this system thermodynamically and structurally. The binding affinities of these ligands (with the exception of one ligand, in which the deviation is understood) to HCA are, despite differences in fluorination pattern, indistinguishable; they nonetheless reflect significant and compensating changes in enthalpy and entropy of binding. Analysis reveals that differences in the structure and thermodynamic properties of the waters surrounding the bound ligands are an important contributor to the observed H/S compensation. These results support the hypothesis that the molecules of water filling the active site of a protein, and surrounding the ligand, are as important as the contact interactions between the protein and the ligand for biomolecular recognition, and in determining the thermodynamics of binding.
Joynt, Suzanne; Morillo, Victor; Leng, Fenfei
2009-01-01
HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)2 is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5′-CCAAAAAAAAAAAAAAAGCCCCCGCTT...
Enthalpy-entropy compensation and the isokinetic temperature in enzyme catalysis.
Cornish-Bowden, Athel
2017-12-01
Enthalpy-entropy compensation supposes that differences in activation enthalpy ΔH++ for different reactions (or, typically in biochemistry, the same reaction catalysed by enzymes obtained from different species) may be compensated for by differences in activation entropy ΔS++. At the isokinetic temperature the compensation is exact, so that all samples have the same activity. These ideas have been controversial for several decades, but examples are still frequently reported as evidence of a real phenomenon, nearly all of the reports ignoring or discounting the possibility of a statistical artefact. Even for measurements in pure chemistry artefacts occur often, and they are almost inescapable in enzyme kinetics and other fields that involve biological macromolecules, on account of limited stability and the fact that kinetic equations are normally valid only over a restricted range of temperature. Here I review the current status and correct an error in a recent book chapter.
Directory of Open Access Journals (Sweden)
Hercigonja R.
2015-01-01
Full Text Available In this work, the values of entropy changes related to n-hexane adsorption onto cation exchanged Y zeolite were calculated from differential heats. Various transition metal cations (Co2+, Ni2+, Zn2+ and Cd2+ were introduced into the lattice of the parent NaY, and the existence of enthalpy-entropy compensation effect related to n-hexane adsorption, id. est, the linearity of -ΔH vs. -ΔS plots was examined. The compensation effect was confirmed for all investigated zeolites. The compensation effect can be comprehended as governed by ion-induced dipole interaction between highly polarizing cationic centers in zeolite and nonopolar n-hexane molecules. Finally, the compensation effect and so the compensation temperature were found to depend on the type of charge-balancing cation (charge, size and electronic configuration. [Projekat Ministarstva nauke Republike Srbije, br. 172018
Discussion of enthalpy, entropy and free energy of formation of GaN
Jacob, K. T.; Rajitha, G.
2009-07-01
Presented in this letter is a critical discussion of a recent paper on experimental investigation of the enthalpy, entropy and free energy of formation of gallium nitride (GaN) published in this journal [T.J. Peshek, J.C. Angus, K. Kash, J. Cryst. Growth 311 (2008) 185-189]. It is shown that the experimental technique employed detects neither the equilibrium partial pressure of N 2 corresponding to the equilibrium between Ga and GaN at fixed temperatures nor the equilibrium temperature at constant pressure of N 2. The results of Peshek et al. are discussed in the light of other information on the Gibbs energy of formation available in the literature. Entropy of GaN is derived from heat-capacity measurements. Based on a critical analysis of all thermodynamic information now available, a set of optimized parameters is identified and a table of thermodynamic data for GaN developed from 298.15 to 1400 K.
The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition.
Fox, Jerome M; Zhao, Mengxia; Fink, Michael J; Kang, Kyungtae; Whitesides, George M
2018-03-05
Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon-termed enthalpy/entropy (H/S) compensation-hinders efforts in biomolecular design, and its incidence-often a surprise to experimentalists-makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting- and, perhaps, avoiding or exploiting-this phenomenon in biophysical systems. Expected final online publication date for the Annual Review of Biophysics Volume 47 is May 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Zinc bioavailability from whey. Enthalpy-entropy compensation in protein binding.
Tang, Ning; Skibsted, Leif H
2016-11-01
Zinc amino acid or peptide complexes improve zinc absorption, however, the thermodynamics behind the interaction between zinc ion and these potential ligands is not well characterized. Therefore, binding of zinc to amino acids, peptides and whey proteins were investigated by isothermal titration calorimetry to provide useful information for improving zinc bioavailability which is lowered by many food components like phytate. Zinc binding to lactoferrin and to bovine serum albumin was found exothermic with ∆H=-100kJ/mol and -30kJ/mol, respectively, in aqueous 0.16M NaCl of pH7.4 at 25°C by isothermal titration calorimetry, while binding to α-lactalbumin and β-lactoglobulin was slightly endothermic. Still the binding constant was for all four proteins found to have a value around 2×10 5 L/mol indicating enthalpy-entropy compensation as also confirmed for zinc binding to amino acids with cysteine being enthalpically favored, while serineenthalpy-entropy compensation makes whey proteins more homogeneous as zinc vehicles counteracting concentration fluctuation and precipitation of zinc. Copyright © 2016 Elsevier Ltd. All rights reserved.
Liu, Guoyu; Gu, Daming; Liu, Haiyan; Ding, Wei; Li, Zhong
2011-06-15
Molecular dynamics simulations and free energy perturbation (FEP) were performed for studying the enthalpy-entropy compensation with a series of ionic liquid-type Gemini imidazolium surfactants (ILGIS), with different carbon atoms of the hydrophobic group or the spacer chain length, in aqueous solutions. According to the law of mass action, the thermodynamic properties of micellization in aqueous solutions for ILGIS were discussed. The results show that the solvation free energy changes calculated from the free energy perturbation are close to the Gibbs free energy calculated from the surface tension method and can be used to discriminate the tendency for micellization and predict the thermodynamic properties of ILGIS. The micellization of ILGIS in aqueous solutions is a spontaneous and entropy-driven process. It is enthalpy-entropy compensated, and the enthalpy-entropy compensation plots exhibit an excellent linearity. The compensation temperature was found to be (307±2) K. As the number carbon atoms in the alkyl chains is increased, the tendency and stability of micellization both increase. At spacer length S≤6, with the spacer chain length increasing, the thermodynamic favorability and stability of the micelles decrease. However, if S>6, thermodynamic favorability and stability increase with raising the spacer chain length. Copyright © 2011 Elsevier Inc. All rights reserved.
DEFF Research Database (Denmark)
Tidemand, Kasper Damgaard; Schonbeck, Christian; Holm, Rene
2014-01-01
in complexation entropy with DS was not able to compensate for this unfavorable change in enthalpy induced by the HP substituents, resulting in a destabilizing effect. This was found to originate from fixation of the HP substituents and decreased free rotation of the bile salts within the CD cavities....... of water molecules in the cavity increased with the DS. Release of water from the cavity resulted in a positive enthalpy change, which correlates qualitatively with the experimentally determined increase in complexation enthalpy and contributes to the enthalpy-entropy compensation. The positive change...
Paul, Bijan K; Ghosh, Narayani; Mukherjee, Saptarshi
2016-04-28
Herein, we present an endeavor toward exploring the lacuna underlying the host:guest chemistry of inclusion complex formation between bile salt(s) and β-cyclodextrin(s) (βCDs). An extensive thermodynamic investigation based on isothermal titration calorimetry (ITC) demonstrates a dominant contribution from exothermic enthalpy change (ΔH enthalpy-entropy compensation behavior showing indication for almost complete compensation. To this end, we have quantified the interaction of two bile salt molecules (namely, sodium deoxycholate and sodium glycocholate) with a series of varying chemical substituents on the host counterpart, namely, βCD, (2-hydroxypropyl)-βCD, and methyl βCD.
Toal, Siobhan E; Verbaro, Daniel J; Schweitzer-Stenner, Reinhard
2014-02-06
The driving forces governing the unique and restricted conformational preferences of amino acid residues in the unfolded state are still not well understood. In this study, we experimentally determine the individual thermodynamic components underlying intrinsic conformational propensities of these residues. Thermodynamic analysis of ultraviolet-circular dichroism (UV-CD) and (1)H NMR data for a series of glycine capped amino acid residues (i.e., G-x-G peptides) reveals the existence of a nearly exact enthalpy-entropy compensation for the polyproline II-β strand equilibrium for all investigated residues. The respective ΔHβ, ΔSβ values exhibit a nearly perfect linear relationship with an apparent compensation temperature of 295 ± 2 K. Moreover, we identified iso-equilibrium points for two subsets of residues at 297 and 305 K. Thus, our data suggest that within this temperature regime, which is only slightly below physiological temperatures, the conformational ensembles of amino acid residues in the unfolded state differ solely with respect to their capability to adopt turn-like conformations. Such iso-equilibria are rarely observed, and their existence herein indicates a common physical origin behind conformational preferences, which we are able to assign to side-chain dependent backbone solvation. Conformational effects such as differences between the number of sterically allowed side chain rotamers can contribute to enthalpy and entropy but not to the Gibbs energy associated with conformational preferences. Interestingly, we found that alanine, aspartic acid, and threonine are the only residues which do not share these iso-equilbiria. The enthalpy-entropy compensation discovered as well as the iso-equilbrium and thermodynamics obtained for each amino acid residue provide a new and informative way of identifying the determinants of amino acid propensities in unfolded and disordered states.
Towards Translating Graph Transformation Approaches by Model Transformations
Hermann, F.; Kastenberg, H.; Modica, T.; Karsai, G.; Taentzer, G.
2006-01-01
Recently, many researchers are working on semantics preserving model transformation. In the field of graph transformation one can think of translating graph grammars written in one approach to a behaviourally equivalent graph grammar in another approach. In this paper we translate graph grammars
Tidemand, Kasper D; Schönbeck, Christian; Holm, René; Westh, Peter; Peters, Günther H
2014-09-18
The inclusion complexes of glycoconjugated bile salts with β-cyclodextrin (β-CD) and 2-hydroxypropyl-β-cyclodextrins (HP-β-CD) in aqueous solution were investigated by molecular dynamics simulations to provide a molecular explanation of the experimentally observed destabilizing effect of the HP substituents. Good agreement with experimental data was found with respect to penetration depths of CDs. An increased degree of HP substitution (DS) resulted in an increased probability of blocking the cavity opening, thereby hindering the bile salt from entering CD. Further, the residence time of water molecules in the cavity increased with the DS. Release of water from the cavity resulted in a positive enthalpy change, which correlates qualitatively with the experimentally determined increase in complexation enthalpy and contributes to the enthalpy-entropy compensation. The positive change in complexation entropy with DS was not able to compensate for this unfavorable change in enthalpy induced by the HP substituents, resulting in a destabilizing effect. This was found to originate from fixation of the HP substituents and decreased free rotation of the bile salts within the CD cavities.
Pera-Titus, M
2016-08-10
The adsorption of CO2 coupled to calorimetry is a state-of-the-art technique for characterizing the basic properties of solids. In this paper, we show that the differential heat and entropy curves measured upon CO2 adsorption on a basic solid can be reasonably estimated from a single CO2 isotherm with no need for any independent heat (calorimetric) measurement. Our method relies on two important observations: (1) formulation of generalized F-H-TS thermodynamic isotherms, the former (F) being directly generated from the raw CO2 isotherms, and (2) the presence of unexpected enthalpy-entropy compensation effects upon CO2 adsorption linking the integral enthalpy and entropy of adsorption until saturation for different solids. Our thermodynamic method has been validated using a broad library of basic solids with variable site strength and heterogeneity. Finally, a new scale of basicity is proposed using the parameters fitted from the thermodynamic isotherm (free energy basis) as descriptors of basic strength. This method opens an avenue to the inference of site strength of basic solids without the need for expensive calorimeters.
An Association-Oriented Partitioning Approach for Streaming Graph Query
Directory of Open Access Journals (Sweden)
Yun Hao
2017-01-01
Full Text Available The volumes of real-world graphs like knowledge graph are increasing rapidly, which makes streaming graph processing a hot research area. Processing graphs in streaming setting poses significant challenges from different perspectives, among which graph partitioning method plays a key role. Regarding graph query, a well-designed partitioning method is essential for achieving better performance. Existing offline graph partitioning methods often require full knowledge of the graph, which is not possible during streaming graph processing. In order to handle this problem, we propose an association-oriented streaming graph partitioning method named Assc. This approach first computes the rank values of vertices with a hybrid approximate PageRank algorithm. After splitting these vertices with an adapted variant affinity propagation algorithm, the process order on vertices in the sliding window can be determined. Finally, according to the level of these vertices and their association, the partition where the vertices should be distributed is decided. We compare its performance with a set of streaming graph partition methods and METIS, a widely adopted offline approach. The results show that our solution can partition graphs with hundreds of millions of vertices in streaming setting on a large collection of graph datasets and our approach outperforms other graph partitioning methods.
Survey of Approaches to Generate Realistic Synthetic Graphs
Energy Technology Data Exchange (ETDEWEB)
Lim, Seung-Hwan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Sangkeun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Powers, Sarah S [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Shankar, Mallikarjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Imam, Neena [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
2016-10-01
A graph is a flexible data structure that can represent relationships between entities. As with other data analysis tasks, the use of realistic graphs is critical to obtaining valid research results. Unfortunately, using the actual ("real-world") graphs for research and new algorithm development is difficult due to the presence of sensitive information in the data or due to the scale of data. This results in practitioners developing algorithms and systems that employ synthetic graphs instead of real-world graphs. Generating realistic synthetic graphs that provide reliable statistical confidence to algorithmic analysis and system evaluation involves addressing technical hurdles in a broad set of areas. This report surveys the state of the art in approaches to generate realistic graphs that are derived from fitted graph models on real-world graphs.
Enthalpy-Entropy Compensation in the Binding of Modulators at Ionotropic Glutamate Receptor GluA2.
Krintel, Christian; Francotte, Pierre; Pickering, Darryl S; Juknaitė, Lina; Pøhlsgaard, Jacob; Olsen, Lars; Frydenvang, Karla; Goffin, Eric; Pirotte, Bernard; Kastrup, Jette S
2016-06-07
The 1,2,4-benzothiadiazine 1,1-dioxide type of positive allosteric modulators of the ionotropic glutamate receptor A2 (GluA2) are promising lead compounds for the treatment of cognitive disorders, e.g., Alzheimer's disease. The modulators bind in a cleft formed by the interface of two neighboring ligand binding domains and act by stabilizing the agonist-bound open-channel conformation. The driving forces behind the binding of these modulators can be significantly altered with only minor substitutions to the parent molecules. In this study, we show that changing the 7-fluorine substituent of modulators BPAM97 (2) and BPAM344 (3) into a hydroxyl group (BPAM557 (4) and BPAM521 (5), respectively), leads to a more favorable binding enthalpy (ΔH, kcal/mol) from -4.9 (2) and -7.5 (3) to -6.2 (4) and -14.5 (5), but also a less favorable binding entropy (-TΔS, kcal/mol) from -2.3 (2) and -1.3 (3) to -0.5 (4) and 4.8 (5). Thus, the dissociation constants (Kd, μM) of 4 (11.2) and 5 (0.16) are similar to those of 2 (5.6) and 3 (0.35). Functionally, 4 and 5 potentiated responses of 10 μM L-glutamate at homomeric rat GluA2(Q)i receptors with EC50 values of 67.3 and 2.45 μM, respectively. The binding mode of 5 was examined with x-ray crystallography, showing that the only change compared to that of earlier compounds was the orientation of Ser-497 pointing toward the hydroxyl group of 5. The favorable enthalpy can be explained by the formation of a hydrogen bond from the side-chain hydroxyl group of Ser-497 to the hydroxyl group of 5, whereas the unfavorable entropy might be due to desolvation effects combined with a conformational restriction of Ser-497 and 5. In summary, this study shows a remarkable example of enthalpy-entropy compensation in drug development accompanied with a likely explanation of the underlying structural mechanism. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Kurhe, Deepti N; Dagade, Dilip H; Jadhav, Jyoti P; Govindwar, Sanjay P; Patil, Kesharsingh J
2009-12-31
Densities and osmotic coefficient measurements for dilute aqueous solutions of glycine, l-leucine, and glycylglycine have been reported at 298.15 K. The partial molar volumes and activity coefficients of solute as well as solvent have been estimated using the density and osmotic coefficient data, respectively. Excess and mixing thermodynamic properties, such as Gibbs free energy, enthalpy, and entropy changes, have been obtained using the activity data from this study and the heat data reported in the literature. The concentration enthalpy-entropy compensation effects have been observed for the studied systems, and the compensation temperatures are reported. It has been observed that the excess free energy change for all the studied systems is almost the same over the studied concentration range, showing that the differences in properties of such solutions are largely decided by the enthalpy-entropy effects. These results, along with partial entropy data, show the effects of the presence of hydrophobic interactions and water structure making effect in the case of aqueous solutions of l-leucine. The application of the Starikov-Norden enthalpy-entropy compensation model yielded information about a "hidden Carnot cycle" and the existence of multiple microphases. Application of the Kirkwood-Buff (KB) theory of solutions for the studied systems yields pair correlation functions between the components. The variation of Kirkwood-Buff integrals with concentration further signifies the concentration dependence of the hydrophobic hydration and interactions in the solution phase. The osmotic second virial coefficients have also been obtained using the KB theory and show good agreement with those obtained using the McMillan-Mayer theory of solutions. The mean square concentration fluctuations is estimated using the KB theory, which gives information about the microheterogeneity in the solution phase, which further reflects the presence of hydration and solute association.
An algebraic approach to graph codes
DEFF Research Database (Denmark)
Pinero, Fernando
theory as evaluation codes. Chapter three consists of the introduction to graph based codes, such as Tanner codes and graph codes. In Chapter four, we compute the dimension of some graph based codes with a result combining graph based codes and subfield subcodes. Moreover, some codes in chapter four...... are optimal or best known for their parameters. In chapter five we study some graph codes with Reed–Solomon component codes. The underlying graph is well known and widely used for its good characteristics. This helps us to compute the dimension of the graph codes. We also introduce a combinatorial concept...... related to the iterative encoding of graph codes with MDS component code. The last chapter deals with affine Grassmann codes and Grassmann codes. We begin with some previously known codes and prove that they are also Tanner codes of the incidence graph of the point–line partial geometry...
Ward, Joshua M; Gorenstein, Nina M; Tian, Jianhua; Martin, Stephen F; Post, Carol Beth
2010-08-18
NMR spectroscopy and molecular dynamics (MD) simulations were used to probe the structure and dynamics of complexes of three phosphotyrosine-derived peptides with the Src SH2 domain in an effort to uncover a structural explanation for enthalpy-entropy compensation observed in the binding thermodynamics. The series of phosphotyrosine peptide derivatives comprises the natural pYEEI Src SH2 ligand, a constrained mimic, in which the phosphotyrosine (pY) residue is preorganized in the bound conformation for the purpose of gaining an entropic advantage to binding, and a flexible analogue of the constrained mimic. The expected gain in binding entropy of the constrained mimic was realized; however, a balancing loss in binding enthalpy was also observed that could not be rationalized from the crystallographic structures. We examined protein dynamics to evaluate whether the observed enthalpic penalty might be the result of effects arising from altered motions in the complex. (15)N-relaxation studies and positional fluctuations from molecular dynamics indicate that the main-chain dynamics of the protein show little variation among the three complexes. Root mean squared (rms) coordinate deviations vary by less than 1.5 A for all non-hydrogen atoms for the crystal structures and in the ensemble average structures calculated from the simulations. In contrast to this striking similarity in the structures and dynamics, there are a number of large chemical shift differences from residues across the binding interface, but particularly from key Src SH2 residues that interact with pY, the "hot spot" residue, which contributes about one-half of the binding free energy. Rank-order correlations between chemical shifts and ligand binding enthalpy for several pY-binding residues, coupled with available mutagenesis and calorimetric data, suggest that subtle structural perturbations (enthalpy, leading to the observed enthalpy-entropy compensation. We find no evidence to support the premise
Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.
2012-08-01
processors) Operating system: Linux/Unix/Mac OS RAM: 2 Mbytes Classification: 16.3, 16.12, 23 Nature of problem: Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperatures) of complex molecules involving multiple torsional motions. Solution method: The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation [1]. Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multi-torsional problems for which one can afford to calculate all the conformations and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes and six utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomain defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 24 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 seconds. J. Zheng, T. Yu, E. Papajak, I.M. Alecu, S.L. Mielke, D.G. Truhlar, Practical methods for including torsional anharmonicity in thermochemical calculations of complex molecules: The internal-coordinate multi
Using graph approach for managing connectivity in integrative landscape modelling
Rabotin, Michael; Fabre, Jean-Christophe; Libres, Aline; Lagacherie, Philippe; Crevoisier, David; Moussa, Roger
2013-04-01
In cultivated landscapes, a lot of landscape elements such as field boundaries, ditches or banks strongly impact water flows, mass and energy fluxes. At the watershed scale, these impacts are strongly conditionned by the connectivity of these landscape elements. An accurate representation of these elements and of their complex spatial arrangements is therefore of great importance for modelling and predicting these impacts.We developped in the framework of the OpenFLUID platform (Software Environment for Modelling Fluxes in Landscapes) a digital landscape representation that takes into account the spatial variabilities and connectivities of diverse landscape elements through the application of the graph theory concepts. The proposed landscape representation consider spatial units connected together to represent the flux exchanges or any other information exchanges. Each spatial unit of the landscape is represented as a node of a graph and relations between units as graph connections. The connections are of two types - parent-child connection and up/downstream connection - which allows OpenFLUID to handle hierarchical graphs. Connections can also carry informations and graph evolution during simulation is possible (connections or elements modifications). This graph approach allows a better genericity on landscape representation, a management of complex connections and facilitate development of new landscape representation algorithms. Graph management is fully operational in OpenFLUID for developers or modelers ; and several graph tools are available such as graph traversal algorithms or graph displays. Graph representation can be managed i) manually by the user (for example in simple catchments) through XML-based files in easily editable and readable format or ii) by using methods of the OpenFLUID-landr library which is an OpenFLUID library relying on common open-source spatial libraries (ogr vector, geos topologic vector and gdal raster libraries). Open
From graphs to tensegrity structures : geometric and symbolic approaches
Guzmán, Miguel de
2006-01-01
A form-finding problem for tensegrity structures is studied; given an abstract graph, we show an algorithm to provide a necessary condition for it to be the underlying graph of a tensegrity in Rd (typically d = 2, 3) with vertices in general position. Furthermore, for a certain class of graphs our algorithm allows to obtain necessary and sufficient conditions on the relative position of the vertices in order to underlie a tensegrity, for what we propose both a geometric and a symbolic approach.
Graph Theory Approach for Studying Food Webs
Longjas, A.; Tejedor, A.; Foufoula-Georgiou, E.
2017-12-01
Food webs are complex networks of feeding interactions among species in ecological communities. Metrics describing food web structure have been proposed to compare and classify food webs ranging from food chain length, connectance, degree distribution, centrality measures, to the presence of motifs (distinct compartments), among others. However, formal methodologies for studying both food web topology and the dynamic processes operating on them are still lacking. Here, we utilize a quantitative framework using graph theory within which a food web is represented by a directed graph, i.e., a collection of vertices (species or trophic species defined as sets of species sharing the same predators and prey) and directed edges (predation links). This framework allows us to identify apex (environmental "source" node) to outlet (top predators) subnetworks and compute the steady-state flux (e.g., carbon, nutrients, energy etc.) in the food web. We use this framework to (1) construct vulnerability maps that quantify the relative change of flux delivery to the top predators in response to perturbations in prey species (2) identify keystone species, whose loss would precipitate further species extinction, and (3) introduce a suite of graph-theoretic metrics to quantify the topologic (imposed by food web connectivity) and dynamic (dictated by the flux partitioning and distribution) components of a food web's complexity. By projecting food webs into a 2D Topodynamic Complexity Space whose coordinates are given by Number of alternative paths (topologic) and Leakage Index (dynamic), we show that this space provides a basis for food web comparison and provide physical insights into their dynamic behavior.
A hierarchical approach to reducing communication in parallel graph algorithms
Harshvardhan,
2015-01-01
Large-scale graph computing has become critical due to the ever-increasing size of data. However, distributed graph computations are limited in their scalability and performance due to the heavy communication inherent in such computations. This is exacerbated in scale-free networks, such as social and web graphs, which contain hub vertices that have large degrees and therefore send a large number of messages over the network. Furthermore, many graph algorithms and computations send the same data to each of the neighbors of a vertex. Our proposed approach recognizes this, and reduces communication performed by the algorithm without change to user-code, through a hierarchical machine model imposed upon the input graph. The hierarchical model takes advantage of locale information of the neighboring vertices to reduce communication, both in message volume and total number of bytes sent. It is also able to better exploit the machine hierarchy to further reduce the communication costs, by aggregating traffic between different levels of the machine hierarchy. Results of an implementation in the STAPL GL shows improved scalability and performance over the traditional level-synchronous approach, with 2.5 × - 8× improvement for a variety of graph algorithms at 12, 000+ cores.
Montgomery, Andrew P; Skropeta, Danielle; Yu, Haibo
2017-10-31
Human β-galactoside α-2,6-sialyltransferase I (ST6Gal I) catalyses the synthesis of sialylated glycoconjugates. Overexpression of ST6Gal I is observed in many cancers, where it promotes metastasis through altered cell surface sialylation. A wide range of sialyltransferase inhibitors have been developed, with analogues structurally similar to the transition state exhibiting the highest inhibitory activity. To improve synthetic accessibility and pharmacokinetics of previously reported inhibitors, the replacement of the charged phosphodiester linker with a potential neutral isostere such as a carbamate or a 1,2,3-triazole has been investigated. Extensive molecular dynamics simulations have demonstrated that compounds with the alternate linkers could maintain key interactions with the human ST6Gal I active site, demonstrating the potential of a carbamate or a 1,2,3-triazole as a phosphodiester isostere. Free energy perturbation calculations provided energetic evidence suggesting that the carbamate and 1,2,3-triazole were slightly more favourable than the phosphodiester. Further exploration with free energy component, quasi-harmonic and cluster analysis suggested that there is an enthalpy-entropy compensation accounting for the replacement of the flexible charged phosphodiester with a neutral and rigid isostere. Overall, these simulations provide a strong rationale for the use of a carbamate or 1,2,3-triazole as a phosphodiester isostere in the development of novel inhibitors of human ST6Gal I.
Kwon, Oh-Hyun; Crnovrsanin, Tarik; Ma, Kwan-Liu
2018-01-01
Using different methods for laying out a graph can lead to very different visual appearances, with which the viewer perceives different information. Selecting a "good" layout method is thus important for visualizing a graph. The selection can be highly subjective and dependent on the given task. A common approach to selecting a good layout is to use aesthetic criteria and visual inspection. However, fully calculating various layouts and their associated aesthetic metrics is computationally expensive. In this paper, we present a machine learning approach to large graph visualization based on computing the topological similarity of graphs using graph kernels. For a given graph, our approach can show what the graph would look like in different layouts and estimate their corresponding aesthetic metrics. An important contribution of our work is the development of a new framework to design graph kernels. Our experimental study shows that our estimation calculation is considerably faster than computing the actual layouts and their aesthetic metrics. Also, our graph kernels outperform the state-of-the-art ones in both time and accuracy. In addition, we conducted a user study to demonstrate that the topological similarity computed with our graph kernel matches perceptual similarity assessed by human users.
Boiocchi, Massimo; Bonizzoni, Marco; Ciarrocchi, Carlo; Fabbrizzi, Luigi; Invernici, Michele; Licchelli, Maurizio
2018-02-11
The dimetallic system [Cu II 2 (L)] 4+ contains two facing equivalent metallocyclam subunits and incorporates ambidentate anions, mono- (halides) and poly-atomic (sulfate), which bridge the two Cu II centres. Isothermal titration calorimetry (ITC) experiments in water showed that the log K values of the inclusion equilibria for halides and sulfate varied over a restricted interval (3.6±0.2), which indicated lack of selectivity and that similarity of ΔG° values resulted from the unbalanced contribution of the ΔH° and TΔS° terms: the more favourable the one, the less favourable the other. In particular, a linear dependence of ΔH° and TΔS° was observed (a typical enthalpy/entropy compensatory diagram), which assigned a major role to hydration terms: 1) a more hydrated anion resulted in a more endothermic dehydration process; and 2) a larger number of water molecules released to the solution resulted in a more positive TΔS°. Limiting cases refer to the complexation 1) of the poorly hydrated iodide (highly exothermic process, entropically disfavoured), and 2) of the highly hydrated sulfate (moderately endothermic process, entropically very favoured). Anion receptors operating in water belong to two main domains: 1) those exhibiting positive ΔH° and positive TΔS° (+/+ signature), and 2) those displaying the opposite behaviour: (-/- signature). The receptor investigated herein connects the two domains, along the ΔH°/TΔS° straight line, thanks to the hidden role of the versatile metal-anion interaction. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
A graph-graph approach to the analysis of the set of associative rules
Belim, S. V.; Smirnova, T. B.; Mironenko, A. N.
2018-01-01
The article proposes a method for processing a set of associative rules, which makes it possible to identify additional relationships between the set of objects under study. The proposed approach consists of three stages. At the first stage, associative rules are revealed from the statistical data. At the second stage, constructed weighted oriented graph of relationships between the objects of the system. The third stage analyses the graph and identifies the community (community), which allows you to determine the groups of the most related objects. As an example, is given an analysis of the activities of public organizations. The result of the work is a method that allows to identify patterns from the analysis of a set of associative rules, and not just from a separate associative rule.
Engineering system dynamics a unified graph-centered approach
Brown, Forbes T
2006-01-01
For today's students, learning to model the dynamics of complex systems is increasingly important across nearly all engineering disciplines. First published in 2001, Forbes T. Brown's Engineering System Dynamics: A Unified Graph-Centered Approach introduced students to a unique and highly successful approach to modeling system dynamics using bond graphs. Updated with nearly one-third new material, this second edition expands this approach to an even broader range of topics. What's New in the Second Edition? In addition to new material, this edition was restructured to build students' competence in traditional linear mathematical methods before they have gone too far into the modeling that still plays a pivotal role. New topics include magnetic circuits and motors including simulation with magnetic hysteresis; extensive new material on the modeling, analysis, and simulation of distributed-parameter systems; kinetic energy in thermodynamic systems; and Lagrangian and Hamiltonian methods. MATLAB(R) figures promi...
A graph-based approach for designing extensible pipelines.
Rodrigues, Maíra R; Magalhães, Wagner C S; Machado, Moara; Tarazona-Santos, Eduardo
2012-07-12
In bioinformatics, it is important to build extensible and low-maintenance systems that are able to deal with the new tools and data formats that are constantly being developed. The traditional and simplest implementation of pipelines involves hardcoding the execution steps into programs or scripts. This approach can lead to problems when a pipeline is expanding because the incorporation of new tools is often error prone and time consuming. Current approaches to pipeline development such as workflow management systems focus on analysis tasks that are systematically repeated without significant changes in their course of execution, such as genome annotation. However, more dynamism on the pipeline composition is necessary when each execution requires a different combination of steps. We propose a graph-based approach to implement extensible and low-maintenance pipelines that is suitable for pipeline applications with multiple functionalities that require different combinations of steps in each execution. Here pipelines are composed automatically by compiling a specialised set of tools on demand, depending on the functionality required, instead of specifying every sequence of tools in advance. We represent the connectivity of pipeline components with a directed graph in which components are the graph edges, their inputs and outputs are the graph nodes, and the paths through the graph are pipelines. To that end, we developed special data structures and a pipeline system algorithm. We demonstrate the applicability of our approach by implementing a format conversion pipeline for the fields of population genetics and genetic epidemiology, but our approach is also helpful in other fields where the use of multiple software is necessary to perform comprehensive analyses, such as gene expression and proteomics analyses. The project code, documentation and the Java executables are available under an open source license at http://code.google.com/p/dynamic-pipeline. The system
A graph-based approach for designing extensible pipelines
Directory of Open Access Journals (Sweden)
Rodrigues Maíra R
2012-07-01
Full Text Available Abstract Background In bioinformatics, it is important to build extensible and low-maintenance systems that are able to deal with the new tools and data formats that are constantly being developed. The traditional and simplest implementation of pipelines involves hardcoding the execution steps into programs or scripts. This approach can lead to problems when a pipeline is expanding because the incorporation of new tools is often error prone and time consuming. Current approaches to pipeline development such as workflow management systems focus on analysis tasks that are systematically repeated without significant changes in their course of execution, such as genome annotation. However, more dynamism on the pipeline composition is necessary when each execution requires a different combination of steps. Results We propose a graph-based approach to implement extensible and low-maintenance pipelines that is suitable for pipeline applications with multiple functionalities that require different combinations of steps in each execution. Here pipelines are composed automatically by compiling a specialised set of tools on demand, depending on the functionality required, instead of specifying every sequence of tools in advance. We represent the connectivity of pipeline components with a directed graph in which components are the graph edges, their inputs and outputs are the graph nodes, and the paths through the graph are pipelines. To that end, we developed special data structures and a pipeline system algorithm. We demonstrate the applicability of our approach by implementing a format conversion pipeline for the fields of population genetics and genetic epidemiology, but our approach is also helpful in other fields where the use of multiple software is necessary to perform comprehensive analyses, such as gene expression and proteomics analyses. The project code, documentation and the Java executables are available under an open source license at http
Information Retrieval and Graph Analysis Approaches for Book Recommendation.
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.
Information Retrieval and Graph Analysis Approaches for Book Recommendation
Chahinez Benkoussas; Patrice Bellot
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 ...
A Factor Graph Approach to Automated GO Annotation.
Directory of Open Access Journals (Sweden)
Flavio E Spetale
Full Text Available 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.
Measuring geographic segregation: a graph-based approach
Hong, Seong-Yun; Sadahiro, Yukio
2014-04-01
Residential segregation is a multidimensional phenomenon that encompasses several conceptually distinct aspects of geographical separation between populations. While various indices have been developed as a response to different definitions of segregation, the reliance on such single-figure indices could oversimplify the complex, multidimensional phenomena. In this regard, this paper suggests an alternative graph-based approach that provides more detailed information than simple indices: The concentration profile graphically conveys information about how evenly a population group is distributed over the study region, and the spatial proximity profile depicts the degree of clustering across different threshold levels. These graphs can also be summarized into single numbers for comparative purposes, but the interpretation can be more accurate by inspecting the additional information. To demonstrate the use of these methods, the residential patterns of three major ethnic groups in Auckland, namely Māori, Pacific peoples, and Asians, are examined using the 2006 census data.
Seiller, Thomas
2014-01-01
In two previous papers, we exposed a combinatorial approach to the program of Geometry of Interaction, a program initiated by Jean-Yves Girard. The strength of our approach lies in the fact that we interpret proofs by simpler structures - graphs - than Girard's constructions, while generalizing the latter since they can be recovered as special cases of our setting. This third paper extends this approach by considering a generalization of graphs named graphings, which is in some way a geometri...
A Community-Aware Approach to Minimizing Dissemination in Graphs
Zhang, Chuxu
2017-08-02
Given a graph, can we minimize the spread of an entity (such as a meme or a virus) while maintaining the graph’s community structure (defined as groups of nodes with denser intra-connectivity than inter-connectivity)? At first glance, these two objectives seem at odds with each other. To minimize dissemination, nodes or links are often deleted to reduce the graph’s connectivity. These deletions can (and often do) destroy the graph’s community structure, which is an important construct in real-world settings (e.g., communities promote trust among their members). We utilize rewiring of links to achieve both objectives. Examples of rewiring in real life are prevalent, such as purchasing products from a new farm since the local farm has signs of mad cow disease; getting information from a new source after a disaster since your usual source is no longer available, etc. Our community-aware approach, called constrCRlink (short for Constraint Community Relink), preserves (on average) 98.6% of the efficacy of the best community-agnostic link-deletion approach (namely, NetMelt+), but changes the original community structure of the graph by only 4.5%. In contrast, NetMelt+ changes 13.6% of the original community structure.
Information Retrieval and Graph Analysis Approaches for Book Recommendation
Directory of Open Access Journals (Sweden)
Chahinez Benkoussas
2015-01-01
Full Text Available 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.
Description of continuous data using bar graphs: a misleading approach.
Martinez, Edson Zangiacomi
2015-01-01
With the ease provided by current computational programs, medical and scientific journals use bar graphs to describe continuous data. This manuscript discusses the inadequacy of bars graphs to present continuous data. Simulated data show that box plots and dot plots are more-feasible tools to describe continuous data. These plots are preferred to represent continuous variables since they effectively describe the range, shape, and variability of observations and clearly identify outliers. By contrast, bar graphs address only measures of central tendency. Bar graphs should be used only to describe qualitative data.
A Hybrid Approach to Processing Big Data Graphs on Memory-Restricted Systems
Harshvardhan,
2015-05-01
With the advent of big-data, processing large graphs quickly has become increasingly important. Most existing approaches either utilize in-memory processing techniques that can only process graphs that fit completely in RAM, or disk-based techniques that sacrifice performance. In this work, we propose a novel RAM-Disk hybrid approach to graph processing that can scale well from a single shared-memory node to large distributed-memory systems. It works by partitioning the graph into sub graphs that fit in RAM and uses a paging-like technique to load sub graphs. We show that without modifying the algorithms, this approach can scale from small memory-constrained systems (such as tablets) to large-scale distributed machines with 16, 000+ cores.
From graphs to tensegrity structures: Geometric and symbolic approaches
de Guzmán, Miguel; Orden, David
2004-01-01
A form-finding problem for tensegrity structures is studied; given an abstract graph, we show an algorithm to provide a necessary condition for it to be the underlying graph of a tensegrity in $\\mathbb{R}^d$ (typically $d=2,3$) with vertices in general position. Furthermore, for a certain class of graphs our algorithm allows to obtain necessary and sufficient conditions on the relative position of the vertices in order to underlie a tensegrity, for what we propose both a geometric and a symbo...
MetricForensics: A Multi-Level Approach for Mining Volatile Graphs
Energy Technology Data Exchange (ETDEWEB)
Henderson, Keith [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Eliassi-Rad, Tina [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Faloutsos, Christos [Carnegie Mellon Univ., Pittsburgh, PA (United States); Akoglu, Leman [Carnegie Mellon Univ., Pittsburgh, PA (United States); Li, Lei [Carnegie Mellon Univ., Pittsburgh, PA (United States); Maruhashi, Koji [Fujitsu Laboratories Ltd., Kanagawa (Japan); Prakash, B. Aditya [Carnegie Mellon Univ., Pittsburgh, PA (United States); Tong, H [Carnegie Mellon Univ., Pittsburgh, PA (United States)
2010-02-08
Advances in data collection and storage capacity have made it increasingly possible to collect highly volatile graph data for analysis. Existing graph analysis techniques are not appropriate for such data, especially in cases where streaming or near-real-time results are required. An example that has drawn significant research interest is the cyber-security domain, where internet communication traces are collected and real-time discovery of events, behaviors, patterns and anomalies is desired. We propose MetricForensics, a scalable framework for analysis of volatile graphs. MetricForensics combines a multi-level “drill down" approach, a collection of user-selected graph metrics and a collection of analysis techniques. At each successive level, more sophisticated metrics are computed and the graph is viewed at a finer temporal resolution. In this way, MetricForensics scales to highly volatile graphs by only allocating resources for computationally expensive analysis when an interesting event is discovered at a coarser resolution first. We test MetricForensics on three real-world graphs: an enterprise IP trace, a trace of legitimate and malicious network traffic from a research institution, and the MIT Reality Mining proximity sensor data. Our largest graph has »3M vertices and »32M edges, spanning 4:5 days. The results demonstrate the scalability and capability of MetricForensics in analyzing volatile graphs; and highlight four novel phenomena in such graphs: elbows, broken correlations, prolonged spikes, and strange stars.
Modified risk graph method using fuzzy rule-based approach
Energy Technology Data Exchange (ETDEWEB)
Nait-Said, R., E-mail: r_nait_said@hotmail.com [LARPI Laboratory, Safety Department, Institute of Health and Occupational Safety, University of Batna, Road Med El-Hadi Boukhlouf, Batna (Algeria); Zidani, F., E-mail: fati_zidani@lycos.com [LSPIE Laboratory, Electrical Engineering Department, Faculty of Engineering, University of Batna, Road Med El-Hadi Boukhlouf, Batna 05000 (Algeria); Ouzraoui, N., E-mail: ouzraoui@yahoo.fr [LARPI Laboratory, Safety Department, Institute of Health and Occupational Safety, University of Batna, Road Med El-Hadi Boukhlouf, Batna (Algeria)
2009-05-30
The risk graph is one of the most popular methods used to determine the safety integrity level for safety instrumented functions. However, conventional risk graph as described in the IEC 61508 standard is subjective and suffers from an interpretation problem of risk parameters. Thus, it can lead to inconsistent outcomes that may result in conservative SILs. To overcome this difficulty, a modified risk graph using fuzzy rule-based system is proposed. This novel version of risk graph uses fuzzy scales to assess risk parameters and calibration may be made by varying risk parameter values. Furthermore, the outcomes which are numerical values of risk reduction factor (the inverse of the probability of failure on demand) can be compared directly with those given by quantitative and semi-quantitative methods such as fault tree analysis (FTA), quantitative risk assessment (QRA) and layers of protection analysis (LOPA).
Modified risk graph method using fuzzy rule-based approach.
Nait-Said, R; Zidani, F; Ouzraoui, N
2009-05-30
The risk graph is one of the most popular methods used to determine the safety integrity level for safety instrumented functions. However, conventional risk graph as described in the IEC 61508 standard is subjective and suffers from an interpretation problem of risk parameters. Thus, it can lead to inconsistent outcomes that may result in conservative SILs. To overcome this difficulty, a modified risk graph using fuzzy rule-based system is proposed. This novel version of risk graph uses fuzzy scales to assess risk parameters and calibration may be made by varying risk parameter values. Furthermore, the outcomes which are numerical values of risk reduction factor (the inverse of the probability of failure on demand) can be compared directly with those given by quantitative and semi-quantitative methods such as fault tree analysis (FTA), quantitative risk assessment (QRA) and layers of protection analysis (LOPA).
A Framework to Measure the Service Quality of Distributor with Fuzzy Graph Theoretic Approach
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Tarun Kumar Gupta
2016-01-01
Full Text Available A combination of fuzzy logic and graph theoretic approach has been used to find the service quality of distributor in a manufacturing supply chain management. This combination is termed as the fuzzy graph theoretic (FGT approach. Initially the identified factors were grouped by SPSS (statistical package for social science software and then the digraph approach was applied. The interaction and inheritance values were calculated by fuzzy graph theory approach in terms of permanent function. Then a single numerical index was calculated by using permanent function which indicates the distributor service quality. This method can be used to compare the service quality of different distributors.
Fractional graph theory a rational approach to the theory of graphs
Scheinerman, Edward R
2013-01-01
A unified treatment of the most important results in the study of fractional graph concepts, this volume explores the various ways in which integer-valued concepts can be modified to derive nonintegral values. It begins with the general fractional theory of hypergraphs and presents in-depth coverage of fundamental and advanced topics. Subjects include fractional matching, fractional coloring, fractional edge coloring, fractional arboricity via matroid methods, and fractional isomorphism. The final chapter examines additional topics such as fractional domination, fractional intersection numbers
A semantic graph-based approach to biomedical summarisation.
Plaza, Laura; Díaz, Alberto; Gervás, Pablo
2011-09-01
Access to the vast body of research literature that is available in biomedicine and related fields may be improved by automatic summarisation. This paper presents a method for summarising biomedical scientific literature that takes into consideration the characteristics of the domain and the type of documents. To address the problem of identifying salient sentences in biomedical texts, concepts and relations derived from the Unified Medical Language System (UMLS) are arranged to construct a semantic graph that represents the document. A degree-based clustering algorithm is then used to identify different themes or topics within the text. Different heuristics for sentence selection, intended to generate different types of summaries, are tested. A real document case is drawn up to illustrate how the method works. A large-scale evaluation is performed using the recall-oriented understudy for gisting-evaluation (ROUGE) metrics. The results are compared with those achieved by three well-known summarisers (two research prototypes and a commercial application) and two baselines. Our method significantly outperforms all summarisers and baselines. The best of our heuristics achieves an improvement in performance of almost 7.7 percentage units in the ROUGE-1 score over the LexRank summariser (0.7862 versus 0.7302). A qualitative analysis of the summaries also shows that our method succeeds in identifying sentences that cover the main topic of the document and also considers other secondary or "satellite" information that might be relevant to the user. The method proposed is proved to be an efficient approach to biomedical literature summarisation, which confirms that the use of concepts rather than terms can be very useful in automatic summarisation, especially when dealing with highly specialised domains. Copyright © 2011 Elsevier B.V. All rights reserved.
A Practical Approach to Constructing a Knowledge Graph for Cybersecurity
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Yan Jia
2018-02-01
Full Text Available Cyberattack forms are complex and varied, and the detection and prediction of dynamic types of attack are always challenging tasks. Research on knowledge graphs is becoming increasingly mature in many fields. At present, it is very significant that certain scholars have combined the concept of the knowledge graph with cybersecurity in order to construct a cybersecurity knowledge base. This paper presents a cybersecurity knowledge base and deduction rules based on a quintuple model. Using machine learning, we extract entities and build ontology to obtain a cybersecurity knowledge base. New rules are then deduced by calculating formulas and using the path-ranking algorithm. The Stanford named entity recognizer (NER is also used to train an extractor to extract useful information. Experimental results show that the Stanford NER provides many features and the useGazettes parameter may be used to train a recognizer in the cybersecurity domain in preparation for future work. Keywords: Cybersecurity, Knowledge graph, Knowledge deduction
A Numerical Approach to Long Cycles in Graphs and Digraphs
Czech Academy of Sciences Publication Activity Database
Fiedler, Miroslav
2001-01-01
Roč. 235, - (2001), s. 233-236 ISSN 0012-365X R&D Projects: GA ČR GA201/98/0222 Institutional research plan: AV0Z1030915 Keywords : graph * diagraph * cycle * Hamilton cycle Subject RIV: BA - General Mathematics Impact factor: 0.301, year: 2001
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Daniele Penteado Rosa
2013-02-01
Full Text Available Orange seeds are a promising agroindustry-waste which can be implemented in the extraction and production of vegetable oil. The relationship between moisture content and water activity provides useful information for the processing and storage of this waste item. The aim of this study was to determine the mechanism of water sorption enthalpy-entropy of orange seeds (C. sinensis cv. Brazilians according to the moisture content. Therefore, desorption isotherms were determined at five different temperature (30, 40, 50, 60, and 70 ºC under a wide range of moisture content (0.005-0.057 kg kg-1 d.b. and water activity (0.02-0.756. Theoretical and empirical models were used for modeling the desorption isotherms. An analytical solution of the Clausius-Clapeyron equation was proposed to compute the isosteric heat of sorption, the differential entropy, and Gibbs free energy using the Oswin model when the effect of temperature on the hygroscopic equilibrium was considered.
Bolel, Priyanka; Datta, Shubhashis; Mahapatra, Niharendu; Halder, Mintu
2012-08-30
Formation of ion pair between charged molecule and protein can lead to interesting biochemical phenomena. We report the evolution of thermodynamics of the binding of tartrazine, a negatively charged azo colorant, and serum albumins with salt. The dye binds predominantly electrostatically in low buffer strengths; however, on increasing salt concentration, affinity decreases considerably. The calculated thermodynamic parameters in high salt indicate manifestation of nonelectrostatic interactions, namely, van der Waals force and hydrogen bonding. Site-marker competitive binding studies and docking simulations indicate that the dye binds with HSA in the warfarin site and with BSA at the interface of warfarin and ibuprofen binding sites. The docked poses indicate nearby amino acid positive side chains, which are possibly responsible for electrostatic interaction. Using the Debye-Hückel interionic attraction theory for binding equilibria, it is shown that, for electrostatic binding the calculated free energy change increases linearly with square root of ionic strength. Also UV-vis, fluorescence, CD data indicate a decrease of interaction with salt concentration. This study quantitatively relates how ionic strength modulates the strength of the protein-ligand electrostatic interaction. The binding enthalpy and entropy have been found to compensate one another. The enthalpy-entropy compensation (EEC), general property of weak intermolecular interactions, has been discussed.
Assessment of tautomer distribution using the condensed reaction graph approach
Gimadiev, T. R.; Madzhidov, T. I.; Nugmanov, R. I.; Baskin, I. I.; Antipin, I. S.; Varnek, A.
2018-03-01
We report the first direct QSPR modeling of equilibrium constants of tautomeric transformations (logK T ) in different solvents and at different temperatures, which do not require intermediate assessment of acidity (basicity) constants for all tautomeric forms. The key step of the modeling consisted in the merging of two tautomers in one sole molecular graph ("condensed reaction graph") which enables to compute molecular descriptors characterizing entire equilibrium. The support vector regression method was used to build the models. The training set consisted of 785 transformations belonging to 11 types of tautomeric reactions with equilibrium constants measured in different solvents and at different temperatures. The models obtained perform well both in cross-validation (Q2 = 0.81 RMSE = 0.7 logK T units) and on two external test sets. Benchmarking studies demonstrate that our models outperform results obtained with DFT B3LYP/6-311 ++ G(d,p) and ChemAxon Tautomerizer applicable only in water at room temperature.
A Parallel Approach for Frequent Subgraph Mining in a Single Large Graph Using Spark
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Fengcai Qiao
2018-02-01
Full Text Available Frequent subgraph mining (FSM plays an important role in graph mining, attracting a great deal of attention in many areas, such as bioinformatics, web data mining and social networks. In this paper, we propose SSiGraM (Spark based Single Graph Mining, a Spark based parallel frequent subgraph mining algorithm in a single large graph. Aiming to approach the two computational challenges of FSM, we conduct the subgraph extension and support evaluation parallel across all the distributed cluster worker nodes. In addition, we also employ a heuristic search strategy and three novel optimizations: load balancing, pre-search pruning and top-down pruning in the support evaluation process, which significantly improve the performance. Extensive experiments with four different real-world datasets demonstrate that the proposed algorithm outperforms the existing GraMi (Graph Mining algorithm by an order of magnitude for all datasets and can work with a lower support threshold.
Saund, Eric
2013-10-01
Effective object and scene classification and indexing depend on extraction of informative image features. This paper shows how large families of complex image features in the form of subgraphs can be built out of simpler ones through construction of a graph lattice—a hierarchy of related subgraphs linked in a lattice. Robustness is achieved by matching many overlapping and redundant subgraphs, which allows the use of inexpensive exact graph matching, instead of relying on expensive error-tolerant graph matching to a minimal set of ideal model graphs. Efficiency in exact matching is gained by exploitation of the graph lattice data structure. Additionally, the graph lattice enables methods for adaptively growing a feature space of subgraphs tailored to observed data. We develop the approach in the domain of rectilinear line art, specifically for the practical problem of document forms recognition. We are especially interested in methods that require only one or very few labeled training examples per category. We demonstrate two approaches to using the subgraph features for this purpose. Using a bag-of-words feature vector we achieve essentially single-instance learning on a benchmark forms database, following an unsupervised clustering stage. Further performance gains are achieved on a more difficult dataset using a feature voting method and feature selection procedure.
A direct mining approach to efficient constrained graph pattern discovery
DEFF Research Database (Denmark)
Zhu, Feida; Zhang, Zequn; Qu, Qiang
2013-01-01
Despite the wealth of research on frequent graph pattern mining, how to efficiently mine the complete set of those with constraints still poses a huge challenge to the existing algorithms mainly due to the inherent bottleneck in the mining paradigm. In essence, mining requests with explicitly...... which short twigs branch out. These patterns, which we formally define as l-long δ-skinny patterns, are able to reveal insightful spatial and temporal trajectory patterns in mobile data mining, information diffusion, adoption propagation, and many others. Based on the key concept of a canonical diameter......, we develop SkinnyMine, an efficient algorithm to mine all the l-long δ-skinny patterns guaranteeing both the completeness of our mining result as well as the unique generation of each target pattern. We also present a general direct mining framework together with two properties of reducibility...
A graph-based approach to detect spatiotemporal dynamics in satellite image time series
Guttler, Fabio; Ienco, Dino; Nin, Jordi; Teisseire, Maguelonne; Poncelet, Pascal
2017-08-01
Enhancing the frequency of satellite acquisitions represents a key issue for Earth Observation community nowadays. Repeated observations are crucial for monitoring purposes, particularly when intra-annual process should be taken into account. Time series of images constitute a valuable source of information in these cases. The goal of this paper is to propose a new methodological framework to automatically detect and extract spatiotemporal information from satellite image time series (SITS). Existing methods dealing with such kind of data are usually classification-oriented and cannot provide information about evolutions and temporal behaviors. In this paper we propose a graph-based strategy that combines object-based image analysis (OBIA) with data mining techniques. Image objects computed at each individual timestamp are connected across the time series and generates a set of evolution graphs. Each evolution graph is associated to a particular area within the study site and stores information about its temporal evolution. Such information can be deeply explored at the evolution graph scale or used to compare the graphs and supply a general picture at the study site scale. We validated our framework on two study sites located in the South of France and involving different types of natural, semi-natural and agricultural areas. The results obtained from a Landsat SITS support the quality of the methodological approach and illustrate how the framework can be employed to extract and characterize spatiotemporal dynamics.
iBGP: A Bipartite Graph Propagation Approach for Mobile Advertising Fraud Detection
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Jinlong Hu
2017-01-01
Full Text Available Online mobile advertising plays a vital financial role in supporting free mobile apps, but detecting malicious apps publishers who generate fraudulent actions on the advertisements hosted on their apps is difficult, since fraudulent traffic often mimics behaviors of legitimate users and evolves rapidly. In this paper, we propose a novel bipartite graph-based propagation approach, iBGP, for mobile apps advertising fraud detection in large advertising system. We exploit the characteristics of mobile advertising user’s behavior and identify two persistent patterns: power law distribution and pertinence and propose an automatic initial score learning algorithm to formulate both concepts to learn the initial scores of non-seed nodes. We propose a weighted graph propagation algorithm to propagate the scores of all nodes in the user-app bipartite graphs until convergence. To extend our approach for large-scale settings, we decompose the objective function of the initial score learning model into separate one-dimensional problems and parallelize the whole approach on an Apache Spark cluster. iBGP was applied on a large synthetic dataset and a large real-world mobile advertising dataset; experiment results demonstrate that iBGP significantly outperforms other popular graph-based propagation methods.
A Graph-Algorithmic Approach for the Study of Metastability in Markov Chains
Gan, Tingyue; Cameron, Maria
2017-06-01
Large continuous-time Markov chains with exponentially small transition rates arise in modeling complex systems in physics, chemistry, and biology. We propose a constructive graph-algorithmic approach to determine the sequence of critical timescales at which the qualitative behavior of a given Markov chain changes, and give an effective description of the dynamics on each of them. This approach is valid for both time-reversible and time-irreversible Markov processes, with or without symmetry. Central to this approach are two graph algorithms, Algorithm 1 and Algorithm 2, for obtaining the sequences of the critical timescales and the hierarchies of Typical Transition Graphs or T-graphs indicating the most likely transitions in the system without and with symmetry, respectively. The sequence of critical timescales includes the subsequence of the reciprocals of the real parts of eigenvalues. Under a certain assumption, we prove sharp asymptotic estimates for eigenvalues (including pre-factors) and show how one can extract them from the output of Algorithm 1. We discuss the relationship between Algorithms 1 and 2 and explain how one needs to interpret the output of Algorithm 1 if it is applied in the case with symmetry instead of Algorithm 2. Finally, we analyze an example motivated by R. D. Astumian's model of the dynamics of kinesin, a molecular motor, by means of Algorithm 2.
RRES: A Novel Approach to the Partitioning Problem for a Typical Subset of System Graphs
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B. Knerr
2008-03-01
Full Text Available The research field of system partitioning in modern electronic system design started to find strong advertence of scientists about fifteen years ago. Since a multitude of formulations for the partitioning problem exist, the same multitude could be found in the number of strategies that address this problem. Their feasibility is highly dependent on the platform abstraction and the degree of realism that it features. This work originated from the intention to identify the most mature and powerful approaches for system partitioning in order to integrate them into a consistent design framework for wireless embedded systems. Within this publication, a thorough characterisation of graph properties typical for task graphs in the field of wireless embedded system design has been undertaken and has led to the development of an entirely new approach for the system partitioning problem. The restricted range exhaustive search algorithm is introduced and compared to popular and well-reputed heuristic techniques based on tabu search, genetic algorithm, and the global criticality/local phase algorithm. It proves superior performance for a set of system graphs featuring specific properties found in human-made task graphs, since it exploits their typical characteristics such as locality, sparsity, and their degree of parallelism.
RRES: A Novel Approach to the Partitioning Problem for a Typical Subset of System Graphs
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Knerr B
2008-01-01
Full Text Available Abstract The research field of system partitioning in modern electronic system design started to find strong advertence of scientists about fifteen years ago. Since a multitude of formulations for the partitioning problem exist, the same multitude could be found in the number of strategies that address this problem. Their feasibility is highly dependent on the platform abstraction and the degree of realism that it features. This work originated from the intention to identify the most mature and powerful approaches for system partitioning in order to integrate them into a consistent design framework for wireless embedded systems. Within this publication, a thorough characterisation of graph properties typical for task graphs in the field of wireless embedded system design has been undertaken and has led to the development of an entirely new approach for the system partitioning problem. The restricted range exhaustive search algorithm is introduced and compared to popular and well-reputed heuristic techniques based on tabu search, genetic algorithm, and the global criticality/local phase algorithm. It proves superior performance for a set of system graphs featuring specific properties found in human-made task graphs, since it exploits their typical characteristics such as locality, sparsity, and their degree of parallelism.
A Unified Bond Graph Modeling Approach for the Ejection Phase of the Cardiovascular System
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LUBNA MOIN
2016-07-01
Full Text Available In this paper the unified Bond Graph model of the left ventricle ejection phase is presented, simulated and validated. The integro-differential and ordinary differential equations obtained from the bond graph models are simulated using ODE45 (Ordinary Differential Equation Solver on MATLAB and Simulink. The results, thus, obtained are compared with CVS (Cardiovascular System physiological data present in Simbiosys (a software for simulating biological systems and also with the CVS Wiggers diagram of heart cycle. As the cardiac activity is a multi domain process that includes mechanical, hydraulic, chemical and electrical events; therefore, for modeling such systems a unified modeling approach is needed. In this paper the unified Bond Graph model of the left ventricle ejection phase is proposed. The Bond Graph conventionalism approach is a graphical method principally powerful to portray multi-energy systems, as it is formulated on the portrayal of power exchanges. The model takes into account a simplified description of the left ventricle which is close to the medical investigation promoting the apperception and the dialogue between engineers and physiologists.
On self-approaching and increasing-chord drawings of 3-connected planar graphs
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Martin Nöllenburg
2016-02-01
Full Text Available An $st$-path in a drawing of a graph is self-approaching if during the traversal of the corresponding curve from $s$ to any point $t'$ on the curve the distance to $t'$ is non-increasing. A path has increasing chords if it is self-approaching in both directions. A drawing is self-approaching (increasing-chord if any pair of vertices is connected by a self-approaching (increasing-chord path.We study self-approaching and increasing-chord drawings of triangulations and 3-connected planar graphs. We show that in the Euclidean plane, triangulations admit increasing-chord drawings, and for planar 3-trees we can ensure planarity. We prove that strongly monotone (and thus increasing-chord drawings of trees and binary cactuses require exponential resolution in the worst case, answering an open question by Kindermann et al. (GD 2014. Moreover, we provide a binary cactus that does not admit a self-approaching drawing. Finally, we show that 3-connected planar graphs admit increasing-chord drawings in the hyperbolic plane and characterize the trees that admit such drawings.
McGibbney, L. J.; Jiang, Y.; Burgess, A. B.
2017-12-01
Big Earth observation data have been produced, archived and made available online, but discovering the right data in a manner that precisely and efficiently satisfies user needs presents a significant challenge to the Earth Science (ES) community. An emerging trend in information retrieval community is to utilize knowledge graphs to assist users in quickly finding desired information from across knowledge sources. This is particularly prevalent within the fields of social media and complex multimodal information processing to name but a few, however building a domain-specific knowledge graph is labour-intensive and hard to keep up-to-date. In this work, we update our progress on the Earth Science Knowledge Graph (ESKG) project; an ESIP-funded testbed project which provides an automatic approach to building a dynamic knowledge graph for ES to improve interdisciplinary data discovery by leveraging implicit, latent existing knowledge present within across several U.S Federal Agencies e.g. NASA, NOAA and USGS. ESKG strengthens ties between observations and user communities by: 1) developing a knowledge graph derived from various sources e.g. Web pages, Web Services, etc. via natural language processing and knowledge extraction techniques; 2) allowing users to traverse, explore, query, reason and navigate ES data via knowledge graph interaction. ESKG has the potential to revolutionize the way in which ES communities interact with ES data in the open world through the entity, spatial and temporal linkages and characteristics that make it up. This project enables the advancement of ESIP collaboration areas including both Discovery and Semantic Technologies by putting graph information right at our fingertips in an interactive, modern manner and reducing the efforts to constructing ontology. To demonstrate the ESKG concept, we will demonstrate use of our framework across NASA JPL's PO.DAAC, NOAA's Earth Observation Requirements Evaluation System (EORES) and various USGS
Graph-based sequence annotation using a data integration approach
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Pesch Robert
2008-06-01
Full Text Available The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara- Cyc which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation.
Graph-based sequence annotation using a data integration approach.
Pesch, Robert; Lysenko, Artem; Hindle, Matthew; Hassani-Pak, Keywan; Thiele, Ralf; Rawlings, Christopher; Köhler, Jacob; Taubert, Jan
2008-08-25
The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara-Cyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation. The methods and algorithms presented in this publication are an integral part of the ONDEX system which is freely available from http://ondex.sf.net/.
A Multi-Level Middle-Out Cross-Zooming Approach for Large Graph Analytics
Energy Technology Data Exchange (ETDEWEB)
Wong, Pak C.; Mackey, Patrick S.; Cook, Kristin A.; Rohrer, Randall M.; Foote, Harlan P.; Whiting, Mark A.
2009-10-11
This paper presents a working graph analytics model that embraces the strengths of the traditional top-down and bottom-up approaches with a resilient crossover concept to exploit the vast middle-ground information overlooked by the two extreme analytical approaches. Our graph analytics model is developed in collaboration with researchers and users, who carefully studied the functional requirements that reflect the critical thinking and interaction pattern of a real-life intelligence analyst. To evaluate the model, we implement a system prototype, known as GreenHornet, which allows our analysts to test the theory in practice, identify the technological and usage-related gaps in the model, and then adapt the new technology in their work space. The paper describes the implementation of GreenHornet and compares its strengths and weaknesses against the other prevailing models and tools.
iBGP: A Bipartite Graph Propagation Approach for Mobile Advertising Fraud Detection
Hu, Jinlong; Liang, Junjie; Dong, Shoubin
2017-01-01
Online mobile advertising plays a vital financial role in supporting free mobile apps, but detecting malicious apps publishers who generate fraudulent actions on the advertisements hosted on their apps is difficult, since fraudulent traffic often mimics behaviors of legitimate users and evolves rapidly. In this paper, we propose a novel bipartite graph-based propagation approach, iBGP, for mobile apps advertising fraud detection in large advertising system. We exploit the characteristics of m...
Zhang, Yongping; Shang, Pengjian; Xiong, Hui; Xia, Jianan
Time irreversibility is an important property of nonequilibrium dynamic systems. A visibility graph approach was recently proposed, and this approach is generally effective to measure time irreversibility of time series. However, its result may be unreliable when dealing with high-dimensional systems. In this work, we consider the joint concept of time irreversibility and adopt the phase-space reconstruction technique to improve this visibility graph approach. Compared with the previous approach, the improved approach gives a more accurate estimate for the irreversibility of time series, and is more effective to distinguish irreversible and reversible stochastic processes. We also use this approach to extract the multiscale irreversibility to account for the multiple inherent dynamics of time series. Finally, we apply the approach to detect the multiscale irreversibility of financial time series, and succeed to distinguish the time of financial crisis and the plateau. In addition, Asian stock indexes away from other indexes are clearly visible in higher time scales. Simulations and real data support the effectiveness of the improved approach when detecting time irreversibility.
Zhang, Huaguang; Feng, Tao; Yang, Guang-Hong; Liang, Hongjing
2015-07-01
In this paper, the inverse optimal approach is employed to design distributed consensus protocols that guarantee consensus and global optimality with respect to some quadratic performance indexes for identical linear systems on a directed graph. The inverse optimal theory is developed by introducing the notion of partial stability. As a result, the necessary and sufficient conditions for inverse optimality are proposed. By means of the developed inverse optimal theory, the necessary and sufficient conditions are established for globally optimal cooperative control problems on directed graphs. Basic optimal cooperative design procedures are given based on asymptotic properties of the resulting optimal distributed consensus protocols, and the multiagent systems can reach desired consensus performance (convergence rate and damping rate) asymptotically. Finally, two examples are given to illustrate the effectiveness of the proposed methods.
An unprecedented multi attribute decision making using graph theory matrix approach
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N.K. Geetha
2018-02-01
Full Text Available A frame work for investigating the best combination of functioning parameters on a variable compression ratio diesel engine is proposed in the present study using a multi attribute optimization methodology, Graph Theory Matrix Approach. The functioning parameters, attributes, sub attributes and functioning variables of sub attributes are chosen based on expert’s opinion and literature review. The directed graphs are developed for attributes and sub attributes. The ‘Parameter Index’ was calculated for all trials to choose the best trial. The experimental results are verified with the theoretical data. Functioning parameters with combination of compression ratio of 17, fuel injection pressure of 20 N/mm2 and fuel injection pressure of 21°bTDC was found to be best. The proposed method allows the decision maker to systematically and logically find the best combination of functioning parameters.
Mining chemical reactions using neighborhood behavior and condensed graphs of reactions approaches.
de Luca, Aurélie; Horvath, Dragos; Marcou, Gilles; Solov'ev, Vitaly; Varnek, Alexandre
2012-09-24
This work addresses the problem of similarity search and classification of chemical reactions using Neighborhood Behavior (NB) and Condensed Graphs of Reaction (CGR) approaches. The CGR formalism represents chemical reactions as a classical molecular graph with dynamic bonds, enabling descriptor calculations on this graph. Different types of the ISIDA fragment descriptors generated for CGRs in combination with two metrics--Tanimoto and Euclidean--were considered as chemical spaces, to serve for reaction dissimilarity scoring. The NB method has been used to select an optimal combination of descriptors which distinguish different types of chemical reactions in a database containing 8544 reactions of 9 classes. Relevance of NB analysis has been validated in generic (multiclass) similarity search and in clustering with Self-Organizing Maps (SOM). NB-compliant sets of descriptors were shown to display enhanced mapping propensities, allowing the construction of better Self-Organizing Maps and similarity searches (NB and classical similarity search criteria--AUC ROC--correlate at a level of 0.7). The analysis of the SOM clusters proved chemically meaningful CGR substructures representing specific reaction signatures.
A Bond Graph Approach for the Modeling and Simulation of a Buck Converter
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Rached Zrafi
2018-01-01
Full Text Available This paper deals with the modeling of bond graph buck converter systems. The bond graph formalism, which represents a heterogeneous formalism for physical modeling, is used to design a sub-model of a power MOSFET and PiN diode switchers. These bond graph models are based on the device’s electrical elements. The application of these models to a bond graph buck converter permit us to obtain an invariant causal structure when the switch devices change state. This paper shows the usefulness of the bond graph device’s modeling to simulate an implicit bond graph buck converter.
Graph-rewriting approach to discrete relaxation: application to music recognition
Fahmy, Hoda M.; Blostein, Dorothea
1994-03-01
In image analysis, low-level recognition of the primitives plays a very important role. Once the primitives of the image are recognized, depending on the application, many types of analyses can take place. It is likely that associated with each object or primitive is a set of possible interpretations, herein referred to as the label set. The low-level recognizer may associate a probability with each label in the label set. We can use the constraints of the application domain to reduce the ambiguity in the object's identity. This process is variously termed constraint satisfaction, labeling, or relaxation. In this paper, we focus on the discrete form of relaxation. Our contribution lies in the development of a graph-rewriting approach which does not assume the degree of localness is high. We apply our approach to the recognition of music notation, where non-local interactions between primitives must be used in order to reduce ambiguity in the identity of the primitives. We use graph-rewriting rules to express not only binary constraints, but also higher-order notational constraints.
A study of brain networks associated with swallowing using graph-theoretical approaches.
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Bo Luan
Full Text Available Functional connectivity between brain regions during swallowing tasks is still not well understood. Understanding these complex interactions is of great interest from both a scientific and a clinical perspective. In this study, functional magnetic resonance imaging (fMRI was utilized to study brain functional networks during voluntary saliva swallowing in twenty-two adult healthy subjects (all females, [Formula: see text] years of age. To construct these functional connections, we computed mean partial correlation matrices over ninety brain regions for each participant. Two regions were determined to be functionally connected if their correlation was above a certain threshold. These correlation matrices were then analyzed using graph-theoretical approaches. In particular, we considered several network measures for the whole brain and for swallowing-related brain regions. The results have shown that significant pairwise functional connections were, mostly, either local and intra-hemispheric or symmetrically inter-hemispheric. Furthermore, we showed that all human brain functional network, although varying in some degree, had typical small-world properties as compared to regular networks and random networks. These properties allow information transfer within the network at a relatively high efficiency. Swallowing-related brain regions also had higher values for some of the network measures in comparison to when these measures were calculated for the whole brain. The current results warrant further investigation of graph-theoretical approaches as a potential tool for understanding the neural basis of dysphagia.
Quantitative graph theory mathematical foundations and applications
Dehmer, Matthias
2014-01-01
The first book devoted exclusively to quantitative graph theory, Quantitative Graph Theory: Mathematical Foundations and Applications presents and demonstrates existing and novel methods for analyzing graphs quantitatively. Incorporating interdisciplinary knowledge from graph theory, information theory, measurement theory, and statistical techniques, this book covers a wide range of quantitative-graph theoretical concepts and methods, including those pertaining to real and random graphs such as:Comparative approaches (graph similarity or distance)Graph measures to characterize graphs quantitat
Directory of Open Access Journals (Sweden)
Eric Vaz
2013-12-01
Full Text Available Urban sprawl and growth has experienced increased concern in geographic and environmental literature. Preceding the existence of robust frameworks found in regional and urban planning, as well as urban geography and economics, the spatial properties of allocation of urban land use are still far from being completely understood. This is largely due to the underlying complexity of the change found at the spatial level of urban land use, merging social, economic and natural drivers. The spatial patterns formed, and the connectivity established among the different subsets of land-use types, becomes a complex network of interactions over time, helping to shape the structure of the city. The possibility to merge the configuration of land-use with complex networks may be assessed elegantly through graph theory. Nodes and edges can become abstract representations of typologies of space and are represented into a topological space of different land use types which traditionally share common spatial boundaries. Within a regional framework, the links between adjacent and neighboring urban land use types become better understood, by means of a KamadaKawai algorithm. This study uses land use in Lisbon over three years, 1990, 2000 and 2006, to develop a Kamada-Kawai graph interpretation of land-use as a result of neighboring power. The rapid change witnessed in Lisbon since the nineties, as well as the availability of CORINE Land Cover data in these three time stamps, permits a reflection on anthropogenic land-use change in urban and semi-urban areas in Portugal’s capital. This paper responds to (1 the structure and connectivity of urban land use over time, demonstrating that most of the agricultural land is stressed to transform to urban, gaining a central role in future. (2 Offer a systemic approach to land-use transitions generating what we call spatial memory, where land use change is often unpredictable over space, but becomes evident in a graph theory
Cavanaugh, Kyle C; Siegel, David A; Raimondi, Peter T; Alberto, Filipe
2014-02-01
The manner in which patches are delineated in spatially realistic metapopulation models will influence the size, connectivity, and extinction and recolonization dynamics of those patches. Most commonly used patch-definition methods focus on identifying discrete, contiguous patches of habitat from a single temporal observation of species occurrence or from a model of habitat suitability. However, these approaches are not suitable for many metapopulation systems where entire patches may not be fully colonized at a given time. For these metapopulation systems, a single large patch of habitat may actually support multiple, interacting subpopulations. The interactions among these subpopulations will be ignored if the patch is treated as a single unit, a situation we term the "mega-patch problem." Mega-patches are characterized by variable intra-patch synchrony, artificially low inter-patch connectivity, and low extinction rates. One way to detect this problem is by using time series data to calculate demographic synchrony within mega-patches. We present a framework for identifying subpopulations in mega-patches using a combination of spatial autocorrelation and graph theory analyses. We apply our approach to southern California giant kelp (Macrocystis pyrifera) forests using a new, long-term (27 years), satellite-based data set of giant kelp canopy biomass. We define metapopulation patches using our method as well as several other commonly used patch delineation methodologies and examine the colonization and extinction dynamics of the metapopulation under each approach. We find that the relationships between patch characteristics such as area and connectivity and the demographic processes of colonizations and extinctions vary among the different patch-definition methods. Our spatial-analysis/graph-theoretic framework produces results that match theoretical expectations better than the other methods. This approach can be used to identify subpopulations in metapopulations
Intraplate seismicity in Canada: a graph theoretic approach to data analysis and interpretation
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K. Vasudevan
2010-10-01
Full Text Available Intraplate seismicity occurs in central and northern Canada, but the underlying origin and dynamics remain poorly understood. Here, we apply a graph theoretic approach to characterize the statistical structure of spatiotemporal clustering exhibited by intraplate seismicity, a direct consequence of the underlying nonlinear dynamics. Using a recently proposed definition of "recurrences" based on record breaking processes (Davidsen et al., 2006, 2008, we have constructed directed graphs using catalogue data for three selected regions (Region 1: 45°−48° N/74°−80° W; Region 2: 51°−55° N/77°−83° W; and Region 3: 56°−70° N/65°−95° W, with attributes drawn from the location, origin time and the magnitude of the events. Based on comparisons with a null model derived from Poisson distribution or Monte Carlo shuffling of the catalogue data, our results provide strong evidence in support of spatiotemporal correlations of seismicity in all three regions considered. Similar evidence for spatiotemporal clustering has been documented using seismicity catalogues for southern California, suggesting possible similarities in underlying earthquake dynamics of both regions despite huge differences in the variability of seismic activity.
DEFF Research Database (Denmark)
Seiller, Thomas
2016-01-01
Interaction graphs were introduced as a general, uniform, construction of dynamic models of linear logic, encompassing all Geometry of Interaction (GoI) constructions introduced so far. This series of work was inspired from Girard's hyperfinite GoI, and develops a quantitative approach that should...... be understood as a dynamic version of weighted relational models. Until now, the interaction graphs framework has been shown to deal with exponentials for the constrained system ELL (Elementary Linear Logic) while keeping its quantitative aspect. Adapting older constructions by Girard, one can clearly define...... "full" exponentials, but at the cost of these quantitative features. We show here that allowing interpretations of proofs to use continuous (yet finite in a measure-theoretic sense) sets of states, as opposed to earlier Interaction Graphs constructions were these sets of states were discrete (and finite...
Forecasting Construction Cost Index based on visibility graph: A network approach
Zhang, Rong; Ashuri, Baabak; Shyr, Yu; Deng, Yong
2018-03-01
Engineering News-Record (ENR), a professional magazine in the field of global construction engineering, publishes Construction Cost Index (CCI) every month. Cost estimators and contractors assess projects, arrange budgets and prepare bids by forecasting CCI. However, fluctuations and uncertainties of CCI cause irrational estimations now and then. This paper aims at achieving more accurate predictions of CCI based on a network approach in which time series is firstly converted into a visibility graph and future values are forecasted relied on link prediction. According to the experimental results, the proposed method shows satisfactory performance since the error measures are acceptable. Compared with other methods, the proposed method is easier to implement and is able to forecast CCI with less errors. It is convinced that the proposed method is efficient to provide considerably accurate CCI predictions, which will make contributions to the construction engineering by assisting individuals and organizations in reducing costs and making project schedules.
Time series analysis of S&P 500 index: A horizontal visibility graph approach
Vamvakaris, Michail D.; Pantelous, Athanasios A.; Zuev, Konstantin M.
2018-05-01
The behavior of stock prices has been thoroughly studied throughout the last century, and contradictory results have been reported in the corresponding literature. In this paper, a network theoretical approach is provided to investigate how crises affected the behavior of US stock prices. We analyze high frequency data from S&P500 via the Horizontal Visibility Graph method, and find that all major crises that took place worldwide in the last twenty years, affected significantly the behavior of the price-index. Nevertheless, we observe that each of those crises impacted the index in a different way and magnitude. Interestingly, our results suggest that the predictability of the price-index series increases during the periods of crises.
An original approach to the mathematical concept of graph from braid crafts
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Albanese Veronica
2016-01-01
Full Text Available In previous researches we found that a community of Argentinean artisans models its own practices of braiding using graphs. Inspired by these findings, we designed an educational activity to introduce the concept of graphs. The study of graphs helps students to develop combinatorial and systematic thinking as well as skills to model reality and abstract and generalize patterns from particular situations. The tasks proposed aim to construct the concept of graphs, then identify characteristics that allow some graphs to be models of braids and finally use them to invent more graphs for new braids. The activity performed in a secondary school teachers’ educational course, had quite satisfactory results due to the number of braids invented and the small amount of mistakes made by the participants.
A Graph Theoretic Approach for Hydraulic Fracturing and Wellbore Leakage Risk Modeling
Glosser, D.; Rose, K.; Bauer, J. R.; Warner, T.
2016-12-01
Recent large scale development of unconventional formations for fossil energy has raised concerns over the potential for fluid leakage between subsurface systems and wellbores. This is particularly true in regions with extensive drilling history, where spatial densities of wellbores are higher, and where significant uncertainties in the location and mechanical integrity of such wellbores exist. The generation of induced fracture networks during hydraulic fracturing may increase subsurface connectivity, and create the potential for unwanted fluid migration between operational and legacy wellbores and subsurface fracture networks. We present a graph theoretic approach for identifying geospatial regions and wellbores at increased risk for subsurface connectivity based on wellbore proximity and local geologic characteristics. The algorithm transforms user inputted geospatial data (geologic and wellbore x,y,z) to graph structure, where wellbores are represented as nodes, and where potential overlapping fracture network zones are represented as edges. The algorithm can be used to complement existing fracture models to better account for the reach of induced fractures, and to identify spatial extents at increased risk for unwanted subsurface connectivity. Additionally, the model can be used to identify regions in need of geophysical detection methods for locating undocumented wells. As a result, the method can be part of a cumulative strategy to reduce uncertainty inherent to combined geologic and engineered systems. The algorithm has been successfully tested against a known leakage scenario in Pennsylvania. In addition to identifying wells associated with the leakage event, the algorithm identified two other higher risk networks in the region. The algorithm output provides valuable information for industry to develop environmentally safe drilling and injection plans; and for regulators to identify specific wellbores at greater risk for leakage, and to develop targeted
Designing a graph-based approach to landscape ecological assessment of linear infrastructures
Energy Technology Data Exchange (ETDEWEB)
Girardet, Xavier, E-mail: xavier.girardet@univ-fcomte.fr; Foltête, Jean-Christophe, E-mail: jean-christophe.foltete@univ-fcomte.fr; Clauzel, Céline, E-mail: celine.clauzel@univ-fcomte.fr
2013-09-15
The development of major linear infrastructures contributes to landscape fragmentation and impacts natural habitats and biodiversity in various ways. To anticipate and minimize such impacts, landscape planning needs to be capable of effective strategic environmental assessment (SEA) and of supporting environmental impact assessment (EIA) decisions. To this end, species distribution models (SDMs) are an effective way of making predictive maps of the presence of a given species. In this paper, we propose to combine SDMs and graph-based representation of landscape networks to integrate the potential long-distance effect of infrastructures on species distribution. A diachronic approach, comparing distribution before and after the linear infrastructure is constructed, leads to the design of a species distribution assessment (SDA), taking into account population isolation. The SDA makes it possible (1) to estimate the local variation in probability of presence and (2) to characterize the impact of the infrastructure in terms of global variation in presence and of distance of disturbance. The method is illustrated by assessing the impact of the construction of a high-speed railway line on the distribution of several virtual species in Franche-Comté (France). The study shows the capacity of the SDA to characterize the impact of a linear infrastructure either as a research concern or as a spatial planning challenge. SDAs could be helpful in deciding among several scenarios for linear infrastructure routes or for the location of mitigation measures. -- Highlights: • Graph connectivity metrics were integrated into a species distribution model. • SDM was performed before and after the implementation of linear infrastructure. • The local variation of presence provides spatial indicators of the impact.
Expert and Novice Approaches to Using Graphs: Evidence from Eye-Track Experiments
Wirth, K. R.; Lindgren, J. M.
2015-12-01
Professionals and students in geology use an array of graphs to study the earth, but relatively little detail is known about how users interact with these graphs. Comprehension of graphical information in the earth sciences is further complicated by the common use of non-traditional formats (e.g., inverted axes, logarithmic scales, normalized plots, ternary diagrams). Many educators consider graph-reading skills an important outcome of general education science curricula, so it is critical that we understand both the development of graph-reading skills and the instructional practices that are most efficacious. Eye-tracking instruments provide quantitative information about eye movements and offer important insights into the development of expertise in graph use. We measured the graph reading skills and eye movements of novices (students with a variety of majors and educational attainment) and experts (faculty and staff from a variety of disciplines) while observing traditional and non-traditional graph formats. Individuals in the expert group consistently demonstrated significantly greater accuracy in responding to questions (e.g., retrieval, interpretation, prediction) about graphs. Among novices, only the number of college math and science courses correlated with response accuracy. Interestingly, novices and experts exhibited similar eye-tracks when they first encountered a new graph; they typically scanned through the title, x and y-axes, and data regions in the first 5-15 seconds. However, experts are readily distinguished from novices by a greater number of eye movements (20-35%) between the data and other graph elements (e.g., title, x-axis, y-axis) both during and after the initial orientation phase. We attribute the greater eye movements between the different graph elements an outcome of the generally better-developed self-regulation skills (goal-setting, monitoring, self-evaluation) that likely characterize individuals in our expert group.
Directory of Open Access Journals (Sweden)
Amine Labriji
2017-07-01
Full Text Available The topic of identifying the similarity of graphs was considered as highly recommended research field in the Web semantic, artificial intelligence, the shape recognition and information research. One of the fundamental problems of graph databases is finding similar graphs to a graph query. Existing approaches dealing with this problem are usually based on the nodes and arcs of the two graphs, regardless of parental semantic links. For instance, a common connection is not identified as being part of the similarity of two graphs in cases like two graphs without common concepts, the measure of similarity based on the union of two graphs, or the one based on the notion of maximum common sub-graph (SCM, or the distance of edition of graphs. This leads to an inadequate situation in the context of information research. To overcome this problem, we suggest a new measure of similarity between graphs, based on the similarity measure of Wu and Palmer. We have shown that this new measure satisfies the properties of a measure of similarities and we applied this new measure on examples. The results show that our measure provides a run time with a gain of time compared to existing approaches. In addition, we compared the relevance of the similarity values obtained, it appears that this new graphs measure is advantageous and offers a contribution to solving the problem mentioned above.
Uniform Single Valued Neutrosophic Graphs
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S. Broumi
2017-09-01
Full Text Available In this paper, we propose a new concept named the uniform single valued neutrosophic graph. An illustrative example and some properties are examined. Next, we develop an algorithmic approach for computing the complement of the single valued neutrosophic graph. A numerical example is demonstrated for computing the complement of single valued neutrosophic graphs and uniform single valued neutrosophic graph.
Gross, Jonathan L
2003-01-01
The Handbook of Graph Theory is the most comprehensive single-source guide to graph theory ever published. Best-selling authors Jonathan Gross and Jay Yellen assembled an outstanding team of experts to contribute overviews of more than 50 of the most significant topics in graph theory-including those related to algorithmic and optimization approaches as well as ""pure"" graph theory. They then carefully edited the compilation to produce a unified, authoritative work ideal for ready reference.Designed and edited with non-experts in mind, the Handbook of Graph Theory makes information easy to fi
Golino, Hudson F; Epskamp, Sacha
2017-01-01
The estimation of the correct number of dimensions is a long-standing problem in psychometrics. Several methods have been proposed, such as parallel analysis (PA), Kaiser-Guttman's eigenvalue-greater-than-one rule, multiple average partial procedure (MAP), the maximum-likelihood approaches that use fit indexes as BIC and EBIC and the less used and studied approach called very simple structure (VSS). In the present paper a new approach to estimate the number of dimensions will be introduced and compared via simulation to the traditional techniques pointed above. The approach proposed in the current paper is called exploratory graph analysis (EGA), since it is based on the graphical lasso with the regularization parameter specified using EBIC. The number of dimensions is verified using the walktrap, a random walk algorithm used to identify communities in networks. In total, 32,000 data sets were simulated to fit known factor structures, with the data sets varying across different criteria: number of factors (2 and 4), number of items (5 and 10), sample size (100, 500, 1000 and 5000) and correlation between factors (orthogonal, .20, .50 and .70), resulting in 64 different conditions. For each condition, 500 data sets were simulated using lavaan. The result shows that the EGA performs comparable to parallel analysis, EBIC, eBIC and to Kaiser-Guttman rule in a number of situations, especially when the number of factors was two. However, EGA was the only technique able to correctly estimate the number of dimensions in the four-factor structure when the correlation between factors were .7, showing an accuracy of 100% for a sample size of 5,000 observations. Finally, the EGA was used to estimate the number of factors in a real dataset, in order to compare its performance with the other six techniques tested in the simulation study.
Noble, S D; Welsh, D J A
2000-01-01
We consider the equivalence classes of graphs induced by the unsigned versions of the Reidemeister moves on knot diagrams. Any graph which is reducible by some finite sequence of these moves, to a graph with no edges is called a knot graph. We show that the class of knot graphs strictly contains the set of delta-wye graphs. We prove that the dimension of the intersection of the cycle and cocycle spaces is an effective numerical invariant of these classes.
A quantum annealing approach for fault detection and diagnosis of graph-based systems
Perdomo-Ortiz, A.; Fluegemann, J.; Narasimhan, S.; Biswas, R.; Smelyanskiy, V. N.
2015-02-01
Diagnosing the minimal set of faults capable of explaining a set of given observations, e.g., from sensor readouts, is a hard combinatorial optimization problem usually tackled with artificial intelligence techniques. We present the mapping of this combinatorial problem to quadratic unconstrained binary optimization (QUBO), and the experimental results of instances embedded onto a quantum annealing device with 509 quantum bits. Besides being the first time a quantum approach has been proposed for problems in the advanced diagnostics community, to the best of our knowledge this work is also the first research utilizing the route Problem → QUBO → Direct embedding into quantum hardware, where we are able to implement and tackle problem instances with sizes that go beyond previously reported toy-model proof-of-principle quantum annealing implementations; this is a significant leap in the solution of problems via direct-embedding adiabatic quantum optimization. We discuss some of the programmability challenges in the current generation of the quantum device as well as a few possible ways to extend this work to more complex arbitrary network graphs.
3D Materials image segmentation by 2D propagation: a graph-cut approach considering homomorphism.
Waggoner, Jarrell; Zhou, Youjie; Simmons, Jeff; De Graef, Marc; Wang, Song
2013-12-01
Segmentation propagation, similar to tracking, is the problem of transferring a segmentation of an image to a neighboring image in a sequence. This problem is of particular importance to materials science, where the accurate segmentation of a series of 2D serial-sectioned images of multiple, contiguous 3D structures has important applications. Such structures may have distinct shape, appearance, and topology, which can be considered to improve segmentation accuracy. For example, some materials images may have structures with a specific shape or appearance in each serial section slice, which only changes minimally from slice to slice, and some materials may exhibit specific inter-structure topology that constrains their neighboring relations. Some of these properties have been individually incorporated to segment specific materials images in prior work. In this paper, we develop a propagation framework for materials image segmentation where each propagation is formulated as an optimal labeling problem that can be efficiently solved using the graph-cut algorithm. Our framework makes three key contributions: 1) a homomorphic propagation approach, which considers the consistency of region adjacency in the propagation; 2) incorporation of shape and appearance consistency in the propagation; and 3) a local non-homomorphism strategy to handle newly appearing and disappearing substructures during this propagation. To show the effectiveness of our framework, we conduct experiments on various 3D materials images, and compare the performance against several existing image segmentation methods.
Directory of Open Access Journals (Sweden)
R. Ramakrishnan
2014-01-01
Full Text Available The availability of natural gas and crude oil resources has been declining over the years. In automobile sector, the consumption of crude oil is 63% of total crude oil production in the world. Hence, automobile industries are placing more emphasis on energy efficient hydraulic hybrid systems, which can replace their conventional transmission systems. Series hydraulic hybrid system (SHHS is a multidomain mechatronics system with two distinct power sources that includes prime mover and hydropneumatic accumulator. It replaces the conventional transmission system to drive the vehicle. The sizing of the subsystems in SHHS plays a major role in improving the energy efficiency of the vehicle. In this paper, a power bond graph approach is used to model the dynamics of the SHHS. The obtained simulation results indicate the energy flow during various modes of operations. It also includes the dynamic response of hydropneumatic accumulator, prime mover, and system output speed. Further, design optimization of the system is carried out to optimize the process parameters for maximizing the system energy efficiency. This leads to increase in fuel economy and environmentally friendly vehicle.
Linear game non-contextuality and Bell inequalities—a graph-theoretic approach
International Nuclear Information System (INIS)
Rosicka, M; Ramanathan, R; Gnaciński, P; Horodecki, M; Horodecki, K; Horodecki, P; Severini, S
2016-01-01
We study the classical and quantum values of a class of one- and two-party unique games, that generalizes the well-known XOR games to the case of non-binary outcomes. In the bipartite case the generalized XOR (XOR-d) games we study are a subclass of the well-known linear games. We introduce a ‘constraint graph’ associated to such a game, with the constraints defining the game represented by an edge-coloring of the graph. We use the graph-theoretic characterization to relate the task of finding equivalent games to the notion of signed graphs and switching equivalence from graph theory. We relate the problem of computing the classical value of single-party anti-correlation XOR games to finding the edge bipartization number of a graph, which is known to be MaxSNP hard, and connect the computation of the classical value of XOR-d games to the identification of specific cycles in the graph. We construct an orthogonality graph of the game from the constraint graph and study its Lovász theta number as a general upper bound on the quantum value even in the case of single-party contextual XOR-d games. XOR-d games possess appealing properties for use in device-independent applications such as randomness of the local correlated outcomes in the optimal quantum strategy. We study the possibility of obtaining quantum algebraic violation of these games, and show that no finite XOR-d game possesses the property of pseudo-telepathy leaving the frequently used chained Bell inequalities as the natural candidates for such applications. We also show this lack of pseudo-telepathy for multi-party XOR-type inequalities involving two-body correlation functions. (paper)
Simplicial complexes of graphs
Jonsson, Jakob
2008-01-01
A graph complex is a finite family of graphs closed under deletion of edges. Graph complexes show up naturally in many different areas of mathematics, including commutative algebra, geometry, and knot theory. Identifying each graph with its edge set, one may view a graph complex as a simplicial complex and hence interpret it as a geometric object. This volume examines topological properties of graph complexes, focusing on homotopy type and homology. Many of the proofs are based on Robin Forman's discrete version of Morse theory. As a byproduct, this volume also provides a loosely defined toolbox for attacking problems in topological combinatorics via discrete Morse theory. In terms of simplicity and power, arguably the most efficient tool is Forman's divide and conquer approach via decision trees; it is successfully applied to a large number of graph and digraph complexes.
Nguyen, Louis H.; Ramakrishnan, Jayant; Granda, Jose J.
2006-01-01
The assembly and operation of the International Space Station (ISS) require extensive testing and engineering analysis to verify that the Space Station system of systems would work together without any adverse interactions. Since the dynamic behavior of an entire Space Station cannot be tested on earth, math models of the Space Station structures and mechanical systems have to be built and integrated in computer simulations and analysis tools to analyze and predict what will happen in space. The ISS Centrifuge Rotor (CR) is one of many mechanical systems that need to be modeled and analyzed to verify the ISS integrated system performance on-orbit. This study investigates using Bond Graph modeling techniques as quick and simplified ways to generate models of the ISS Centrifuge Rotor. This paper outlines the steps used to generate simple and more complex models of the CR using Bond Graph Computer Aided Modeling Program with Graphical Input (CAMP-G). Comparisons of the Bond Graph CR models with those derived from Euler-Lagrange equations in MATLAB and those developed using multibody dynamic simulation at the National Aeronautics and Space Administration (NASA) Johnson Space Center (JSC) are presented to demonstrate the usefulness of the Bond Graph modeling approach for aeronautics and space applications.
A graph signal filtering-based approach for detection of different edge types on airborne lidar data
Bayram, Eda; Vural, Elif; Alatan, Aydin
2017-10-01
Airborne Laser Scanning is a well-known remote sensing technology, which provides a dense and highly accurate, yet unorganized point cloud of earth surface. During the last decade, extracting information from the data generated by airborne LiDAR systems has been addressed by many studies in geo-spatial analysis and urban monitoring applications. However, the processing of LiDAR point clouds is challenging due to their irregular structure and 3D geometry. In this study, we propose a novel framework for the detection of the boundaries of an object or scene captured by LiDAR. Our approach is motivated by edge detection techniques in vision research and it is established on graph signal filtering which is an exciting and promising field of signal processing for irregular data types. Due to the convenient applicability of graph signal processing tools on unstructured point clouds, we achieve the detection of the edge points directly on 3D data by using a graph representation that is constructed exclusively to answer the requirements of the application. Moreover, considering the elevation data as the (graph) signal, we leverage aerial characteristic of the airborne LiDAR data. The proposed method can be employed both for discovering the jump edges on a segmentation problem and for exploring the crease edges on a LiDAR object on a reconstruction/modeling problem, by only adjusting the filter characteristics.
de Mol, M.J.; Rensink, Arend; Hunt, James J.
This paper introduces an approach for adding graph transformation-based functionality to existing JAVA programs. The approach relies on a set of annotations to identify the intended graph structure, as well as on user methods to manipulate that structure, within the user’s own JAVA class
CD30 cell graphs of Hodgkin lymphoma are not scale-free--an image analysis approach.
Schäfer, Hendrik; Schäfer, Tim; Ackermann, Jörg; Dichter, Norbert; Döring, Claudia; Hartmann, Sylvia; Hansmann, Martin-Leo; Koch, Ina
2016-01-01
Hodgkin lymphoma (HL) is a type of B-cell lymphoma. To diagnose the subtypes, biopsies are taken and immunostained. The slides are scanned to produce high-resolution digital whole slide images (WSI). Pathologists manually inspect the spatial distribution of cells, but little is known on the statistical properties of cell distributions in WSIs. Such properties would give valuable information for the construction of theoretical models that describe the invasion of malignant cells in the lymph node and the intercellular interactions. In this work, we define and discuss HL cell graphs. We identify CD30(+) cells in HL WSIs, bringing together the fields of digital imaging and network analysis. We define special graphs based on the positions of the immunostained cells. We present an automatic analysis of complete WSIs to determine significant morphological and immunohistochemical features of HL cells and their spatial distribution in the lymph node tissue under three different medical conditions: lymphadenitis (LA) and two types of HL. We analyze the vertex degree distributions of CD30 cell graphs and compare them to a null model. CD30 cell graphs show higher vertex degrees than expected by a random unit disk graph, suggesting clustering of the cells. We found that a gamma distribution is suitable to model the vertex degree distributions of CD30 cell graphs, meaning that they are not scale-free. Moreover, we compare the graphs for LA and two subtypes of HL. LA and classical HL showed different vertex degree distributions. The vertex degree distributions of the two HL subtypes NScHL and mixed cellularity HL (MXcHL) were similar. The CellProfiler pipeline used for cell detection is available at https://sourceforge.net/projects/cellgraphs/. ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
A Graph-Based Approach for 3D Building Model Reconstruction from Airborne LiDAR Point Clouds
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Bin Wu
2017-01-01
Full Text Available 3D building model reconstruction is of great importance for environmental and urban applications. Airborne light detection and ranging (LiDAR is a very useful data source for acquiring detailed geometric and topological information of building objects. In this study, we employed a graph-based method based on hierarchical structure analysis of building contours derived from LiDAR data to reconstruct urban building models. The proposed approach first uses a graph theory-based localized contour tree method to represent the topological structure of buildings, then separates the buildings into different parts by analyzing their topological relationships, and finally reconstructs the building model by integrating all the individual models established through the bipartite graph matching process. Our approach provides a more complete topological and geometrical description of building contours than existing approaches. We evaluated the proposed method by applying it to the Lujiazui region in Shanghai, China, a complex and large urban scene with various types of buildings. The results revealed that complex buildings could be reconstructed successfully with a mean modeling error of 0.32 m. Our proposed method offers a promising solution for 3D building model reconstruction from airborne LiDAR point clouds.
Tejedor, Alejandro; Longjas, Anthony; Zaliapin, Ilya; Foufoula-Georgiou, Efi
2015-04-01
River deltas are landforms with complex channel networks that deliver water, sediment and nutrient fluxes from rivers to oceans or inland water bodies via multiple pathways. Most of the deltas are subject to anthropogenic and natural perturbations causing topological and dynamical changes in the delta structure and function. We present a quantitative framework based on spectral graph theory within which a systematic study of the topology, transport dynamics and response to change of river deltas can be performed, as well as computation of sub-networks (from apex to shoreline outlets), and contributing/nourishing areas. We introduce metrics of topologic and dynamic complexity and define a multidimensional complexity space where each delta projects. By analysis of seven deltas of different morphodynamic and environmental settings, we report a surprising power law relationship between sub-network size and its dynamic exchange with surrounding sub-networks within the deltaic system. The exponent of the relationship is universal (predicting that a sub-network twice as large leaks out to other sub-networks only 1.3 times its total flux) and the pre-exponent depends on the topologic complexity of the delta network as a whole, i.e., the ensemble of the interacting sub-sub-networks. We also use the developed framework to construct vulnerability maps that quantify the relative change of sediment and water delivery to the shoreline outlets in response to possible perturbations in hundreds of upstream links. This enables us to evaluate which links (hotspots) and what management scenarios would most influence flux delivery to the outlets, paving the way for systematically examining how local or spatially distributed delta interventions can be studied within a systems approach for delta sustainability.
Using Graph Transformations and Graph Abstractions for Software Verification
Zambon, Eduardo; Rensink, Arend
In this paper we describe our intended approach for the verification of software written in imperative programming languages. We base our approach on model checking of graph transition systems, where each state is a graph and the transitions are specified by graph transformation rules. We believe
Graphing trillions of triangles.
Burkhardt, Paul
2017-07-01
The increasing size of Big Data is often heralded but how data are transformed and represented is also profoundly important to knowledge discovery, and this is exemplified in Big Graph analytics. Much attention has been placed on the scale of the input graph but the product of a graph algorithm can be many times larger than the input. This is true for many graph problems, such as listing all triangles in a graph. Enabling scalable graph exploration for Big Graphs requires new approaches to algorithms, architectures, and visual analytics. A brief tutorial is given to aid the argument for thoughtful representation of data in the context of graph analysis. Then a new algebraic method to reduce the arithmetic operations in counting and listing triangles in graphs is introduced. Additionally, a scalable triangle listing algorithm in the MapReduce model will be presented followed by a description of the experiments with that algorithm that led to the current largest and fastest triangle listing benchmarks to date. Finally, a method for identifying triangles in new visual graph exploration technologies is proposed.
Graph structure and monadic second-order logic. A language-theoretic approach.
Courcelle, Bruno; Engelfriet, Joost
2012-01-01
Collection Encyclopedia of Mathematics and Applications, Vol. 138; International audience; Livre sur les décompositions de graphes et la logique du second-ordre monadique. Applications algorithmiques et en théorie des langages. Cambridge University Press, Juin 2012
A Comparison of Two Approaches to Training Visual Analysis of AB Graphs
Wolfe, Katie; Slocum, Timothy A.
2015-01-01
Visual analysis is the primary method of evaluating data in single-subject research. Few studies have evaluated interventions to teach visual analysis skills. The purpose of this study was to evaluate systematic instruction, delivered using computer-based intervention or a recorded lecture, on identifying changes in slope and level in AB graphs.…
A Graph-Based Approach to Action Scheduling in a Parallel Database System
Grefen, P.W.P.J.; Apers, Peter M.G.
Parallel database machines are meant to obtain high performance in transaction processing, both in terms of response time adn throughput. To obtain high performance, a good scheduling of the execution of the various actions in transactions is crucial. This paper describes a graph-based technique for
Row—column visibility graph approach to two-dimensional landscapes
International Nuclear Information System (INIS)
Xiao Qin; Pan Xue; Li Xin-Li; Stephen Mutua; Yang Hui-Jie; Jiang Yan; Wang Jian-Yong; Zhang Qing-Jun
2014-01-01
A new concept, called the row—column visibility graph, is proposed to map two-dimensional landscapes to complex networks. A cluster coverage is introduced to describe the extensive property of node clusters on a Euclidean lattice. Graphs mapped from fractals generated with the probability redistribution model behave scale-free. They have pattern-induced hierarchical organizations and comparatively much more extensive structures. The scale-free exponent has a negative correlation with the Hurst exponent, however, there is no deterministic relation between them. Graphs for fractals generated with the midpoint displacement model are exponential networks. When the Hurst exponent is large enough (e.g., H > 0.5), the degree distribution decays much more slowly, the average coverage becomes significant large, and the initially hierarchical structure at H < 0.5 is destroyed completely. Hence, the row—column visibility graph can be used to detect the pattern-related new characteristics of two-dimensional landscapes. (interdisciplinary physics and related areas of science and technology)
Mal-Netminer: Malware Classification Approach Based on Social Network Analysis of System Call Graph
Directory of Open Access Journals (Sweden)
Jae-wook Jang
2015-01-01
Full Text Available As the security landscape evolves over time, where thousands of species of malicious codes are seen every day, antivirus vendors strive to detect and classify malware families for efficient and effective responses against malware campaigns. To enrich this effort and by capitalizing on ideas from the social network analysis domain, we build a tool that can help classify malware families using features driven from the graph structure of their system calls. To achieve that, we first construct a system call graph that consists of system calls found in the execution of the individual malware families. To explore distinguishing features of various malware species, we study social network properties as applied to the call graph, including the degree distribution, degree centrality, average distance, clustering coefficient, network density, and component ratio. We utilize features driven from those properties to build a classifier for malware families. Our experimental results show that “influence-based” graph metrics such as the degree centrality are effective for classifying malware, whereas the general structural metrics of malware are less effective for classifying malware. Our experiments demonstrate that the proposed system performs well in detecting and classifying malware families within each malware class with accuracy greater than 96%.
Proxy Graph: Visual Quality Metrics of Big Graph Sampling.
Nguyen, Quan Hoang; Hong, Seok-Hee; Eades, Peter; Meidiana, Amyra
2017-06-01
Data sampling has been extensively studied for large scale graph mining. Many analyses and tasks become more efficient when performed on graph samples of much smaller size. The use of proxy objects is common in software engineering for analysis and interaction with heavy objects or systems. In this paper, we coin the term 'proxy graph' and empirically investigate how well a proxy graph visualization can represent a big graph. Our investigation focuses on proxy graphs obtained by sampling; this is one of the most common proxy approaches. Despite the plethora of data sampling studies, this is the first evaluation of sampling in the context of graph visualization. For an objective evaluation, we propose a new family of quality metrics for visual quality of proxy graphs. Our experiments cover popular sampling techniques. Our experimental results lead to guidelines for using sampling-based proxy graphs in visualization.
Fundamentals of algebraic graph transformation
Ehrig, Hartmut; Prange, Ulrike; Taentzer, Gabriele
2006-01-01
Graphs are widely used to represent structural information in the form of objects and connections between them. Graph transformation is the rule-based manipulation of graphs, an increasingly important concept in computer science and related fields. This is the first textbook treatment of the algebraic approach to graph transformation, based on algebraic structures and category theory. Part I is an introduction to the classical case of graph and typed graph transformation. In Part II basic and advanced results are first shown for an abstract form of replacement systems, so-called adhesive high-level replacement systems based on category theory, and are then instantiated to several forms of graph and Petri net transformation systems. Part III develops typed attributed graph transformation, a technique of key relevance in the modeling of visual languages and in model transformation. Part IV contains a practical case study on model transformation and a presentation of the AGG (attributed graph grammar) tool envir...
DEFF Research Database (Denmark)
Hartnell, B.L.; Vestergaard, Preben Dahl
There are many results dealing with the problem of decomposing a fixed graph into isomorphic subgraphs. There has also been work on characterizing graphs with the property that one can delete the edges of a number of edge disjoint copies of the subgraph and, regardless of how that is done......, the graph that remains can still be decomposed (such graphs are called or ). In this paper we consider the follwing variation. Given a fixed graph H, determine which graphs (call them ) have the property that every edge disjoint packing with H is maximum. In the case that the graph H is isomorphic...... to the path on 3 nodes, we characterize the equipackable graphs of girth 5 or more. randomly packable randomly decomposable equipackable maximal...
DEFF Research Database (Denmark)
Vestergaard, Preben Dahl; Hartnell, Bert L.
2006-01-01
There are many results dealing with the problem of decomposing a fixed graph into isomorphic subgraphs. There has also been work on characterizing graphs with the property that one can delete the edges of a number of edge disjoint copies of the subgraph and, regardless of how that is done......, the graph that remains can still be decomposed (such graphs are called randomly packable or randomly decomposable). In this paper we consider the following variation. Given a fixed graph H, determine which graphs (call them equipackable) have the property that every maximal edge disjoint packing with H...... is maximum. In the case that the graph H is isomorphic to the path on 3 nodes, we characterize the equipackable graphs of girth 5 or more....
Yoo, Illhoi; Hu, Xiaohua; Song, Il-Yeol
2007-11-27
A huge amount of biomedical textual information has been produced and collected in MEDLINE for decades. In order to easily utilize biomedical information in the free text, document clustering and text summarization together are used as a solution for text information overload problem. In this paper, we introduce a coherent graph-based semantic clustering and summarization approach for biomedical literature. Our extensive experimental results show the approach shows 45% cluster quality improvement and 72% clustering reliability improvement, in terms of misclassification index, over Bisecting K-means as a leading document clustering approach. In addition, our approach provides concise but rich text summary in key concepts and sentences. Our coherent biomedical literature clustering and summarization approach that takes advantage of ontology-enriched graphical representations significantly improves the quality of document clusters and understandability of documents through summaries.
Gysel, Rob; Gusfield, Dan
2011-01-01
The multistate perfect phylogeny problem is a classic problem in computational biology. When no perfect phylogeny exists, it is of interest to find a set of characters to remove in order to obtain a perfect phylogeny in the remaining data. This is known as the character removal problem. We show how to use chordal graphs and triangulations to solve the character removal problem for an arbitrary number of states, which was previously unsolved. We outline a preprocessing technique that speeds up the computation of the minimal separators of a graph. Minimal separators are used in our solution to the missing data character removal problem and to Gusfield's solution of the perfect phylogeny problem with missing data.
A covering-graph approach to epidemics on SIS and SIS-like networks.
Floyd, William; Kay, Leslie; Shapiro, Michael
2012-01-01
In this paper, we introduce a new class of epidemics on networks which we call SI(S/I). SI(S/I) networks differ from SIS networks in allowing an infected individual to become reinfected without first passing to the susceptible state. We use a covering-graph construction to compare SIR, SIS, and SI(S/I) networks. Like the SIR networks that cover them, SI(S/I) networks exhibit infection probabilities that are monotone with respect to both transmission probabilities and the initial set of infectives. The same covering-graph construction allows us to characterize the recurrent states in an SIS or SI(S/I) network with reinfection.
Agha-mohammadi, Ali-akbar
2013-06-01
This paper is concerned with the problem of stochastic optimal control (possibly with imperfect measurements) in the presence of constraints. We propose a computationally tractable framework to address this problem. The method lends itself to sampling-based methods where we construct a graph in the state space of the problem, on which a Dynamic Programming (DP) is solved and a closed-loop feedback policy is computed. The constraints are seamlessly incorporated to the control policy selection by including their effect on the transition probabilities of the graph edges. We present a unified framework that is applicable both in the state space (with perfect measurements) and in the information space (with imperfect measurements).
Learning Based Approach for Optimal Clustering of Distributed Program's Call Flow Graph
Abofathi, Yousef; Zarei, Bager; Parsa, Saeed
Optimal clustering of call flow graph for reaching maximum concurrency in execution of distributable components is one of the NP-Complete problems. Learning automatas (LAs) are search tools which are used for solving many NP-Complete problems. In this paper a learning based algorithm is proposed to optimal clustering of call flow graph and appropriate distributing of programs in network level. The algorithm uses learning feature of LAs to search in state space. It has been shown that the speed of reaching to solution increases remarkably using LA in search process, and it also prevents algorithm from being trapped in local minimums. Experimental results show the superiority of proposed algorithm over others.
A Semantic Graph-Based Approach for Radicalisation Detection on Social Media
Saif, Hassan; Dickinson, Thomas; Kastler, Leon; Fernandez, Miriam; Alani, Harith
2017-01-01
From its start, the so-called Islamic State of Iraq and the Levant (ISIL/ISIS) has been successfully exploiting social media networks, most notoriously Twitter, to promote its propaganda and recruit new members, resulting in thousands of social media users adopting a pro-ISIS stance every year. Automatic identification of pro-ISIS users on social media has, thus, become the centre of interest for various governmental and research organisations. In this paper we propose a semantic graph-based ...
Task-linked Diurnal Brain Network Reorganization in Older Adults: A Graph Theoretical Approach.
Anderson, John A E; Sarraf, Saman; Amer, Tarek; Bellana, Buddhika; Man, Vincent; Campbell, Karen L; Hasher, Lynn; Grady, Cheryl L
2017-03-01
Testing older adults in the morning generally improves behavioral performance relative to afternoon testing. Morning testing is also associated with brain activity similar to that of young adults. Here, we used graph theory to explore how time of day (TOD) affects the organization of brain networks in older adults across rest and task states. We used nodes from the automated anatomical labeling atlas to construct participant-specific correlation matrices of fMRI data obtained during 1-back tasks with interference and rest. We computed pairwise group differences for key graph metrics, including small-worldness and modularity. We found that older adults tested in the morning and young adults did not differ on any graph metric. Both of these groups differed from older adults tested in the afternoon during the tasks-but not rest. Specifically, the latter group had lower modularity and small-worldness (indices of more efficient network organization). Across all groups, higher modularity and small-worldness strongly correlated with reduced distractibility on an implicit priming task. Increasingly, TOD is seen as important for interpreting and reproducing neuroimaging results. Our study emphasizes how TOD affects brain network organization and executive control in older adults.
Functional Organization of the Action Observation Network in Autism: A Graph Theory Approach.
Alaerts, Kaat; Geerlings, Franca; Herremans, Lynn; Swinnen, Stephan P; Verhoeven, Judith; Sunaert, Stefan; Wenderoth, Nicole
2015-01-01
The ability to recognize, understand and interpret other's actions and emotions has been linked to the mirror system or action-observation-network (AON). Although variations in these abilities are prevalent in the neuro-typical population, persons diagnosed with autism spectrum disorders (ASD) have deficits in the social domain and exhibit alterations in this neural network. Here, we examined functional network properties of the AON using graph theory measures and region-to-region functional connectivity analyses of resting-state fMRI-data from adolescents and young adults with ASD and typical controls (TC). Overall, our graph theory analyses provided convergent evidence that the network integrity of the AON is altered in ASD, and that reductions in network efficiency relate to reductions in overall network density (i.e., decreased overall connection strength). Compared to TC, individuals with ASD showed significant reductions in network efficiency and increased shortest path lengths and centrality. Importantly, when adjusting for overall differences in network density between ASD and TC groups, participants with ASD continued to display reductions in network integrity, suggesting that also network-level organizational properties of the AON are altered in ASD. While differences in empirical connectivity contributed to reductions in network integrity, graph theoretical analyses provided indications that also changes in the high-level network organization reduced integrity of the AON.
Functional Organization of the Action Observation Network in Autism: A Graph Theory Approach.
Directory of Open Access Journals (Sweden)
Kaat Alaerts
Full Text Available The ability to recognize, understand and interpret other's actions and emotions has been linked to the mirror system or action-observation-network (AON. Although variations in these abilities are prevalent in the neuro-typical population, persons diagnosed with autism spectrum disorders (ASD have deficits in the social domain and exhibit alterations in this neural network.Here, we examined functional network properties of the AON using graph theory measures and region-to-region functional connectivity analyses of resting-state fMRI-data from adolescents and young adults with ASD and typical controls (TC.Overall, our graph theory analyses provided convergent evidence that the network integrity of the AON is altered in ASD, and that reductions in network efficiency relate to reductions in overall network density (i.e., decreased overall connection strength. Compared to TC, individuals with ASD showed significant reductions in network efficiency and increased shortest path lengths and centrality. Importantly, when adjusting for overall differences in network density between ASD and TC groups, participants with ASD continued to display reductions in network integrity, suggesting that also network-level organizational properties of the AON are altered in ASD.While differences in empirical connectivity contributed to reductions in network integrity, graph theoretical analyses provided indications that also changes in the high-level network organization reduced integrity of the AON.
Summary 2: Graph Grammar Verification through Abstraction
Baldan, P.; Koenig, B.; Rensink, A.; Rensink, Arend; König, B.; Montanari, U.; Gardner, P.
2005-01-01
Until now there have been few contributions concerning the verification of graph grammars, specifically of infinite-state graph grammars. This paper compares two existing approaches, based on abstractions of graph transformation systems. While in the unfolding approach graph grammars are
Graph passing in graph transformation
Ghamarian, A.H.; Rensink, Arend; Fish, Andrew; Lambers, Leen
Graph transformation works under the whole world assumption. Therefore, in realistic systems, both the individual graphs and the set of all such graphs can grow very large. In reactive formalisms such as process algebra, on the other hand, each system is split into smaller components which
Graph Passing in Graph Transformation
Ghamarian, A.H.; Rensink, Arend
2012-01-01
Graph transformation works under the whole world assumption. Therefore, in realistic systems, both the individual graphs and the set of all such graphs can grow very large. In reactive formalisms such as process algebra, on the other hand, each system is split into smaller components which
DEFF Research Database (Denmark)
Merker, Martin
The topic of this PhD thesis is graph decompositions. While there exist various kinds of decompositions, this thesis focuses on three problems concerning edgedecompositions. Given a family of graphs H we ask the following question: When can the edge-set of a graph be partitioned so that each part...... k(T)-edge-connected graph whose size is divisible by the size of T admits a T-decomposition. This proves a conjecture by Barát and Thomassen from 2006. Moreover, we introduce a new arboricity notion where we restrict the diameter of the trees in a decomposition into forests. We conjecture......-connected planar graph contains two edge-disjoint 18/19 -thin spanning trees. Finally, we make progress on a conjecture by Baudon, Bensmail, Przybyło, and Wozniak stating that if a graph can be decomposed into locally irregular graphs, then there exists such a decomposition with at most 3 parts. We show...
Interface Enthalpy-Entropy Competition in Nanoscale Metal Hydrides
Directory of Open Access Journals (Sweden)
Nicola Patelli
2018-01-01
Full Text Available We analyzed the effect of the interfacial free energy on the thermodynamics of hydrogen sorption in nano-scaled materials. When the enthalpy and entropy terms are the same for all interfaces, as in an isotropic bi-phasic system, one obtains a compensation temperature, which does not depend on the system size nor on the relative phase abundance. The situation is different and more complex in a system with three or more phases, where the interfaces have different enthalpy and entropy. We also consider the possible effect of elastic strains on the stability of the hydride phase and on hysteresis. We compare a simple model with experimental data obtained on two different systems: (1 bi-phasic nanocomposites where ultrafine TiH2 crystallite are dispersed within a Mg nanoparticle and (2 Mg nanodots encapsulated by different phases.
Enthalpy-Entropy Compensation (EEC) Effect: A Revisit.
Pan, Animesh; Biswas, Tapas; Rakshit, Animesh K; Moulik, Satya P
2015-12-31
A short account of the developments and perspectives of IKR (iso-kinetic relation) and EEC (enthalpy (H) - entropy (S) compensation) has been presented. The IKR and EEC are known to be extra thermodynamic or empirical correlations though linear H-S correlation can be thermodynamically deduced. Attempt has also been made to explain the phenomena in terms of statistical thermodynamics. In this study, we have briefly revisited the fundamentals of both IKR and EEC from kinetic and thermodynamic grounds. A detailed revisit of the EEC phenomenon on varied kinetic and equilibrium processes has been also presented. Possible correlations among the free energy (ΔG), enthalpy (ΔH), and entropy (ΔS) changes of different similar and nonsimilar chemical processes under varied conditions have been discussed with possible future projections.
Graph Theory and ANT Colony Optimization Approach for Forest Patch Connectivity Analysis
Shantala Devi, B. S.; Murthy, M. S. R.; Pujar, G. S.; Debnath, B.
2011-08-01
Forest connectivity is necessary for prioritizing biodiversity conservation. Connectivity indices facilitate to predict the movement pattern of species across complex landscapes. Change in area and inter-patch distance in forest affects the biodiversity, wildlife movement, seed dispersal and other ecological factors. In graph theory components play an important role to analyze the group of patches and its impact with reference to the threshold distance between the patches. The study on link, threshold distance and components showed that with the increase in threshold distance, number of components decreased and number of links increased. Also Integral index of connectivity importance value (dIIC > 0.05) is high for big forest patches and considered to be intact forest. For those less than 0.05 importance value requires protection and conservation. Hence dIIC is categorised into Very low, low, Medium, high and Very high to analyze the degree of connectivity. Choosing correct threshold distance based on the requirement of species movement is preferred. Based on the selection of potential habitat patches shortest path between them is determined using Ant Colony Optimization (ACO) Technique. Vegetation type Map, Slope, Elevation, Disturbance Index, Biological Richness Map and DIIC layers facilitated to analyze the optimal path of the species through ACO for connectivity. Graph Theory and ACO works as a robust tool for Biodiversity Conservation.
Foodsheds in Virtual Water Flow Networks: A Spectral Graph Theory Approach
Directory of Open Access Journals (Sweden)
Nina Kshetry
2017-06-01
Full Text Available A foodshed is a geographic area from which a population derives its food supply, but a method to determine boundaries of foodsheds has not been formalized. Drawing on the food–water–energy nexus, we propose a formal network science definition of foodsheds by using data from virtual water flows, i.e., water that is virtually embedded in food. In particular, we use spectral graph partitioning for directed graphs. If foodsheds turn out to be geographically compact, it suggests the food system is local and therefore reduces energy and externality costs of food transport. Using our proposed method we compute foodshed boundaries at the global-scale, and at the national-scale in the case of two of the largest agricultural countries: India and the United States. Based on our determination of foodshed boundaries, we are able to better understand commodity flows and whether foodsheds are contiguous and compact, and other factors that impact environmental sustainability. The formal method we propose may be used more broadly to study commodity flows and their impact on environmental sustainability.
Monitoring Effective Connectivity in the Preterm Brain: A Graph Approach to Study Maturation
Directory of Open Access Journals (Sweden)
M. Lavanga
2017-01-01
Full Text Available In recent years, functional connectivity in the developmental science received increasing attention. Although it has been reported that the anatomical connectivity in the preterm brain develops dramatically during the last months of pregnancy, little is known about how functional and effective connectivity change with maturation. The present study investigated how effective connectivity in premature infants evolves. To assess it, we use EEG measurements and graph-theory methodologies. We recorded data from 25 preterm babies, who underwent long-EEG monitoring at least twice during their stay in the NICU. The recordings took place from 27 weeks postmenstrual age (PMA until 42 weeks PMA. Results showed that the EEG-connectivity, assessed using graph-theory indices, moved from a small-world network to a random one, since the clustering coefficient increases and the path length decreases. This shift can be due to the development of the thalamocortical connections and long-range cortical connections. Based on the network indices, we developed different age-prediction models. The best result showed that it is possible to predict the age of the infant with a root mean-squared error (MSE equal to 2.11 weeks. These results are similar to the ones reported in the literature for age prediction in preterm babies.
Bounding the HL-index of a graph: a majorization approach.
Clemente, Gian Paolo; Cornaro, Alessandra
2016-01-01
In mathematical chemistry, the median eigenvalues of the adjacency matrix of a molecular graph are strictly related to orbital energies and molecular orbitals. In this regard, the difference between the occupied orbital of highest energy (HOMO) and the unoccupied orbital of lowest energy (LUMO) has been investigated (see Fowler and Pisansky in Acta Chim. Slov. 57:513-517, 2010). Motivated by the HOMO-LUMO separation problem, Jaklič et al. in (Ars Math. Contemp. 5:99-115, 2012) proposed the notion of HL -index that measures how large in absolute value are the median eigenvalues of the adjacency matrix. Several bounds for this index have been provided in the literature. The aim of the paper is to derive alternative inequalities to bound the HL -index. By applying majorization techniques and making use of some known relations, we derive new and sharper upper bounds for this index. Analytical and numerical results show the performance of these bounds on different classes of graphs.
Arosio, Marcello; Martina, Mario L. V.
2017-04-01
In the last years, the relations and interactions between multi-hazards, vulnerability, exposure and resilience spheres are assuming more and more attention and the scientific community recognized that they are very dynamic, complex and interconnected. The traditional approaches define risk as the potential economic, social and environmental consequences due to a hazardous phenomenon in a specific period. Although there have been major improvements in recent years, there are still some limitation in term of a holistic approach that is able to include the emergent value hidden in the relation and interaction between the different spheres. Furthermore, the emergent behaviour of a society makes the collective risk greater than the sum of the parts and this requires a holistic, systematic and integrated approach. For this reason, it is important to consider the connections between elements to assess properly the vulnerability of systems. In a system (e.g. road, hospital and ecological network, etc.), or in a System of System (e.g. socio-technical urban service), there are critical elements that, beyond the intrinsic vulnerability, can be characterize by greater or lower vulnerability because of their physical, geographical, cyber or logical connections. To understand the system response to a perturbation, and therefore its resilience, is necessary not only to represent but also to quantify the relative importance of the elements and their interconnections. To this aim, we propose an innovative approach in the field of natural risk assessment based on the properties of graph G=(N,L). A graph consists of two sets N (nodes) and L (links): the nodes represent the single exposed elements (physical, social, environmental, etc.) to a hazard, while the links (or connections) represent the interaction between the elements. This approach encourages the risk assessment to a new prospective: from reductionist to holistic. The final goal is to provide insight in understanding how
Tarasevich, Yu Yu; Burmistrov, A. S.; Goltseva, V. A.; Gordeev, I. I.; Serbin, V. I.; Sizova, A. A.; Vodolazskaya, I. V.; Zholobov, D. A.
2018-01-01
A set of current-carrying bonds of a random resistor network (RRN) is called the (effective) backbone. The (geometrical) backbone can be defined as a union of all self-avoiding walks between two given points on a network or between its opposite borders. These two definitions provide two different approaches for identification of backbones. On the one hand, one can treat an arbitrary network as RRN and calculate potentials and currents in this RRN. On the other hand, one can apply to the network some search algorithms on graphs. Each of these approaches are known to have both advantages and drawbacks. We have implemented several different algorithms for backbone identification. The algorithms were applied to backbone identification for different system sizes and concentrations of conducting bonds. Our analysis suggests that a universal algorithm suitable for any problem is hardly possible to offer. Most likely, each particular task needs a specific algorithm.
Graph theory approach to the eigenvalue problem of large space structures
Reddy, A. S. S. R.; Bainum, P. M.
1981-01-01
Graph theory is used to obtain numerical solutions to eigenvalue problems of large space structures (LSS) characterized by a state vector of large dimensions. The LSS are considered as large, flexible systems requiring both orientation and surface shape control. Graphic interpretation of the determinant of a matrix is employed to reduce a higher dimensional matrix into combinations of smaller dimensional sub-matrices. The reduction is implemented by means of a Boolean equivalent of the original matrices formulated to obtain smaller dimensional equivalents of the original numerical matrix. Computation time becomes less and more accurate solutions are possible. An example is provided in the form of a free-free square plate. Linearized system equations and numerical values of a stiffness matrix are presented, featuring a state vector with 16 components.
A graph modification approach for finding core-periphery structures in protein interaction networks.
Bruckner, Sharon; Hüffner, Falk; Komusiewicz, Christian
2015-01-01
The core-periphery model for protein interaction (PPI) networks assumes that protein complexes in these networks consist of a dense core and a possibly sparse periphery that is adjacent to vertices in the core of the complex. In this work, we aim at uncovering a global core-periphery structure for a given PPI network. We propose two exact graph-theoretic formulations for this task, which aim to fit the input network to a hypothetical ground truth network by a minimum number of edge modifications. In one model each cluster has its own periphery, and in the other the periphery is shared. We first analyze both models from a theoretical point of view, showing their NP-hardness. Then, we devise efficient exact and heuristic algorithms for both models and finally perform an evaluation on subnetworks of the S. cerevisiae PPI network.
Abnormalities of functional brain networks in pathological gambling: a graph-theoretical approach
Tschernegg, Melanie; Crone, Julia S.; Eigenberger, Tina; Schwartenbeck, Philipp; Fauth-Bühler, Mira; Lemènager, Tagrid; Mann, Karl; Thon, Natasha; Wurst, Friedrich M.; Kronbichler, Martin
2013-01-01
Functional neuroimaging studies of pathological gambling (PG) demonstrate alterations in frontal and subcortical regions of the mesolimbic reward system. However, most investigations were performed using tasks involving reward processing or executive functions. Little is known about brain network abnormalities during task-free resting state in PG. In the present study, graph-theoretical methods were used to investigate network properties of resting state functional magnetic resonance imaging data in PG. We compared 19 patients with PG to 19 healthy controls (HCs) using the Graph Analysis Toolbox (GAT). None of the examined global metrics differed between groups. At the nodal level, pathological gambler showed a reduced clustering coefficient in the left paracingulate cortex and the left juxtapositional lobe (supplementary motor area, SMA), reduced local efficiency in the left SMA, as well as an increased node betweenness for the left and right paracingulate cortex and the left SMA. At an uncorrected threshold level, the node betweenness in the left inferior frontal gyrus was decreased and increased in the caudate. Additionally, increased functional connectivity between fronto-striatal regions and within frontal regions has also been found for the gambling patients. These findings suggest that regions associated with the reward system demonstrate reduced segregation but enhanced integration while regions associated with executive functions demonstrate reduced integration. The present study makes evident that PG is also associated with abnormalities in the topological network structure of the brain during rest. Since alterations in PG cannot be explained by direct effects of abused substances on the brain, these findings will be of relevance for understanding functional connectivity in other addictive disorders. PMID:24098282
Klados, Manousos A; Kanatsouli, Kassia; Antoniou, Ioannis; Babiloni, Fabio; Tsirka, Vassiliki; Bamidis, Panagiotis D; Micheloyannis, Sifis
2013-01-01
The two core systems of mathematical processing (subitizing and retrieval) as well as their functionality are already known and published. In this study we have used graph theory to compare the brain network organization of these two core systems in the cortical layer during difficult calculations. We have examined separately all the EEG frequency bands in healthy young individuals and we found that the network organization at rest, as well as during mathematical tasks has the characteristics of Small World Networks for all the bands, which is the optimum organization required for efficient information processing. The different mathematical stimuli provoked changes in the graph parameters of different frequency bands, especially the low frequency bands. More specific, in Delta band the induced network increases it's local and global efficiency during the transition from subitizing to retrieval system, while results suggest that difficult mathematics provoke networks with higher cliquish organization due to more specific demands. The network of the Theta band follows the same pattern as before, having high nodal and remote organization during difficult mathematics. Also the spatial distribution of the network's weights revealed more prominent connections in frontoparietal regions, revealing the working memory load due to the engagement of the retrieval system. The cortical networks of the alpha brainwaves were also more efficient, both locally and globally, during difficult mathematics, while the fact that alpha's network was more dense on the frontparietal regions as well, reveals the engagement of the retrieval system again. Concluding, this study gives more evidences regarding the interaction of the two core systems, exploiting the produced functional networks of the cerebral cortex, especially for the difficult mathematics.
A Modal-Logic Based Graph Abstraction
Bauer, J.; Boneva, I.B.; Kurban, M.E.; Rensink, Arend; Ehrig, H; Heckel, R.; Rozenberg, G.; Taentzer, G.
2008-01-01
Infinite or very large state spaces often prohibit the successful verification of graph transformation systems. Abstract graph transformation is an approach that tackles this problem by abstracting graphs to abstract graphs of bounded size and by lifting application of productions to abstract
Interaction Graphs: Exponentials
Seiller, Thomas
2013-01-01
This paper is the fourth of a series exposing a systematic combinatorial approach to Girard's Geometry of Interaction program. This program aims at obtaining particular realizability models for linear logic that accounts for the dynamics of cut-elimination. This fourth paper tackles the complex issue of defining exponential connectives in this framework. In order to succeed in this, we use the notion of graphings, a generalization of graphs which was defined in earlier work. We explain how we...
Graph Sampling for Covariance Estimation
Chepuri, Sundeep Prabhakar
2017-04-25
In this paper the focus is on subsampling as well as reconstructing the second-order statistics of signals residing on nodes of arbitrary undirected graphs. Second-order stationary graph signals may be obtained by graph filtering zero-mean white noise and they admit a well-defined power spectrum whose shape is determined by the frequency response of the graph filter. Estimating the graph power spectrum forms an important component of stationary graph signal processing and related inference tasks such as Wiener prediction or inpainting on graphs. The central result of this paper is that by sampling a significantly smaller subset of vertices and using simple least squares, we can reconstruct the second-order statistics of the graph signal from the subsampled observations, and more importantly, without any spectral priors. To this end, both a nonparametric approach as well as parametric approaches including moving average and autoregressive models for the graph power spectrum are considered. The results specialize for undirected circulant graphs in that the graph nodes leading to the best compression rates are given by the so-called minimal sparse rulers. A near-optimal greedy algorithm is developed to design the subsampling scheme for the non-parametric and the moving average models, whereas a particular subsampling scheme that allows linear estimation for the autoregressive model is proposed. Numerical experiments on synthetic as well as real datasets related to climatology and processing handwritten digits are provided to demonstrate the developed theory.
Khaouch, Zakaria; Zekraoui, Mustapha; Bengourram, Jamaa; Kouider, Nourreeddine; Mabrouki, Mustapha
2016-11-01
In this paper, we would like to focus on modeling main parts of the wind turbines (blades, gearbox, tower, generator and pitching system) from a mechatronics viewpoint using the Bond-Graph Approach (BGA). Then, these parts are combined together in order to simulate the complete system. Moreover, the real dynamic behavior of the wind turbine is taken into account and with the new model; final load simulation is more realistic offering benefits and reliable system performance. This model can be used to develop control algorithms to reduce fatigue loads and enhance power production. Different simulations are carried-out in order to validate the proposed wind turbine model, using real data provided in the open literature (blade profile and gearbox parameters for a 750 kW wind turbine). Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
Simoens Frederik
2006-01-01
Full Text Available This paper concerns channel tracking in a multiantenna context for correlated flat-fading channels obeying a Gauss-Markov model. It is known that data-aided tracking of fast-fading channels requires a lot of pilot symbols in order to achieve sufficient accuracy, and hence decreases the spectral efficiency. To overcome this problem, we design a code-aided estimation scheme which exploits information from both the pilot symbols and the unknown coded data symbols. The algorithm is derived based on a factor graph representation of the system and application of the sum-product algorithm. The sum-product algorithm reveals how soft information from the decoder should be exploited for the purpose of estimation and how the information bits can be detected. Simulation results illustrate the effectiveness of our approach.
A graph theoretic approach to the analysis of DNA sequencing data.
Berno, A J
1996-02-01
The analysis of data from automated DNA sequencing instruments has been a limiting factor in the development of new sequencing technology. A new base-calling algorithm that is intended to be independent of any particular sequencing technology has been developed and shown to be effective with data from the Applied Biosystems 373 sequencing system. This algorithm makes use of a nonlinear deconvolution filter to detect likely oligomer events and a graph theoretic editing strategy to find the subset of those events that is most likely to correspond to the correct sequence. Metrics evaluating the quality and accuracy of the resulting sequence are also generated and have been shown to be predictive of measured error rates. Compared to the Applied Biosystems Analysis software, this algorithm generates 18% fewer insertion errors, 80% more deletion errors, and 4% fewer mismatches. The tradeoff between different types of errors can be controlled through a secondary editing step that inserts or deletes base calls depending on their associated confidence values.
Modelling of Non-Linear Pilot Disinfection Water System: A Bond Graph Approach
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Naoufel ZITOUNI
2012-08-01
Full Text Available The ultraviolet (UV irradiations are used to solve the bacteriological problem of the drinking water quality. A discharge-gas lamp is used to produce this type of irradiation. The UV lamp is fed by photovoltaic (PV energy via electronic ballast composed by an inverter, a transformer and resonant circuit (RLC. The aim of this work is to give a useful global model of the system. In particular, we introduce the complicated UV lamp model and the water disinfection kinetics, where the radiant energy flux emitted by the discharge-gas lamp and the arc voltage are a complex functions of the current and time. This system is intended to be mainly used in rural zones, the photovoltaic modules as source of energy is an adequate solution. To optimise the power transfer from the PV array to ballast and UV lamp, a Maximum Power Point Tracking (MPPT device may be located between PV array and the loads. In this paper, we developed a bond-graph model which gives the water quality from UV flow, gas type, pressure, lamp current and geometrical characteristic. Finally reliable simulations are established and compared with experimental tests.
Vignola, Emanuele; Steinmann, Stephan N.; Vandegehuchte, Bart D.; Curulla, Daniel; Stamatakis, Michail; Sautet, Philippe
2017-08-01
The accurate description of the energy of adsorbate layers is crucial for the understanding of chemistry at interfaces. For heterogeneous catalysis, not only the interaction of the adsorbate with the surface but also the adsorbate-adsorbate lateral interactions significantly affect the activation energies of reactions. Modeling the interactions of the adsorbates with the catalyst surface and with each other can be efficiently achieved in the cluster expansion Hamiltonian formalism, which has recently been implemented in a graph-theoretical kinetic Monte Carlo (kMC) scheme to describe multi-dentate species. Automating the development of the cluster expansion Hamiltonians for catalytic systems is challenging and requires the mapping of adsorbate configurations for extended adsorbates onto a graphical lattice. The current work adopts machine learning methods to reach this goal. Clusters are automatically detected based on formalized, but intuitive chemical concepts. The corresponding energy coefficients for the cluster expansion are calculated by an inversion scheme. The potential of this method is demonstrated for the example of ethylene adsorption on Pd(111), for which we propose several expansions, depending on the graphical lattice. It turns out that for this system, the best description is obtained as a combination of single molecule patterns and a few coupling terms accounting for lateral interactions.
Hendrix, William; Jenkins, John; Padmanabhan, Kanchana; Chakraborty, Arpan
2014-01-01
Practical Graph Mining with R presents a "do-it-yourself" approach to extracting interesting patterns from graph data. It covers many basic and advanced techniques for the identification of anomalous or frequently recurring patterns in a graph, the discovery of groups or clusters of nodes that share common patterns of attributes and relationships, the extraction of patterns that distinguish one category of graphs from another, and the use of those patterns to predict the category of new graphs. Hands-On Application of Graph Data Mining Each chapter in the book focuses on a graph mining task, such as link analysis, cluster analysis, and classification. Through applications using real data sets, the book demonstrates how computational techniques can help solve real-world problems. The applications covered include network intrusion detection, tumor cell diagnostics, face recognition, predictive toxicology, mining metabolic and protein-protein interaction networks, and community detection in social networks. De...
Using Graph Transformations and Graph Abstractions for Software Verification
Zambon, Eduardo; Ehrig, Hartmut; Rensink, Arend; Rozenberg, Grzegorz; Schurr, Andy
In this abstract we present an overview of our intended approach for the verification of software written in imperative programming languages. This approach is based on model checking of graph transition systems (GTS), where each program state is modeled as a graph and the exploration engine is
International Nuclear Information System (INIS)
Texier, Christophe
2008-01-01
We consider a metric graph G made of two graphs G 1 and G 2 attached at one point. We derive a formula relating the spectral determinant of the Laplace operator S G (γ)=det(γ-Δ) in terms of the spectral determinants of the two subgraphs. The result is generalized to describe the attachment of n graphs. The formulae are also valid for the spectral determinant of the Schroedinger operator det(γ-Δ+V(x))
Mechatronics by bond graphs an object-oriented approach to modelling and simulation
Damić, Vjekoslav
2015-01-01
This book presents a computer-aided approach to the design of mechatronic systems. Its subject is an integrated modeling and simulation in a visual computer environment. Since the first edition, the simulation software changed enormously, became more user-friendly and easier to use. Therefore, a second edition became necessary taking these improvements into account. The modeling is based on system top-down and bottom-up approach. The mathematical models are generated in a form of differential-algebraic equations and solved using numerical and symbolic algebra methods. The integrated approach developed is applied to mechanical, electrical and control systems, multibody dynamics, and continuous systems. .
An Efficient Monte Carlo Approach to Compute PageRank for Large Graphs on a Single PC
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Sonobe Tomohiro
2016-03-01
Full Text Available This paper describes a novel Monte Carlo based random walk to compute PageRanks of nodes in a large graph on a single PC. The target graphs of this paper are ones whose size is larger than the physical memory. In such an environment, memory management is a difficult task for simulating the random walk among the nodes. We propose a novel method that partitions the graph into subgraphs in order to make them fit into the physical memory, and conducts the random walk for each subgraph. By evaluating the walks lazily, we can conduct the walks only in a subgraph and approximate the random walk by rotating the subgraphs. In computational experiments, the proposed method exhibits good performance for existing large graphs with several passes of the graph data.
Reorganization in Multi-Agent Architectures: An Active Graph Grammar Approach
Markus, Schatten
2013-01-01
Background: Organizational architecture is a holistic approach to design of humane organizations and studies an organization from five perspectives: structure, culture, processes, strategy and individuals. In this paper the concept of organizational architecture is firstly formalized using the fractal principle and then applied to multi-agent systems’ (MAS) organizations. Objectives: Providing a holistic framework for modelling all aspects of MASreorganization. Methods/Approach: MAS organizat...
International Nuclear Information System (INIS)
Vincze, Arpad; Nemeth, Andras
2013-01-01
According to a recent statement, the IAEA seeks to develop a more effective safeguards system to achieve greater deterrence, because deterrence of proliferation is much more effective than detection. To achieve this goal, a less predictive safeguards system is being developed based on the advanced state-level approach that is driven by all available safeguards-relevant information. The 'directed graph analysis' is recommended as a possible methodology to implement acquisition path analysis by the IAEA to support the State evaluation process. The basic methodology is simple, well established, powerful, and its adaptation to the modelling of the nuclear profile of a State requires minimum software development. Based on this methodology the material flow network model has been developed under the Hungarian Support Programme to the IAEA, which is described in detail. In the proposed model, materials in different chemical and physical form can flow through pipes representing declared processes, material transports, diversions or undeclared processes. The nodes of the network are the material types, while the edges of the network are the pipes. A state parameter (p) is assigned to each node and edge representing the probability of their existence in the State. The possible application of this model in the State-level analytical approach will be discussed and outlook for further work will be given. The paper is followed by the slides of the presentation
International Nuclear Information System (INIS)
Rand, C.P. du; Schoor, G. van
2012-01-01
Highlights: ► Different uncorrelated fault signatures are derived for HTGR component faults. ► A multiple classifier ensemble increases confidence in classification accuracy. ► Detailed simulation model of system is not required for fault diagnosis. - Abstract: The second paper in a two part series presents the area error method for generation of representative enthalpy–entropy (h–s) fault signatures to classify malfunctions in generation IV nuclear high temperature gas-cooled reactor (HTGR) components. The second classifier is devised to ultimately address the fault diagnosis (FD) problem via the proposed methods in a multiple classifier (MC) ensemble. FD is realized by way of different input feature sets to the classification algorithm based on the area and trajectory of the residual shift between the fault-free and the actual operating h–s graph models. The application of the proposed technique is specifically demonstrated for 24 single fault transients considered in the main power system (MPS) of the Pebble Bed Modular Reactor (PBMR). The results show that the area error technique produces different fault signatures with low correlation for all the examined component faults. A brief evaluation of the two fault signature generation techniques is presented and the performance of the area error method is documented using the fault classification index (FCI) presented in Part I of the series. The final part of this work reports the application of the proposed approach for classification of an emulated fault transient in data from the prototype Pebble Bed Micro Model (PBMM) plant. Reference data values are calculated for the plant via a thermo-hydraulic simulation model of the MPS. The results show that the correspondence between the fault signatures, generated via experimental plant data and simulated reference values, are generally good. The work presented in the two part series, related to the classification of component faults in the MPS of different
Trudeau, Richard J
1994-01-01
Preface1. Pure Mathematics Introduction; Euclidean Geometry as Pure Mathematics; Games; Why Study Pure Mathematics?; What's Coming; Suggested Reading2. Graphs Introduction; Sets; Paradox; Graphs; Graph diagrams; Cautions; Common Graphs; Discovery; Complements and Subgraphs; Isomorphism; Recognizing Isomorphic Graphs; Semantics The Number of Graphs Having a Given nu; Exercises; Suggested Reading3. Planar Graphs Introduction; UG, K subscript 5, and the Jordan Curve Theorem; Are there More Nonplanar Graphs?; Expansions; Kuratowski's Theorem; Determining Whether a Graph is Planar or
Directory of Open Access Journals (Sweden)
Zabiniako Vitaly
2014-12-01
Full Text Available In this article, the authors perform an analysis in order to assess adaptation of magnetic force-directed algorithms for context-based information extraction from multi-attributed graphs during visualization sessions. Theoretic standings behind magnetic force-directed approach are stated together with review on how particular features of respective algorithms in combination with appropriate visual techniques are especially suitable for improved processing and presenting of knowledge that is captured in form of graphs. The complexity of retrieving multi-attributed information within the proposed approach is handled with dedicated tools, such as selective attraction of nodes to MFE (Magnetic Force Emitter based on search criteria, localization of POI (Point of Interest regions, graph node anchoring, etc. Implicit compatibility of aforementioned tools with interactive nature of data exploration is distinguished. Description of case study, based on bibliometric network analysis is given, which is followed by the review of existing related works in this field. Conclusions are made and further studies in the field of visualization of multi-attributed graphs are defined.
Sotiropoulos, Stamatios N; Bai, Li; Morgan, Paul S; Constantinescu, Cris S; Tench, Christopher R
2010-02-01
Brain tractography techniques utilize a set of diffusion-weighted magnetic resonance images to reconstruct white matter tracts, non-invasively and in-vivo. Streamline tracking techniques propagate curves from a seed to imply connectivity to distal voxels. Alternative approaches have been developed that attempt to quantify connection strength between all voxels and the seed. Tractography based on graph theory is amongst them. Despite its potential, graph-based tracking through complex fibre configurations has not been extensively studied and existing methods have inherent limitations. Anatomically unlikely connections may be identified in fibre crossing regions, by assigning relatively high connection strengths to all crossing populations. In this study, we discuss these limitations and present a new approach for robustly propagating through fibre crossings, as described by the orientation distribution functions (ODFs) derived from Q-ball imaging. Each image voxel is treated as a graph node and graph arcs connect neighbouring voxels. Weights representative of both structural and diffusivity features are assigned to each arc. To account for the existence of crossing fibre populations within a voxel, complex ODFs are decomposed into components representative of single-fibre populations and an image multigraph is created. The multigraph is searched exhaustively, but efficiently, to find the strongest paths and assign connectivity strengths between a seed and all the other image voxels. A comparison with the existing graph-based tractography as well as Q-ball driven front evolution tractography is performed on simulated data, and on human Q-ball imaging data acquired from five healthy volunteers. The new approach improves the connection strengths through fibre crossing regions, reducing the strengths of paths that are less anatomically plausible. Copyright (c) 2009 Elsevier Inc. All rights reserved.
Directory of Open Access Journals (Sweden)
Carlos A. Sánchez-Catasús
2017-01-01
Full Text Available There is growing support that cerebrovascular reactivity (CVR in response to a vasodilatory challenge, also defined as the cerebrovascular reserve, is reduced in Alzheimer's disease dementia. However, this is less clear in patients with mild cognitive impairment (MCI. The current standard analysis may not reflect subtle abnormalities in CVR. In this study, we aimed to investigate vasodilatory-induced changes in the topology of the cerebral blood flow correlation (CBFcorr network to study possible network-related CVR abnormalities in MCI. For this purpose, four CBFcorr networks were constructed: two using CBF SPECT data at baseline and under the vasodilatory challenge of acetazolamide (ACZ, obtained from a group of 26 MCI patients; and two equivalent networks from a group of 26 matched cognitively normal controls. The mean strength of association (SA and clustering coefficient (C were used to evaluate ACZ-induced changes on the topology of CBFcorr networks. We found that cognitively normal adults and MCI patients show different patterns of C and SA changes. The observed differences included the medial prefrontal cortices and inferior parietal lobe, which represent areas involved in MCI's cognitive dysfunction. In contrast, no substantial differences were detected by standard CVR analysis. These results suggest that graph theoretical analysis of ACZ-induced changes in the topology of the CBFcorr networks allows the identification of subtle network-related CVR alterations in MCI, which couldn't be detected by the standard approach.
Trend Motif: A Graph Mining Approach for Analysis of Dynamic Complex Networks
Energy Technology Data Exchange (ETDEWEB)
Jin, R; McCallen, S; Almaas, E
2007-05-28
Complex networks have been used successfully in scientific disciplines ranging from sociology to microbiology to describe systems of interacting units. Until recently, studies of complex networks have mainly focused on their network topology. However, in many real world applications, the edges and vertices have associated attributes that are frequently represented as vertex or edge weights. Furthermore, these weights are often not static, instead changing with time and forming a time series. Hence, to fully understand the dynamics of the complex network, we have to consider both network topology and related time series data. In this work, we propose a motif mining approach to identify trend motifs for such purposes. Simply stated, a trend motif describes a recurring subgraph where each of its vertices or edges displays similar dynamics over a userdefined period. Given this, each trend motif occurrence can help reveal significant events in a complex system; frequent trend motifs may aid in uncovering dynamic rules of change for the system, and the distribution of trend motifs may characterize the global dynamics of the system. Here, we have developed efficient mining algorithms to extract trend motifs. Our experimental validation using three disparate empirical datasets, ranging from the stock market, world trade, to a protein interaction network, has demonstrated the efficiency and effectiveness of our approach.
Tong, Yubing; Udupa, Jayaram K; Ciesielski, Krzysztof C; Wu, Caiyun; McDonough, Joseph M; Mong, David A; Campbell, Robert M
2017-01-01
Dynamic or 4D imaging of the thorax has many applications. Both prospective and retrospective respiratory gating and tracking techniques have been developed for 4D imaging via CT and MRI. For pediatric imaging, due to radiation concerns, MRI becomes the de facto modality of choice. In thoracic insufficiency syndrome (TIS), patients often suffer from extreme malformations of the chest wall, diaphragm, and/or spine with inability of the thorax to support normal respiration or lung growth (Campbell et al., 2003, Campbell and Smith, 2007), as such patient cooperation needed by some of the gating and tracking techniques are difficult to realize without causing patient discomfort and interference with the breathing mechanism itself. Therefore (ventilator-supported) free-breathing MRI acquisition is currently the best choice for imaging these patients. This, however, raises a question of how to create a consistent 4D image from such acquisitions. This paper presents a novel graph-based technique for compiling the best 4D image volume representing the thorax over one respiratory cycle from slice images acquired during unencumbered natural tidal-breathing of pediatric TIS patients. In our approach, for each coronal (or sagittal) slice position, images are acquired at a rate of about 200-300ms/slice over several natural breathing cycles which yields over 2000 slices. A weighted graph is formed where each acquired slice constitutes a node and the weight of the arc between two nodes defines the degree of contiguity in space and time of the two slices. For each respiratory phase, an optimal 3D spatial image is constructed by finding the best path in the graph in the spatial direction. The set of all such 3D images for a given respiratory cycle constitutes a 4D image. Subsequently, the best 4D image among all such constructed images is found over all imaged respiratory cycles. Two types of evaluation studies are carried out to understand the behavior of this algorithm and in
Diestel, Reinhard
2017-01-01
This standard textbook of modern graph theory, now in its fifth edition, combines the authority of a classic with the engaging freshness of style that is the hallmark of active mathematics. It covers the core material of the subject with concise yet reliably complete proofs, while offering glimpses of more advanced methods in each field by one or two deeper results, again with proofs given in full detail. The book can be used as a reliable text for an introductory course, as a graduate text, and for self-study. From the reviews: “This outstanding book cannot be substituted with any other book on the present textbook market. It has every chance of becoming the standard textbook for graph theory.”Acta Scientiarum Mathematiciarum “Deep, clear, wonderful. This is a serious book about the heart of graph theory. It has depth and integrity. ”Persi Diaconis & Ron Graham, SIAM Review “The book has received a very enthusiastic reception, which it amply deserves. A masterly elucidation of modern graph theo...
Tracking and graph-cut based approach for panoramic background construction
Fadaeieslam, Mohammad Javad; Soryani, Mohsen; Fathy, Mahmood
2013-10-01
An efficient method is presented for extracting motion behaviors and contours of moving objects in a wide view and for creating panoramic background. In the field of making panorama, the main goal of existing methods is to create a pleasing wide view. For this purpose, such methods do not track moving objects. They attempt to find optimal seams so that the result does not contain cut objects or blurring. Hence, moving objects are removed, repeated, or placed in an arbitrary location in the final panoramic image. We expand panorama applications from artistic views to surveillance usages. To investigate moving object behavior, the proposed method attempts to find correspondences between positions of a moving object in different selected frames by using SIFT features. It also presents a new approach to combine various types of information in order to extract the exact boundary of moving objects in moving cameras. The required information is obtained from the moving object's corresponding areas in other frames. Experiments were arranged to demonstrate the effectiveness and robustness of this method. The results show that this method, which uses fewer frames, is able to create better panoramic background compared with the existing methods.
Directory of Open Access Journals (Sweden)
Hossien Pourghassem
2011-04-01
Full Text Available Relevance feedback approaches is used to improve the performance of content-based image retrieval systems. In this paper, a novel relevance feedback approach based on similarity measure modification in an X-ray image retrieval system based on fuzzy representation using fuzzy attributed relational graph (FARG is presented. In this approach, optimum weight of each feature in feature vector is calculated using similarity rate between query image and relevant and irrelevant images in user feedback. The calculated weight is used to tune fuzzy graph matching algorithm as a modifier parameter in similarity measure. The standard deviation of the retrieved image features is applied to calculate the optimum weight. The proposed image retrieval system uses a FARG for representation of images, a fuzzy matching graph algorithm as similarity measure and a semantic classifier based on merging scheme for determination of the search space in image database. To evaluate relevance feedback approach in the proposed system, a standard X-ray image database consisting of 10000 images in 57 classes is used. The improvement of the evaluation parameters shows proficiency and efficiency of the proposed system.
Maximal outerplanar graphs as chordal graphs, path-neighborhood graphs, and triangle graphs
R.C. Laskar (R.C.); H.M. Mulder (Martyn); B. Novick (Beth)
2011-01-01
textabstractMaximal outerplanar graphs are characterized using three different classes of graphs. A path-neighborhood graph is a connected graph in which every neighborhood induces a path. The triangle graph $T(G)$ has the triangles of the graph $G$ as its vertices, two of these being adjacent
Witman, Matthew; Ling, Sanliang; Boyd, Peter; Barthel, Senja; Haranczyk, Maciej; Slater, Ben; Smit, Berend
2018-02-28
Scientific interest in two-dimensional (2D) materials, ranging from graphene and other single layer materials to atomically thin crystals, is quickly increasing for a large variety of technological applications. While in silico design approaches have made a large impact in the study of 3D crystals, algorithms designed to discover atomically thin 2D materials from their parent 3D materials are by comparison more sparse. We hypothesize that determining how to cut a 3D material in half (i.e., which Miller surface is formed) by severing a minimal number of bonds or a minimal amount of total bond energy per unit area can yield insight into preferred crystal faces. We answer this question by implementing a graph theory technique to mathematically formalize the enumeration of minimum cut surfaces of crystals. While the algorithm is generally applicable to different classes of materials, we focus on zeolitic materials due to their diverse structural topology and because 2D zeolites have promising catalytic and separation performance compared to their 3D counterparts. We report here a simple descriptor based only on structural information that predicts whether a zeolite is likely to be synthesizable in the 2D form and correctly identifies the expressed surface in known layered 2D zeolites. The discovery of this descriptor allows us to highlight other zeolites that may also be synthesized in the 2D form that have not been experimentally realized yet. Finally, our method is general since the mathematical formalism can be applied to find the minimum cut surfaces of other crystallographic materials such as metal-organic frameworks, covalent-organic frameworks, zeolitic-imidazolate frameworks, metal oxides, etc.
Bond graph modeling of centrifugal compression systems
Uddin, Nur; Gravdahl, Jan Tommy
2015-01-01
A novel approach to model unsteady fluid dynamics in a compressor network by using a bond graph is presented. The model is intended in particular for compressor control system development. First, we develop a bond graph model of a single compression system. Bond graph modeling offers a different perspective to previous work by modeling the compression system based on energy flow instead of fluid dynamics. Analyzing the bond graph model explains the energy flow during compressor surge. Two pri...
Gould, Ronald
2012-01-01
This introduction to graph theory focuses on well-established topics, covering primary techniques and including both algorithmic and theoretical problems. The algorithms are presented with a minimum of advanced data structures and programming details. This thoroughly corrected 1988 edition provides insights to computer scientists as well as advanced undergraduates and graduate students of topology, algebra, and matrix theory. Fundamental concepts and notation and elementary properties and operations are the first subjects, followed by examinations of paths and searching, trees, and networks. S
Chartrand, Gary; Zhang, Ping
2010-01-01
Gary Chartrand has influenced the world of Graph Theory for almost half a century. He has supervised more than a score of Ph.D. dissertations and written several books on the subject. The most widely known of these texts, Graphs and Digraphs, … has much to recommend it, with clear exposition, and numerous challenging examples [that] make it an ideal textbook for the advanced undergraduate or beginning graduate course. The authors have updated their notation to reflect the current practice in this still-growing area of study. By the authors' estimation, the 5th edition is approximately 50% longer than the 4th edition. … the legendary Frank Harary, author of the second graph theory text ever produced, is one of the figures profiled. His book was the standard in the discipline for several decades. Chartrand, Lesniak and Zhang have produced a worthy successor.-John T. Saccoman, MAA Reviews, June 2012 (This book is in the MAA's basic library list.)As with the earlier editions, the current text emphasizes clear...
Large networks and graph limits
Lovász, László
2012-01-01
Recently, it became apparent that a large number of the most interesting structures and phenomena of the world can be described by networks. Developing a mathematical theory of very large networks is an important challenge. This book describes one recent approach to this theory, the limit theory of graphs, which has emerged over the last decade. The theory has rich connections with other approaches to the study of large networks, such as "property testing" in computer science and regularity partition in graph theory. It has several applications in extremal graph theory, including the exact for
Graph theory and combinatorial optimization
Marcotte, Odile; Avis, David
2006-01-01
A current treatment of cutting-edge topics in Graph Theory and Combinatorial Optimization by leading researchersIncludes heuristic advances and novel approaches to solving combinatorial optimization problems.
CHARACTERISATION OF REGULAR GRAPHS AS LOOP GRAPHS ...
African Journals Online (AJOL)
There have been various generalisations of Cayley graphs, prototypes of transitive graphs. The most generalised is the description of graphs on general groupoids. What has clearly emerged in this exercise is that the philosophy of constructing graphs on groupoids offers a fruitful avenue from which we may understand ...
De Bruijn graphs and DNA graphs
Pendavingh, Rudi; Schuurman, Petra; Woeginger, Gerhard; Brandstädt, Andreas; Le, Van Bang
2001-01-01
In this paper we prove the NP-hardness of various recognition problems for subgraphs of De Bruijn graphs. In particular, the recognition of DNA graphs is shown to be NP-hard; DNA graphs are the vertex induced subgraphs of De Bruijn graphs over a four letter alphabet. As a consequence, two open
Appel, Robin; Folmer, Hendrik Hendrikus; Kuper, Jan; Wester, Rinse; Broenink, Johannes F.
2017-01-01
SLAM is a fundamental problem in robotics that can be solved by a set of algorithms that are known to have large computational complexity. GraphSLAM contains a rapidly growing system of equations which are often solved by sparse evaluation techniques. This paper proposes a technique to evaluate
DEFF Research Database (Denmark)
Blanke, Mogens
2005-01-01
This paper addresses the design process of diagnosis and fault-tolerant control when a system should operate despite multiple failures in sensors or actuators. Graph-theory based analysis of system's structure is demonstrated to be a unique design methodology that can cope with the diagnosis desi...
Colored graphs and matrix integrals
International Nuclear Information System (INIS)
Artamkin, I.V.
2007-12-01
In this article we discuss two different asymptotic expansions of matrix integrals. The original approach using the so-called Feynman diagram techniques leads to sums over isomorphism classes of ribbon graphs. Asymptotic expansions of more general Gaussian integrals are sums over isomorphism classes of colored graphs without ribbon structure. Here we derive the former expansion from the latter one. This provides an independent proof for the expansion used by Kontsevich. It might be very interesting to compare the algebra arising in these two approaches. The asymptotic expansion using ribbon graphs leads to the tau function of the KDV hierarchy while the sums over colored graphs satisfy simple partial differential equations which generalize the Burgers equation. We describe the general approach using colored graphs in the second section. In the third section we specialize the results of the second section for the matrix integral. In this section we also derive the expansion over ribbon graphs. The proof is based on simple topological considerations which are contained in section 5. In the last section we give an explicit calculation of the first term of the expansion using colored graphs
Diestel, Reinhard
2012-01-01
HauptbeschreibungThis standard textbook of modern graph theory, now in its fourth edition, combinesthe authority of a classic with the engaging freshness of style that is the hallmarkof active mathematics. It covers the core material of the subject with concise yetreliably complete proofs, while offering glimpses of more advanced methodsin each field by one or two deeper results, again with proofs given in full detail.The book can be used as a reliable text for an introductory course, as a graduatetext, and for self-study. Rezension"Deep, clear, wonderful. This is a serious book about the
Graph limits and hereditary properties
Janson, Svante
2011-01-01
We collect some general results on graph limits associated to hereditary classes of graphs. As examples, we consider some classes defined by forbidden subgraphs and some classes of intersection graphs, including triangle-free graphs, chordal graphs, cographs, interval graphs, unit interval graphs, threshold graphs, and line graphs.
On characterizing terrain visibility graphs
Directory of Open Access Journals (Sweden)
William Evans
2015-06-01
Full Text Available A terrain is an $x$-monotone polygonal line in the $xy$-plane. Two vertices of a terrain are mutually visible if and only if there is no terrain vertex on or above the open line segment connecting them. A graph whose vertices represent terrain vertices and whose edges represent mutually visible pairs of terrain vertices is called a terrain visibility graph. We would like to find properties that are both necessary and sufficient for a graph to be a terrain visibility graph; that is, we would like to characterize terrain visibility graphs.Abello et al. [Discrete and Computational Geometry, 14(3:331--358, 1995] showed that all terrain visibility graphs are “persistent”. They showed that the visibility information of a terrain point set implies some ordering requirements on the slopes of the lines connecting pairs of points in any realization, and as a step towards showing sufficiency, they proved that for any persistent graph $M$ there is a total order on the slopes of the (pseudo lines in a generalized configuration of points whose visibility graph is $M$.We give a much simpler proof of this result by establishing an orientation to every triple of vertices, reflecting some slope ordering requirements that are consistent with $M$ being the visibility graph, and prove that these requirements form a partial order. We give a faster algorithm to construct a total order on the slopes. Our approach attempts to clarify the implications of the graph theoretic properties on the ordering of the slopes, and may be interpreted as defining properties on an underlying oriented matroid that we show is a restricted type of $3$-signotope.
Quick Mining of Isomorphic Exact Large Patterns from Large Graphs
Almasri, Islam
2014-12-01
The applications of the sub graph isomorphism search are growing with the growing number of areas that model their systems using graphs or networks. Specifically, many biological systems, such as protein interaction networks, molecular structures and protein contact maps, are modeled as graphs. The sub graph isomorphism search is concerned with finding all sub graphs that are isomorphic to a relevant query graph, the existence of such sub graphs can reflect on the characteristics of the modeled system. The most computationally expensive step in the search for isomorphic sub graphs is the backtracking algorithm that traverses the nodes of the target graph. In this paper, we propose a pruning approach that is inspired by the minimum remaining value heuristic that achieves greater scalability over large query and target graphs. Our testing on various biological networks shows that performance enhancement of our approach over existing state-of-the-art approaches varies between 6x and 53x. © 2014 IEEE.
Energy Technology Data Exchange (ETDEWEB)
Kou, Qiang; Wu, Si; Tolić, Nikola; Paša-Tolić, Ljiljana; Liu, Yunlong; Liu, Xiaowen
2016-12-21
Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird’s eye view” of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry data sets showed that TopMG outperformed existing methods in identifying complex proteoforms.
Olayan, Rawan S.
2017-11-23
Motivation Finding computationally drug-target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer the high false positive prediction rate. Results We developed DDR, a novel method that improves the DTI prediction accuracy. DDR is based on the use of a heterogeneous graph that contains known DTIs with multiple similarities between drugs and multiple similarities between target proteins. DDR applies non-linear similarity fusion method to combine different similarities. Before fusion, DDR performs a pre-processing step where a subset of similarities is selected in a heuristic process to obtain an optimized combination of similarities. Then, DDR applies a random forest model using different graph-based features extracted from the DTI heterogeneous graph. Using five repeats of 10-fold cross-validation, three testing setups, and the weighted average of area under the precision-recall curve (AUPR) scores, we show that DDR significantly reduces the AUPR score error relative to the next best start-of-the-art method for predicting DTIs by 34% when the drugs are new, by 23% when targets are new, and by 34% when the drugs and the targets are known but not all DTIs between them are not known. Using independent sources of evidence, we verify as correct 22 out of the top 25 DDR novel predictions. This suggests that DDR can be used as an efficient method to identify correct DTIs.
Chartrand, Gary; Rosen, Kenneth H
2008-01-01
Beginning with the origin of the four color problem in 1852, the field of graph colorings has developed into one of the most popular areas of graph theory. Introducing graph theory with a coloring theme, Chromatic Graph Theory explores connections between major topics in graph theory and graph colorings as well as emerging topics. This self-contained book first presents various fundamentals of graph theory that lie outside of graph colorings, including basic terminology and results, trees and connectivity, Eulerian and Hamiltonian graphs, matchings and factorizations, and graph embeddings. The remainder of the text deals exclusively with graph colorings. It covers vertex colorings and bounds for the chromatic number, vertex colorings of graphs embedded on surfaces, and a variety of restricted vertex colorings. The authors also describe edge colorings, monochromatic and rainbow edge colorings, complete vertex colorings, several distinguishing vertex and edge colorings, and many distance-related vertex coloring...
Graph theory and its applications
Gross, Jonathan L
2006-01-01
Gross and Yellen take a comprehensive approach to graph theory that integrates careful exposition of classical developments with emerging methods, models, and practical needs. Their unparalleled treatment provides a text ideal for a two-semester course and a variety of one-semester classes, from an introductory one-semester course to courses slanted toward classical graph theory, operations research, data structures and algorithms, or algebra and topology.
Analytical Treatment of Higher-Order Graphs: A Path Ordinal Method for Solving Graphs
Directory of Open Access Journals (Sweden)
Hala Kamal
2017-11-01
Full Text Available Analytical treatment of the composition of higher-order graphs representing linear relations between variables is developed. A path formalism to deal with problems in graph theory is introduced. It is shown how paths in the composed graph representing individual contributions to variables relation can be enumerated and represented by ordinals. The method allows for one to extract partial information and gives an alternative to classical graph approach.
On the centrality of vertices of molecular graphs.
Randić, Milan; Novič, Marjana; Vračko, Marjan; Plavšić, Dejan
2013-11-05
For acyclic systems the center of a graph has been known to be either a single vertex of two adjacent vertices, that is, an edge. It has not been quite clear how to extend the concept of graph center to polycyclic systems. Several approaches to the graph center of molecular graphs of polycyclic graphs have been proposed in the literature. In most cases alternative approaches, however, while being apparently equally plausible, gave the same results for many molecules, but occasionally they differ in their characterization of molecular center. In order to reduce the number of vertices that would qualify as forming the center of the graph, a hierarchy of rules have been considered in the search for graph centers. We reconsidered the problem of "the center of a graph" by using a novel concept of graph theory, the vertex "weights," defined by counting the number of pairs of vertices at the same distance from the vertex considered. This approach gives often the same results for graph centers of acyclic graphs as the standard definition of graph center based on vertex eccentricities. However, in some cases when two nonequivalent vertices have been found as graph center, the novel approach can discriminate between the two. The same approach applies to cyclic graphs without additional rules to locate the vertex or vertices forming the center of polycyclic graphs, vertices referred to as central vertices of a graph. In addition, the novel vertex "weights," in the case of acyclic, cyclic, and polycyclic graphs can be interpreted as vertex centralities, a measure for how close or distant vertices are from the center or central vertices of the graph. Besides illustrating the centralities of a number of smaller polycyclic graphs, we also report on several acyclic graphs showing the same centrality values of their vertices. Copyright © 2013 Wiley Periodicals, Inc.
Software for Graph Analysis and Visualization
Directory of Open Access Journals (Sweden)
M. I. Kolomeychenko
2014-01-01
Full Text Available This paper describes the software for graph storage, analysis and visualization. The article presents a comparative analysis of existing software for analysis and visualization of graphs, describes the overall architecture of application and basic principles of construction and operation of the main modules. Furthermore, a description of the developed graph storage oriented to storage and processing of large-scale graphs is presented. The developed algorithm for finding communities and implemented algorithms of autolayouts of graphs are the main functionality of the product. The main advantage of the developed software is high speed processing of large size networks (up to millions of nodes and links. Moreover, the proposed graph storage architecture is unique and has no analogues. The developed approaches and algorithms are optimized for operating with big graphs and have high productivity.
Triangle Counting in Dynamic Graph Streams
DEFF Research Database (Denmark)
Bulteau, Laurent; Froese, Vincent; Pagh, Rasmus
2015-01-01
Estimating the number of triangles in graph streams using a limited amount of memory has become a popular topic in the last decade. Different variations of the problem have been studied, depending on whether the graph edges are provided in an arbitrary order or as incidence lists. However......, with a few exceptions, the algorithms have considered insert-only streams. We present a new algorithm estimating the number of triangles in dynamic graph streams where edges can be both inserted and deleted. We show that our algorithm achieves better time and space complexity than previous solutions...... for various graph classes, for example sparse graphs with a relatively small number of triangles. Also, for graphs with constant transitivity coefficient, a common situation in real graphs, this is the first algorithm achieving constant processing time per edge. The result is achieved by a novel approach...
Olayan, Rawan S; Ashoor, Haitham; Bajic, Vladimir B
2018-04-01
Finding computationally drug-target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer the high false positive prediction rate. We developed DDR, a novel method that improves the DTI prediction accuracy. DDR is based on the use of a heterogeneous graph that contains known DTIs with multiple similarities between drugs and multiple similarities between target proteins. DDR applies non-linear similarity fusion method to combine different similarities. Before fusion, DDR performs a pre-processing step where a subset of similarities is selected in a heuristic process to obtain an optimized combination of similarities. Then, DDR applies a random forest model using different graph-based features extracted from the DTI heterogeneous graph. Using 5-repeats of 10-fold cross-validation, three testing setups, and the weighted average of area under the precision-recall curve (AUPR) scores, we show that DDR significantly reduces the AUPR score error relative to the next best start-of-the-art method for predicting DTIs by 34% when the drugs are new, by 23% when targets are new and by 34% when the drugs and the targets are known but not all DTIs between them are not known. Using independent sources of evidence, we verify as correct 22 out of the top 25 DDR novel predictions. This suggests that DDR can be used as an efficient method to identify correct DTIs. The data and code are provided at https://bitbucket.org/RSO24/ddr/. vladimir.bajic@kaust.edu.sa. Supplementary data are available at Bioinformatics online.
Graph Model Based Indoor Tracking
DEFF Research Database (Denmark)
Jensen, Christian Søndergaard; Lu, Hua; Yang, Bin
2009-01-01
The tracking of the locations of moving objects in large indoor spaces is important, as it enables a range of applications related to, e.g., security and indoor navigation and guidance. This paper presents a graph model based approach to indoor tracking that offers a uniform data management...... infrastructure for different symbolic positioning technologies, e.g., Bluetooth and RFID. More specifically, the paper proposes a model of indoor space that comprises a base graph and mappings that represent the topology of indoor space at different levels. The resulting model can be used for one or several...... indoor positioning technologies. Focusing on RFID-based positioning, an RFID specific reader deployment graph model is built from the base graph model. This model is then used in several algorithms for constructing and refining trajectories from raw RFID readings. Empirical studies with implementations...
Generating random networks and graphs
Coolen, Ton; Roberts, Ekaterina
2017-01-01
This book supports researchers who need to generate random networks, or who are interested in the theoretical study of random graphs. The coverage includes exponential random graphs (where the targeted probability of each network appearing in the ensemble is specified), growth algorithms (i.e. preferential attachment and the stub-joining configuration model), special constructions (e.g. geometric graphs and Watts Strogatz models) and graphs on structured spaces (e.g. multiplex networks). The presentation aims to be a complete starting point, including details of both theory and implementation, as well as discussions of the main strengths and weaknesses of each approach. It includes extensive references for readers wishing to go further. The material is carefully structured to be accessible to researchers from all disciplines while also containing rigorous mathematical analysis (largely based on the techniques of statistical mechanics) to support those wishing to further develop or implement the theory of rand...
Arosio, Marcello; Martina, Mario L. V.
2017-04-01
The emergent behaviour of the contemporary complex, socio-technical and interconnected society makes the collective risk greater than the sum of the parts and this requires a holistic, systematic and integrated approach. Although there have been major improvements in recent years, there are still some limitation in term of a holistic approach that is able to include the emergent value hidden in the connections between exposed elements and the interactions between the different spheres of the multi-hazards, vulnerability, exposure and resilience. To deal with these challenges it is necessary to consider the connections between the exposed elements (e.g. populations, schools, hospital, etc.) and to quantify the relative importance of the elements and their interconnections (e.g. the need of injured people to go to hospital or children to school). In a system (e.g. road, hospital and ecological network, etc.), or in a System of System (e.g. socio-technical urban service), there are critical elements that, beyond the intrinsic vulnerability, can be characterized by greater or lower vulnerability because of their physical, geographical, cyber or logical connections. To this aim, we propose in this study a comparative analysis between traditional reductionist approach and a new holistic approach to vulnerability assessment to natural hazards. The analysis considers a study case of a socio-economic complex system through an innovative approach based on the properties of graph G=(N,L). A graph consists of two sets N (nodes) and L (links): the nodes represent the single exposed elements (physical, social, environmental, etc.) to a hazard, while the links (or connections) represent the interaction between the elements. The final goal is to illustrate an application of this innovative approach of integrated collective vulnerability assessment.
International Nuclear Information System (INIS)
Creyx, M.; Delacourt, E.; Morin, C.; Desmet, B.
2016-01-01
A dynamic model using the bond graph formalism of the expansion cylinder of an open Joule cycle Ericsson engine intended for a biomass-fuelled micro-CHP system is presented. Dynamic phenomena, such as the thermodynamic evolution of air, the instantaneous air mass flow rates linked to pressure drops crossing the valves, the heat transferred through the expansion cylinder wall and the mechanical friction losses, are included in the model. The influence on the Ericsson engine performances of the main operating conditions (intake air pressure and temperature, timing of intake and exhaust valve closing, rotational speed, mechanical friction losses and heat transfer at expansion cylinder wall) is studied. The operating conditions maximizing the performances of the Ericsson engine used in the a biomass-fuelled micro-CHP unit are an intake air pressure between 6 and 8 bar, a maximized intake air temperature, an adjustment of the intake and exhaust valve closing corresponding to an expansion cycle close to the theoretical Joule cycle, a rotational speed close to 800 rpm. The heat transfer at the expansion cylinder wall reduces the engine performances. - Highlights: • A bond graph dynamic model of the Ericsson engine expansion cylinder is presented. • Dynamic aspects are modelled: pressure drops, friction losses, wall heat transfer. • Influent factors and phenomena on the engine performances are investigated. • Expansion cycles close to the theoretical Joule cycle maximize the performances. • The heat transfer at the expansion chamber wall reduces the performances.
Ahmadlou, Mehran; Rostami, Reza; Sadeghi, Vahid
2012-05-10
Neurofeedback training is increasingly used for ADHD treatment. However some ADHD patients are not treated through the long-time neurofeedback trainings with common protocols. In this paper a new graph theoretical approach is presented for EEG-based prediction of ADHD patients' responses to a common neurofeedback training: rewarding SMR activity (12-15 Hz) with inhibiting theta activity (4-8 Hz) and beta2 activity (18-25 Hz). Eyes closed EEGs of two groups before and after neurofeedback training were studied: ADHD patients with (15 children) and without (15 children) positive response to neurofeedback training. Employing a recent method to measure synchronization, fuzzy synchronization likelihood, functional connectivity graphs of the patients' brains were constructed in the full-band EEGs and 6 common EEG sub-bands produced by wavelet decomposition. Then, efficiencies of the brain networks in synchronizability and high speed information transmission were computed based on mean path length of the graphs, before and after neurofeedback training. The results were analyzed by ANOVA and showed synchronizability of the neocortex activity network at beta band in ADHDs with positive response is obviously less than that of ADHDs resistant to neurofeedback therapy, before treatment. The accuracy of linear discriminant analysis (LDA) in distinguishing these patients based on this feature is so high (84.2%) that this feature can be considered as reliable characteristics for prediction of responses of ADHDs to the neurofeedback trainings. Also difference between flexibility of the neocortex in beta band before and after treatment is obviously larger in the ADHDs with positive response in comparison to those with negative response which may be a neurophysiologic reason for dissatisfaction of the last group to the neurofeedback therapy. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
Chemical Graph Transformation with Stereo-Information
DEFF Research Database (Denmark)
Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel
2017-01-01
Double Pushout graph transformation naturally facilitates the modelling of chemical reactions: labelled undirected graphs model molecules and direct derivations model chemical reactions. However, the most straightforward modelling approach ignores the relative placement of atoms and their neighbo......Double Pushout graph transformation naturally facilitates the modelling of chemical reactions: labelled undirected graphs model molecules and direct derivations model chemical reactions. However, the most straightforward modelling approach ignores the relative placement of atoms...... and their neighbours in space. Stereoisomers of chemical compounds thus cannot be distinguished, even though their chemical activity may differ substantially. In this contribution we propose an extended chemical graph transformation system with attributes that encode information about local geometry. The modelling...... of graph transformation, but we here propose a framework that also allows for partially specified stereoinformation. While there are several stereochemical configurations to be considered, we focus here on the tetrahedral molecular shape, and suggest general principles for how to treat all other chemically...
Visual Adjacency Lists for Dynamic Graphs.
Hlawatsch, Marcel; Burch, Michael; Weiskopf, Daniel
2014-11-01
We present a visual representation for dynamic, weighted graphs based on the concept of adjacency lists. Two orthogonal axes are used: one for all nodes of the displayed graph, the other for the corresponding links. Colors and labels are employed to identify the nodes. The usage of color allows us to scale the visualization to single pixel level for large graphs. In contrast to other techniques, we employ an asymmetric mapping that results in an aligned and compact representation of links. Our approach is independent of the specific properties of the graph to be visualized, but certain graphs and tasks benefit from the asymmetry. As we show in our results, the strength of our technique is the visualization of dynamic graphs. In particular, sparse graphs benefit from the compact representation. Furthermore, our approach uses visual encoding by size to represent weights and therefore allows easy quantification and comparison. We evaluate our approach in a quantitative user study that confirms the suitability for dynamic and weighted graphs. Finally, we demonstrate our approach for two examples of dynamic graphs.
Quantum information processing with graph states
International Nuclear Information System (INIS)
Schlingemann, Dirk-Michael
2005-04-01
Graph states are multiparticle states which are associated with graphs. Each vertex of the graph corresponds to a single system or particle. The links describe quantum correlations (entanglement) between pairs of connected particles. Graph states were initiated independently by two research groups: On the one hand, graph states were introduced by Briegel and Raussendorf as a resource for a new model of one-way quantum computing, where algorithms are implemented by a sequence of measurements at single particles. On the other hand, graph states were developed by the author of this thesis and ReinhardWerner in Braunschweig, as a tool to build quantum error correcting codes, called graph codes. The connection between the two approaches was fully realized in close cooperation of both research groups. This habilitation thesis provides a survey of the theory of graph codes, focussing mainly, but not exclusively on the author's own research work. We present the theoretical and mathematical background for the analysis of graph codes. The concept of one-way quantum computing for general graph states is discussed. We explicitly show how to realize the encoding and decoding device of a graph code on a one-way quantum computer. This kind of implementation is to be seen as a mathematical description of a quantum memory device. In addition to that, we investigate interaction processes, which enable the creation of graph states on very large systems. Particular graph states can be created, for instance, by an Ising type interaction between next neighbor particles which sits at the points of an infinitely extended cubic lattice. Based on the theory of quantum cellular automata, we give a constructive characterization of general interactions which create a translationally invariant graph state. (orig.)
Visibility graphs and landscape visibility analysis
O Sullivan, D.; Turner, A.
2001-01-01
Visibility analysis based on viewsheds is one of the most frequently used GIS analysis tools. In this paper we present an approach to visibility analysis based on the visibility graph. A visibility graph records the pattern of mutual visibility relations in a landscape, and provides a convenient way of storing and further analysing the results of multiple viewshed analyses for a particular landscape region. We describe how a visibility graph may be calculated for a landscape. We then give exa...
Dynamic Programming on Nominal Graphs
Directory of Open Access Journals (Sweden)
Nicklas Hoch
2015-04-01
Full Text Available Many optimization problems can be naturally represented as (hyper graphs, where vertices correspond to variables and edges to tasks, whose cost depends on the values of the adjacent variables. Capitalizing on the structure of the graph, suitable dynamic programming strategies can select certain orders of evaluation of the variables which guarantee to reach both an optimal solution and a minimal size of the tables computed in the optimization process. In this paper we introduce a simple algebraic specification with parallel composition and restriction whose terms up to structural axioms are the graphs mentioned above. In addition, free (unrestricted vertices are labelled with variables, and the specification includes operations of name permutation with finite support. We show a correspondence between the well-known tree decompositions of graphs and our terms. If an axiom of scope extension is dropped, several (hierarchical terms actually correspond to the same graph. A suitable graphical structure can be found, corresponding to every hierarchical term. Evaluating such a graphical structure in some target algebra yields a dynamic programming strategy. If the target algebra satisfies the scope extension axiom, then the result does not depend on the particular structure, but only on the original graph. We apply our approach to the parking optimization problem developed in the ASCENS e-mobility case study, in collaboration with Volkswagen. Dynamic programming evaluations are particularly interesting for autonomic systems, where actual behavior often consists of propagating local knowledge to obtain global knowledge and getting it back for local decisions.
Chromatic polynomials of random graphs
International Nuclear Information System (INIS)
Van Bussel, Frank; Fliegner, Denny; Timme, Marc; Ehrlich, Christoph; Stolzenberg, Sebastian
2010-01-01
Chromatic polynomials and related graph invariants are central objects in both graph theory and statistical physics. Computational difficulties, however, have so far restricted studies of such polynomials to graphs that were either very small, very sparse or highly structured. Recent algorithmic advances (Timme et al 2009 New J. Phys. 11 023001) now make it possible to compute chromatic polynomials for moderately sized graphs of arbitrary structure and number of edges. Here we present chromatic polynomials of ensembles of random graphs with up to 30 vertices, over the entire range of edge density. We specifically focus on the locations of the zeros of the polynomial in the complex plane. The results indicate that the chromatic zeros of random graphs have a very consistent layout. In particular, the crossing point, the point at which the chromatic zeros with non-zero imaginary part approach the real axis, scales linearly with the average degree over most of the density range. While the scaling laws obtained are purely empirical, if they continue to hold in general there are significant implications: the crossing points of chromatic zeros in the thermodynamic limit separate systems with zero ground state entropy from systems with positive ground state entropy, the latter an exception to the third law of thermodynamics.
Multi-Centrality Graph Spectral Decompositions and Their Application to Cyber Intrusion Detection
Energy Technology Data Exchange (ETDEWEB)
Chen, Pin-Yu; Choudhury, Sutanay; Hero, Alfred
2016-03-01
Many modern datasets can be represented as graphs and hence spectral decompositions such as graph principal component analysis (PCA) can be useful. Distinct from previous graph decomposition approaches based on subspace projection of a single topological feature, e.g., the centered graph adjacency matrix (graph Laplacian), we propose spectral decomposition approaches to graph PCA and graph dictionary learning that integrate multiple features, including graph walk statistics, centrality measures and graph distances to reference nodes. In this paper we propose a new PCA method for single graph analysis, called multi-centrality graph PCA (MC-GPCA), and a new dictionary learning method for ensembles of graphs, called multi-centrality graph dictionary learning (MC-GDL), both based on spectral decomposition of multi-centrality matrices. As an application to cyber intrusion detection, MC-GPCA can be an effective indicator of anomalous connectivity pattern and MC-GDL can provide discriminative basis for attack classification.
GraphMeta: Managing HPC Rich Metadata in Graphs
Energy Technology Data Exchange (ETDEWEB)
Dai, Dong; Chen, Yong; Carns, Philip; Jenkins, John; Zhang, Wei; Ross, Robert
2016-01-01
High-performance computing (HPC) systems face increasingly critical metadata management challenges, especially in the approaching exascale era. These challenges arise not only from exploding metadata volumes, but also from increasingly diverse metadata, which contains data provenance and arbitrary user-defined attributes in addition to traditional POSIX metadata. This ‘rich’ metadata is becoming critical to supporting advanced data management functionality such as data auditing and validation. In our prior work, we identified a graph-based model as a promising solution to uniformly manage HPC rich metadata due to its flexibility and generality. However, at the same time, graph-based HPC rich metadata anagement also introduces significant challenges to the underlying infrastructure. In this study, we first identify the challenges on the underlying infrastructure to support scalable, high-performance rich metadata management. Based on that, we introduce GraphMeta, a graphbased engine designed for this use case. It achieves performance scalability by introducing a new graph partitioning algorithm and a write-optimal storage engine. We evaluate GraphMeta under both synthetic and real HPC metadata workloads, compare it with other approaches, and demonstrate its advantages in terms of efficiency and usability for rich metadata management in HPC systems.
Relations between the set-complexity and the structure of graphs and their sub-graphs.
Ignac, Tomasz M; Sakhanenko, Nikita A; Galas, David J
2012-09-21
: We describe some new conceptual tools for the rigorous, mathematical description of the "set-complexity" of graphs. This set-complexity has been shown previously to be a useful measure for analyzing some biological networks, and in discussing biological information in a quantitative fashion. The advances described here allow us to define some significant relationships between the set-complexity measure and the structure of graphs, and of their component sub-graphs. We show here that modular graph structures tend to maximize the set-complexity of graphs. We point out the relationship between modularity and redundancy, and discuss the significance of set-complexity in this regard. We specifically discuss the relationship between complexity and entropy in the case of complete-bipartite graphs, and present a new method for constructing highly complex, binary graphs. These results can be extended to the case of ternary graphs, and to other multi-edge graphs, which are fundamentally more relevant to biological structures and systems. Finally, our results lead us to an approach for extracting high complexity modular graphs from large, noisy graphs with low information content. We illustrate this approach with two examples.
Bapat, Ravindra B
2014-01-01
This new edition illustrates the power of linear algebra in the study of graphs. The emphasis on matrix techniques is greater than in other texts on algebraic graph theory. Important matrices associated with graphs (for example, incidence, adjacency and Laplacian matrices) are treated in detail. Presenting a useful overview of selected topics in algebraic graph theory, early chapters of the text focus on regular graphs, algebraic connectivity, the distance matrix of a tree, and its generalized version for arbitrary graphs, known as the resistance matrix. Coverage of later topics include Laplacian eigenvalues of threshold graphs, the positive definite completion problem and matrix games based on a graph. Such an extensive coverage of the subject area provides a welcome prompt for further exploration. The inclusion of exercises enables practical learning throughout the book. In the new edition, a new chapter is added on the line graph of a tree, while some results in Chapter 6 on Perron-Frobenius theory are reo...
Tejedor, Alejandro; Longjas, Anthony; Zaliapin, Ilya; Foufoula-Georgiou, Efi
2015-06-01
River deltas are intricate landscapes with complex channel networks that self-organize to deliver water, sediment, and nutrients from the apex to the delta top and eventually to the coastal zone. The natural balance of material and energy fluxes, which maintains a stable hydrologic, geomorphologic, and ecological state of a river delta, is often disrupted by external perturbations causing topological and dynamical changes in the delta structure and function. A formal quantitative framework for studying delta channel network connectivity and transport dynamics and their response to change is lacking. Here we present such a framework based on spectral graph theory and demonstrate its value in computing delta's steady state fluxes and identifying upstream (contributing) and downstream (nourishment) areas and fluxes from any point in the network. We use this framework to construct vulnerability maps that quantify the relative change of sediment and water delivery to the shoreline outlets in response to possible perturbations in hundreds of upstream links. The framework is applied to the Wax Lake delta in the Louisiana coast of the U.S. and the Niger delta in West Africa. In a companion paper, we present a comprehensive suite of metrics that quantify topologic and dynamic complexity of delta channel networks and, via application to seven deltas in diverse environments, demonstrate their potential to reveal delta morphodynamics and relate to notions of vulnerability and robustness.
PRIVATE GRAPHS – ACCESS RIGHTS ON GRAPHS FOR SEAMLESS NAVIGATION
Directory of Open Access Journals (Sweden)
W. Dorner
2016-06-01
Full Text Available After the success of GNSS (Global Navigational Satellite Systems and navigation services for public streets, indoor seems to be the next big development in navigational services, relying on RTLS – Real Time Locating Services (e.g. WIFI and allowing seamless navigation. In contrast to navigation and routing services on public streets, seamless navigation will cause an additional challenge: how to make routing data accessible to defined users or restrict access rights for defined areas or only to parts of the graph to a defined user group? The paper will present case studies and data from literature, where seamless and especially indoor navigation solutions are presented (hospitals, industrial complexes, building sites, but the problem of restricted access rights was only touched from a real world, but not a technical perspective. The analysis of case studies will show, that the objective of navigation and the different target groups for navigation solutions will demand well defined access rights and require solutions, how to make only parts of a graph to a user or application available to solve a navigational task. The paper will therefore introduce the concept of private graphs, which is defined as a graph for navigational purposes covering the street, road or floor network of an area behind a public street and suggest different approaches how to make graph data for navigational purposes available considering access rights and data protection, privacy and security issues as well.
Integral trees and integral graphs
Wang, Ligong
2005-01-01
This monograph deals with integral graphs, Laplacian integral regular graphs, cospectral graphs and cospectral integral graphs. The organization of this work, which consists of eight chapters, is as follows.
Loukas, A.
2015-01-01
We have recently seen a surge of research focusing on the processing of graph data. The emerging field of signal processing on graphs focuses on the extension of classical discrete signal processing techniques to the graph setting. Arguably, the greatest breakthrough of the field has been the
Indian Academy of Sciences (India)
IAS Admin
graph. We also note before closing this general discus- sion that among the family of regular and connected graphs, the graphs in the family of SRGs are character- ized by having exactly three distinct eigenvalues of the adjacency matrix. The friendship theorem asserts that if friendship in a community is a symmetric relation ...
Brouwer, A.E.; Haemers, W.H.
2012-01-01
This book gives an elementary treatment of the basic material about graph spectra, both for ordinary, and Laplace and Seidel spectra. The text progresses systematically, by covering standard topics before presenting some new material on trees, strongly regular graphs, two-graphs, association
Graphing Inequalities, Connecting Meaning
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…
Pluhař, Z; Weidenmüller, H A
2014-04-11
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.
Sotirov, Renata
2017-01-01
The graph bisection problem is the problem of partitioning the vertex set of a graph into two sets of given sizes such that the sum of weights of edges joining these two sets is optimized. We present a semidefinite programming relaxation for the graph bisection problem with a matrix variable of
Hyperbolicity in median graphs
Indian Academy of Sciences (India)
If is hyperbolic, we denote by () the sharp hyperbolicity constant of , i.e., ( X ) = inf { ≥ 0 : X is − hyperbolic } . In this paper we study the hyperbolicity of median graphs and we also obtain some results about general hyperbolic graphs. In particular, we prove that a median graph is hyperbolic if and only if its ...
Joint Graph Layouts for Visualizing Collections of Segmented Meshes
Ren, Jing
2017-09-12
We present a novel and efficient approach for computing joint graph layouts and then use it to visualize collections of segmented meshes. Our joint graph layout algorithm takes as input the adjacency matrices for a set of graphs along with partial, possibly soft, correspondences between nodes of different graphs. We then use a two stage procedure, where in the first step, we extend spectral graph drawing to include a consistency term so that a collection of graphs can be handled jointly. Our second step extends metric multi-dimensional scaling with stress majorization to the joint layout setting, while using the output of the spectral approach as initialization. Further, we discuss a user interface for exploring a collection of graphs. Finally, we show multiple example visualizations of graphs stemming from collections of segmented meshes and we present qualitative and quantitative comparisons with previous work.
Hell, Pavol
2004-01-01
This is a book about graph homomorphisms. Graph theory is now an established discipline but the study of graph homomorphisms has only recently begun to gain wide acceptance and interest. The subject gives a useful perspective in areas such as graph reconstruction, products, fractional and circular colourings, and has applications in complexity theory, artificial intelligence, telecommunication, and, most recently, statistical physics.Based on the authors' lecture notes for graduate courses, this book can be used as a textbook for a second course in graph theory at 4th year or master's level an
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.
Kundu, Kousik; Costa, Fabrizio; Backofen, Rolf
2013-07-01
State-of-the-art experimental data for determining binding specificities of peptide recognition modules (PRMs) is obtained by high-throughput approaches like peptide arrays. Most prediction tools applicable to this kind of data are based on an initial multiple alignment of the peptide ligands. Building an initial alignment can be error-prone, especially in the case of the proline-rich peptides bound by the SH3 domains. Here, we present a machine-learning approach based on an efficient graph-kernel technique to predict the specificity of a large set of 70 human SH3 domains, which are an important class of PRMs. The graph-kernel strategy allows us to (i) integrate several types of physico-chemical information for each amino acid, (ii) consider high-order correlations between these features and (iii) eliminate the need for an initial peptide alignment. We build specialized models for each human SH3 domain and achieve competitive predictive performance of 0.73 area under precision-recall curve, compared with 0.27 area under precision-recall curve for state-of-the-art methods based on position weight matrices. We show that better models can be obtained when we use information on the noninteracting peptides (negative examples), which is currently not used by the state-of-the art approaches based on position weight matrices. To this end, we analyze two strategies to identify subsets of high confidence negative data. The techniques introduced here are more general and hence can also be used for any other protein domains, which interact with short peptides (i.e. other PRMs). The program with the predictive models can be found at http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/SH3PepInt.tar.gz. We also provide a genome-wide prediction for all 70 human SH3 domains, which can be found under http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/Genome-Wide-Predictions.tar.gz. Supplementary data are available at Bioinformatics online.
Integer Flows and Circuit Covers of Graphs and Signed Graphs
Cheng, Jian
The work in Chapter 2 is motivated by Tutte and Jaeger's pioneering work on converting modulo flows into integer-valued flows for ordinary graphs. For a signed graphs (G, sigma), we first prove that for each k ∈ {2, 3}, if (G, sigma) is (k - 1)-edge-connected and contains an even number of negative edges when k = 2, then every modulo k-flow of (G, sigma) can be converted into an integer-valued ( k + 1)-ow with a larger or the same support. We also prove that if (G, sigma) is odd-(2p+1)-edge-connected, then (G, sigma) admits a modulo circular (2 + 1/ p)-flows if and only if it admits an integer-valued circular (2 + 1/p)-flows, which improves all previous result by Xu and Zhang (DM2005), Schubert and Steffen (EJC2015), and Zhu (JCTB2015). Shortest circuit cover conjecture is one of the major open problems in graph theory. It states that every bridgeless graph G contains a set of circuits F such that each edge is contained in at least one member of F and the length of F is at most 7/5∥E(G)∥. This concept was recently generalized to signed graphs by Macajova et al. (JGT2015). In Chapter 3, we improve their upper bound from 11∥E( G)∥ to 14/3 ∥E(G)∥, and if G is 2-edgeconnected and has even negativeness, then it can be further reduced to 11/3 ∥E(G)∥. Tutte's 3-flow conjecture has been studied by many graph theorists in the last several decades. As a new approach to this conjecture, DeVos and Thomassen considered the vectors as ow values and found that there is a close relation between vector S1-flows and integer 3-NZFs. Motivated by their observation, in Chapter 4, we prove that if a graph G admits a vector S1-flow with rank at most two, then G admits an integer 3-NZF. The concept of even factors is highly related to the famous Four Color Theorem. We conclude this dissertation in Chapter 5 with an improvement of a recent result by Chen and Fan (JCTB2016) on the upperbound of even factors. We show that if a graph G contains an even factor, then it
Enabling Graph Appliance for Genome Assembly
Energy Technology Data Exchange (ETDEWEB)
Singh, Rina [ORNL; Graves, Jeffrey A [ORNL; Lee, Sangkeun (Matt) [ORNL; Sukumar, Sreenivas R [ORNL; Shankar, Mallikarjun [ORNL
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.
Incremental View Maintenance for Deductive Graph Databases Using Generalized Discrimination Networks
Directory of Open Access Journals (Sweden)
Thomas Beyhl
2016-12-01
Full Text Available Nowadays, graph databases are employed when relationships between entities are in the scope of database queries to avoid performance-critical join operations of relational databases. Graph queries are used to query and modify graphs stored in graph databases. Graph queries employ graph pattern matching that is NP-complete for subgraph isomorphism. Graph database views can be employed that keep ready answers in terms of precalculated graph pattern matches for often stated and complex graph queries to increase query performance. However, such graph database views must be kept consistent with the graphs stored in the graph database. In this paper, we describe how to use incremental graph pattern matching as technique for maintaining graph database views. We present an incremental maintenance algorithm for graph database views, which works for imperatively and declaratively specified graph queries. The evaluation shows that our maintenance algorithm scales when the number of nodes and edges stored in the graph database increases. Furthermore, our evaluation shows that our approach can outperform existing approaches for the incremental maintenance of graph query results.
Chartrand, Gary
1984-01-01
Graph theory is used today in the physical sciences, social sciences, computer science, and other areas. Introductory Graph Theory presents a nontechnical introduction to this exciting field in a clear, lively, and informative style. Author Gary Chartrand covers the important elementary topics of graph theory and its applications. In addition, he presents a large variety of proofs designed to strengthen mathematical techniques and offers challenging opportunities to have fun with mathematics. Ten major topics - profusely illustrated - include: Mathematical Models, Elementary Concepts of Grap
Uncertain Graph Sparsification
Parchas, Panos; Papailiou, Nikolaos; Papadias, Dimitris; Bonchi, Francesco
2016-01-01
Uncertain graphs are prevalent in several applications including communications systems, biological databases and social networks. The ever increasing size of the underlying data renders both graph storage and query processing extremely expensive. Sparsification has often been used to reduce the size of deterministic graphs by maintaining only the important edges. However, adaptation of deterministic sparsification methods fails in the uncertain setting. To overcome this problem, we introduce...
Directory of Open Access Journals (Sweden)
Aleks Kissinger
2014-03-01
Full Text Available String diagrams are a powerful tool for reasoning about physical processes, logic circuits, tensor networks, and many other compositional structures. Dixon, Duncan and Kissinger introduced string graphs, which are a combinatoric representations of string diagrams, amenable to automated reasoning about diagrammatic theories via graph rewrite systems. In this extended abstract, we show how the power of such rewrite systems can be greatly extended by introducing pattern graphs, which provide a means of expressing infinite families of rewrite rules where certain marked subgraphs, called !-boxes ("bang boxes", on both sides of a rule can be copied any number of times or removed. After reviewing the string graph formalism, we show how string graphs can be extended to pattern graphs and how pattern graphs and pattern rewrite rules can be instantiated to concrete string graphs and rewrite rules. We then provide examples demonstrating the expressive power of pattern graphs and how they can be applied to study interacting algebraic structures that are central to categorical quantum mechanics.
Creating more effective graphs
Robbins, Naomi B
2012-01-01
A succinct and highly readable guide to creating effective graphs The right graph can be a powerful tool for communicating information, improving a presentation, or conveying your point in print. If your professional endeavors call for you to present data graphically, here's a book that can help you do it more effectively. Creating More Effective Graphs gives you the basic knowledge and techniques required to choose and create appropriate graphs for a broad range of applications. Using real-world examples everyone can relate to, the author draws on her years of experience in gr
DEFF Research Database (Denmark)
Mansutti, Alessio; Miculan, Marino; Peressotti, Marco
2017-01-01
We introduce loose graph simulations (LGS), a new notion about labelled graphs which subsumes in an intuitive and natural way subgraph isomorphism (SGI), regular language pattern matching (RLPM) and graph simulation (GS). Being a unification of all these notions, LGS allows us to express directly...... also problems which are “mixed” instances of previous ones, and hence which would not fit easily in any of them. After the definition and some examples, we show that the problem of finding loose graph simulations is NP-complete, we provide formal translation of SGI, RLPM, and GS into LGSs, and we give...
DEFF Research Database (Denmark)
Thomassen, Carsten
2014-01-01
We prove a general result on graph factors modulo k . A special case says that, for each natural number k , every (12k−7)-edge-connected graph with an even number of vertices contains a spanning subgraph in which each vertex has degree congruent to k modulo 2k.......We prove a general result on graph factors modulo k . A special case says that, for each natural number k , every (12k−7)-edge-connected graph with an even number of vertices contains a spanning subgraph in which each vertex has degree congruent to k modulo 2k....
Gelfand, I M; Shnol, E E
1969-01-01
The second in a series of systematic studies by a celebrated mathematician I. M. Gelfand and colleagues, this volume presents students with a well-illustrated sequence of problems and exercises designed to illuminate the properties of functions and graphs. Since readers do not have the benefit of a blackboard on which a teacher constructs a graph, the authors abandoned the customary use of diagrams in which only the final form of the graph appears; instead, the book's margins feature step-by-step diagrams for the complete construction of each graph. The first part of the book employs simple fu
Energy Technology Data Exchange (ETDEWEB)
Lothian, Joshua [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Powers, Sarah S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sullivan, Blair D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Baker, Matthew B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Schrock, Jonathan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Poole, Stephen W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
2013-10-01
The benchmarking effort within the Extreme Scale Systems Center at Oak Ridge National Laboratory seeks to provide High Performance Computing benchmarks and test suites of interest to the DoD sponsor. The work described in this report is a part of the effort focusing on graph generation. A previously developed benchmark, SystemBurn, allowed the emulation of different application behavior profiles within a single framework. To complement this effort, similar capabilities are desired for graph-centric problems. This report examines existing synthetic graph generator implementations in preparation for further study on the properties of their generated synthetic graphs.
Characterisations of Intersection Graphs by Vertex Orderings
Wood, David R.
2004-01-01
Characterisations of interval graphs, comparability graphs, co-comparability graphs, permutation graphs, and split graphs in terms of linear orderings of the vertex set are presented. As an application, it is proved that interval graphs, co-comparability graphs, AT-free graphs, and split graphs have bandwidth bounded by their maximum degree.
High Dimensional Spectral Graph Theory and Non-backtracking Random Walks on Graphs
Kempton, Mark
This thesis has two primary areas of focus. First we study connection graphs, which are weighted graphs in which each edge is associated with a d-dimensional rotation matrix for some fixed dimension d, in addition to a scalar weight. Second, we study non-backtracking random walks on graphs, which are random walks with the additional constraint that they cannot return to the immediately previous state at any given step. Our work in connection graphs is centered on the notion of consistency, that is, the product of rotations moving from one vertex to another is independent of the path taken, and a generalization called epsilon-consistency. We present higher dimensional versions of the combinatorial Laplacian matrix and normalized Laplacian matrix from spectral graph theory, and give results characterizing the consistency of a connection graph in terms of the spectra of these matrices. We generalize several tools from classical spectral graph theory, such as PageRank and effective resistance, to apply to connection graphs. We use these tools to give algorithms for sparsification, clustering, and noise reduction on connection graphs. In non-backtracking random walks, we address the question raised by Alon et. al. concerning how the mixing rate of a non-backtracking random walk to its stationary distribution compares to the mixing rate for an ordinary random walk. Alon et. al. address this question for regular graphs. We take a different approach, and use a generalization of Ihara's Theorem to give a new proof of Alon's result for regular graphs, and to extend the result to biregular graphs. Finally, we give a non-backtracking version of Polya's Random Walk Theorem for 2-dimensional grids.
Graph Embedded Extreme Learning Machine.
Iosifidis, Alexandros; Tefas, Anastasios; Pitas, Ioannis
2016-01-01
In this paper, we propose a novel extension of the extreme learning machine (ELM) algorithm for single-hidden layer feedforward neural network training that is able to incorporate subspace learning (SL) criteria on the optimization process followed for the calculation of the network's output weights. The proposed graph embedded ELM (GEELM) algorithm is able to naturally exploit both intrinsic and penalty SL criteria that have been (or will be) designed under the graph embedding framework. In addition, we extend the proposed GEELM algorithm in order to be able to exploit SL criteria in arbitrary (even infinite) dimensional ELM spaces. We evaluate the proposed approach on eight standard classification problems and nine publicly available datasets designed for three problems related to human behavior analysis, i.e., the recognition of human face, facial expression, and activity. Experimental results denote the effectiveness of the proposed approach, since it outperforms other ELM-based classification schemes in all the cases.
A first course in graph theory
Chartrand, Gary
2012-01-01
This comprehensive text offers undergraduates a remarkably student-friendly introduction to graph theory. Written by two of the field's most prominent experts, it takes an engaging approach that emphasizes graph theory's history. Unique examples and lucid proofs provide a sound yet accessible treatment that stimulates interest in an evolving subject and its many applications.Optional sections designated as ""excursion"" and ""exploration"" present interesting sidelights of graph theory and touch upon topics that allow students the opportunity to experiment and use their imaginations. Three app
Crossed products for interactions and graph algebras
DEFF Research Database (Denmark)
Kwasniewski, Bartosz
2014-01-01
. These results cover the case of crossed products by endomorphisms with hereditary ranges and complemented kernels. As model examples of interactions not coming from endomorphisms we introduce and study in detail interactions arising from finite graphs. The interaction (V,H) associated to a graph E acts...... on the core F_E of the graph algebra C*(E). By describing a partial homeomorphism dual to (V,H) we find the fundamental structure theorems for C*(E), such as Cuntz–Krieger uniqueness theorem, as results concerning reversible noncommutative dynamics on F_E . We also provide a new approach to calculation of K...
Graph representation of protein free energy landscape
International Nuclear Information System (INIS)
Li, Minghai; Duan, Mojie; Fan, Jue; Huo, Shuanghong; Han, Li
2013-01-01
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
Determining X-chains in graph states
International Nuclear Information System (INIS)
Wu, Jun-Yi; Kampermann, Hermann; Bruß, Dagmar
2016-01-01
The representation of graph states in the X-basis as well as the calculation of graph state overlaps can efficiently be performed by using the concept of X-chains (Wu et al 2015 Phys. Rev. A 92 012322). We present a necessary and sufficient criterion for X-chains and show that they can efficiently be determined by the Bareiss algorithm. An analytical approach for searching X-chain groups of a graph state is proposed. Furthermore we generalize the concept of X-chains to so-called Euler chains, whose induced subgraphs are Eulerian. This approach helps to determine if a given vertex set is an X-chain and we show how Euler chains can be used in the construction of multipartite Bell inequalities for graph states. (paper)
Directory of Open Access Journals (Sweden)
A. Assari
2016-01-01
Full Text Available In this paper, a graph is assigned to any probability measure on the σ-algebra of Borel sets of a topological space. Using this construction, it is proved that given any number n (finite or infinite there exists a nonregular graph such that its clique, chromatic, and dominating number equals n.
De Jong, Marvin L.
1993-01-01
Describes the powerful graphing ability of computer algebra systems (CAS) to create three-dimensional graphs or surface graphics of electric potentials. Provides equations along with examples of the printouts. Lists the programs Mathematica, Maple, Derive, Theorist, MathCad, and MATLAB as promising CAS systems. (MVL)
Perepelitsa, VA; Sergienko, [No Value; Kochkarov, AM
1999-01-01
Definitions of prefractal and fractal graphs are introduced, and they are used to formulate mathematical models in different fields of knowledge. The topicality of fractal-graph recognition from the point of view, of fundamental improvement in the efficiency of the solution of algorithmic problems
Joyner, W David
2017-01-01
This textbook acts as a pathway to higher mathematics by seeking and illuminating the connections between graph theory and diverse fields of mathematics, such as calculus on manifolds, group theory, algebraic curves, Fourier analysis, cryptography and other areas of combinatorics. An overview of graph theory definitions and polynomial invariants for graphs prepares the reader for the subsequent dive into the applications of graph theory. To pique the reader’s interest in areas of possible exploration, recent results in mathematics appear throughout the book, accompanied with examples of related graphs, how they arise, and what their valuable uses are. The consequences of graph theory covered by the authors are complicated and far-reaching, so topics are always exhibited in a user-friendly manner with copious graphs, exercises, and Sage code for the computation of equations. Samples of the book’s source code can be found at github.com/springer-math/adventures-in-graph-theory. The text is geared towards ad...
Packing Degenerate Graphs Greedily
Czech Academy of Sciences Publication Activity Database
Allen, P.; Böttcher, J.; Hladký, J.; Piguet, Diana
2017-01-01
Roč. 61, August (2017), s. 45-51 ISSN 1571-0653 R&D Projects: GA ČR GJ16-07822Y Institutional support: RVO:67985807 Keywords : tree packing conjecture * graph packing * graph processes Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics
DEFF Research Database (Denmark)
Husfeldt, Thore
2015-01-01
This chapter presents an introduction to graph colouring algorithms. The focus is on vertex-colouring algorithms that work for general classes of graphs with worst-case performance guarantees in a sequential model of computation. The presentation aims to demonstrate the breadth of available...
Moment graphs and representations
DEFF Research Database (Denmark)
Jantzen, Jens Carsten
2012-01-01
Moment graphs and sheaves on moment graphs are basically combinatorial objects that have be used to describe equivariant intersectiion cohomology. In these lectures we are going to show that they can be used to provide a direct link from this cohomology to the representation theory of simple Lie...
Directory of Open Access Journals (Sweden)
Behnaz Tolue
2018-07-01
Full Text Available In this paper we introduce stable subgroup graph associated to the group $G$. It is a graph with vertex set all subgroups of $G$ and two distinct subgroups $H_1$ and $H_2$ are adjacent if $St_{G}(H_1\\cap H_2\
Generalized connectivity of graphs
Li, Xueliang
2016-01-01
Noteworthy results, proof techniques, open problems and conjectures in generalized (edge-) connectivity are discussed in this book. Both theoretical and practical analyses for generalized (edge-) connectivity of graphs are provided. Topics covered in this book include: generalized (edge-) connectivity of graph classes, algorithms, computational complexity, sharp bounds, Nordhaus-Gaddum-type results, maximum generalized local connectivity, extremal problems, random graphs, multigraphs, relations with the Steiner tree packing problem and generalizations of connectivity. This book enables graduate students to understand and master a segment of graph theory and combinatorial optimization. Researchers in graph theory, combinatorics, combinatorial optimization, probability, computer science, discrete algorithms, complexity analysis, network design, and the information transferring models will find this book useful in their studies.
GoFFish: A Sub-Graph Centric Framework for Large-Scale Graph Analytics1
Energy Technology Data Exchange (ETDEWEB)
Simmhan, Yogesh; Kumbhare, Alok; Wickramaarachchi, Charith; Nagarkar, Soonil; Ravi, Santosh; Raghavendra, Cauligi; Prasanna, Viktor
2014-08-25
Large scale graph processing is a major research area for Big Data exploration. Vertex centric programming models like Pregel are gaining traction due to their simple abstraction that allows for scalable execution on distributed systems naturally. However, there are limitations to this approach which cause vertex centric algorithms to under-perform due to poor compute to communication overhead ratio and slow convergence of iterative superstep. In this paper we introduce GoFFish a scalable sub-graph centric framework co-designed with a distributed persistent graph storage for large scale graph analytics on commodity clusters. We introduce a sub-graph centric programming abstraction that combines the scalability of a vertex centric approach with the flexibility of shared memory sub-graph computation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation.
Querying 3D Data by Adjacency Graphs
Bore, Nils; Jensfelt, Patric; Folkesson, John
2015-01-01
The need for robots to search the 3D data they have saved is becoming more apparent. We present an approach for finding structures in 3D models such as those built by robots of their environment. The method extracts geometric primitives from point cloud data. An attributed graph over these primitives forms our representation of the surface structures. Recurring substructures are found with frequent graph mining techniques. We investigate if a model invariant to changes in size and reflection ...
Product of Locally Primitive Graphs
Directory of Open Access Journals (Sweden)
Amir Assari
2014-01-01
Full Text Available Many large graphs can be constructed from existing smaller graphs by using graph operations, such as the product of two graphs. Many properties of such large graphs are closely related to those of the corresponding smaller ones. In this paper we consider the product of two locally primitive graphs and prove that only tensor product of them will also be locally primitive.
Graph Abstraction and Abstract Graph Transformation
Boneva, I.B.; Rensink, Arend; Kurban, M.E.; Bauer, J.
2007-01-01
Many important systems like concurrent heap-manipulating programs, communication networks, or distributed algorithms are hard to verify due to their inherent dynamics and unboundedness. Graphs are an intuitive representation of states of these systems, where transitions can be conveniently described
Spanners for geometric intersection graphs with applications
Directory of Open Access Journals (Sweden)
Martin Fürer
2012-05-01
Full Text Available A ball graph is an intersection graph of a set of balls with arbitrary radii. Given a real numbert>1, we say that a subgraph G' of a graph G is a t-spanner of G, if for every pair of verticesu,v in G, there exists a path in G' of length at most t times the distance between u and v inG. In this paper, we consider the problem of efficiently constructing sparse spanners of ball graphs which supports fast shortest path distance queries.We present the first algorithm for constructing spanners of ball graphs. For a ball graph in Rk, we construct a (1+ε-spanner for any ε>0 with O(nε-k+1 edges in O(n2ℓ+δε-k logℓ S time, using an efficient partitioning of space into hypercubes and solving intersection problems. Here ℓ=1-1/(⌊k/2⌋+2, δ is any positive constant, and S is the ratio between the largest and smallest radius. For the special case when the balls all have unit size, we show that the complexity of constructing a (1+ε-spanner is almost equal to the complexity of constructing a Euclidean minimum spanning tree. The algorithm extends naturally to other disk-likeobjects, also in higher dimensions.The algorithm uses an efficient subdivision of space to construct a sparse graph having many of the same distance properties as the input ball graph. Additionally, the constructed spanners have a small vertex separator decomposition (hereditary. In dimension k=2, the disk graph spanner has an O(n1/2ε-3/2+ε-3log S separator. The presence of a small separator is then exploited to obtain very efficient data structures for approximate distance queries. The results on geometric graph separators might be of independent interest. For example, since complete Euclidean graphs are just a special case of (unit ball graphs, our results also provide a new approach for constructing spanners with small separators in these graphs.
Subgraph detection using graph signals
Chepuri, Sundeep Prabhakar
2017-03-06
In this paper we develop statistical detection theory for graph signals. In particular, given two graphs, namely, a background graph that represents an usual activity and an alternative graph that represents some unusual activity, we are interested in answering the following question: To which of the two graphs does the observed graph signal fit the best? To begin with, we assume both the graphs are known, and derive an optimal Neyman-Pearson detector. Next, we derive a suboptimal detector for the case when the alternative graph is not known. The developed theory is illustrated with numerical experiments.
Bollobas, Bela
2004-01-01
The ever-expanding field of extremal graph theory encompasses a diverse array of problem-solving methods, including applications to economics, computer science, and optimization theory. This volume, based on a series of lectures delivered to graduate students at the University of Cambridge, presents a concise yet comprehensive treatment of extremal graph theory.Unlike most graph theory treatises, this text features complete proofs for almost all of its results. Further insights into theory are provided by the numerous exercises of varying degrees of difficulty that accompany each chapter. A
Probabilistic Graph Layout for Uncertain Network Visualization.
Schulz, Christoph; Nocaj, Arlind; Goertler, Jochen; Deussen, Oliver; Brandes, Ulrik; Weiskopf, Daniel
2017-01-01
We present a novel uncertain network visualization technique based on node-link diagrams. Nodes expand spatially in our probabilistic graph layout, depending on the underlying probability distributions of edges. The visualization is created by computing a two-dimensional graph embedding that combines samples from the probabilistic graph. A Monte Carlo process is used to decompose a probabilistic graph into its possible instances and to continue with our graph layout technique. Splatting and edge bundling are used to visualize point clouds and network topology. The results provide insights into probability distributions for the entire network-not only for individual nodes and edges. We validate our approach using three data sets that represent a wide range of network types: synthetic data, protein-protein interactions from the STRING database, and travel times extracted from Google Maps. Our approach reveals general limitations of the force-directed layout and allows the user to recognize that some nodes of the graph are at a specific position just by chance.
Directory of Open Access Journals (Sweden)
Aaron Fong
2013-02-01
Full Text Available Previous theoretical studies of Mislow’s doubly-bridged biphenyl ketone 1 and dihydrodimethylphenanthrene 2 have determined significant entropic contributions to their normal (1 and inverse (2 conformational kinetic isotope effects (CKIEs. To broaden our investigation, we have used density functional methods to characterize the potential energy surfaces and vibrational frequencies for ground and transition structures of additional systems with measured CKIEs, including [2.2]-metaparacyclophane-d (3, 1,1'-binaphthyl (4, 2,2'-dibromo-[1,1'-biphenyl]-4,4'-dicarboxylic acid (5, and the 2-(N,N,N-trimethyl-2'-(N,N-dimethyl-diaminobiphenyl cation (6. We have also computed CKIEs in a number of systems whose experimental CKIEs are unknown. These include analogs of 1 in which the C=O groups have been replaced with CH2 (7, O (8, and S (9 atoms and ring-expanded variants of 2 containing CH2 (10, O (11, S (12, or C=O (13 groups. Vibrational entropy contributes to the CKIEs in all of these systems with the exception of cyclophane 3, whose isotope effect is predicted to be purely enthalpic in origin and whose Bigeleisen-Mayer ZPE term is equivalent to ΔΔ H‡. There is variable correspondence between these terms in the other molecules studied, thus identifying additional examples of systems in which the Bigeleisen-Mayer formalism does not correlate with ΔH/ΔS dissections.
Korolev, Alexander A; Shiryaeva, Valeria E; Popova, Tamara P; Kurganov, Alexander A
2011-08-01
Enthalpy and entropy of adsorption of light hydrocarbons C1-C4 have been measured for three monoliths of different polarity and for five different carrier gases: helium, hydrogen, nitrogen, carbon dioxide and dinitrogen oxide. Using carrier gas helium the highest values of enthalpy and entropy were observed for monolith based on ethylenedimethacrylate and the lowest values were observed for monolith based on silica, while monolith based on divinylbenzene demonstrated intermediate values. Entropy-enthalpy correlations were observed with carrier gas helium for all thee monoliths and possess similar slope indicating similar adsorption mechanism on all monoliths studied. Comparing different carrier gases entropy-enthalpy correlations within a homological series of solutes were observed for light carrier gases (He, H2 and N2) and were not observed for heavy carrier gases (CO2 and N2O). Instead, entropy-enthalpy correlations for heavy carrier gases were observed with pressure as variable and the higher the carrier gas pressure the lower the values of enthalpy and entropy observed. The observed changes in entropy-enthalpy correlations were explained by competitive adsorption of heavy carrier gas on monoliths. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Thermodynamics of Aβ16-21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties.
Rao Jampani, Srinivasa; Mahmoudinobar, Farbod; Su, Zhaoqian; Dias, Cristiano L
2015-11-01
Here, we provide insights into the thermodynamic properties of A β16-21 dissociation from an amyloid fibril using all-atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers-of-mass of the A β16-21 peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard-Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A β16-21. © 2015 Wiley Periodicals, Inc.
Decomposing Oriented Graphs into Six Locally Irregular Oriented Graphs
DEFF Research Database (Denmark)
Bensmail, Julien; Renault, Gabriel
2016-01-01
An undirected graph G is locally irregular if every two of its adjacent vertices have distinct degrees. We say that G is decomposable into k locally irregular graphs if there exists a partition E1∪E2∪⋯∪Ek of the edge set E(G) such that each Ei induces a locally irregular graph. It was recently...... conjectured by Baudon et al. that every undirected graph admits a decomposition into at most three locally irregular graphs, except for a well-characterized set of indecomposable graphs. We herein consider an oriented version of this conjecture. Namely, can every oriented graph be decomposed into at most...... three locally irregular oriented graphs, i.e. whose adjacent vertices have distinct outdegrees? We start by supporting this conjecture by verifying it for several classes of oriented graphs. We then prove a weaker version of this conjecture. Namely, we prove that every oriented graph can be decomposed...
Graph Transformation for Consolidation of Creativity Sessions Results
DEFF Research Database (Denmark)
Dolog, Peter
2010-01-01
Graph transformation approach for consolidation of creativity sessions results is part of the FP7 EU/IST project idSpace: Tooling of and training for collaborative, distributed product innovation. The goal of graph transformation approach is to provide a tool for merging results of various sessions...
Alspach, BR
1985-01-01
This volume deals with a variety of problems involving cycles in graphs and circuits in digraphs. Leading researchers in this area present here 3 survey papers and 42 papers containing new results. There is also a collection of unsolved problems.
Tailored Random Graph Ensembles
International Nuclear Information System (INIS)
Roberts, E S; Annibale, A; Coolen, A C C
2013-01-01
Tailored graph ensembles are a developing bridge between biological networks and statistical mechanics. The aim is to use this concept to generate a suite of rigorous tools that can be used to quantify and compare the topology of cellular signalling networks, such as protein-protein interaction networks and gene regulation networks. We calculate exact and explicit formulae for the leading orders in the system size of the Shannon entropies of random graph ensembles constrained with degree distribution and degree-degree correlation. We also construct an ergodic detailed balance Markov chain with non-trivial acceptance probabilities which converges to a strictly uniform measure and is based on edge swaps that conserve all degrees. The acceptance probabilities can be generalized to define Markov chains that target any alternative desired measure on the space of directed or undirected graphs, in order to generate graphs with more sophisticated topological features.
Learning Probabilistic Decision Graphs
DEFF Research Database (Denmark)
Jaeger, Manfred; Dalgaard, Jens; Silander, Tomi
2004-01-01
Probabilistic decision graphs (PDGs) are a representation language for probability distributions based on binary decision diagrams. PDGs can encode (context-specific) independence relations that cannot be captured in a Bayesian network structure, and can sometimes provide computationally more...
Wilson, Robin J
1985-01-01
Graph Theory has recently emerged as a subject in its own right, as well as being an important mathematical tool in such diverse subjects as operational research, chemistry, sociology and genetics. This book provides a comprehensive introduction to the subject.
Efficiently Controllable Graphs.
Gokler, Can; Lloyd, Seth; Shor, Peter; Thompson, Kevin
2017-06-30
We investigate graphs that can be disconnected into small components by removing a vanishingly small fraction of their vertices. We show that, when a controllable quantum network is described by such a graph and the gaps in eigenfrequencies and in transition frequencies are bounded exponentially in the number of vertices, the network is efficiently controllable, in the sense that universal quantum computation can be performed using a control sequence polynomial in the size of the network while controlling a vanishingly small fraction of subsystems. We show that networks corresponding to finite-dimensional lattices are efficiently controllable and explore generalizations to percolation clusters and random graphs. We show that the classical computational complexity of estimating the ground state of Hamiltonians described by controllable graphs is polynomial in the number of subsystems or qubits.
DEFF Research Database (Denmark)
Bakhshesh, Davood; Barba, Luis; Bose, Prosenjit
2018-01-01
In this paper, we introduce a variation of the well-studied Yao graphs. Given a set of points S⊂R2 and an angle 0Yao graph cY(θ) with vertex set S and angle θ as follows. For each p,q∈S, we add an edge from p to q in cY(θ) if there exists a cone with apex p...
Local Interaction on Random Graphs
Directory of Open Access Journals (Sweden)
Hans Haller
2010-08-01
Full Text Available We analyze dynamic local interaction in population games where the local interaction structure (modeled as a graph can change over time: A stochastic process generates a random sequence of graphs. This contrasts with models where the initial interaction structure (represented by a deterministic graph or the realization of a random graph cannot change over time.
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.
Categorical constructions in graph theory
Directory of Open Access Journals (Sweden)
Richard T. Bumby
1986-01-01
Full Text Available This paper presents some graph-theoretic questions from the viewpoint of the portion of category theory which has become common knowledge. In particular, the reader is encouraged to consider whether there is only one natural category of graphs and how theories of directed graphs and undirected graphs are related.
Commuting projections on graphs
Energy Technology Data Exchange (ETDEWEB)
Vassilevski, Panayot S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing; Zikatanov, Ludmil T. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Mathematics
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 ℓ_{2}-projection Q_{H} 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 Q_{H} commute with the discrete divergence operator, i.e., we have div π _{H} = Q_{H} 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.
Bollobás, Béla
1998-01-01
The time has now come when graph theory should be part of the education of every serious student of mathematics and computer science, both for its own sake and to enhance the appreciation of mathematics as a whole. This book is an in-depth account of graph theory, written with such a student in mind; it reflects the current state of the subject and emphasizes connections with other branches of pure mathematics. The volume grew out of the author's earlier book, Graph Theory -- An Introductory Course, but its length is well over twice that of its predecessor, allowing it to reveal many exciting new developments in the subject. Recognizing that graph theory is one of several courses competing for the attention of a student, the book contains extensive descriptive passages designed to convey the flavor of the subject and to arouse interest. In addition to a modern treatment of the classical areas of graph theory such as coloring, matching, extremal theory, and algebraic graph theory, the book presents a detailed ...
Hierarchy of graph matchbox manifolds
Lukina, Olga
2011-01-01
We study a class of graph foliated spaces, or graph matchbox manifolds, initially constructed by Kenyon and Ghys. For graph foliated spaces we introduce a quantifier of dynamical complexity which we call its level. We develop the fusion construction, which allows us to associate to every two graph foliated spaces a third one which contains the former two in its closure. Although the underlying idea of the fusion is simple, it gives us a powerful tool to study graph foliated spaces. Using fusi...
Linear representation of a graph
Directory of Open Access Journals (Sweden)
Eduardo Montenegro
2019-10-01
Full Text Available In this paper the linear representation of a graph is defined. A linear representation of a graph is a subgroup of $GL(p,\\mathbb{R}$, the group of invertible matrices of order $ p $ and real coefficients. It will be demonstrated that every graph admits a linear representation. In this paper, simple and finite graphs will be used, framed in the graphs theory's area
Directory of Open Access Journals (Sweden)
Daniele Penteado Rosa
2013-02-01
Full Text Available Orange seeds are a promising agroindustry-waste which can be implemented in the extraction and production of vegetable oil. The relationship between moisture content and water activity provides useful information for the processing and storage of this waste item. The aim of this study was to determine the mechanism of water sorption enthalpy-entropy of orange seeds (C. sinensis cv. Brazilians according to the moisture content. Therefore, desorption isotherms were determined at five different temperature (30, 40, 50, 60, and 70 ºC under a wide range of moisture content (0.005-0.057 kg kg-1 d.b. and water activity (0.02-0.756. Theoretical and empirical models were used for modeling the desorption isotherms. An analytical solution of the Clausius-Clapeyron equation was proposed to compute the isosteric heat of sorption, the differential entropy, and Gibbs free energy using the Oswin model when the effect of temperature on the hygroscopic equilibrium was considered.As sementes de laranja são resíduos promissores da agroindústria com um alto potencial de aplicação na produção de óleo vegetal. A relação entre o conteúdo de umidade de equilíbrio e a atividade de água fornece informações úteis para seu processamento e armazenamento. O objetivo deste trabalho foi determinar o mecanismo entalpia-entropia de sorção da água de sementes de laranja (C. sinensis cv. Brasileiros em função do teor de umidade. Para isso, isotermas de dessorção das sementes de laranja foram determinados em cinco níveis de temperaturas (30, 40, 50, 60 e 70 ºC em um intervalo de umidade de equilíbrio (0.005-0.057 kg kg-1 d.b. e atividade de água de 0,02-0,756. Modelos teóricos e empíricos foram usados para a modelagem das isotermas de dessorção. A solução analítica da equação de Clausius-Clapeyron foi proposta para calcular o calor isostérico de sorção, a entropia diferencial e a energia livre de Gibbs através do modelo de Oswin quando o
Signal Processing for Time-Series Functions on a Graph
2018-02-01
ARL-TR-8276• FEB 2018 US Army Research Laboratory Signal Processing for Time-Series Functions on a Graph by Humberto Muñoz-Barona, Jean Vettel, and...ARL-TR-8276• FEB 2018 US Army Research Laboratory Signal Processing for Time-Series Functions on a Graph by Humberto Muñoz-Barona Southern University...addison.w.bohannon.civ@mail.mil>. Previous research introduced signal processing on graphs, an approach to generalize signal processing tools such
Towards Scalable Graph Computation on Mobile Devices
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
Generating Realistic Labelled, Weighted Random Graphs
Directory of Open Access Journals (Sweden)
Michael Charles Davis
2015-12-01
Full Text Available Generative algorithms for random graphs have yielded insights into the structure and evolution of real-world networks. Most networks exhibit a well-known set of properties, such as heavy-tailed degree distributions, clustering and community formation. Usually, random graph models consider only structural information, but many real-world networks also have labelled vertices and weighted edges. In this paper, we present a generative model for random graphs with discrete vertex labels and numeric edge weights. The weights are represented as a set of Beta Mixture Models (BMMs with an arbitrary number of mixtures, which are learned from real-world networks. We propose a Bayesian Variational Inference (VI approach, which yields an accurate estimation while keeping computation times tractable. We compare our approach to state-of-the-art random labelled graph generators and an earlier approach based on Gaussian Mixture Models (GMMs. Our results allow us to draw conclusions about the contribution of vertex labels and edge weights to graph structure.
Towards Scalable Graph Computation on Mobile Devices.
Chen, Yiqi; Lin, Zhiyuan; Pienta, Robert; Kahng, Minsuk; Chau, Duen Horng
2014-10-01
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.
Czech Academy of Sciences Publication Activity Database
Exner, Pavel; Lipovský, J.
2017-01-01
Roč. 58, č. 4 (2017), č. článku 042101. ISSN 0022-2488 R&D Projects: GA ČR GA17-01706S Institutional support: RVO:61389005 Keywords : self-adjoint coupling * high-energy regime * resonances in quantum graphs Subject RIV: BE - Theoretical Physics OBOR OECD: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 1.077, year: 2016
Ringo: Interactive Graph Analytics on Big-Memory Machines
Perez, Yonathan; Sosič, Rok; Banerjee, Arijit; Puttagunta, Rohan; Raison, Martin; Shah, Pararth; Leskovec, Jure
2016-01-01
We present Ringo, a system for analysis of large graphs. Graphs provide a way to represent and analyze systems of interacting objects (people, proteins, webpages) with edges between the objects denoting interactions (friendships, physical interactions, links). Mining graphs provides valuable insights about individual objects as well as the relationships among them. In building Ringo, we take advantage of the fact that machines with large memory and many cores are widely available and also relatively affordable. This allows us to build an easy-to-use interactive high-performance graph analytics system. Graphs also need to be built from input data, which often resides in the form of relational tables. Thus, Ringo provides rich functionality for manipulating raw input data tables into various kinds of graphs. Furthermore, Ringo also provides over 200 graph analytics functions that can then be applied to constructed graphs. We show that a single big-memory machine provides a very attractive platform for performing analytics on all but the largest graphs as it offers excellent performance and ease of use as compared to alternative approaches. With Ringo, we also demonstrate how to integrate graph analytics with an iterative process of trial-and-error data exploration and rapid experimentation, common in data mining workloads. PMID:27081215
Parallel Algorithm for Incremental Betweenness Centrality on Large Graphs
Jamour, Fuad Tarek
2017-10-17
Betweenness centrality quantifies the importance of nodes in a graph in many applications, including network analysis, community detection and identification of influential users. Typically, graphs in such applications evolve over time. Thus, the computation of betweenness centrality should be performed incrementally. This is challenging because updating even a single edge may trigger the computation of all-pairs shortest paths in the entire graph. Existing approaches cannot scale to large graphs: they either require excessive memory (i.e., quadratic to the size of the input graph) or perform unnecessary computations rendering them prohibitively slow. We propose iCentral; a novel incremental algorithm for computing betweenness centrality in evolving graphs. We decompose the graph into biconnected components and prove that processing can be localized within the affected components. iCentral is the first algorithm to support incremental betweeness centrality computation within a graph component. This is done efficiently, in linear space; consequently, iCentral scales to large graphs. We demonstrate with real datasets that the serial implementation of iCentral is up to 3.7 times faster than existing serial methods. Our parallel implementation that scales to large graphs, is an order of magnitude faster than the state-of-the-art parallel algorithm, while using an order of magnitude less computational resources.
The STAPL Parallel Graph Library
Harshvardhan,
2013-01-01
This paper describes the stapl Parallel Graph Library, a high-level framework that abstracts the user from data-distribution and parallelism details and allows them to concentrate on parallel graph algorithm development. It includes a customizable distributed graph container and a collection of commonly used parallel graph algorithms. The library introduces pGraph pViews that separate algorithm design from the container implementation. It supports three graph processing algorithmic paradigms, level-synchronous, asynchronous and coarse-grained, and provides common graph algorithms based on them. Experimental results demonstrate improved scalability in performance and data size over existing graph libraries on more than 16,000 cores and on internet-scale graphs containing over 16 billion vertices and 250 billion edges. © Springer-Verlag Berlin Heidelberg 2013.
Graph rewriting using a single pushout: a comparison
van den Broek, P.M.; Kuper, Jan; Dietz, J.L.G.
1992-01-01
Recently two algebraic approaches to graph rewriting have been given which use only single pushouts. Here we compare both approaches. We show that they are almost the same, the only difference being the way dangling arcs are treated.
Embedding graphs in Lorentzian spacetime.
Directory of Open Access Journals (Sweden)
James R Clough
Full Text Available Geometric approaches to network analysis combine simply defined models with great descriptive power. In this work we provide a method for embedding directed acyclic graphs (DAG into Minkowski spacetime using Multidimensional scaling (MDS. First we generalise the classical MDS algorithm, defined only for metrics with a Riemannian signature, to manifolds of any metric signature. We then use this general method to develop an algorithm which exploits the causal structure of a DAG to assign space and time coordinates in a Minkowski spacetime to each vertex. As in the causal set approach to quantum gravity, causal connections in the discrete graph correspond to timelike separation in the continuous spacetime. The method is demonstrated by calculating embeddings for simple models of causal sets and random DAGs, as well as real citation networks. We find that the citation networks we test yield significantly more accurate embeddings that random DAGs of the same size. Finally we suggest a number of applications in citation analysis such as paper recommendation, identifying missing citations and fitting citation models to data using this geometric approach.
Learning molecular energies using localized graph kernels
Ferré, Grégoire; Haut, Terry; Barros, Kipton
2017-03-01
Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.
FSG: Fast String Graph Construction for De Novo Assembly.
Bonizzoni, Paola; Vedova, Gianluca Della; Pirola, Yuri; Previtali, Marco; Rizzi, Raffaella
2017-10-01
The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradigm. In this article, we explore a novel approach to compute the string graph, based on the FM-index and Burrows and Wheeler Transform. We describe a simple algorithm that uses only the FM-index representation of the collection of reads to construct the string graph, without accessing the input reads. Our algorithm has been integrated into the string graph assembler (SGA) as a standalone module to construct the string graph. The new integrated assembler has been assessed on a standard benchmark, showing that fast string graph (FSG) is significantly faster than SGA while maintaining a moderate use of main memory, and showing practical advantages in running FSG on multiple threads. Moreover, we have studied the effect of coverage rates on the running times.
Ribes, Luis
2017-01-01
This book offers a detailed introduction to graph theoretic methods in profinite groups and applications to abstract groups. It is the first to provide a comprehensive treatment of the subject. The author begins by carefully developing relevant notions in topology, profinite groups and homology, including free products of profinite groups, cohomological methods in profinite groups, and fixed points of automorphisms of free pro-p groups. The final part of the book is dedicated to applications of the profinite theory to abstract groups, with sections on finitely generated subgroups of free groups, separability conditions in free and amalgamated products, and algorithms in free groups and finite monoids. Profinite Graphs and Groups will appeal to students and researchers interested in profinite groups, geometric group theory, graphs and connections with the theory of formal languages. A complete reference on the subject, the book includes historical and bibliographical notes as well as a discussion of open quest...
White, AT
1985-01-01
The field of topological graph theory has expanded greatly in the ten years since the first edition of this book appeared. The original nine chapters of this classic work have therefore been revised and updated. Six new chapters have been added, dealing with: voltage graphs, non-orientable imbeddings, block designs associated with graph imbeddings, hypergraph imbeddings, map automorphism groups and change ringing.Thirty-two new problems have been added to this new edition, so that there are now 181 in all; 22 of these have been designated as ``difficult'''' and 9 as ``unsolved''''. Three of the four unsolved problems from the first edition have been solved in the ten years between editions; they are now marked as ``difficult''''.
Graph theory and interconnection networks
Hsu, Lih-Hsing
2008-01-01
The advancement of large scale integrated circuit technology has enabled the construction of complex interconnection networks. Graph theory provides a fundamental tool for designing and analyzing such networks. Graph Theory and Interconnection Networks provides a thorough understanding of these interrelated topics. After a brief introduction to graph terminology, the book presents well-known interconnection networks as examples of graphs, followed by in-depth coverage of Hamiltonian graphs. Different types of problems illustrate the wide range of available methods for solving such problems. The text also explores recent progress on the diagnosability of graphs under various models.
On support relations and semantic scene graphs
Yang, Michael Ying; Liao, Wentong; Ackermann, Hanno; Rosenhahn, Bodo
2017-09-01
Scene understanding is one of the essential and challenging topics in computer vision and photogrammetry. Scene graph provides valuable information for such scene understanding. This paper proposes a novel framework for automatic generation of semantic scene graphs which interpret indoor environments. First, a Convolutional Neural Network is used to detect objects of interest in the given image. Then, the precise support relations between objects are inferred by taking two important auxiliary information in the indoor environments: the physical stability and the prior support knowledge between object categories. Finally, a semantic scene graph describing the contextual relations within a cluttered indoor scene is constructed. In contrast to the previous methods for extracting support relations, our approach provides more accurate results. Furthermore, we do not use pixel-wise segmentation to obtain objects, which is computation costly. We also propose different methods to evaluate the generated scene graphs, which lacks in this community. Our experiments are carried out on the NYUv2 dataset. The experimental results demonstrated that our approach outperforms the state-of-the-art methods in inferring support relations. The estimated scene graphs are accurately compared with ground truth.
Linear Time Vertex Partitioning on Massive Graphs
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
Endomorphisms of graph algebras
DEFF Research Database (Denmark)
Conti, Roberto; Hong, Jeong Hee; Szymanski, Wojciech
2012-01-01
We initiate a systematic investigation of endomorphisms of graph C*-algebras C*(E), extending several known results on endomorphisms of the Cuntz algebras O_n. Most but not all of this study is focused on endomorphisms which permute the vertex projections and globally preserve the diagonal MASA D......_E of C*(E). Our results pertain both automorphisms and proper endomorphisms. Firstly, the Weyl group and the restricted Weyl group of a graph C*-algebra are introduced and investigated. In particular, criteria of outerness for automorphisms in the restricted Weyl group are found. We also show...
Stevanovic, Dragan
2015-01-01
Spectral Radius of Graphs provides a thorough overview of important results on the spectral radius of adjacency matrix of graphs that have appeared in the literature in the preceding ten years, most of them with proofs, and including some previously unpublished results of the author. The primer begins with a brief classical review, in order to provide the reader with a foundation for the subsequent chapters. Topics covered include spectral decomposition, the Perron-Frobenius theorem, the Rayleigh quotient, the Weyl inequalities, and the Interlacing theorem. From this introduction, the
The Role of Graphing Calculators in Mathematics Reform.
Waits, Bert K.; Demana, Franklin
This essay describes the role of graphing calculators in mathematics reform. Among the topics discussed are the history of graphing calculators in mathematics education, recent technological innovations, and professional development opportunities. The case is made for a balanced approach between calculator use and paper-and-pencil techniques.…
Handbook of graph grammars and computing by graph transformation
Engels, G; Kreowski, H J; Rozenberg, G
1999-01-01
Graph grammars originated in the late 60s, motivated by considerations about pattern recognition and compiler construction. Since then, the list of areas which have interacted with the development of graph grammars has grown quite impressively. Besides the aforementioned areas, it includes software specification and development, VLSI layout schemes, database design, modeling of concurrent systems, massively parallel computer architectures, logic programming, computer animation, developmental biology, music composition, visual languages, and many others.The area of graph grammars and graph tran
Topics in graph theory graphs and their Cartesian product
Imrich, Wilfried; Rall, Douglas F
2008-01-01
From specialists in the field, you will learn about interesting connections and recent developments in the field of graph theory by looking in particular at Cartesian products-arguably the most important of the four standard graph products. Many new results in this area appear for the first time in print in this book. Written in an accessible way, this book can be used for personal study in advanced applications of graph theory or for an advanced graph theory course.
Robustness of random graphs based on graph spectra.
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.
Codes related to line graphs of triangular graphs and permutation ...
African Journals Online (AJOL)
For any prime p, we consider p-ary linear codes obtained from the row span of incidence matrices of line graphs of triangular graphs and adjacency matrices of their line graphs. We determine parameters of the codes, their automorphism groups and exhibit permutation decoding sets (PD-sets) for partial permutation ...
Feature Tracking Using Reeb Graphs
Energy Technology Data Exchange (ETDEWEB)
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.
Visualizing automorphisms of graph algebras
DEFF Research Database (Denmark)
Avery, James Emil; Johansen, Rune; Szymanski, Wojciech
2018-01-01
Graph C*-algebras have been celebrated as C*-algebras that can be seen, because many important properties may be determined by looking at the underlying graph. This paper introduces the permutation graph for a permutative endomorphism of a graph C*-algebra as a labeled directed multigraph...... that gives a visual representation of the endomorphism and facilitates computations. Combinatorial criteria have previously been developed for deciding when such an endomorphism is an automorphism, but here the question is reformulated in terms of the permutation graph and new proofs are given. Furthermore......, it is shown how to use permutation graphs to efficiently generate exhaustive collections of permutative automorphisms. Permutation graphs provide a natural link to the textile systems representing induced endomorphisms on the edge shift of the given graph, and this allows the powerful tools of the theory...
Rensink, Arend; Schmidt, David
2004-01-01
Graphs are an intuitive model for states of a (software) system that include pointer structures | for instance, object-oriented programs. However, a naive encoding results in large individual states and large, or even unbounded, state spaces. As usual, some form of abstraction is necessary in order
Rensink, Arend; Schmidt, D.A.
2004-01-01
Abstract. Graphs are an intuitive model for states of a (software) system that include pointer structures — for instance, object-oriented programs. However, a naive encoding results in large individual states and large, or even unbounded, state spaces. As usual, some form of abstraction is necessary
Dujmović, Vida; Sidiropoulos, Anastasios; Wood, David R.
2015-01-01
Bourgain and Yehudayoff recently constructed $O(1)$-monotone bipartite expanders. By combining this result with a generalisation of the unraveling method of Kannan, we construct 3-monotone bipartite expanders, which is best possible. We then show that the same graphs admit 3-page book embeddings, 2-queue layouts, 4-track layouts, and have simple thickness 2. All these results are best possible.
S.M. Heditniemi (Sandra); R.C. Laskar (R.C.); H.M. Mulder (Martyn)
2012-01-01
textabstractLet $G = (V,E)$ be a graph. A partition $\\pi = \\{V_1, V_2, \\ldots, V_k \\}$ of the vertices $V$ of $G$ into $k$ {\\it color classes} $V_i$, with $1 \\leq i \\leq k$, is called a {\\it quorum coloring} if for every vertex $v \\in V$, at least half of the vertices in the closed neighborhood
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…
Grabmayer, C.A.; van Oostrom, V.
2014-01-01
We report on work in progress on `nested term graphs' for formalizing higher-order terms (e.g. finite or infinite lambda-terms), including those expressing recursion (e.g. terms in the lambda-calculus with letrec). The idea is to represent the nested scope structure of a higher-order term by a
Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 9. Decoding Codes on Graphs - Low Density Parity Check Codes. A S Madhu Aditya Nori. General Article Volume 8 Issue 9 September 2003 pp 49-59. Fulltext. Click here to view fulltext PDF. Permanent link:
Energy Technology Data Exchange (ETDEWEB)
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.
String graph construction using incremental hashing.
Ben-Bassat, Ilan; Chor, Benny
2014-12-15
New sequencing technologies generate larger amount of short reads data at decreasing cost. De novo sequence assembly is the problem of combining these reads back to the original genome sequence, without relying on a reference genome. This presents algorithmic and computational challenges, especially for long and repetitive genome sequences. Most existing approaches to the assembly problem operate in the framework of de Bruijn graphs. Yet, a number of recent works use the paradigm of string graph, using a variety of methods for storing and processing suffixes and prefixes, like suffix arrays, the Burrows-Wheeler transform or the FM index. Our work is motivated by a search for new approaches to constructing the string graph, using alternative yet simple data structures and algorithmic concepts. We introduce a novel hash-based method for constructing the string graph. We use incremental hashing, and specifically a modification of the Karp-Rabin fingerprint, and Bloom filters. Using these probabilistic methods might create false-positive and false-negative edges during the algorithm's execution, but these are all detected and corrected. The advantages of the proposed approach over existing methods are its simplicity and the incorporation of established probabilistic techniques in the context of de novo genome sequencing. Our preliminary implementation is favorably comparable with the first string graph construction of Simpson and Durbin (2010) (but not with subsequent improvements). Further research and optimizations will hopefully enable the algorithm to be incorporated, with noticeable performance improvement, in state-of-the-art string graph-based assemblers. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Temporal Representation in Semantic Graphs
Energy Technology Data Exchange (ETDEWEB)
Levandoski, J J; Abdulla, G M
2007-08-07
A wide range of knowledge discovery and analysis applications, ranging from business to biological, make use of semantic graphs when modeling relationships and concepts. Most of the semantic graphs used in these applications are assumed to be static pieces of information, meaning temporal evolution of concepts and relationships are not taken into account. Guided by the need for more advanced semantic graph queries involving temporal concepts, this paper surveys the existing work involving temporal representations in semantic graphs.
On dominator colorings in graphs
Indian Academy of Sciences (India)
Graph coloring and domination are two major areas in graph theory that have been ... independent set if no two vertices in S are adjacent. ... independent set. The corona G1 ◦ G2 of two graphs G1 and G2 is defined to be the graph. G obtained by taking one copy of G1 and |V(G1)| copies of G2, and then joining the i-th.
Hamiltonian paths on Platonic graphs
Directory of Open Access Journals (Sweden)
Brian Hopkins
2004-07-01
Full Text Available We develop a combinatorial method to show that the dodecahedron graph has, up to rotation and reflection, a unique Hamiltonian cycle. Platonic graphs with this property are called topologically uniquely Hamiltonian. The same method is used to demonstrate topologically distinct Hamiltonian cycles on the icosahedron graph and to show that a regular graph embeddable on the 2-holed torus is topologically uniquely Hamiltonian.
Proving correctness of compilers using structured graphs
DEFF Research Database (Denmark)
Bahr, Patrick
2014-01-01
We present an approach to compiler implementation using Oliveira and Cook’s structured graphs that avoids the use of explicit jumps in the generated code. The advantage of our method is that it takes the implementation of a compiler using a tree type along with its correctness proof and turns...
Probabilistic Transcriptome Assembly and Variant Graph Genotyping
DEFF Research Database (Denmark)
Sibbesen, Jonas Andreas
that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...
Energy Technology Data Exchange (ETDEWEB)
Winlaw, Manda [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); De Sterck, Hans [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-10-26
In very simple terms a network can be de ned as a collection of points joined together by lines. Thus, networks can be used to represent connections between entities in a wide variety of elds including engi- neering, science, medicine, and sociology. Many large real-world networks share a surprising number of properties, leading to a strong interest in model development research and techniques for building synthetic networks have been developed, that capture these similarities and replicate real-world graphs. Modeling these real-world networks serves two purposes. First, building models that mimic the patterns and prop- erties of real networks helps to understand the implications of these patterns and helps determine which patterns are important. If we develop a generative process to synthesize real networks we can also examine which growth processes are plausible and which are not. Secondly, high-quality, large-scale network data is often not available, because of economic, legal, technological, or other obstacles [7]. Thus, there are many instances where the systems of interest cannot be represented by a single exemplar network. As one example, consider the eld of cybersecurity, where systems require testing across diverse threat scenarios and validation across diverse network structures. In these cases, where there is no single exemplar network, the systems must instead be modeled as a collection of networks in which the variation among them may be just as important as their common features. By developing processes to build synthetic models, so-called graph generators, we can build synthetic networks that capture both the essential features of a system and realistic variability. Then we can use such synthetic graphs to perform tasks such as simulations, analysis, and decision making. We can also use synthetic graphs to performance test graph analysis algorithms, including clustering algorithms and anomaly detection algorithms.
An introduction to grids, graphs, and networks
Pozrikidis, C
2014-01-01
An Introduction to Grids, Graphs, and Networks aims to provide a concise introduction to graphs and networks at a level that is accessible to scientists, engineers, and students. In a practical approach, the book presents only the necessary theoretical concepts from mathematics and considers a variety of physical and conceptual configurations as prototypes or examples. The subject is timely, as the performance of networks is recognized as an important topic in the study of complex systems with applications in energy, material, and information grid transport (epitomized by the internet). The bo
Nullspace embeddings for outerplanar graphs
L. Lovász (László); A. Schrijver (Alexander)
2017-01-01
textabstractWe study relations between geometric embeddings of graphs and the spectrum of associated matrices, focusing on outerplanar embeddings of graphs. For a simple connected graph G=(V,E), we define a "good" G-matrix as a V×V matrix with negative entries corresponding to adjacent nodes, zero
Nullspace embeddings for outerplanar graphs
L. Lovász (László); A. Schrijver (Alexander); M. Loebl (Martin); J. Nešetřil (Jaroslav); R. Thomas (Robin)
2017-01-01
htmlabstractWe study relations between geometric embeddings of graphs and the spectrum of associated matrices, focusing on outerplanar embeddings of graphs. For a simple connected graph G = (V, E), we define a "good” G-matrix as a V × V matrix with negative
Nullspace embeddings for outerplanar graphs
Lovász, L.; Schrijver, A.; Loebl, M.; Nešetřil, J.; Thomas, R.
2017-01-01
We study relations between geometric embeddings of graphs and the spectrum of associated matrices, focusing on outerplanar embeddings of graphs. For a simple connected graph G = (V, E), we define a “good” G-matrix as a V × V matrix with negative entries corresponding to adjacent nodes, zero entries
Pattern-Based Graph Abstraction
Rensink, Arend; Zambon, Eduardo; Ehrig, H; Engels, G.; Kreowski, H.J.; Rozenberg, G.
We present a new abstraction technique for the exploration of graph transformation systems with infinite state spaces. This technique is based on patterns, simple graphs describing structures of interest that should be preserved by the abstraction. Patterns are collected into pattern graphs, layered
Generalised compositionality in graph transformation
Ghamarian, A.H.; Rensink, Arend; Ehrig, H; Engels, G.; Kreowski, H.J.; Rozenberg, G.
We present a notion of composition applying both to graphs and to rules, based on graph and rule interfaces along which they are glued. The current paper generalises a previous result in two different ways. Firstly, rules do not have to form pullbacks with their interfaces; this enables graph
Hopkins, Brian
2004-01-01
The interconnected world of actors and movies is a familiar, rich example for graph theory. This paper gives the history of the "Kevin Bacon Game" and makes extensive use of a Web site to analyze the underlying graph. The main content is the classroom development of the weighted average to determine the best choice of "center" for the graph. The…
Mining and Indexing Graph Databases
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.…
Graph transformation tool contest 2008
Rensink, Arend; van Gorp, Pieter
This special section is the outcome of the graph transformation tool contest organised during the Graph-Based Tools (GraBaTs) 2008 workshop, which took place as a satellite event of the International Conference on Graph Transformation (ICGT) 2008. The contest involved two parts: three “off-line case
Submanifolds weakly associated with graphs
Indian Academy of Sciences (India)
We establish an interesting link between differential geometry and graph theory by defining submanifolds weakly associated with graphs. We prove that, in a local sense, every submanifold satisfies such an association, and other general results. Finally, we study submanifolds associated with graphs either in low ...
Incremental Frequent Subgraph Mining on Large Evolving Graphs
Abdelhamid, Ehab
2017-08-22
Frequent subgraph mining is a core graph operation used in many domains, such as graph data management and knowledge exploration, bioinformatics and security. Most existing techniques target static graphs. However, modern applications, such as social networks, utilize large evolving graphs. Mining these graphs using existing techniques is infeasible, due to the high computational cost. In this paper, we propose IncGM+, a fast incremental approach for continuous frequent subgraph mining problem on a single large evolving graph. We adapt the notion of “fringe” to the graph context, that is the set of subgraphs on the border between frequent and infrequent subgraphs. IncGM+ maintains fringe subgraphs and exploits them to prune the search space. To boost the efficiency, we propose an efficient index structure to maintain selected embeddings with minimal memory overhead. These embeddings are utilized to avoid redundant expensive subgraph isomorphism operations. Moreover, the proposed system supports batch updates. Using large real-world graphs, we experimentally verify that IncGM+ outperforms existing methods by up to three orders of magnitude, scales to much larger graphs and consumes less memory.
GRAMI: Generalized Frequent Subgraph Mining in Large Graphs
El Saeedy, Mohammed El Sayed
2011-07-24
Mining frequent subgraphs is an important operation on graphs. Most existing work assumes a database of many small graphs, but modern applications, such as social networks, citation graphs or protein-protein interaction in bioinformatics, are modeled as a single large graph. Interesting interactions in such applications may be transitive (e.g., friend of a friend). Existing methods, however, search for frequent isomorphic (i.e., exact match) subgraphs and cannot discover many useful patterns. In this paper we propose GRAMI, a framework that generalizes frequent subgraph mining in a large single graph. GRAMI discovers frequent patterns. A pattern is a graph where edges are generalized to distance-constrained paths. Depending on the definition of the distance function, many instantiations of the framework are possible. Both directed and undirected graphs, as well as multiple labels per vertex, are supported. We developed an efficient implementation of the framework that models the frequency resolution phase as a constraint satisfaction problem, in order to avoid the costly enumeration of all instances of each pattern in the graph. We also implemented CGRAMI, a version that supports structural and semantic constraints; and AGRAMI, an approximate version that supports very large graphs. Our experiments on real data demonstrate that our framework is up to 3 orders of magnitude faster and discovers more interesting patterns than existing approaches.
Transduction on Directed Graphs via Absorbing Random Walks.
De, Jaydeep; Zhang, Xiaowei; Lin, Feng; Cheng, Li
2017-08-11
In this paper we consider the problem of graph-based transductive classification, and we are particularly interested in the directed graph scenario which is a natural form for many real world applications.Different from existing research efforts that either only deal with undirected graphs or circumvent directionality by means of symmetrization, we propose a novel random walk approach on directed graphs using absorbing Markov chains, which can be regarded as maximizing the accumulated expected number of visits from the unlabeled transient states. Our algorithm is simple, easy to implement, and works with large-scale graphs on binary, multiclass, and multi-label prediction problems. Moreover, it is capable of preserving the graph structure even when the input graph is sparse and changes over time, as well as retaining weak signals presented in the directed edges. We present its intimate connections to a number of existing methods, including graph kernels, graph Laplacian based methods, and interestingly, spanning forest of graphs. Its computational complexity and the generalization error are also studied. Empirically our algorithm is systematically evaluated on a wide range of applications, where it has shown to perform competitively comparing to a suite of state-of-the-art methods. In particular, our algorithm is shown to work exceptionally well with large sparse directed graphs with e.g. millions of nodes and tens of millions of edges, where it significantly outperforms other state-of-the-art methods. In the dynamic graph setting involving insertion or deletion of nodes and edge-weight changes over time, it also allows efficient online updates that produce the same results as of the batch update counterparts.
Asteroidal Quadruples in non Rooted Path Graphs
Directory of Open Access Journals (Sweden)
Gutierrez Marisa
2015-11-01
Full Text Available A directed path graph is the intersection graph of a family of directed subpaths of a directed tree. A rooted path graph is the intersection graph of a family of directed subpaths of a rooted tree. Rooted path graphs are directed path graphs. Several characterizations are known for directed path graphs: one by forbidden induced subgraphs and one by forbidden asteroids. It is an open problem to find such characterizations for rooted path graphs. For this purpose, we are studying in this paper directed path graphs that are non rooted path graphs. We prove that such graphs always contain an asteroidal quadruple.
A New Graph Drawing Scheme for Social Network
Directory of Open Access Journals (Sweden)
Eric Ke Wang
2014-01-01
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.
A Robust PTAS for Maximum Weight Independent Sets in Unit Disk Graphs
Nieberg, T.; Hurink, Johann L.; Kern, Walter; Hromkovič, Juraj; Nagel, Manfred; Westfechtel, Bernhard
2004-01-01
A unit disk graph is the intersection graph of unit disks in the euclidean plane. We present a polynomial-time approximation scheme for the maximum weight independent set problem in unit disk graphs. In contrast to previously known approximation schemes, our approach does not require a geometric
A new PTAS for maximum independent sets in unit disk graphs
Nieberg, T.; Hurink, Johann L.; Kern, Walter
2003-01-01
A unit disk graph is an intersection graph of unit disks in the euclidean plane. We present a polynomial-time approximation scheme for the maximum independent set problem in unit disk graphs. In contrast to previously known approximation schemes, our approach does not require a geometric
Harary, Frank
2015-01-01
Presented in 1962-63 by experts at University College, London, these lectures offer a variety of perspectives on graph theory. Although the opening chapters form a coherent body of graph theoretic concepts, this volume is not a text on the subject but rather an introduction to the extensive literature of graph theory. The seminar's topics are geared toward advanced undergraduate students of mathematics.Lectures by this volume's editor, Frank Harary, include ""Some Theorems and Concepts of Graph Theory,"" ""Topological Concepts in Graph Theory,"" ""Graphical Reconstruction,"" and other introduc
Domination criticality in product graphs
Directory of Open Access Journals (Sweden)
M.R. Chithra
2015-07-01
Full Text Available A connected dominating set is an important notion and has many applications in routing and management of networks. Graph products have turned out to be a good model of interconnection networks. This motivated us to study the Cartesian product of graphs G with connected domination number, γc(G=2,3 and characterize such graphs. Also, we characterize the k−γ-vertex (edge critical graphs and k−γc-vertex (edge critical graphs for k=2,3 where γ denotes the domination number of G. We also discuss the vertex criticality in grids.
Dynamic Representations of Sparse Graphs
DEFF Research Database (Denmark)
Brodal, Gerth Stølting; Fagerberg, Rolf
1999-01-01
We present a linear space data structure for maintaining graphs with bounded arboricity—a large class of sparse graphs containing e.g. planar graphs and graphs of bounded treewidth—under edge insertions, edge deletions, and adjacency queries. The data structure supports adjacency queries in worst...... case O(c) time, and edge insertions and edge deletions in amortized O(1) and O(c+log n) time, respectively, where n is the number of nodes in the graph, and c is the bound on the arboricity....
Graph Creation, Visualisation and Transformation
Directory of Open Access Journals (Sweden)
Maribel Fernández
2010-03-01
Full Text Available We describe a tool to create, edit, visualise and compute with interaction nets - a form of graph rewriting systems. The editor, called GraphPaper, allows users to create and edit graphs and their transformation rules using an intuitive user interface. The editor uses the functionalities of the TULIP system, which gives us access to a wealth of visualisation algorithms. Interaction nets are not only a formalism for the specification of graphs, but also a rewrite-based computation model. We discuss graph rewriting strategies and a language to express them in order to perform strategic interaction net rewriting.
Video tracking based on sequential particle filtering on graphs.
Pan, Pan; Schonfeld, Dan
2011-06-01
In this paper, we develop a novel solution for particle filtering on general graphs. We provide an exact solution for particle filtering on directed cycle-free graphs. The proposed approach relies on a partial-order relation in an antichain decomposition that forms a high-order Markov chain over the partitioned graph. We subsequently derive a closed-form sequential updating scheme for conditional density propagation using particle filtering on directed cycle-free graphs. We also provide an approximate solution for particle filtering on general graphs by splitting graphs with cycles into multiple directed cycle-free subgraphs. We then use the sequential updating scheme by alternating among the directed cycle-free subgraphs to obtain an estimate of the density propagation. We rely on the proposed method for particle filtering on general graphs for two video tracking applications: 1) object tracking using high-order Markov chains; and 2) distributed multiple object tracking based on multi-object graphical interaction models. Experimental results demonstrate the improved performance of the proposed approach to particle filtering on graphs compared with existing methods for video tracking.
Canonical Labelling of Site Graphs
Directory of Open Access Journals (Sweden)
Nicolas Oury
2013-06-01
Full Text Available We investigate algorithms for canonical labelling of site graphs, i.e. graphs in which edges bind vertices on sites with locally unique names. We first show that the problem of canonical labelling of site graphs reduces to the problem of canonical labelling of graphs with edge colourings. We then present two canonical labelling algorithms based on edge enumeration, and a third based on an extension of Hopcroft's partition refinement algorithm. All run in quadratic worst case time individually. However, one of the edge enumeration algorithms runs in sub-quadratic time for graphs with "many" automorphisms, and the partition refinement algorithm runs in sub-quadratic time for graphs with "few" bisimulation equivalences. This suite of algorithms was chosen based on the expectation that graphs fall in one of those two categories. If that is the case, a combined algorithm runs in sub-quadratic worst case time. Whether this expectation is reasonable remains an interesting open problem.
Bogiatzis, P.; Ishii, M.; Davis, T. A.
2016-12-01
Seismic tomography inverse problems are among the largest high-dimensional parameter estimation tasks in Earth science. We show how combinatorics and graph theory can be used to analyze the structure of such problems, and to effectively decompose them into smaller ones that can be solved efficiently by means of the least squares method. In combination with recent high performance direct sparse algorithms, this reduction in dimensionality allows for an efficient computation of the model resolution and covariance matrices using limited resources. Furthermore, we show that a new sparse singular value decomposition method can be used to obtain the complete spectrum of the singular values. This procedure provides the means for more objective regularization and further dimensionality reduction of the problem. We apply this methodology to a moderate size, non-linear seismic tomography problem to image the structure of the crust and the upper mantle beneath Japan using local deep earthquakes recorded by the High Sensitivity Seismograph Network stations.
Directory of Open Access Journals (Sweden)
Burhan Selçuk
2017-06-01
Full Text Available Hypercube is a popular interconnection network. Due to the popularity of hypercube, more researchers pay a great effort to develop the different variants of hypercube. In this paper, we have proposed a variant of hypercube which is called as “Connected Cubic Network Graphs”, and have investigated the Hamilton-like properties of Connected Cubic Network Graphs (CCNG. Firstly, we defined CCNG and showed the characteristic analyses of CCNG. Then, we showed that the CCNG has the properties of Hamilton graph, and can be labeled using a Gray coding based recursive algorithm. Finally, we gave the comparison results, a routing algorithm and a bitonic sort algorithm for CCNG. In case of sparsity and cost, CCNG is better than Hypercube.
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…
Directory of Open Access Journals (Sweden)
Falcon Seth
2007-09-01
Full Text Available Abstract Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network.
2010-12-02
evaluating the function ΘP (A) for any fixed A,P is equivalent to solving the so-called Quadratic Assignment Problem ( QAP ), and thus we can employ various...tractable linear programming, spectral, and SDP relaxations of QAP [40, 11, 33]. In particular we discuss recent work [14] on exploiting group...symmetry in SDP relaxations of QAP , which is useful for approximately computing elementary convex graph invariants in many interesting cases. Finally in
Zhou, Feng; de la Torre, Fernando
2015-11-19
Graph matching (GM) is a fundamental problem in computer science, and it plays a central role to solve correspondence problems in computer vision. GM problems that incorporate pairwise constraints can be formulated as a quadratic assignment problem (QAP). Although widely used, solving the correspondence problem through GM has two main limitations: (1) the QAP is NP-hard and difficult to approximate; (2) GM algorithms do not incorporate geometric constraints between nodes that are natural in computer vision problems. To address aforementioned problems, this paper proposes factorized graph matching (FGM). FGM factorizes the large pairwise affinity matrix into smaller matrices that encode the local structure of each graph and the pairwise affinity between edges. Four are the benefits that follow from this factorization: (1) There is no need to compute the costly (in space and time) pairwise affinity matrix; (2) The factorization allows the use of a path-following optimization algorithm, that leads to improved optimization strategies and matching performance; (3) Given the factorization, it becomes straight-forward to incorporate geometric transformations (rigid and non-rigid) to the GM problem. (4) Using a matrix formulation for the GM problem and the factorization, it is easy to reveal commonalities and differences between different GM methods. The factorization also provides a clean connection with other matching algorithms such as iterative closest point; Experimental results on synthetic and real databases illustrate how FGM outperforms state-of-the-art algorithms for GM. The code is available at http://humansensing.cs.cmu.edu/fgm.
Toussaint, Paule-Joanne; Maiz, Sofiane; Coynel, David; Doyon, Julien; Messé, Arnaud; de Souza, Leonardo Cruz; Sarazin, Marie; Perlbarg, Vincent; Habert, Marie-Odile; Benali, Habib
2014-11-01
Cognitive decline in normal ageing and Alzheimer's disease (AD) emerges from functional disruption in the coordination of large-scale brain systems sustaining cognition. Integrity of these systems can be examined by correlation methods based on analysis of resting state functional magnetic resonance imaging (fMRI). Here we investigate functional connectivity within the default mode network (DMN) in normal ageing and AD using resting state fMRI. Images from young and elderly controls, and patients with AD were processed using spatial independent component analysis to identify the DMN. Functional connectivity was quantified using integration and indices derived from graph theory. Four DMN sub-systems were identified: Frontal (medial and superior), parietal (precuneus-posterior cingulate, lateral parietal), temporal (medial temporal), and hippocampal (bilateral). There was a decrease in antero-posterior interactions (lower global efficiency), but increased interactions within the frontal and parietal sub-systems (higher local clustering) in elderly compared to young controls. This decreased antero-posterior integration was more pronounced in AD patients compared to elderly controls, particularly in the precuneus-posterior cingulate region. Conjoint knowledge of integration measures and graph indices in the same data helps in the interpretation of functional connectivity results, as comprehension of one measure improves with understanding of the other. The approach allows for complete characterisation of connectivity changes and could be applied to other resting state networks and different pathologies. Copyright © 2014 Elsevier Inc. All rights reserved.
Typed lambda-terms in categorical attributed graph transformation
Directory of Open Access Journals (Sweden)
Bertrand Boisvert
2011-06-01
Full Text Available This paper deals with model transformation based on attributed graph rewriting. Our contribution investigates a single pushout approach for applying the rewrite rules. The computation of graph attributes is obtained through the use of typed lambda-calculus with inductive types. In this paper we present solutions to cope with single pushout construction for the graph structure and the computations functions. As this rewrite system uses inductive types, the expressiveness of attribute computations is facilitated and appears more efficient than the one based on Sigma-algebras. Some examples showing the interest of our computation approach are described in this paper.
Self-stabilizing mutual exclusion on directed graphs
D. Alstein; J.H. Hoepman (Jaap-Henk); B.E. Olivier; P.I.A. van der Put
1995-01-01
textabstractThis paper investigates the complexity of self-stabilizing mutual exclusion protocols for distributed systems, where processors communicate through shared memory according to a strongly connected directed communication graph. Tchuente's approach of covering a network with one directed
Directory of Open Access Journals (Sweden)
Unil Yun
2016-05-01
Full Text Available Frequent graph mining has been proposed to find interesting patterns (i.e., frequent sub-graphs from databases composed of graph transaction data, which can effectively express complex and large data in the real world. In addition, various applications for graph mining have been suggested. Traditional graph pattern mining methods use a single minimum support threshold factor in order to check whether or not mined patterns are interesting. However, it is not a sufficient factor that can consider valuable characteristics of graphs such as graph sizes and features of graph elements. That is, previous methods cannot consider such important characteristics in their mining operations since they only use a fixed minimum support threshold in the mining process. For this reason, in this paper, we propose a novel graph mining algorithm that can consider various multiple, minimum support constraints according to the types of graph elements and changeable minimum support conditions, depending on lengths of graph patterns. In addition, the proposed algorithm performs in mining operations more efficiently because it can minimize duplicated operations and computational overheads by considering symmetry features of graphs. Experimental results provided in this paper demonstrate that the proposed algorithm outperforms previous mining approaches in terms of pattern generation, runtime and memory usage.
Modeling flow and transport in fracture networks using graphs
Karra, S.; O'Malley, D.; Hyman, J. D.; Viswanathan, H. S.; Srinivasan, G.
2018-03-01
Fractures form the main pathways for flow in the subsurface within low-permeability rock. For this reason, accurately predicting flow and transport in fractured systems is vital for improving the performance of subsurface applications. Fracture sizes in these systems can range from millimeters to kilometers. Although modeling flow and transport using the discrete fracture network (DFN) approach is known to be more accurate due to incorporation of the detailed fracture network structure over continuum-based methods, capturing the flow and transport in such a wide range of scales is still computationally intractable. Furthermore, if one has to quantify uncertainty, hundreds of realizations of these DFN models have to be run. To reduce the computational burden, we solve flow and transport on a graph representation of a DFN. We study the accuracy of the graph approach by comparing breakthrough times and tracer particle statistical data between the graph-based and the high-fidelity DFN approaches, for fracture networks with varying number of fractures and degree of heterogeneity. Due to our recent developments in capabilities to perform DFN high-fidelity simulations on fracture networks with large number of fractures, we are in a unique position to perform such a comparison. We show that the graph approach shows a consistent bias with up to an order of magnitude slower breakthrough when compared to the DFN approach. We show that this is due to graph algorithm's underprediction of the pressure gradients across intersections on a given fracture, leading to slower tracer particle speeds between intersections and longer travel times. We present a bias correction methodology to the graph algorithm that reduces the discrepancy between the DFN and graph predictions. We show that with this bias correction, the graph algorithm predictions significantly improve and the results are very accurate. The good accuracy and the low computational cost, with O (104) times lower times than
Graphs cospectral with a friendship graph or its complement
Directory of Open Access Journals (Sweden)
Alireza Abdollahi
2013-12-01
Full Text Available Let $n$ be any positive integer and let $F_n$ be the friendship (or Dutch windmill graph with $2n+1$ vertices and $3n$ edges. Here we study graphs with the same adjacency spectrum as the $F_n$. Two graphs are called cospectral if the eigenvalues multiset of their adjacency matrices are the same. Let $G$ be a graph cospectral with $F_n$. Here we prove that if $G$ has no cycle of length $4$ or $5$, then $Gcong F_n$. Moreover if $G$ is connected and planar then $Gcong F_n$.All but one of connected components of $G$ are isomorphic to $K_2$.The complement $overline{F_n}$ of the friendship graph is determined by its adjacency eigenvalues, that is, if $overline{F_n}$ is cospectral with a graph $H$, then $Hcong overline{F_n}$.
Query optimization for graph analytics on linked data using SPARQL
Energy Technology Data Exchange (ETDEWEB)
Hong, Seokyong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Sangkeun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lim, Seung -Hwan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sukumar, Sreenivas R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Vatsavai, Ranga Raju [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
2015-07-01
Triplestores that support query languages such as SPARQL are emerging as the preferred and scalable solution to represent data and meta-data as massive heterogeneous graphs using Semantic Web standards. With increasing adoption, the desire to conduct graph-theoretic mining and exploratory analysis has also increased. Addressing that desire, this paper presents a solution that is the marriage of Graph Theory and the Semantic Web. We present software that can analyze Linked Data using graph operations such as counting triangles, finding eccentricity, testing connectedness, and computing PageRank directly on triple stores via the SPARQL interface. We describe the process of optimizing performance of the SPARQL-based implementation of such popular graph algorithms by reducing the space-overhead, simplifying iterative complexity and removing redundant computations by understanding query plans. Our optimized approach shows significant performance gains on triplestores hosted on stand-alone workstations as well as hardware-optimized scalable supercomputers such as the Cray XMT.
X-Graphs: Language and Algorithms for Heterogeneous Graph Streams
2017-09-01
parallel implementations for many key graph algorithms, conversions between tables and graphs and Python language bindings. SNAP is widely deployed...1. We have used Delite to develop a suite of DSLs for data analysis (query processing, machine learning , and graph processing). Approved for Public...range of users, interested in network analysis: support for Python - a major programming language for data scientists, documentation, tutorials, and
Fast construction of voxel-level functional connectivity graphs.
Loewe, Kristian; Grueschow, Marcus; Stoppel, Christian M; Kruse, Rudolf; Borgelt, Christian
2014-06-19
Graph-based analysis of fMRI data has recently emerged as a promising approach to study brain networks. Based on the assessment of synchronous fMRI activity at separate brain sites, functional connectivity graphs are constructed and analyzed using graph-theoretical concepts. Most previous studies investigated region-level graphs, which are computationally inexpensive, but bring along the problem of choosing sensible regions and involve blurring of more detailed information. In contrast, voxel-level graphs provide the finest granularity attainable from the data, enabling analyses at superior spatial resolution. They are, however, associated with considerable computational demands, which can render high-resolution analyses infeasible. In response, many existing studies investigating functional connectivity at the voxel-level reduced the computational burden by sacrificing spatial resolution. Here, a novel, time-efficient method for graph construction is presented that retains the original spatial resolution. Performance gains are instead achieved through data reduction in the temporal domain based on dichotomization of voxel time series combined with tetrachoric correlation estimation and efficient implementation. By comparison with graph construction based on Pearson's r, the technique used by the majority of previous studies, we find that the novel approach produces highly similar results an order of magnitude faster. Its demonstrated performance makes the proposed approach a sensible and efficient alternative to customary practice. An open source software package containing the created programs is freely available for download.
GOGrapher: A Python library for GO graph representation and analysis.
Muller, Brian; Richards, Adam J; Jin, Bo; Lu, Xinghua
2009-07-07
The Gene Ontology is the most commonly used controlled vocabulary for annotating proteins. The concepts in the ontology are organized as a directed acyclic graph, in which a node corresponds to a biological concept and a directed edge denotes the parent-child semantic relationship between a pair of terms. A large number of protein annotations further create links between proteins and their functional annotations, reflecting the contemporary knowledge about proteins and their functional relationships. This leads to a complex graph consisting of interleaved biological concepts and their associated proteins. What is needed is a simple, open source library that provides tools to not only create and view the Gene Ontology graph, but to analyze and manipulate it as well. Here we describe the development and use of GOGrapher, a Python library that can be used for the creation, analysis, manipulation, and visualization of Gene Ontology related graphs. An object-oriented approach was adopted to organize the hierarchy of the graphs types and associated classes. An Application Programming Interface is provided through which different types of graphs can be pragmatically created, manipulated, and visualized. GOGrapher has been successfully utilized in multiple research projects, e.g., a graph-based multi-label text classifier for protein annotation. The GOGrapher project provides a reusable programming library designed for the manipulation and analysis of Gene Ontology graphs. The library is freely available for the scientific community to use and improve.
Improving Attack Graph Visualization through Data Reduction and Attack Grouping
Energy Technology Data Exchange (ETDEWEB)
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.
GOGrapher: A Python library for GO graph representation and analysis
Directory of Open Access Journals (Sweden)
Lu Xinghua
2009-07-01
Full Text Available Abstract Background The Gene Ontology is the most commonly used controlled vocabulary for annotating proteins. The concepts in the ontology are organized as a directed acyclic graph, in which a node corresponds to a biological concept and a directed edge denotes the parent-child semantic relationship between a pair of terms. A large number of protein annotations further create links between proteins and their functional annotations, reflecting the contemporary knowledge about proteins and their functional relationships. This leads to a complex graph consisting of interleaved biological concepts and their associated proteins. What is needed is a simple, open source library that provides tools to not only create and view the Gene Ontology graph, but to analyze and manipulate it as well. Here we describe the development and use of GOGrapher, a Python library that can be used for the creation, analysis, manipulation, and visualization of Gene Ontology related graphs. Findings An object-oriented approach was adopted to organize the hierarchy of the graphs types and associated classes. An Application Programming Interface is provided through which different types of graphs can be pragmatically created, manipulated, and visualized. GOGrapher has been successfully utilized in multiple research projects, e.g., a graph-based multi-label text classifier for protein annotation. Conclusion The GOGrapher project provides a reusable programming library designed for the manipulation and analysis of Gene Ontology graphs. The library is freely available for the scientific community to use and improve.
Gallerani, Luigi
2015-01-01
Abstract The CERN Technical Network (TN) TN was intended to be a network for accelerator and infrastructure operations. However, today, more than 60 million IP packets are routed every hour between the General Purpose Network (GPN) and the TN, involving more than 6000 different hosts. In order to improve the security of the accelerator control system, it is fundamental to understand the network traffic between the two networks and to define new appropriate routing and firewall rules without impacting operations. The complexity and huge size of the infrastructure and the number of protocols and services involved, have discouraged for years any attempt to understand and control the network traffic between the GPN and the TN. In this paper, we show a new way to solve the problem graphically. Combining the network traffic analysis with the use of large graph visualization algorithms we produced usable 2D large color topology maps of the network identifying the inter-relations of the control system machines and s...
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
Graphs Theory and Applications
Fournier, Jean-Claude
2008-01-01
This book provides a pedagogical and comprehensive introduction to graph theory and its applications. It contains all the standard basic material and develops significant topics and applications, such as: colorings and the timetabling problem, matchings and the optimal assignment problem, and Hamiltonian cycles and the traveling salesman problem, to name but a few. Exercises at various levels are given at the end of each chapter, and a final chapter presents a few general problems with hints for solutions, thus providing the reader with the opportunity to test and refine their knowledge on the
Directory of Open Access Journals (Sweden)
Porcheron F.
2013-03-01
Full Text Available Amine scrubbing is usually considered as the most efficient technology for CO2 mitigation through postcombustion Carbon Capture and Storage (CCS. However, optimization of the amine structure to improve the solvent properties requires to sample a large number of possible candidates and hence to gather a large amount of experimental data. In this context, the use of QSAR (Quantitative Structure Activity Relationship statistical modeling is a powerful tool as it performs a mapping of a set of input vectors (i.e. the characteristics or the properties of the molecules under consideration to a set of output vectors (i.e. their targeted properties. In this work, we used a high throughput screening experimental device to measure CO2 solubility data on a set of 46 amine aqueous solutions. Absorption isotherms are represented using a thermodynamic model based on two thermodynamic constants, pKa* and pKc* , accounting for the main chemical reactions occurring in the liquid phase between amine and CO2. Then, we used a statistical approach named Graph Machines at the same time to cluster the molecules and to model the variation of the acidity constant pKa* as a function of the molecular structure. The originality of our approach is the use of graphs to represent molecules in multidimensional spaces and simultaneously construct predictive models of their physicochemical properties based on these graphs. This approach is applied in this paper to predict the thermodynamic properties of a set of 5 new molecules. Le procédé d’absorption aux amines est considéré comme la technologie la plus efficace pour limiter les rejets de CO2 dans le cadre du captage en postcombustion puis du stockage du CO2. Cependant, l’optimisation des propriétés du solvant nécessite d’évaluer un grand nombre de candidats potentiels et donc de collecter une quantité importante de propriétés expérimentales. Dans ce contexte, l’utilisation de méthodes de mod
Nested Dynamic Condition Response Graphs
DEFF Research Database (Denmark)
Hildebrandt, Thomas; Mukkamala, Raghava Rao; Slaats, Tijs
2012-01-01
We present an extension of the recently introduced declarative process model Dynamic Condition Response Graphs ( DCR Graphs) to allow nested subgraphs and a new milestone relation between events. The extension was developed during a case study carried out jointly with our industrial partner...... Exformatics, a danish provider of case and workflow management systems. We formalize the semantics by giving first a map from Nested to (flat) DCR Graphs with milestones, and then extending the previously given mapping from DCR Graphs to Buchi-automata to include the milestone relation....
Spectral partitioning in equitable graphs.
Barucca, Paolo
2017-06-01
Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous. An exact solution to graph partitioning for two equal-sized communities is proposed and verified numerically, and a conjecture on the absence of an efficient recovery detectability transition in equitable graphs is suggested. A final discussion summarizes results and outlines their relevance for the solution of graph partitioning problems in other graph ensembles, in particular for the study of detectability thresholds and resolution limits in stochastic block models.
Qualitative Comparison of Graph-Based and Logic-Based Multi-Relational Data Mining: A Case Study
National Research Council Canada - National Science Library
Ketkar, Nikhil S; Holder, Lawrence B; Cook, Diane J
2005-01-01
The goal of this paper is to generate insights about the differences between graph-based and logic-based approaches to multi-relational data mining by performing a case study of the graph-based system...
BootGraph: probabilistic fiber tractography using bootstrap algorithms and graph theory.
Vorburger, Robert S; Reischauer, Carolin; Boesiger, Peter
2013-02-01
Bootstrap methods have recently been introduced to diffusion-weighted magnetic resonance imaging to estimate the measurement uncertainty of ensuing diffusion parameters directly from the acquired data without the necessity to assume a noise model. These methods have been previously combined with deterministic streamline tractography algorithms to allow for the assessment of connection probabilities in the human brain. Thereby, the local noise induced disturbance in the diffusion data is accumulated additively due to the incremental progression of streamline tractography algorithms. Graph based approaches have been proposed to overcome this drawback of streamline techniques. For this reason, the bootstrap method is in the present work incorporated into a graph setup to derive a new probabilistic fiber tractography method, called BootGraph. The acquired data set is thereby converted into a weighted, undirected graph by defining a vertex in each voxel and edges between adjacent vertices. By means of the cone of uncertainty, which is derived using the wild bootstrap, a weight is thereafter assigned to each edge. Two path finding algorithms are subsequently applied to derive connection probabilities. While the first algorithm is based on the shortest path approach, the second algorithm takes all existing paths between two vertices into consideration. Tracking results are compared to an established algorithm based on the bootstrap method in combination with streamline fiber tractography and to another graph based algorithm. The BootGraph shows a very good performance in crossing situations with respect to false negatives and permits incorporating additional constraints, such as a curvature threshold. By inheriting the advantages of the bootstrap method and graph theory, the BootGraph method provides a computationally efficient and flexible probabilistic tractography setup to compute connection probability maps and virtual fiber pathways without the drawbacks of
Community detection by graph Voronoi diagrams
Deritei, Dávid; Lázár, Zsolt I.; Papp, István; Járai-Szabó, Ferenc; Sumi, Róbert; Varga, Levente; Ravasz Regan, Erzsébet; Ercsey-Ravasz, Mária
2014-06-01
Accurate and efficient community detection in networks is a key challenge for complex network theory and its applications. The problem is analogous to cluster analysis in data mining, a field rich in metric space-based methods. Common to these methods is a geometric, distance-based definition of clusters or communities. Here we propose a new geometric approach to graph community detection based on graph Voronoi diagrams. Our method serves as proof of principle that the definition of appropriate distance metrics on graphs can bring a rich set of metric space-based clustering methods to network science. We employ a simple edge metric that reflects the intra- or inter-community character of edges, and a graph density-based rule to identify seed nodes of Voronoi cells. Our algorithm outperforms most network community detection methods applicable to large networks on benchmark as well as real-world networks. In addition to offering a computationally efficient alternative for community detection, our method opens new avenues for adapting a wide range of data mining algorithms to complex networks from the class of centroid- and density-based clustering methods.
Bodner, Todd E.
2016-01-01
This article revisits how the end points of plotted line segments should be selected when graphing interactions involving a continuous target predictor variable. Under the standard approach, end points are chosen at ±1 or 2 standard deviations from the target predictor mean. However, when the target predictor and moderator are correlated or the…
Energy Technology Data Exchange (ETDEWEB)
Maunz, Peter Lukas Wilhelm [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sterk, Jonathan David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lobser, Daniel [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Parekh, Ojas D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ryan-Anderson, Ciaran [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2016-01-01
In recent years, advanced network analytics have become increasingly important to na- tional security with applications ranging from cyber security to detection and disruption of ter- rorist networks. While classical computing solutions have received considerable investment, the development of quantum algorithms to address problems, such as data mining of attributed relational graphs, is a largely unexplored space. Recent theoretical work has shown that quan- tum algorithms for graph analysis can be more efficient than their classical counterparts. Here, we have implemented a trapped-ion-based two-qubit quantum information proces- sor to address these goals. Building on Sandia's microfabricated silicon surface ion traps, we have designed, realized and characterized a quantum information processor using the hyperfine qubits encoded in two 171 Yb + ions. We have implemented single qubit gates using resonant microwave radiation and have employed Gate set tomography (GST) to characterize the quan- tum process. For the first time, we were able to prove that the quantum process surpasses the fault tolerance thresholds of some quantum codes by demonstrating a diamond norm distance of less than 1 . 9 x 10 [?] 4 . We used Raman transitions in order to manipulate the trapped ions' motion and realize two-qubit gates. We characterized the implemented motion sensitive and insensitive single qubit processes and achieved a maximal process infidelity of 6 . 5 x 10 [?] 5 . We implemented the two-qubit gate proposed by Molmer and Sorensen and achieved a fidelity of more than 97 . 7%.
ILIGRA : An Efficient Inverse Line Graph Algorithm
Liu, D.; Trajanovski, S.; Van Mieghem, P.
2014-01-01
This paper presents a new and efficient algorithm, ILIGRA, for inverse line graph construction. Given a line graph H, ILIGRA constructs its root graph G with the time complexity being linear in the number of nodes in H. If ILIGRA does not know whether the given graph H is a line graph, it firstly
On Graph Rewriting, Reduction and Evaluation
DEFF Research Database (Denmark)
Zerny, Ian
2010-01-01
We inter-derive two prototypical styles of graph reduction: reduction machines à la Turner and graph rewriting systems à la Barendregt et al. To this end, we adapt Danvy et al.'s mechanical program derivations from the world of terms to the world of graphs. We also outline how to inter......-derive a third style of graph reduction: a graph evaluator....
ON BIPOLAR SINGLE VALUED NEUTROSOPHIC GRAPHS
Broumi, Said; Talea, Mohamed; Bakali, Assia; Smarandache, Florentin
2016-01-01
In this article, we combine the concept of bipolar neutrosophic set and graph theory. We introduce the notions of bipolar single valued neutrosophic graphs, strong bipolar single valued neutrosophic graphs, complete bipolar single valued neutrosophic graphs, regular bipolar single valued neutrosophic graphs and investigate some of their related properties.
Kirchhoff index of graphs and some graph operations
Indian Academy of Sciences (India)
We define the -repetition of to be the graph obtained by joining y i to x j for each i ∈ V ( T ) and each child of . In this paper, we compute the Kirchhoff index of the -repetition of in terms of parameters of and . Also we study how K f ( G ) behaves under some graph operations such as joining vertices or ...
Quantum Probability and Spectral Analysis of Graphs
Hora, Akihito
2007-01-01
This is the first book to comprehensively cover the quantum probabilistic approach to spectral analysis of graphs. This approach has been developed by the authors and has become an interesting research area in applied mathematics and physics. The book can be used as a concise introduction to quantum probability from an algebraic aspect. Here readers will learn several powerful methods and techniques of wide applicability, which have been recently developed under the name of quantum probability. The exercises at the end of each chapter help to deepen understanding. Among the topics discussed along the way are: quantum probability and orthogonal polynomials; asymptotic spectral theory (quantum central limit theorems) for adjacency matrices; the method of quantum decomposition; notions of independence and structure of graphs; and asymptotic representation theory of the symmetric groups.
Graph Theory. 2. Vertex Descriptors and Graph Coloring
Directory of Open Access Journals (Sweden)
Lorentz JÄNTSCHI
2002-12-01
Full Text Available This original work presents the construction of a set of ten sequence matrices and their applications for ordering vertices in graphs. For every sequence matrix three ordering criteria are applied: lexicographic ordering, based on strings of numbers, corresponding to every vertex, extracted as rows from sequence matrices; ordering by the sum of path lengths from a given vertex; and ordering by the sum of paths, starting from a given vertex. We also examine a graph that has different orderings for the above criteria. We then proceed to demonstrate that every criterion induced its own partition of graph vertex. We propose the following theoretical result: both LAVS and LVDS criteria generate identical partitioning of vertices in any graph. Finally, a coloring of graph vertices according to introduced ordering criteria was proposed.
Calculating Graph Algorithms for Dominance and Shortest Path
DEFF Research Database (Denmark)
Sergey, Ilya; Midtgaard, Jan; Clarke, Dave
2012-01-01
We calculate two iterative, polynomial-time graph algorithms from the literature: a dominance algorithm and an algorithm for the single-source shortest path problem. Both algorithms are calculated directly from the definition of the properties by fixed-point fusion of (1) a least fixed point...... expressing all finite paths through a directed graph and (2) Galois connections that capture dominance and path length. The approach illustrates that reasoning in the style of fixed-point calculus extends gracefully to the domain of graph algorithms. We thereby bridge common practice from the school...
Infinitary term graph rewriting is simple, sound and complete
DEFF Research Database (Denmark)
Bahr, Patrick
2012-01-01
Based on a simple metric and a simple partial order on term graphs, we develop two infinitary calculi of term graph rewriting. We show that, similarly to infinitary term rewriting, the partial order formalisation yields a conservative extension of the metric formalisation of the calculus. By show....... By showing that the resulting calculi simulate the corresponding well-established infinitary calculi of term rewriting in a sound and complete manner, we argue for the appropriateness of our approach to capture the notion of infinitary term graph rewriting....
Yu, Qingbao; Du, Yuhui; Chen, Jiayu; He, Hao; Sui, Jing; Pearlson, Godfrey; Calhoun, Vince D
2017-11-01
A key challenge in building a brain graph using fMRI data is how to define the nodes. Spatial brain components estimated by independent components analysis (ICA) and regions of interest (ROIs) determined by brain atlas are two popular methods to define nodes in brain graphs. It is difficult to evaluate which method is better in real fMRI data. Here we perform a simulation study and evaluate the accuracies of a few graph metrics in graphs with nodes of ICA components, ROIs, or modified ROIs in four simulation scenarios. Graph measures with ICA nodes are more accurate than graphs with ROI nodes in all cases. Graph measures with modified ROI nodes are modulated by artifacts. The correlations of graph metrics across subjects between graphs with ICA nodes and ground truth are higher than the correlations between graphs with ROI nodes and ground truth in scenarios with large overlapped spatial sources. Moreover, moving the location of ROIs would largely decrease the correlations in all scenarios. Evaluating graphs with different nodes is promising in simulated data rather than real data because different scenarios can be simulated and measures of different graphs can be compared with a known ground truth. Since ROIs defined using brain atlas may not correspond well to real functional boundaries, overall findings of this work suggest that it is more appropriate to define nodes using data-driven ICA than ROI approaches in real fMRI data. Copyright © 2017 Elsevier B.V. All rights reserved.
Drawing Large Graphs by Multilevel Maxent-Stress Optimization.
Meyerhenke, Henning; Nollenburg, Martin; Schulz, Christian
2017-03-29
Drawing large graphs appropriately is an important step for the visual analysis of data from real-world networks. Here we present a novel multilevel algorithm to compute a graph layout with respect to the maxent-stress metric proposed by Gansner et al. (2013) that combines layout stress and entropy. As opposed to previous work, we do not solve the resulting linear systems of the maxent-stress metric with a typical numerical solver. Instead we use a simple local iterative scheme within a multilevel approach. To accelerate local optimization, we approximate long-range forces and use shared-memory parallelism. Our experiments validate the high potential of our approach, which is particularly appealing for dynamic graphs. In comparison to the previously best maxent-stress optimizer, which is sequential, our parallel implementation is on average 30 times faster already for static graphs (and still faster if executed on a single thread) while producing a comparable solution quality.
Chordal Graphs and Semidefinite Optimization
DEFF Research Database (Denmark)
Vandenberghe, Lieven; Andersen, Martin Skovgaard
2015-01-01
Chordal graphs play a central role in techniques for exploiting sparsity in large semidefinite optimization problems and in related con-vex optimization problems involving sparse positive semidefinite matrices. Chordal graph properties are also fundamental to several classical results in combinat...
DYNAMICALLY MAINTAINING THE VISIBILITY GRAPH
VEGTER, G
1991-01-01
An algorithm is presented to maintain the visibility graph of a set of N line segments in the plane in O(log2 N + K log N) time, where K is the total number of arcs of the visibility graph that are destroyed or created upon insertion or deletion of a line segment. The line segments should be
A cluster algorithm for graphs
S. van Dongen
2000-01-01
textabstractA cluster algorithm for graphs called the emph{Markov Cluster algorithm (MCL~algorithm) is introduced. The algorithm provides basically an interface to an algebraic process defined on stochastic matrices, called the MCL~process. The graphs may be both weighted (with nonnegative weight)
The planar cubic Cayley graphs
Georgakopoulos, Agelos
2018-01-01
The author obtains a complete description of the planar cubic Cayley graphs, providing an explicit presentation and embedding for each of them. This turns out to be a rich class, comprising several infinite families. He obtains counterexamples to conjectures of Mohar, Bonnington and Watkins. The author's analysis makes the involved graphs accessible to computation, corroborating a conjecture of Droms.
The planar cubic cayley graphs
Georgakopoulos, Agelos
2018-01-01
The author obtains a complete description of the planar cubic Cayley graphs, providing an explicit presentation and embedding for each of them. This turns out to be a rich class, comprising several infinite families. He obtains counterexamples to conjectures of Mohar, Bonnington and Watkins. The author's analysis makes the involved graphs accessible to computation, corroborating a conjecture of Droms.
Hoede, C.; Liu, X
1998-01-01
In continuation of the paper of Hoede and Li on word graphs for a set of prepositions, word graphs are given for adjectives, adverbs and Chinese classifier words. It is argued that these three classes of words belong to a general class of words that may be called adwords. These words express the
2005-06-01
relationship, trust, etc.) between people. • User Psychology : Clickstream graphs are bipartite graphs connecting Internet users to the websites they visit...document groups (say, science fiction novels and thrillers ), based on the word groups that occur most frequently in them. A user who prefers one
Bell inequalities for graph states
International Nuclear Information System (INIS)
Toth, G.; Hyllus, P.; Briegel, H.J.; Guehne, O.
2005-01-01
Full text: In the last years graph states have attracted an increasing interest in the field of quantum information theory. Graph states form a family of multi-qubit states which comprises many popular states such as the GHZ states and the cluster states. They also play an important role in applications. For instance, measurement based quantum computation uses graph states as resources. From a theoretical point of view, it is remarkable that graph states allow for a simple description in terms of stabilizing operators. In this contribution, we investigate the non-local properties of graph states. We derive a family of Bell inequalities which require three measurement settings for each party and are maximally violated by graph states. In turn, any graph state violates at least one of the inequalities. We show that for certain types of graph states the violation of these inequalities increases exponentially with the number of qubits. We also discuss connections to other entanglement properties such as the positively of the partial transpose or the geometric measure of entanglement. (author)
Submanifolds weakly associated with graphs
Indian Academy of Sciences (India)
theory by defining submanifolds weakly associated with graphs. We prove that, in a local sense, every submanifold satisfies such an association, and other general results. Finally, we study submanifolds associated with graphs either in low dimensions or belonging to some special families. Keywords. Almost Hermitian ...
Subgraph Enumeration in Massive Graphs
DEFF Research Database (Denmark)
Silvestri, Francesco
We consider the problem of enumerating all instances of a given sample graph in a large data graph. Our focus is on determining the input/output (I/O) complexity of this problem. Let $E$ be the number of edges in the data graph, $k=\\BO{1}$ be the number of vertexes in the sample graph, $B......$ be the block length, and $M$ be the main memory size. The main result of the paper is a randomized algorithm that enumerates all instances of the sample graph in $\\BO{E^{k/2}/\\left(BM^{k/2-1}\\right)}$ expected I/Os if the maximum vertex degree of the data graph is $\\sqrt{EM}$. Under some assumptions, the same...... bound also applies with high probability. Our algorithm is I/O optimal, in the worst-case, when the sample graph belongs to the Alon class, which includes cliques, cycles and every graph with a perfect matching: indeed, we show that any algorithm enumerating $T$ instances must always use $\\BOM...
Xu, Zhiqiang
2017-02-16
Attributed graph clustering, also known as community detection on attributed graphs, attracts much interests recently due to the ubiquity of attributed graphs in real life. Many existing algorithms have been proposed for this problem, which are either distance based or model based. However, model selection in attributed graph clustering has not been well addressed, that is, most existing algorithms assume the cluster number to be known a priori. In this paper, we propose two efficient approaches for attributed graph clustering with automatic model selection. The first approach is a popular Bayesian nonparametric method, while the second approach is an asymptotic method based on a recently proposed model selection criterion, factorized information criterion. Experimental results on both synthetic and real datasets demonstrate that our approaches for attributed graph clustering with automatic model selection significantly outperform the state-of-the-art algorithm.
A Collection of Features for Semantic Graphs
Energy Technology Data Exchange (ETDEWEB)
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.
Directory of Open Access Journals (Sweden)
Marco Raberto
Full Text Available 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.
RJSplot: Interactive Graphs with R.
Barrios, David; Prieto, Carlos
2018-03-01
Data visualization techniques provide new methods for the generation of interactive graphs. These graphs allow a better exploration and interpretation of data but their creation requires advanced knowledge of graphical libraries. Recent packages have enabled the integration of interactive graphs in R. However, R provides limited graphical packages that allow the generation of interactive graphs for computational biology applications. The present project has joined the analytical power of R with the interactive graphical features of JavaScript in a new R package (RJSplot). It enables the easy generation of interactive graphs in R, provides new visualization capabilities, and contributes to the advance of computational biology analytical methods. At present, 16 interactive graphics are available in RJSplot, such as the genome viewer, Manhattan plots, 3D plots, heatmaps, dendrograms, networks, and so on. The RJSplot package is freely available online at http://rjsplot.net. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Quantum chaos on discrete graphs
Energy Technology Data Exchange (ETDEWEB)
Smilansky, Uzy [Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100 (Israel); Isaac Newton Institute for Mathematical Sciences, 20 Clarkson Road, Cambridge CB3 0EH (United Kingdom)
2007-07-06
Adapting a method developed for the study of quantum chaos on quantum (metric) graphs (Kottos and Smilansky 1997 Phys. Rev. Lett. 79 4794, Kottos and Smilansky 1999 Ann. Phys., NY 274 76), spectral {zeta} functions and trace formulae for discrete Laplacians on graphs are derived. This is achieved by expressing the spectral secular equation in terms of the periodic orbits of the graph and obtaining functions which belong to the class of {zeta} functions proposed originally by Ihara (1966 J. Mat. Soc. Japan 18 219) and expanded by subsequent authors (Stark and Terras 1996 Adv. Math. 121 124, Kotani and Sunada 2000 J. Math. Sci. Univ. Tokyo 7 7). Finally, a model of 'classical dynamics' on the discrete graph is proposed. It is analogous to the corresponding classical dynamics derived for quantum graphs (Kottos and Smilansky 1997 Phys. Rev. Lett. 79 4794, Kottos and Smilansky 1999 Ann. Phys., NY 274 76). (fast track communication)
Directory of Open Access Journals (Sweden)
I. Sahul Hamid
2016-07-01
Full Text Available A set D of vertices of a graph G is called a dominating set of G if every vertex in V(G−D is adjacent to a vertex in D. A dominating set S such that the subgraph 〈S〉 induced by S has at least one isolated vertex is called an isolate dominating set. An isolate dominating set none of whose proper subset is an isolate dominating set is a minimal isolate dominating set. The minimum and maximum cardinality of a minimal isolate dominating set are called the isolate domination number γ0 and the upper isolate domination number Γ0 respectively. In this paper we initiate a study on these parameters.
Environmental evolutionary graph theory.
Maciejewski, Wes; Puleo, Gregory J
2014-11-07
Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have received relatively less attention. Here we present a structured population model where different individuals are best suited to different regions of their environment. The underlying structure is a graph: individuals occupy vertices, which are connected by edges. If an individual is suited for their vertex, they receive an increase in fecundity. This framework allows attention to be restricted to the spatial arrangement of suitable habitat. We prove some basic properties of this model and find some counter-intuitive results. Notably, (1) the arrangement of suitable sites is as important as their proportion, and (2) decreasing the proportion of suitable sites may result in a decrease in the fixation time of an allele. Copyright © 2014 Elsevier Ltd. All rights reserved.
Word Similarity from Dictionaries: Inferring Fuzzy Measures from Fuzzy Graphs
Directory of Open Access Journals (Sweden)
Vicenc Torra
2008-01-01
Full Text Available WORD SIMILARITY FROM DICTIONARIES: INFERRING FUZZY MEASURES FROM FUZZY GRAPHS The computation of similarities between words is a basic element of information retrieval systems, when retrieval is not solely based on word matching. In this work we consider a measure between words based on dictionaries. This is achieved assuming that a dictionary is formalized as a fuzzy graph. We show that the approach permits to compute measures not only for pairs of words but for sets of them.
Graph embedding with rich information through heterogeneous graph
Sun, Guolei
2017-11-12
Graph embedding, aiming to learn low-dimensional representations for nodes in graphs, has attracted increasing attention due to its critical application including node classification, link prediction and clustering in social network analysis. Most existing algorithms for graph embedding only rely on the topology information and fail to use the copious information in nodes as well as edges. As a result, their performance for many tasks may not be satisfactory. In this thesis, we proposed a novel and general framework for graph embedding with rich text information (GERI) through constructing a heterogeneous network, in which we integrate node and edge content information with graph topology. Specially, we designed a novel biased random walk to explore the constructed heterogeneous network with the notion of flexible neighborhood. Our sampling strategy can compromise between BFS and DFS local search on heterogeneous graph. To further improve our algorithm, we proposed semi-supervised GERI (SGERI), which learns graph embedding in an discriminative manner through heterogeneous network with label information. The efficacy of our method is demonstrated by extensive comparison experiments with 9 baselines over multi-label and multi-class classification on various datasets including Citeseer, Cora, DBLP and Wiki. It shows that GERI improves the Micro-F1 and Macro-F1 of node classification up to 10%, and SGERI improves GERI by 5% in Wiki.
Max-plus algebraic throughput analysis of synchronous dataflow graphs
de Groote, Robert; Kuper, Jan; Broersma, Haitze J.; Smit, Gerardus Johannes Maria
2012-01-01
In this paper we present a novel approach to throughput analysis of synchronous dataflow (SDF) graphs. Our approach is based on describing the evolution of actor firing times as a linear time-invariant system in max-plus algebra. Experimental results indicate that our approach is faster than
On some properties of doughnut graphs
Directory of Open Access Journals (Sweden)
Md. Rezaul Karim
2016-08-01
Full Text Available The class of doughnut graphs is a subclass of 5-connected planar graphs. It is known that a doughnut graph admits a straight-line grid drawing with linear area, the outerplanarity of a doughnut graph is 3, and a doughnut graph is k-partitionable. In this paper we show that a doughnut graph exhibits a recursive structure. We also give an efficient algorithm for finding a shortest path between any pair of vertices in a doughnut graph. We also propose a nice application of a doughnut graph based on its properties.
Completeness and regularity of generalized fuzzy graphs.
Samanta, Sovan; Sarkar, Biswajit; Shin, Dongmin; Pal, Madhumangal
2016-01-01
Fuzzy graphs are the backbone of many real systems like networks, image, scheduling, etc. But, due to some restriction on edges, fuzzy graphs are limited to represent for some systems. Generalized fuzzy graphs are appropriate to avoid such restrictions. In this study generalized fuzzy graphs are introduced. In this study, matrix representation of generalized fuzzy graphs is described. Completeness and regularity are two important parameters of graph theory. Here, regular and complete generalized fuzzy graphs are introduced. Some properties of them are discussed. After that, effective regular graphs are exemplified.
Comparison and Enumeration of Chemical Graphs
Akutsu, Tatsuya; Nagamochi, Hiroshi
2013-01-01
Chemical compounds are usually represented as graph structured data in computers. In this review article, we overview several graph classes relevant to chemical compounds and the computational complexities of several fundamental problems for these graph classes. In particular, we consider the following problems: determining whether two chemical graphs are identical, determining whether one input chemical graph is a part of the other input chemical graph, finding a maximum common part of two input graphs, finding a reaction atom mapping, enumerating possible chemical graphs, and enumerating stereoisomers. We also discuss the relationship between the fifth problem and kernel functions for chemical compounds. PMID:24688697
Zhao, Jian; Glueck, Michael; Breslav, Simon; Chevalier, Fanny; Khan, Azam
2017-01-01
User-authored annotations of data can support analysts in the activity of hypothesis generation and sensemaking, where it is not only critical to document key observations, but also to communicate insights between analysts. We present annotation graphs, a dynamic graph visualization that enables meta-analysis of data based on user-authored annotations. The annotation graph topology encodes annotation semantics, which describe the content of and relations between data selections, comments, and tags. We present a mixed-initiative approach to graph layout that integrates an analyst's manual manipulations with an automatic method based on similarity inferred from the annotation semantics. Various visual graph layout styles reveal different perspectives on the annotation semantics. Annotation graphs are implemented within C8, a system that supports authoring annotations during exploratory analysis of a dataset. We apply principles of Exploratory Sequential Data Analysis (ESDA) in designing C8, and further link these to an existing task typology in the visualization literature. We develop and evaluate the system through an iterative user-centered design process with three experts, situated in the domain of analyzing HCI experiment data. The results suggest that annotation graphs are effective as a method of visually extending user-authored annotations to data meta-analysis for discovery and organization of ideas.
Hierarchy of modular graph identities
Energy Technology Data Exchange (ETDEWEB)
D’Hoker, Eric; Kaidi, Justin [Mani L. Bhaumik Institute for Theoretical Physics, Department of Physics and Astronomy,University of California,Los Angeles, CA 90095 (United States)
2016-11-09
The low energy expansion of Type II superstring amplitudes at genus one is organized in terms of modular graph functions associated with Feynman graphs of a conformal scalar field on the torus. In earlier work, surprising identities between two-loop graphs at all weights, and between higher-loop graphs of weights four and five were constructed. In the present paper, these results are generalized in two complementary directions. First, all identities at weight six and all dihedral identities at weight seven are obtained and proven. Whenever the Laurent polynomial at the cusp is available, the form of these identities confirms the pattern by which the vanishing of the Laurent polynomial governs the full modular identity. Second, the family of modular graph functions is extended to include all graphs with derivative couplings and worldsheet fermions. These extended families of modular graph functions are shown to obey a hierarchy of inhomogeneous Laplace eigenvalue equations. The eigenvalues are calculated analytically for the simplest infinite sub-families and obtained by Maple for successively more complicated sub-families. The spectrum is shown to consist solely of eigenvalues s(s−1) for positive integers s bounded by the weight, with multiplicities which exhibit rich representation-theoretic patterns.
Identifying vertex covers in graphs
DEFF Research Database (Denmark)
Henning, Michael A.; Yeo, Anders
2012-01-01
An identifying vertex cover in a graph G is a subset T of vertices in G that has a nonempty intersection with every edge of G such that T distinguishes the edges, that is, e∩T ≠ 0 for every edge e in G and e∩T ≠ f∩T for every two distinct edges e and f in G. The identifying vertex cover number TD......(G) of G is the minimum size of an identifying vertex cover in G. We observe that TD(G)+ρ(G) = |V (G)|, where ρ(G) denotes the packing number of G. We conjecture that if G is a graph of order n and size m with maximum degree Δ, then TD(G) ≤(Δ(Δ-1)/ Δ2+1)n + (2/Δ2+1) m. If the conjecture is true......, then the bound is best possible for all Δ ≥ 1. We prove this conjecture when Δ ≥ 1 and G is a Δ-regular graph. The three known Moore graphs of diameter 2, namely the 5-cycle, the Petersen graph and the Hoffman-Singleton graph, are examples of regular graphs that achieves equality in the upper bound. We also...
Mizan: Optimizing Graph Mining in Large Parallel Systems
Kalnis, Panos
2012-03-01
Extracting information from graphs, from nding shortest paths to complex graph mining, is essential for many ap- plications. Due to the shear size of modern graphs (e.g., social networks), processing must be done on large paral- lel computing infrastructures (e.g., the cloud). Earlier ap- proaches relied on the MapReduce framework, which was proved inadequate for graph algorithms. More recently, the message passing model (e.g., Pregel) has emerged. Although the Pregel model has many advantages, it is agnostic to the graph properties and the architecture of the underlying com- puting infrastructure, leading to suboptimal performance. In this paper, we propose Mizan, a layer between the users\\' code and the computing infrastructure. Mizan considers the structure of the input graph and the architecture of the in- frastructure in order to: (i) decide whether it is bene cial to generate a near-optimal partitioning of the graph in a pre- processing step, and (ii) choose between typical point-to- point message passing and a novel approach that puts com- puting nodes in a virtual overlay ring. We deployed Mizan on a small local Linux cluster, on the cloud (256 virtual machines in Amazon EC2), and on an IBM Blue Gene/P supercomputer (1024 CPUs). We show that Mizan executes common algorithms on very large graphs 1-2 orders of mag- nitude faster than MapReduce-based implementations and up to one order of magnitude faster than implementations relying on Pregel-like hash-based graph partitioning.
Graph theoretical model of a sensorimotor connectome in zebrafish.
Directory of Open Access Journals (Sweden)
Michael Stobb
Full Text Available Mapping the detailed connectivity patterns (connectomes of neural circuits is a central goal of neuroscience. The best quantitative approach to analyzing connectome data is still unclear but graph theory has been used with success. We present a graph theoretical model of the posterior lateral line sensorimotor pathway in zebrafish. The model includes 2,616 neurons and 167,114 synaptic connections. Model neurons represent known cell types in zebrafish larvae, and connections were set stochastically following rules based on biological literature. Thus, our model is a uniquely detailed computational representation of a vertebrate connectome. The connectome has low overall connection density, with 2.45% of all possible connections, a value within the physiological range. We used graph theoretical tools to compare the zebrafish connectome graph to small-world, random and structured random graphs of the same size. For each type of graph, 100 randomly generated instantiations were considered. Degree distribution (the number of connections per neuron varied more in the zebrafish graph than in same size graphs with less biological detail. There was high local clustering and a short average path length between nodes, implying a small-world structure similar to other neural connectomes and complex networks. The graph was found not to be scale-free, in agreement with some other neural connectomes. An experimental lesion was performed that targeted three model brain neurons, including the Mauthner neuron, known to control fast escape turns. The lesion decreased the number of short paths between sensory and motor neurons analogous to the behavioral effects of the same lesion in zebrafish. This model is expandable and can be used to organize and interpret a growing database of information on the zebrafish connectome.
XML Graphs in Program Analysis
DEFF Research Database (Denmark)
Møller, Anders; Schwartzbach, Michael I.
2011-01-01
XML graphs have shown to be a simple and effective formalism for representing sets of XML documents in program analysis. It has evolved through a six year period with variants tailored for a range of applications. We present a unified definition, outline the key properties including validation...... of XML graphs against different XML schema languages, and provide a software package that enables others to make use of these ideas. We also survey the use of XML graphs for program analysis with four very different languages: XACT (XML in Java), Java Servlets (Web application programming), XSugar...... (transformations between XML and non-XML data), and XSLT (stylesheets for transforming XML documents)....
Kirchhoff index of graphs and some graph operations
Indian Academy of Sciences (India)
Abstract. Let T be a rooted tree, G a connected graph, x,y ∈ V(G) be fixed and Gi's be |V(T )| disjoint copies of G with xi and yi denoting the corresponding copies of x and y in Gi, respectively. We define the T -repetition of G to be the graph obtained by joining yi to xj for each i ∈ V(T ) and each child j of i. In this paper, we ...
Parallel Algorithms for Graph Optimization using Tree Decompositions
Energy Technology Data Exchange (ETDEWEB)
Sullivan, Blair D [ORNL; Weerapurage, Dinesh P [ORNL; Groer, Christopher S [ORNL
2012-06-01
Although many $\\cal{NP}$-hard graph optimization problems can be solved in polynomial time on graphs of bounded tree-width, the adoption of these techniques into mainstream scientific computation has been limited due to the high memory requirements of the necessary dynamic programming tables and excessive runtimes of sequential implementations. This work addresses both challenges by proposing a set of new parallel algorithms for all steps of a tree decomposition-based approach to solve the maximum weighted independent set problem. A hybrid OpenMP/MPI implementation includes a highly scalable parallel dynamic programming algorithm leveraging the MADNESS task-based runtime, and computational results demonstrate scaling. This work enables a significant expansion of the scale of graphs on which exact solutions to maximum weighted independent set can be obtained, and forms a framework for solving additional graph optimization problems with similar techniques.
A Graph Based Backtracking Algorithm for Solving General CSPs
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.
Bond graph model-based fault diagnosis of hybrid systems
Borutzky, Wolfgang
2015-01-01
This book presents a bond graph model-based approach to fault diagnosis in mechatronic systems appropriately represented by a hybrid model. The book begins by giving a survey of the fundamentals of fault diagnosis and failure prognosis, then recalls state-of-art developments referring to latest publications, and goes on to discuss various bond graph representations of hybrid system models, equations formulation for switched systems, and simulation of their dynamic behavior. The structured text: • focuses on bond graph model-based fault detection and isolation in hybrid systems; • addresses isolation of multiple parametric faults in hybrid systems; • considers system mode identification; • provides a number of elaborated case studies that consider fault scenarios for switched power electronic systems commonly used in a variety of applications; and • indicates that bond graph modelling can also be used for failure prognosis. In order to facilitate the understanding of fault diagnosis and the presented...
Hyperspectral image classification through bilayer graph-based learning.
Gao, Yue; Ji, Rongrong; Cui, Peng; Dai, Qionghai; Hua, Gang
2014-07-01
Hyperspectral image classification with limited number of labeled pixels is a challenging task. In this paper, we propose a bilayer graph-based learning framework to address this problem. For graph-based classification, how to establish the neighboring relationship among the pixels from the high dimensional features is the key toward a successful classification. Our graph learning algorithm contains two layers. The first-layer constructs a simple graph, where each vertex denotes one pixel and the edge weight encodes the similarity between two pixels. Unsupervised learning is then conducted to estimate the grouping relations among different pixels. These relations are subsequently fed into the second layer to form a hypergraph structure, on top of which, semisupervised transductive learning is conducted to obtain the final classification results. Our experiments on three data sets demonstrate the merits of our proposed approach, which compares favorably with state of the art.
Fracture and Fragmentation of Simplicial Finite Elements Meshes using Graphs
Energy Technology Data Exchange (ETDEWEB)
Mota, A; Knap, J; Ortiz, M
2006-10-18
An approach for the topological representation of simplicial finite element meshes as graphs is presented. It is shown that by using a graph, the topological changes induced by fracture reduce to a few, local kernel operations. The performance of the graph representation is demonstrated and analyzed, using as reference the 3D fracture algorithm by Pandolfi and Ortiz [22]. It is shown that the graph representation initializes in O(N{sub E}{sup 1.1}) time and fractures in O(N{sub I}{sup 1.0}) time, while the reference implementation requires O(N{sub E}{sup 2.1}) time to initialize and O(N{sub I}{sup 1.9}) time to fracture, where NE is the number of elements in the mesh and N{sub I} is the number of interfaces to fracture.
Multiple Illuminant Colour Estimation via Statistical Inference on Factor Graphs.
Mutimbu, Lawrence; Robles-Kelly, Antonio
2016-08-31
This paper presents a method to recover a spatially varying illuminant colour estimate from scenes lit by multiple light sources. Starting with the image formation process, we formulate the illuminant recovery problem in a statistically datadriven setting. To do this, we use a factor graph defined across the scale space of the input image. In the graph, we utilise a set of illuminant prototypes computed using a data driven approach. As a result, our method delivers a pixelwise illuminant colour estimate being devoid of libraries or user input. The use of a factor graph also allows for the illuminant estimates to be recovered making use of a maximum a posteriori (MAP) inference process. Moreover, we compute the probability marginals by performing a Delaunay triangulation on our factor graph. We illustrate the utility of our method for pixelwise illuminant colour recovery on widely available datasets and compare against a number of alternatives. We also show sample colour correction results on real-world images.
Scalable force directed graph layout algorithms using fast multipole methods
Yunis, Enas Abdulrahman
2012-06-01
We present an extension to ExaFMM, a Fast Multipole Method library, as a generalized approach for fast and scalable execution of the Force-Directed Graph Layout algorithm. The Force-Directed Graph Layout algorithm is a physics-based approach to graph layout that treats the vertices V as repelling charged particles with the edges E connecting them acting as springs. Traditionally, the amount of work required in applying the Force-Directed Graph Layout algorithm is O(|V|2 + |E|) using direct calculations and O(|V| log |V| + |E|) using truncation, filtering, and/or multi-level techniques. Correct application of the Fast Multipole Method allows us to maintain a lower complexity of O(|V| + |E|) while regaining most of the precision lost in other techniques. Solving layout problems for truly large graphs with millions of vertices still requires a scalable algorithm and implementation. We have been able to leverage the scalability and architectural adaptability of the ExaFMM library to create a Force-Directed Graph Layout implementation that runs efficiently on distributed multicore and multi-GPU architectures. © 2012 IEEE.
Entropy and the Complexity of Graphs Revisited
Directory of Open Access Journals (Sweden)
Matthias Dehmer
2012-03-01
Full Text Available This paper presents a taxonomy and overview of approaches to the measurement of graph and network complexity. The taxonomy distinguishes between deterministic (e.g., Kolmogorov complexity and probabilistic approaches with a view to placing entropy-based probabilistic measurement in context. Entropy-based measurement is the main focus of the paper. Relationships between the different entropy functions used to measure complexity are examined; and intrinsic (e.g., classical measures and extrinsic (e.g., Körner entropy variants of entropy-based models are discussed in some detail.
Application-Specific Graph Sampling for Frequent Subgraph Mining and Community Detection
Energy Technology Data Exchange (ETDEWEB)
Purohit, Sumit; Choudhury, Sutanay; Holder, Lawrence B.
2017-12-11
Graph mining is an important data analysis methodology, but struggles as the input graph size increases. The scalability and usability challenges posed by such large graphs make it imperative to sample the input graph and reduce its size. The critical challenge in sampling is to identify the appropriate algorithm to insure the resulting analysis does not suffer heavily from the data reduction. Predicting the expected performance degradation for a given graph and sampling algorithm is also useful. In this paper, we present different sampling approaches for graph mining applications such as Frequent Subgrpah Mining (FSM), and Community Detection (CD). We explore graph metrics such as PageRank, Triangles, and Diversity to sample a graph and conclude that for heterogeneous graphs Triangles and Diversity perform better than degree based metrics. We also present two new sampling variations for targeted graph mining applications. We present empirical results to show that knowledge of the target application, along with input graph properties can be used to select the best sampling algorithm. We also conclude that performance degradation is an abrupt, rather than gradual phenomena, as the sample size decreases. We present the empirical results to show that the performance degradation follows a logistic function.
Open Graphs and Computational Reasoning
Directory of Open Access Journals (Sweden)
Lucas Dixon
2010-06-01
Full Text Available We present a form of algebraic reasoning for computational objects which are expressed as graphs. Edges describe the flow of data between primitive operations which are represented by vertices. These graphs have an interface made of half-edges (edges which are drawn with an unconnected end and enjoy rich compositional principles by connecting graphs along these half-edges. In particular, this allows equations and rewrite rules to be specified between graphs. Particular computational models can then be encoded as an axiomatic set of such rules. Further rules can be derived graphically and rewriting can be used to simulate the dynamics of a computational system, e.g. evaluating a program on an input. Examples of models which can be formalised in this way include traditional electronic circuits as well as recent categorical accounts of quantum information.
Submanifolds weakly associated with graphs
Indian Academy of Sciences (India)
Leuven: Katholieke Universiteit Leuven). (1990). [5] Etayo F, On quasi-slant submanifolds of an almost Hermitian manifold, Publ. Math. Debrecen 53 (1998) 217–223. [6] Harary F, Graph Theory (Reading: Addison-Wesley) (1972). [7] Papaghiuc N ...
Graph anomalies in cyber communications
Energy Technology Data Exchange (ETDEWEB)
Vander Wiel, Scott A [Los Alamos National Laboratory; Storlie, Curtis B [Los Alamos National Laboratory; Sandine, Gary [Los Alamos National Laboratory; Hagberg, Aric A [Los Alamos National Laboratory; Fisk, Michael [Los Alamos National Laboratory
2011-01-11
Enterprises monitor cyber traffic for viruses, intruders and stolen information. Detection methods look for known signatures of malicious traffic or search for anomalies with respect to a nominal reference model. Traditional anomaly detection focuses on aggregate traffic at central nodes or on user-level monitoring. More recently, however, traffic is being viewed more holistically as a dynamic communication graph. Attention to the graph nature of the traffic has expanded the types of anomalies that are being sought. We give an overview of several cyber data streams collected at Los Alamos National Laboratory and discuss current work in modeling the graph dynamics of traffic over the network. We consider global properties and local properties within the communication graph. A method for monitoring relative entropy on multiple correlated properties is discussed in detail.
A contribution to queens graphs
DEFF Research Database (Denmark)
Barat, Janos
A graph $G$ is a queens graph if the vertices of $G$ can be mapped to queens on the chessboard such that two vertices are adjacent if and only if the corresponding queens attack each other, i.e. they are in horizontal, vertical or diagonal position. We prove a conjecture of Beineke, Broere...... and Henning that the Cartesian product of an odd cycle and a path is a queens graph. We show that the same does not hold for two odd cycles. % is not representable in the same way. The representation of the Cartesian product of an odd cycle and an even cycle remains an open problem. We also prove...... constructively that any finite subgraph of the grid or the hexagonal grid is a queens graph....
SOUR graphs for efficient completion
Lynch, Christopher; Strogova, Polina
1998-01-01
International audience; We introduce a data structure called \\emphSOUR graphs and present an efficient Knuth-Bendix completion procedure based on it. \\emphSOUR graphs allow for a maximal structure sharing of terms in rewriting systems. The term representation is a dag representation, except that edges are labelled with equational constraints and variable renamings. The rewrite rules correspond to rewrite edges, the unification problems to unification edges. The Critical Pair and Simplificatio...
Rectilinear Graphs and Angular Resolution
Bodlaender, H.L.; Tel, G.
2003-01-01
In this note we show that a planar graph with angular resolution at least π/2 can be drawn with all angles an integer multiple of π/2, that is, in a rectilinear manner. Moreover, we show that for d ≠ 4, d › 2, having an angular resolution of 2π/d does not imply that the graph can be drawn with all
On dominator colorings in graphs
Indian Academy of Sciences (India)
A dominator coloring of a graph G is a proper coloring of G in which every vertex dominates every vertex of at least one color class. The minimum number of colors required for a dominator coloring of G is called the dominator chromatic number of G and is denoted by χd(G). In this paper we present several results on graphs ...
a generalization of total graphs
Indian Academy of Sciences (India)
8
Abstract. Let R be a commutative ring with nonzero identity, Ln(R) be the set of all lower triangular n × n matrices, and U be a triangular subset of. Rn i.e. the product of any lower triangular matrix with the transpose of any element of U, belongs to U. The graph GTn. U (Rn) is a simple graph whose ver- tices consists of all ...
Port-Hamiltonian Systems on Open Graphs
Schaft, A.J. van der; Maschke, B.M.
2010-01-01
In this talk we discuss how to define in an intrinsic manner port-Hamiltonian dynamics on open graphs. Open graphs are graphs where some of the vertices are boundary vertices (terminals), which allow interconnection with other systems. We show that a directed graph carries two natural Dirac
On Graph Rewriting, Reduction and Evaluation
DEFF Research Database (Denmark)
Zerny, Ian
2009-01-01
We inter-derive two prototypical styles of graph reduction: reduction machines à la Turner and graph rewriting systems à la Barendregt. To this end, we adapt Danvy et al.'s mechanical program derivations from the world of terms to the world of graphs. We also inter-derive a graph evaluator....
Graphs with branchwidth at most three
Bodlaender, H.L.; Thilikos, D.M.
1997-01-01
In this paper we investigate both the structure of graphs with branchwidth at most three, as well as algorithms to recognise such graphs. We show that a graph has branchwidth at most three, if and only if it has treewidth at most three and does not contain the three-dimensional binary cube graph
A faithful functor among algebras and graphs
Falcón Ganfornina, Óscar Jesús; Falcón Ganfornina, Raúl Manuel; Núñez Valdés, Juan; Pacheco Martínez, Ana María; Villar Liñán, María Trinidad; Vigo Aguiar, Jesús (Coordinador)
2016-01-01
The problem of identifying a functor between the categories of algebras and graphs is currently open. Based on a known algorithm that identifies isomorphisms of Latin squares with isomorphism of vertex-colored graphs, we describe here a pair of graphs that enable us to find a faithful functor between finite-dimensional algebras over finite fields and these graphs.
Constructing Dense Graphs with Unique Hamiltonian Cycles
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…
Hard graphs for the maximum clique problem
Hoede, C.
1988-01-01
The maximum clique problem is one of the NP-complete problems. There are graphs for which a reduction technique exists that transforms the problem for these graphs into one for graphs with specific properties in polynomial time. The resulting graphs do not grow exponentially in order and number.
Frog: Asynchronous Graph Processing on GPU with Hybrid Coloring Model
Energy Technology Data Exchange (ETDEWEB)
Shi, Xuanhua; Luo, Xuan; Liang, Junling; Zhao, Peng; Di, Sheng; He, Bingsheng; Jin, Hai
2018-01-01
GPUs have been increasingly used to accelerate graph processing for complicated computational problems regarding graph theory. Many parallel graph algorithms adopt the asynchronous computing model to accelerate the iterative convergence. Unfortunately, the consistent asynchronous computing requires locking or atomic operations, leading to significant penalties/overheads when implemented on GPUs. As such, coloring algorithm is adopted to separate the vertices with potential updating conflicts, guaranteeing the consistency/correctness of the parallel processing. Common coloring algorithms, however, may suffer from low parallelism because of a large number of colors generally required for processing a large-scale graph with billions of vertices. We propose a light-weight asynchronous processing framework called Frog with a preprocessing/hybrid coloring model. The fundamental idea is based on Pareto principle (or 80-20 rule) about coloring algorithms as we observed through masses of realworld graph coloring cases. We find that a majority of vertices (about 80%) are colored with only a few colors, such that they can be read and updated in a very high degree of parallelism without violating the sequential consistency. Accordingly, our solution separates the processing of the vertices based on the distribution of colors. In this work, we mainly answer three questions: (1) how to partition the vertices in a sparse graph with maximized parallelism, (2) how to process large-scale graphs that cannot fit into GPU memory, and (3) how to reduce the overhead of data transfers on PCIe while processing each partition. We conduct experiments on real-world data (Amazon, DBLP, YouTube, RoadNet-CA, WikiTalk and Twitter) to evaluate our approach and make comparisons with well-known non-preprocessed (such as Totem, Medusa, MapGraph and Gunrock) and preprocessed (Cusha) approaches, by testing four classical algorithms (BFS, PageRank, SSSP and CC). On all the tested applications and
Exploratory Item Classification Via Spectral Graph Clustering.
Chen, Yunxiao; Li, Xiaoou; Liu, Jingchen; Xu, Gongjun; Ying, Zhiliang
2017-01-01
Large-scale assessments are supported by a large item pool. An important task in test development is to assign items into scales that measure different characteristics of individuals, and a popular approach is cluster analysis of items. Classical methods in cluster analysis, such as the hierarchical clustering, K-means method, and latent-class analysis, often induce a high computational overhead and have difficulty handling missing data, especially in the presence of high-dimensional responses. In this article, the authors propose a spectral clustering algorithm for exploratory item cluster analysis. The method is computationally efficient, effective for data with missing or incomplete responses, easy to implement, and often outperforms traditional clustering algorithms in the context of high dimensionality. The spectral clustering algorithm is based on graph theory, a branch of mathematics that studies the properties of graphs. The algorithm first constructs a graph of items, characterizing the similarity structure among items. It then extracts item clusters based on the graphical structure, grouping similar items together. The proposed method is evaluated through simulations and an application to the revised Eysenck Personality Questionnaire.
Citation graph based ranking in Invenio
Marian, Ludmila; Rajman, Martin; Vesely, Martin
2010-01-01
Invenio is the web-based integrated digital library system developed at CERN. Within this framework, we present four types of ranking models based on the citation graph that complement the simple approach based on citation counts: time-dependent citation counts, a relevancy ranking which extends the PageRank model, a time-dependent ranking which combines the freshness of citations with PageRank and a ranking that takes into consideration the external citations. We present our analysis and results obtained on two main data sets: Inspire and CERN Document Server. Our main contributions are: (i) a study of the currently available ranking methods based on the citation graph; (ii) the development of new ranking methods that correct some of the identified limitations of the current methods such as treating all citations of equal importance, not taking time into account or considering the citation graph complete; (iii) a detailed study of the key parameters for these ranking methods. (The original publication is ava...
Graph Quasicontinuous Functions and Densely Continuous Forms
Directory of Open Access Journals (Sweden)
Lubica Hola
2017-07-01
Full Text Available Let $X, Y$ be topological spaces. A function $f: X \\to Y$ is said to be graph quasicontinuous if there is a quasicontinuous function $g: X \\to Y$ with the graph of $g$ contained in the closure of the graph of $f$. There is a close relation between the notions of graph quasicontinuous functions and minimal usco maps as well as the notions of graph quasicontinuous functions and densely continuous forms. Every function with values in a compact Hausdorff space is graph quasicontinuous; more generally every locally compact function is graph quasicontinuous.
On P-transitive graphs and applications
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Giacomo Lenzi
2011-06-01
Full Text Available We introduce a new class of graphs which we call P-transitive graphs, lying between transitive and 3-transitive graphs. First we show that the analogue of de Jongh-Sambin Theorem is false for wellfounded P-transitive graphs; then we show that the mu-calculus fixpoint hierarchy is infinite for P-transitive graphs. Both results contrast with the case of transitive graphs. We give also an undecidability result for an enriched mu-calculus on P-transitive graphs. Finally, we consider a polynomial time reduction from the model checking problem on arbitrary graphs to the model checking problem on P-transitive graphs. All these results carry over to 3-transitive graphs.
Phage, Itumeleng B.; Lemmer, Miriam; Hitge, Mariette
2017-01-01
Students' graph comprehension may be affected by the background of the students who are the readers or interpreters of the graph, their knowledge of the context in which the graph is set, and the inferential processes required by the graph operation. This research study investigated these aspects of graph comprehension for 152 first year…
Geometry of Graph Edit Distance Spaces
Jain, Brijnesh J.
2015-01-01
In this paper we study the geometry of graph spaces endowed with a special class of graph edit distances. The focus is on geometrical results useful for statistical pattern recognition. The main result is the Graph Representation Theorem. It states that a graph is a point in some geometrical space, called orbit space. Orbit spaces are well investigated and easier to explore than the original graph space. We derive a number of geometrical results from the orbit space representation, translate ...
Directory of Open Access Journals (Sweden)
Luan Yihui
2009-09-01
Full Text Available Abstract Background Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks. Results Recent studies have shown that the degree distribution of the nodes is not an adequate statistic in many molecular networks. We sought to extend this statistic with 2nd and 3rd order degree correlations and developed a pseudo-likelihood approach to estimate the parameters. The approach was used to analyze the MIPS and BIOGRID yeast protein interaction networks, and two yeast coexpression networks. We showed that 2nd order degree correlation information gave better predictions of gene interactions in both protein interaction and gene coexpression networks. However, in the biologically important task of predicting functionally homogeneous modules, degree correlation information performs marginally better in the case of the MIPS and BIOGRID protein interaction networks, but worse in the case of gene coexpression networks. Conclusion Our use of dK models showed that incorporation of degree correlations could increase predictive power in some contexts, albeit sometimes marginally, but, in all contexts, the use of third-order degree correlations decreased accuracy. However, it is possible that other parameter estimation methods, such as maximum likelihood, will show the usefulness of incorporating 2nd and 3rd degree correlations in predicting functionally homogeneous modules.
Neuro-symbolic representation learning on biological knowledge graphs
Alshahrani, Mona
2017-04-21
Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge.We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of SemanticWeb based knowledge bases in biology to use in machine learning and data analytics.https://github.com/bio-ontology-research-group/walking-rdf-and-owl.robert.hoehndorf@kaust.edu.sa.Supplementary data are available at Bioinformatics online.
Bounds for percolation thresholds on directed and undirected graphs
Hamilton, Kathleen; Pryadko, Leonid
2015-03-01
Percolation theory is an efficient approach to problems with strong disorder, e.g., in quantum or classical transport, composite materials, and diluted magnets. Recently, the growing role of big data in scientific and industrial applications has led to a renewed interest in graph theory as a tool for describing complex connections in various kinds of networks: social, biological, technological, etc. In particular, percolation on graphs has been used to describe internet stability, spread of contagious diseases and computer viruses; related models describe market crashes and viral spread in social networks. We consider site-dependent percolation on directed and undirected graphs, and present several exact bounds for location of the percolation transition in terms of the eigenvalues of matrices associated with graphs, including the adjacency matrix and the Hashimoto matrix used to enumerate non-backtracking walks. These bounds correspond t0 a mean field approximation and become asymptotically exact for graphs with no short cycles. We illustrate this convergence numerically by simulating percolation on several families of graphs with different cycle lengths. This research was supported in part by the NSF Grant PHY-1416578 and by the ARO Grant W911NF-11-1-0027.
Neuro-symbolic representation learning on biological knowledge graphs.
Alshahrani, Mona; Khan, Mohammad Asif; Maddouri, Omar; Kinjo, Akira R; Queralt-Rosinach, Núria; Hoehndorf, Robert
2017-09-01
Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of Semantic Web based knowledge bases in biology to use in machine learning and data analytics. https://github.com/bio-ontology-research-group/walking-rdf-and-owl. robert.hoehndorf@kaust.edu.sa. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.
Predicting Treatment Relations with Semantic Patterns over Biomedical Knowledge Graphs.
Bakal, Gokhan; Kavuluru, Ramakanth
2015-12-01
Identifying new potential treatment options (say, medications and procedures) for known medical conditions that cause human disease burden is a central task of biomedical research. Since all candidate drugs cannot be tested with animal and clinical trials, in vitro approaches are first attempted to identify promising candidates. Even before this step, due to recent advances, in silico or computational approaches are also being employed to identify viable treatment options. Generally, natural language processing (NLP) and machine learning are used to predict specific relations between any given pair of entities using the distant supervision approach. In this paper, we report preliminary results on predicting treatment relations between biomedical entities purely based on semantic patterns over biomedical knowledge graphs. As such, we refrain from explicitly using NLP, although the knowledge graphs themselves may be built from NLP extractions. Our intuition is fairly straightforward - entities that participate in a treatment relation may be connected using similar path patterns in biomedical knowledge graphs extracted from scientific literature. Using a dataset of treatment relation instances derived from the well known Unified Medical Language System (UMLS), we verify our intuition by employing graph path patterns from a well known knowledge graph as features in machine learned models. We achieve a high recall (92 %) but precision, however, decreases from 95% to an acceptable 71% as we go from uniform class distribution to a ten fold increase in negative instances. We also demonstrate models trained with patterns of length ≤ 3 result in statistically significant gains in F-score over those trained with patterns of length ≤ 2. Our results show the potential of exploiting knowledge graphs for relation extraction and we believe this is the first effort to employ graph patterns as features for identifying biomedical relations.
High-performance analysis of filtered semantic graphs
Energy Technology Data Exchange (ETDEWEB)
Buluc, Aydin [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Fox, Armando [Univ. of California, Berkeley, CA (United States); Gilbert, John R. [Univ. of California, Santa Barbara, CA (United States); Kamil, Shoaib A. [Univ. of California, Berkeley, CA (United States); Lugowski, Adam [Univ. of California, Santa Barbara, CA (United States); Oliker, Leonid [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Williams, Samuel W. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
2012-01-01
High performance is a crucial consideration when executing a complex analytic query on a massive semantic graph. In a semantic graph, vertices and edges carry "attributes" of various types. Analytic queries on semantic graphs typically depend on the values of these attributes; thus, the computation must either view the graph through a filter that passes only those individual vertices and edges of interest, or else must first materialize a subgraph or subgraphs consisting of only the vertices and edges of interest. The filtered approach is superior due to its generality, ease of use, and memory efficiency, but may carry a performance cost. In the Knowledge Discovery Toolbox (KDT), a Python library for parallel graph computations, the user writes filters in a high-level language, but those filters result in relatively low performance due to the bottleneck of having to call into the Python interpreter for each edge. In this work, we use the Selective Embedded JIT Specialization (SEJITS) approach to automatically translate filters defined by programmers into a lower-level efficiency language, bypassing the upcall into Python. We evaluate our approach by comparing it with the high-performance C++ /MPI Combinatorial BLAS engine, and show that the productivity gained by using a high-level filtering language comes without sacrificing performance.
Graph based techniques for tag cloud generation
DEFF Research Database (Denmark)
Leginus, Martin; Dolog, Peter; Lage, Ricardo Gomes
2013-01-01
Tag cloud is one of the navigation aids for exploring documents. Tag cloud also link documents through the user defined terms. We explore various graph based techniques to improve the tag cloud generation. Moreover, we introduce relevance measures based on underlying data such as ratings...... or citation counts for improved measurement of relevance of tag clouds. We show, that on the given data sets, our approach outperforms the state of the art baseline methods with respect to such relevance by 41 % on Movielens dataset and by 11 % on Bibsonomy data set....
Directory of Open Access Journals (Sweden)
Andreas P. Braun
2016-04-01
Full Text Available Box graphs succinctly and comprehensively characterize singular fibers of elliptic fibrations in codimension two and three, as well as flop transitions connecting these, in terms of representation theoretic data. We develop a framework that provides a systematic map between a box graph and a crepant algebraic resolution of the singular elliptic fibration, thus allowing an explicit construction of the fibers from a singular Weierstrass or Tate model. The key tool is what we call a fiber face diagram, which shows the relevant information of a (partial toric triangulation and allows the inclusion of more general algebraic blowups. We shown that each such diagram defines a sequence of weighted algebraic blowups, thus providing a realization of the fiber defined by the box graph in terms of an explicit resolution. We show this correspondence explicitly for the case of SU(5 by providing a map between box graphs and fiber faces, and thereby a sequence of algebraic resolutions of the Tate model, which realizes each of the box graphs.
Hierarchical organisation of causal graphs
International Nuclear Information System (INIS)
Dziopa, P.
1993-01-01
This paper deals with the design of a supervision system using a hierarchy of models formed by graphs, in which the variables are the nodes and the causal relations between the variables of the arcs. To obtain a representation of the variables evolutions which contains only the relevant features of their real evolutions, the causal relations are completed with qualitative transfer functions (QTFs) which produce roughly the behaviour of the classical transfer functions. Major improvements have been made in the building of the hierarchical organization. First, the basic variables of the uppermost level and the causal relations between them are chosen. The next graph is built by adding intermediary variables to the upper graph. When the undermost graph has been built, the transfer functions parameters corresponding to its causal relations are identified. The second task consists in the upwelling of the information from the undermost graph to the uppermost one. A fusion procedure of the causal relations has been designed to compute the QFTs relevant for each level. This procedure aims to reduce the number of parameters needed to represent an evolution at a high level of abstraction. These techniques have been applied to the hierarchical modelling of nuclear process. (authors). 8 refs., 12 figs
Algorithms for Planar Graphs and Graphs in Metric Spaces
DEFF Research Database (Denmark)
Wulff-Nilsen, Christian
preprocessing time, an O(n log n) time algorithm for the replacement paths problem, and a min st-cut oracle with nearlinear preprocessing time. We also give improved time bounds for computing various graph invariants such as diameter and girth. In the second part, we consider stretch factor problems...... a graph with new edges while minimizing stretch factor. The third and final part of the thesis deals with the Steiner tree problem in the plane equipped with a weighted fixed orientation metric. Here, we give an improved theoretical analysis of the strength of pruning techniques applied by many Steiner...
Enthalpy-Entropy Compensation in the Binding of Modulators at Ionotropic Glutamate Receptor GluA2
DEFF Research Database (Denmark)
Krintel, Christian; Francotte, Pierre; Pickering, Darryl S
2016-01-01
The 1,2,4-benzothiadiazine 1,1-dioxide type of positive allosteric modulators of the ionotropic glutamate receptor A2 (GluA2) are promising lead compounds for the treatment of cognitive disorders, e.g., Alzheimer’s disease. The modulators bind in a cleft formed by the interface of two neighboring...
Ferrante, Andrea; Gorski, Jack
2012-01-01
Ligand binding is a thermodynamically cooperative process in many biochemical systems characterized by the conformational flexibility of the reactants. However the contribution of conformational entropy to cooperativity of ligation needs to be elucidated. Here we perform kinetic and thermodynamic analyses on a panel of cycle-mutated peptides, derived from influenza H3 HA306-319, interacting with wild type and a mutant HLA-DR. We observe that within a certain range of peptide affinity, this system shows isothermal entropy-enthalpy compensation (iEEC). The incremental increases in conformational entropy measured as disruptive mutations are added in the ligand or receptor are more than sufficient in magnitude to account for the experimentally observed lack of free energy decrease cooperativity. Beyond this affinity range, compensation is not observed, and therefore the ability of the residual interactions to form a stable complex decreases in an exponential fashion. Taken together, our results indicate that cooperativity and iEEC constitute the thermodynamic epiphenomena of the structural fluctuation that accompanies ligand/receptor complex formation in flexible systems. Therefore, ligand binding affinity prediction needs to consider how each source of binding energy contributes synergistically to the folding and kinetic stability of the complex in a process based on the trade-off between structural tightening and restraint of conformational mobility. PMID:22342886
Zhu, Tiantian; Zhang, Xiaoyan; Li, Zhikai; Hsu, Chih-Hao; Chen, Wei; Miyoshi, Toshikazu; Li, Xiaohong; Yang, Xiaoming; Tu, Yingfeng; Li, Christopher Y
2017-07-20
We present here that in two-dimensional (2D) fullerene supramolecular liquid crystals (SLCs), the phase diagram and lamella thickness of SLCs and 2D crystals can be tuned by the flexible alkyl tail and spacer length, due to their different effects on enthalpy and entropy changes during SLC formation.
Athawale, Manoj V; Sarupria, Sapna; Garde, Shekhar
2008-05-08
Salts and additives can significantly affect the strength of water-mediated interactions in solution. We present results from molecular dynamics simulations focused on the thermodynamics of hydrophobic hydration, association, and the folding-unfolding of a hydrophobic polymer in water and in aqueous solutions of NaCl and of an osmolyte trimethylamine oxide (TMAO). It is known that addition of NaCl makes the hydration of hydrophobic solutes unfavorable and, correspondingly, strengthens their association at the pair as well as the many-body level (Ghosh, T.; Kalra, A.; Garde, S. J. Phys. Chem. B 2005, 109, 642), whereas the osmolyte TMAO has an almost negligible effect on the hydrophobic hydration and association (Athawale, M. V.; Dordick, J. S.; Garde, S. Biophys. J. 2005, 89, 858). Whether these effects are enthalpic or entropic in origin is not fully known. Here we perform temperature-dependent simulations to resolve the free energy into entropy and enthalpy contributions. We find that in TMAO solutions, there is an almost precise entropy-enthalpy compensation leading to the negligible effect of TMAO on hydrophobic phenomena. In contrast, in NaCl solutions, changes in enthalpy dominate, making the salt-induced strengthening of hydrophobic interactions enthalpic in origin. The resolution of total enthalpy into solute-solvent and solvent-solvent terms further shows that enthalpy changes originate primarily from solvent-solvent energy terms. Our results are consistent with experimental data on the hydration of small hydrophobic solutes by Ben-Naim and Yaacobi (Ben-Naim, A.; Yaacobi, M. J. Phys. Chem. 1974, 78, 170). In combination with recent work by Zangi, Hagen, and Berne (Zangi, R.; Hagen, M.; Berne, B. J. J. Am. Chem. Soc. 2007, 129, 4678) and the experimental data on surface tensions of salt solutions by Matubayasi et al. (Matubayasi, N.; Matsuo, H.; Yamamoto, K.; Yamaguchi, S.; Matuzawa, A. J. Colloid Interface Sci. 1999, 209, 398), our results highlight interesting length scale dependences of salt effects on hydrophobic phenomena. Although NaCl strengthens hydrophobic interactions at both small and large length scales, that effect is enthalpy-dominated at small length scales and entropy-dominated for large solutes and interfaces. Our results have implications for understanding of additive effects on water-mediated interactions, as well as on biocompatibility of osmolyte molecules in aqueous solutions.
Procedural Content Graphs for Urban Modeling
Directory of Open Access Journals (Sweden)
Pedro Brandão Silva
2015-01-01
Full Text Available Massive procedural content creation, for example, for virtual urban environments, is a difficult, yet important challenge. While shape grammars are a popular example of effectiveness in architectural modeling, they have clear limitations regarding readability, manageability, and expressive power when addressing a variety of complex structural designs. Moreover, shape grammars aim at geometry specification and do not facilitate integration with other types of content, such as textures or light sources, which could rather accompany the generation process. We present procedural content graphs, a graph-based solution for procedural generation that addresses all these issues in a visual, flexible, and more expressive manner. Besides integrating handling of diverse types of content, this approach introduces collective entity manipulation as lists, seamlessly providing features such as advanced filtering, grouping, merging, ordering, and aggregation, essentially unavailable in shape grammars. Hereby, separated entities can be easily merged or just analyzed together in order to perform a variety of context-based decisions and operations. The advantages of this approach are illustrated via examples of tasks that are either very cumbersome or simply impossible to express with previous grammar approaches.
Graph methods for the investigation of metabolic networks in parasitology.
Cottret, Ludovic; Jourdan, Fabien
2010-08-01
Recently, a way was opened with the development of many mathematical methods to model and analyze genome-scale metabolic networks. Among them, methods based on graph models enable to us quickly perform large-scale analyses on large metabolic networks. However, it could be difficult for parasitologists to select the graph model and methods adapted to their biological questions. In this review, after briefly addressing the problem of the metabolic network reconstruction, we propose an overview of the graph-based approaches used in whole metabolic network analyses. Applications highlight the usefulness of this kind of approach in the field of parasitology, especially by suggesting metabolic targets for new drugs. Their development still represents a major challenge to fight against the numerous diseases caused by parasites.
Nodal Statistics on Quantum Graphs
Alon, Lior; Band, Ram; Berkolaiko, Gregory
2018-03-01
It has been suggested that the distribution of the suitably normalized number of zeros of Laplacian eigenfunctions contains information about the geometry of the underlying domain. We study this distribution (more precisely, the distribution of the "nodal surplus") for Laplacian eigenfunctions of a metric graph. The existence of the distribution is established, along with its symmetry. One consequence of the symmetry is that the graph's first Betti number can be recovered as twice the average nodal surplus of its eigenfunctions. Furthermore, for graphs with disjoint cycles it is proven that the distribution has a universal form—it is binomial over the allowed range of values of the surplus. To prove the latter result, we introduce the notion of a local nodal surplus and study its symmetry and dependence properties, establishing that the local nodal surpluses of disjoint cycles behave like independent Bernoulli variables.
Graph modeling systems and methods
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.
Feder, Tomás
2009-06-01
Results on graph turnpike problem without distinctness, including its NP-completeness, and an O(m+n log n) algorithm, is presented. The usual turnpike problem has all pairwise distances given, but does not specify which pair of vertices w e corresponds to. There are two other problems that can be viewed as special cases of the graph turnpike problem, including the bandwidth problem and the low-distortion graph embedding problem. The aim for the turnpike problem in the NP-complete is to orient the edges with weights w i in either direction so that when the whole cycle is transversed in the real line, it returns to a chosen starting point for the cycle. An instance of the turnpike problem with or without distinctness is uniquely mappable if there exists at most one solution up to translation and choice of orientation.
Negation switching invariant signed graphs
Directory of Open Access Journals (Sweden)
Deepa Sinha
2014-04-01
Full Text Available A signed graph (or, $sigraph$ in short is a graph G in which each edge x carries a value $\\sigma(x \\in \\{-, +\\}$ called its sign. Given a sigraph S, the negation $\\eta(S$ of the sigraph S is a sigraph obtained from S by reversing the sign of every edge of S. Two sigraphs $S_{1}$ and $S_{2}$ on the same underlying graph are switching equivalent if it is possible to assign signs `+' (`plus' or `-' (`minus' to vertices of $S_{1}$ such that by reversing the sign of each of its edges that has received opposite signs at its ends, one obtains $S_{2}$. In this paper, we characterize sigraphs which are negation switching invariant and also see for what sigraphs, S and $\\eta (S$ are signed isomorphic.
The fascinating world of graph theory
Benjamin, Arthur; Zhang, Ping
2015-01-01
Graph theory goes back several centuries and revolves around the study of graphs-mathematical structures showing relations between objects. With applications in biology, computer science, transportation science, and other areas, graph theory encompasses some of the most beautiful formulas in mathematics-and some of its most famous problems. The Fascinating World of Graph Theory explores the questions and puzzles that have been studied, and often solved, through graph theory. This book looks at graph theory's development and the vibrant individuals responsible for the field's growth. Introducin
An intersection graph of straight lines
DEFF Research Database (Denmark)
Thomassen, Carsten
2002-01-01
G. Ehrlich, S. Even, and R.E. Tarjan conjectured that the graph obtained from a complete 3 partite graph K4,4,4 by deleting the edges of four disjoint triangles is not the intersection graph of straight line segments in the plane. We show that it is.......G. Ehrlich, S. Even, and R.E. Tarjan conjectured that the graph obtained from a complete 3 partite graph K4,4,4 by deleting the edges of four disjoint triangles is not the intersection graph of straight line segments in the plane. We show that it is....
Graph-based modelling in engineering
Rysiński, Jacek
2017-01-01
This book presents versatile, modern and creative applications of graph theory in mechanical engineering, robotics and computer networks. Topics related to mechanical engineering include e.g. machine and mechanism science, mechatronics, robotics, gearing and transmissions, design theory and production processes. The graphs treated are simple graphs, weighted and mixed graphs, bond graphs, Petri nets, logical trees etc. The authors represent several countries in Europe and America, and their contributions show how different, elegant, useful and fruitful the utilization of graphs in modelling of engineering systems can be. .
Graph Processing on GPUs: A Survey
DEFF Research Database (Denmark)
Shi, Xuanhua; Zheng, Zhigao; Zhou, Yongluan
2018-01-01
In the big data era, much real-world data can be naturally represented as graphs. Consequently, many application domains can be modeled as graph processing. Graph processing, especially the processing of the large-scale graphs with the number of vertices and edges in the order of billions or even......, utilizing GPU to accelerate graph processing proves to be a promising solution. This article surveys the key issues of graph processing on GPUs, including data layout, memory access pattern, workload mapping, and specific GPU programming. In this article, we summarize the state-of-the-art research on GPU...
Exformatics Declarative Case Management Workflows as DCR Graphs
DEFF Research Database (Denmark)
Slaats, Tijs; Mukkamala, Raghava Rao; Hildebrandt, Thomas
2013-01-01
Declarative workflow languages have been a growing research subject over the past ten years, but applications of the declarative approach in industry are still uncommon. Over the past two years Exformatics A/S, a Danish provider of Electronic Case Management systems, has been cooperating with res......Declarative workflow languages have been a growing research subject over the past ten years, but applications of the declarative approach in industry are still uncommon. Over the past two years Exformatics A/S, a Danish provider of Electronic Case Management systems, has been cooperating...... with researchers at IT University of Copenhagen (ITU) to create tools for the declarative workflow language Dynamic Condition Response Graphs (DCR Graphs) and incorporate them into their products and in teaching at ITU. In this paper we give a status report over the work. We start with an informal introduction...... to DCR Graphs. We then show how DCR Graphs are being used by Exformatics to model workflows through a case study of an invoice workflow. Finally we give an overview of the tools that have been developed by Exformatics to support working with DCR Graphs and evaluate their use in capturing requirements...
Graph topologies on closed multifunctions
Directory of Open Access Journals (Sweden)
Giuseppe Di Maio
2003-10-01
Full Text Available In this paper we study function space topologies on closed multifunctions, i.e. closed relations on X x Y using various hypertopologies. The hypertopologies are in essence, graph topologies i.e topologies on functions considered as graphs which are subsets of X x Y . We also study several topologies, including one that is derived from the Attouch-Wets filter on the range. We state embedding theorems which enable us to generalize and prove some recent results in the literature with the use of known results in the hyperspace of the range space and in the function space topologies of ordinary functions.
XML Graphs in Program Analysis
DEFF Research Database (Denmark)
Møller, Anders; Schwartzbach, Michael Ignatieff
2007-01-01
XML graphs have shown to be a simple and effective formalism for representing sets of XML documents in program analysis. It has evolved through a six year period with variants tailored for a range of applications. We present a unified definition, outline the key properties including validation...... of XML graphs against different XML schema languages, and provide a software package that enables others to make use of these ideas. We also survey four very different applications: XML in Java, Java Servlets and JSP, transformations between XML and non-XML data, and XSLT....
Andersson, Mattias
2011-01-01
A star graph consists of a vertex to which a set of edges are connected. Such an object can be used to, among other things, model the electromagnetic properties of quantum wires. A scalar field theory is constructed on the star graph and its properties are investigated. It turns out that there exist Kirchoff's rules for the conserved charges in the system leading to restrictions of the possible type of boundary conditions at the vertex. Scale invariant boundary conditions are investigated in...
Completely Described Undirected Graph Structure
Directory of Open Access Journals (Sweden)
G. S. Ivanova
2016-01-01
Full Text Available The objects of research are undirected graphs. The paper considers a problem of their isomorphism. A literature analysis of its solution, has shown that there is no way to define a complete graph invariant in the form of unique structural characteristics of each its vertex, which has a computational complexity of definition better than О (n 4 .The work objective is to provide the characteristics of the graph structure, which could be used to solve the problem of their isomorphism for a time better than О (n 4 . As such characteristics, the paper proposes to use the set of codes of tree roots of all the shortest - in terms of the number of edges - paths from each vertex to the others, uniquely defining the structure of each tree. It proves the theorem that it is possible to reduce the problem of isomorphism of the undirected graphs to the isomorphism problem of their splitting into the trees of all the shortest - in terms of the number of edges - paths of each vertex to the others. An algorithm to construct the shortest paths from each vertex to all others and to compute codes of their vertices has been developed. As the latter, are used Aho-codes, which find application in recognising the isomorphism of trees. The computational complexity to obtain structural characteristics of vertices has been estimated to be about О (n 3 .The pilot studies involved the full-scale experiment using the developed complex programmes to generate raw data, i.e. analytic representation of the graph with the number of vertices equal to 1200, and a programme to provide codes of the tree roots. To have an estimate of - "the worst" in terms of time - complexity of expansion algorithm of graphs into trees of the shortest paths and define the codes of their roots has been an experimentally studied how the number of tree vertices depends on the graph density. For the worst case was obtained a dependence of the number of tree vertices on the number of graph vertices
Some Invariants of Jahangir Graphs
Directory of Open Access Journals (Sweden)
Mobeen Munir
2017-01-01
Full Text Available In this report, we compute closed forms of M-polynomial, first and second Zagreb polynomials and forgotten polynomial for Jahangir graphs Jn,m for all values of m and n. From the M-polynomial, we recover many degree-based topological indices such as first and second Zagreb indices, modified Zagreb index, Symmetric division index, etc. We also compute harmonic index, first and second multiple Zagreb indices and forgotten index of Jahangir graphs. Our results are extensions of many existing results.
Graph abstraction and abstract graph transformations (Amended version)
Boneva, I.B.; Kreiker, Jörg; Kurban, M.E.; Rensink, Arend; Zambon, Eduardo
2012-01-01
Many important systems such as concurrent heap-manipulating programs, communication networks, or distributed algorithms, are hard to verify due to their inherent dynamics and unboundedness. Graphs are an intuitive representation for the states of these systems, where transitions can be conveniently
Multiple graph regularized protein domain ranking
Wang, Jim Jing-Yan
2012-11-19
Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.
Multiple graph regularized protein domain ranking.
Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin
2012-11-19
Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.
Multiple graph regularized protein domain ranking
Directory of Open Access Journals (Sweden)
Wang Jim
2012-11-01
Full Text Available Abstract Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.
Systems information management: graph theoretical approach
Temel, T.
2006-01-01
This study proposes a new method for characterising the underlying information structure of a multi-sector system. A complete characterisation is accomplished by identifying information gaps and cause-effect information pathways in the system, and formulating critical testable hypotheses.
Query Optimizations over Decentralized RDF Graphs
Abdelaziz, Ibrahim
2017-05-18
Applications in life sciences, decentralized social networks, Internet of Things, and statistical linked dataspaces integrate data from multiple decentralized RDF graphs via SPARQL queries. Several approaches have been proposed to optimize query processing over a small number of heterogeneous data sources by utilizing schema information. In the case of schema similarity and interlinks among sources, these approaches cause unnecessary data retrieval and communication, leading to poor scalability and response time. This paper addresses these limitations and presents Lusail, a system for scalable and efficient SPARQL query processing over decentralized graphs. Lusail achieves scalability and low query response time through various optimizations at compile and run times. At compile time, we use a novel locality-aware query decomposition technique that maximizes the number of query triple patterns sent together to a source based on the actual location of the instances satisfying these triple patterns. At run time, we use selectivity-awareness and parallel query execution to reduce network latency and to increase parallelism by delaying the execution of subqueries expected to return large results. We evaluate Lusail using real and synthetic benchmarks, with data sizes up to billions of triples on an in-house cluster and a public cloud. We show that Lusail outperforms state-of-the-art systems by orders of magnitude in terms of scalability and response time.
Graph reconstruction with a betweenness oracle
DEFF Research Database (Denmark)
Abrahamsen, Mikkel; Bodwin, Greg; Rotenberg, Eva
2016-01-01
Graph reconstruction algorithms seek to learn a hidden graph by repeatedly querying a blackbox oracle for information about the graph structure. Perhaps the most well studied and applied version of the problem uses a distance oracle, which can report the shortest path distance between any pair....... Despite this, we are able to develop betweenness reconstruction algorithms that match the current state of the art for distance reconstruction, and even improve it for certain types of graphs. We obtain the following algorithms: 1. Reconstruction of general graphs in O(n2) queries 2. Reconstruction...... of degree-bounded graphs in Õ(n3/2) queries 3. Reconstruction of geodetic degree-bounded graphs in Õ(n) queries In addition to being a fundamental graph theoretic problem with some natural applications, our new results shed light on some avenues for progress in the distance reconstruction problem....
Use of Spatial Transformations in Graph Comprehension
National Research Council Canada - National Science Library
Trickett, Susan B; Trafton, J. G
2004-01-01
Current theories of graph comprehension are largely silent about the processes by which inferences are made from graphs, although it is apparent that people are able to make such inferences. In Trickett & Trafton (2004...
Humidity Graphs for All Seasons.
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)
Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 1. A Problem in Graph Theory. K P Savithri. Think It Over Volume 12 Issue 1 January 2007 pp 81-81. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/012/01/0081-0081. Author Affiliations.
Box graphs and singular fibers
International Nuclear Information System (INIS)
Hayashi, Hirotaka; Lawrie, Craig; Morrison, David R.; Schäfer-Nameki, Sakura
2014-01-01
We determine the higher codimension fibers of elliptically fibered Calabi-Yau fourfolds with section by studying the three-dimensional N=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 , E 7 and E 8
Ancestral Genres of Mathematical Graphs
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…
Constructing Knowledge Graphs of Depression
Huang, Zhisheng; Yang, Jie; van Harmelen, Frank; Hu, Qing
2017-01-01
Knowledge Graphs have been shown to be useful tools for integrating multiple medical knowledge sources, and to support such tasks as medical decision making, literature retrieval, determining healthcare quality indicators, co-morbodity analysis and many others. A large number of medical knowledge
Contracting a planar graph efficiently
DEFF Research Database (Denmark)
Holm, Jacob; Italiano, Giuseppe F.; Karczmarz, Adam
2017-01-01
We present a data structure that can maintain a simple planar graph under edge contractions in linear total time. The data structure supports adjacency queries and provides access to neighbor lists in O(1) time. Moreover, it can report all the arising self-loops and parallel edges. By applying th...
Fixation Time for Evolutionary Graphs
Nie, Pu-Yan; Zhang, Pei-Ai
Evolutionary graph theory (EGT) is recently proposed by Lieberman et al. in 2005. EGT is successful for explaining biological evolution and some social phenomena. It is extremely important to consider the time of fixation for EGT in many practical problems, including evolutionary theory and the evolution of cooperation. This study characterizes the time to asymptotically reach fixation.
Indian Academy of Sciences (India)
Examples: Some explicit computations. Throughout this section, we will assume that ( , μ) is a finite, connected, weighted graph. The adjacency matrix of (which, by abuse of notation, will also be denoted by ) is, as usual, the symmetric matrix with rows and columns indexed by the vertex set V of and. (v, w) = |{e ∈ E : s(e) = v, ...
Affect and Graphing Calculator Use
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…
On dominator colorings in graphs
Indian Academy of Sciences (India)
A dominator coloring of a graph is a proper coloring of in which every vertex dominates every vertex of at least one color class. The minimum number of colors required for a dominator coloring of is called the dominator chromatic number of and is denoted by d ( G ) . In this paper we present several results on ...
Czech Academy of Sciences Publication Activity Database
Hussein, A.; Krejčiřík, David; Siegl, P.
2015-01-01
Roč. 367, č. 4 (2015), s. 2921-2957 ISSN 0002-9947 R&D Projects: GA ČR GAP203/11/0701 Institutional support: RVO:61389005 Keywords : Laplacians on metric graphs * non-self-adjoint boundary conditions * similarity transforms to self-adjoint operators * Riesz basis Subject RIV: BE - Theoretical Physics Impact factor: 1.196, year: 2015
Application of graph database for analytical tasks
Günzl, Richard
2014-01-01
This diploma thesis is about graph databases, which belong to the category of database systems known as NoSQL databases, but graph databases are beyond NoSQL databases. Graph databases are useful in many cases thanks to native storing of interconnections between data, which brings advantageous properties in comparison with traditional relational database system, especially in querying. The main goal of the thesis is: to describe principles, properties and advantages of graph database; to desi...
A Graph Calculus for Predicate Logic
Directory of Open Access Journals (Sweden)
Paulo A. S. Veloso
2013-03-01
Full Text Available We introduce a refutation graph calculus for classical first-order predicate logic, which is an extension of previous ones for binary relations. One reduces logical consequence to establishing that a constructed graph has empty extension, i. e. it represents bottom. Our calculus establishes that a graph has empty extension by converting it to a normal form, which is expanded to other graphs until we can recognize conflicting situations (equivalent to a formula and its negation.
Unsupervised Deep Haar Scattering on Graphs
Chen, Xu; Cheng, Xiuyuan; Mallat, Stéphane
2014-01-01
The classification of high-dimensional data defined on graphs is particularly difficult when the graph geometry is unknown. We introduce a Haar scattering transform on graphs, which computes invariant signal descriptors. It is implemented with a deep cascade of additions, subtractions and absolute values, which iteratively compute orthogonal Haar wavelet transforms. Multiscale neighborhoods of unknown graphs are estimated by minimizing an average total variation, with a pair matching algorith...