WorldWideScience

Sample records for boolean network models

  1. Boolean networks as modelling framework

    Directory of Open Access Journals (Sweden)

    Florian eGreil

    2012-08-01

    Full Text Available In a network, the components of a given system are represented as nodes, the interactions are abstracted as links between the nodes. Boolean networks refer to a class of dynamics on networks, in fact it is the simplest possible dynamics where each node has a value 0 or 1. This allows to investigate extensively the dynamics both analytically and by numerical experiments. The present article focuses on the theoretical concept of relevant components and the immediate application in plant biology, references for more in-depths treatment of the mathematical details are also given.

  2. Boolean network model predicts knockout mutant phenotypes of fission yeast.

    Directory of Open Access Journals (Sweden)

    Maria I Davidich

    Full Text Available BOOLEAN NETWORKS (OR: networks of switches are extremely simple mathematical models of biochemical signaling networks. Under certain circumstances, Boolean networks, despite their simplicity, are capable of predicting dynamical activation patterns of gene regulatory networks in living cells. For example, the temporal sequence of cell cycle activation patterns in yeasts S. pombe and S. cerevisiae are faithfully reproduced by Boolean network models. An interesting question is whether this simple model class could also predict a more complex cellular phenomenology as, for example, the cell cycle dynamics under various knockout mutants instead of the wild type dynamics, only. Here we show that a Boolean network model for the cell cycle control network of yeast S. pombe correctly predicts viability of a large number of known mutants. So far this had been left to the more detailed differential equation models of the biochemical kinetics of the yeast cell cycle network and was commonly thought to be out of reach for models as simplistic as Boolean networks. The new results support our vision that Boolean networks may complement other mathematical models in systems biology to a larger extent than expected so far, and may fill a gap where simplicity of the model and a preference for an overall dynamical blueprint of cellular regulation, instead of biochemical details, are in the focus.

  3. Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

    Directory of Open Access Journals (Sweden)

    Natalie Berestovsky

    Full Text Available The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them

  4. Dynamical modeling of the cholesterol regulatory pathway with Boolean networks

    Directory of Open Access Journals (Sweden)

    Corcos Laurent

    2008-11-01

    Full Text Available Abstract Background Qualitative dynamics of small gene regulatory networks have been studied in quite some details both with synchronous and asynchronous analysis. However, both methods have their drawbacks: synchronous analysis leads to spurious attractors and asynchronous analysis lacks computational efficiency, which is a problem to simulate large networks. We addressed this question through the analysis of a major biosynthesis pathway. Indeed the cholesterol synthesis pathway plays a pivotal role in dislypidemia and, ultimately, in cancer through intermediates such as mevalonate, farnesyl pyrophosphate and geranyl geranyl pyrophosphate, but no dynamic model of this pathway has been proposed until now. Results We set up a computational framework to dynamically analyze large biological networks. This framework associates a classical and computationally efficient synchronous Boolean analysis with a newly introduced method based on Markov chains, which identifies spurious cycles among the results of the synchronous simulation. Based on this method, we present here the results of the analysis of the cholesterol biosynthesis pathway and its physiological regulation by the Sterol Response Element Binding Proteins (SREBPs, as well as the modeling of the action of statins, inhibitor drugs, on this pathway. The in silico experiments show the blockade of the cholesterol endogenous synthesis by statins and its regulation by SREPBs, in full agreement with the known biochemical features of the pathway. Conclusion We believe that the method described here to identify spurious cycles opens new routes to compute large and biologically relevant models, thanks to the computational efficiency of synchronous simulation. Furthermore, to the best of our knowledge, we present here the first dynamic systems biology model of the human cholesterol pathway and several of its key regulatory control elements, hoping it would provide a good basis to perform in silico

  5. Random Boolean Networks

    OpenAIRE

    Drossel, Barbara

    2007-01-01

    This review explains in a self-contained way the properties of random Boolean networks and their attractors, with a special focus on critical networks. Using small example networks, analytical calculations, phenomenological arguments, and problems to solve, the basic concepts are introduced and important results concerning phase diagrams, numbers of relevant nodes and attractor properties are derived.

  6. Mapping Complex Networks: Exploring Boolean Modeling of Signal Transduction Pathways

    OpenAIRE

    Bhardwaj, Gaurav; Wells, Christine P.; Albert, Reka; van Rossum, Damian B.; Patterson, Randen L

    2009-01-01

    In this study, we explored the utility of a descriptive and predictive bionetwork model for phospholipase C-coupled calcium signaling pathways, built with non-kinetic experimental information. Boolean models generated from these data yield oscillatory activity patterns for both the endoplasmic reticulum resident inositol-1,4,5-trisphosphate receptor (IP3R) and the plasma-membrane resident canonical transient receptor potential channel 3 (TRPC3). These results are specific as randomization of ...

  7. Relative stability of network states in Boolean network models of gene regulation in development.

    Science.gov (United States)

    Zhou, Joseph Xu; Samal, Areejit; d'Hérouël, Aymeric Fouquier; Price, Nathan D; Huang, Sui

    2016-01-01

    Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x), derived from interactions in the gene regulatory network (GRN) of a cell, quantifies the relative stability of network states, which determine the effort required for state transitions in a multi-stable dynamical system. However, quasi-potential landscapes, originally developed for continuous systems, are not suitable for discrete-valued networks which are important tools to study complex systems. In this paper, we provide a framework to quantify the landscape for discrete Boolean networks (BNs). We apply our framework to study pancreas cell differentiation where an ensemble of BN models is considered based on the structure of a minimal GRN for pancreas development. We impose biologically motivated structural constraints (corresponding to specific type of Boolean functions) and dynamical constraints (corresponding to stable attractor states) to limit the space of BN models for pancreas development. In addition, we enforce a novel functional constraint corresponding to the relative ordering of attractor states in BN models to restrict the space of BN models to the biological relevant class. We find that BNs with canalyzing/sign-compatible Boolean functions best capture the dynamics of pancreas cell differentiation. This framework can also determine the genes' influence on cell state transitions, and thus can facilitate the rational design of cell reprogramming protocols. PMID:26965665

  8. Autonomous Modeling, Statistical Complexity and Semi-annealed Treatment of Boolean Networks

    Science.gov (United States)

    Gong, Xinwei

    This dissertation presents three studies on Boolean networks. Boolean networks are a class of mathematical systems consisting of interacting elements with binary state variables. Each element is a node with a Boolean logic gate, and the presence of interactions between any two nodes is represented by directed links. Boolean networks that implement the logic structures of real systems are studied as coarse-grained models of the real systems. Large random Boolean networks are studied with mean field approximations and used to provide a baseline of possible behaviors of large real systems. This dissertation presents one study of the former type, concerning the stable oscillation of a yeast cell-cycle oscillator, and two studies of the latter type, respectively concerning the statistical complexity of large random Boolean networks and an extension of traditional mean field techniques that accounts for the presence of short loops. In the cell-cycle oscillator study, a novel autonomous update scheme is introduced to study the stability of oscillations in small networks. A motif that corrects pulse-growing perturbations and a motif that grows pulses are identified. A combination of the two motifs is capable of sustaining stable oscillations. Examining a Boolean model of the yeast cell-cycle oscillator using an autonomous update scheme yields evidence that it is endowed with such a combination. Random Boolean networks are classified as ordered, critical or disordered based on their response to small perturbations. In the second study, random Boolean networks are taken as prototypical cases for the evaluation of two measures of complexity based on a criterion for optimal statistical prediction. One measure, defined for homogeneous systems, does not distinguish between the static spatial inhomogeneity in the ordered phase and the dynamical inhomogeneity in the disordered phase. A modification in which complexities of individual nodes are calculated yields vanishing

  9. From Boolean Network Model to Continuous Model Helps in Design of Functional Circuits

    OpenAIRE

    Bin Shao; Xiang Liu; Dongliang Zhang; Jiayi Wu; Qi Ouyang

    2015-01-01

    Computational circuit design with desired functions in a living cell is a challenging task in synthetic biology. To achieve this task, numerous methods that either focus on small scale networks or use evolutionary algorithms have been developed. Here, we propose a two-step approach to facilitate the design of functional circuits. In the first step, the search space of possible topologies for target functions is reduced by reverse engineering using a Boolean network model. In the second step, ...

  10. Reverse engineering Boolean networks: from Bernoulli mixture models to rule based systems.

    Directory of Open Access Journals (Sweden)

    Mehreen Saeed

    Full Text Available A Boolean network is a graphical model for representing and analyzing the behavior of gene regulatory networks (GRN. In this context, the accurate and efficient reconstruction of a Boolean network is essential for understanding the gene regulation mechanism and the complex relations that exist therein. In this paper we introduce an elegant and efficient algorithm for the reverse engineering of Boolean networks from a time series of multivariate binary data corresponding to gene expression data. We call our method ReBMM, i.e., reverse engineering based on Bernoulli mixture models. The time complexity of most of the existing reverse engineering techniques is quite high and depends upon the indegree of a node in the network. Due to the high complexity of these methods, they can only be applied to sparsely connected networks of small sizes. ReBMM has a time complexity factor, which is independent of the indegree of a node and is quadratic in the number of nodes in the network, a big improvement over other techniques and yet there is little or no compromise in accuracy. We have tested ReBMM on a number of artificial datasets along with simulated data derived from a plant signaling network. We also used this method to reconstruct a network from real experimental observations of microarray data of the yeast cell cycle. Our method provides a natural framework for generating rules from a probabilistic model. It is simple, intuitive and illustrates excellent empirical results.

  11. Exploring phospholipase C-coupled Ca(2+) signalling networks using Boolean modelling.

    Science.gov (United States)

    Bhardwaj, G; Wells, C P; Albert, R; van Rossum, D B; Patterson, R L

    2011-05-01

    In this study, the authors explored the utility of a descriptive and predictive bionetwork model for phospholipase C-coupled calcium signalling pathways, built with non-kinetic experimental information. Boolean models generated from these data yield oscillatory activity patterns for both the endoplasmic reticulum resident inositol-1,4,5-trisphosphate receptor (IP(3)R) and the plasma-membrane resident canonical transient receptor potential channel 3 (TRPC3). These results are specific as randomisation of the Boolean operators ablates oscillatory pattern formation. Furthermore, knock-out simulations of the IP(3)R, TRPC3 and multiple other proteins recapitulate experimentally derived results. The potential of this approach can be observed by its ability to predict previously undescribed cellular phenotypes using in vitro experimental data. Indeed, our cellular analysis of the developmental and calcium-regulatory protein, DANGER1a, confirms the counter-intuitive predictions from our Boolean models in two highly relevant cellular models. Based on these results, the authors theorise that with sufficient legacy knowledge and/or computational biology predictions, Boolean networks can provide a robust method for predictive modelling of any biological system. [Includes supplementary material]. PMID:21639591

  12. Dynamical modeling of the cholesterol regulatory pathway with Boolean networks

    OpenAIRE

    Corcos Laurent; Kervizic Gwenael

    2008-01-01

    Abstract Background Qualitative dynamics of small gene regulatory networks have been studied in quite some details both with synchronous and asynchronous analysis. However, both methods have their drawbacks: synchronous analysis leads to spurious attractors and asynchronous analysis lacks computational efficiency, which is a problem to simulate large networks. We addressed this question through the analysis of a major biosynthesis pathway. Indeed the cholesterol synthesis pathway plays a pivo...

  13. The receptor mosaic hypothesis of the engram: possible relevance of Boolean network modeling.

    Science.gov (United States)

    Zoli, M; Guidolin, D; Fuxe, K; Agnati, L F

    1996-09-01

    In the past 15 years, several lines of evidence have shown that receptors for chemical signals can interact in domains of the plasma membrane and possibly form molecular circuits encoding logical operators. In this frame, the receptor mosaic hypothesis of the engram was advanced. According to this proposal, aggregates of different receptor species (mosaics) may form in neuronal membranes (typically synapses) and constitute a memory trace (engram) of its activity. In the present paper, we present an attempt to model the functioning of aggregates of interacting receptors in membrane domains by means of random Boolean networks. PMID:8968825

  14. Effect of memory in non-Markovian Boolean networks

    CERN Document Server

    Ebadi, Haleh; Ausloos, Marcel; Jafari, GholamReza

    2016-01-01

    One successful model of interacting biological systems is the Boolean network. The dynamics of a Boolean network, controlled with Boolean functions, is usually considered to be a Markovian (memory-less) process. However, both self organizing features of biological phenomena and their intelligent nature should raise some doubt about ignoring the history of their time evolution. Here, we extend the Boolean network Markovian approach: we involve the effect of memory on the dynamics. This can be explored by modifying Boolean functions into non-Markovian functions, for example, by investigating the usual non-Markovian threshold function, - one of the most applied Boolean functions. By applying the non-Markovian threshold function on the dynamical process of a cell cycle network, we discover a power law memory with a more robust dynamics than the Markovian dynamics.

  15. Modeling and controlling the two-phase dynamics of the p53 network: a Boolean network approach

    International Nuclear Information System (INIS)

    Although much empirical evidence has demonstrated that p53 plays a key role in tumor suppression, the dynamics and function of the regulatory network centered on p53 have not yet been fully understood. Here, we develop a Boolean network model to reproduce the two-phase dynamics of the p53 network in response to DNA damage. In particular, we map the fates of cells into two types of Boolean attractors, and we find that the apoptosis attractor does not exist for minor DNA damage, reflecting that the cell is reparable. As the amount of DNA damage increases, the basin of the repair attractor shrinks, accompanied by the rising of the apoptosis attractor and the expansion of its basin, indicating that the cell becomes more irreparable with more DNA damage. For severe DNA damage, the repair attractor vanishes, and the apoptosis attractor dominates the state space, accounting for the exclusive fate of death. Based on the Boolean network model, we explore the significance of links, in terms of the sensitivity of the two-phase dynamics, to perturbing the weights of links and removing them. We find that the links are either critical or ordinary, rather than redundant. This implies that the p53 network is irreducible, but tolerant of small mutations at some ordinary links, and this can be interpreted with evolutionary theory. We further devised practical control schemes for steering the system into the apoptosis attractor in the presence of DNA damage by pinning the state of a single node or perturbing the weight of a single link. Our approach offers insights into understanding and controlling the p53 network, which is of paramount importance for medical treatment and genetic engineering. (paper)

  16. Modeling and controlling the two-phase dynamics of the p53 network: a Boolean network approach

    Science.gov (United States)

    Lin, Guo-Qiang; Ao, Bin; Chen, Jia-Wei; Wang, Wen-Xu; Di, Zeng-Ru

    2014-12-01

    Although much empirical evidence has demonstrated that p53 plays a key role in tumor suppression, the dynamics and function of the regulatory network centered on p53 have not yet been fully understood. Here, we develop a Boolean network model to reproduce the two-phase dynamics of the p53 network in response to DNA damage. In particular, we map the fates of cells into two types of Boolean attractors, and we find that the apoptosis attractor does not exist for minor DNA damage, reflecting that the cell is reparable. As the amount of DNA damage increases, the basin of the repair attractor shrinks, accompanied by the rising of the apoptosis attractor and the expansion of its basin, indicating that the cell becomes more irreparable with more DNA damage. For severe DNA damage, the repair attractor vanishes, and the apoptosis attractor dominates the state space, accounting for the exclusive fate of death. Based on the Boolean network model, we explore the significance of links, in terms of the sensitivity of the two-phase dynamics, to perturbing the weights of links and removing them. We find that the links are either critical or ordinary, rather than redundant. This implies that the p53 network is irreducible, but tolerant of small mutations at some ordinary links, and this can be interpreted with evolutionary theory. We further devised practical control schemes for steering the system into the apoptosis attractor in the presence of DNA damage by pinning the state of a single node or perturbing the weight of a single link. Our approach offers insights into understanding and controlling the p53 network, which is of paramount importance for medical treatment and genetic engineering.

  17. Boolean network robotics: a proof of concept

    CERN Document Server

    Roli, Andrea; Pinciroli, Carlo; Birattari, Mauro

    2011-01-01

    Dynamical systems theory and complexity science provide powerful tools for analysing artificial agents and robots. Furthermore, they have been recently proposed also as a source of design principles and guidelines. Boolean networks are a prominent example of complex dynamical systems and they have been shown to effectively capture important phenomena in gene regulation. From an engineering perspective, these models are very compelling, because they can exhibit rich and complex behaviours, in spite of the compactness of their description. In this paper, we propose the use of Boolean networks for controlling robots' behaviour. The network is designed by means of an automatic procedure based on stochastic local search techniques. We show that this approach makes it possible to design a network which enables the robot to accomplish a task that requires the capability of navigating the space using a light stimulus, as well as the formation and use of an internal memory.

  18. Boolean networks with reliable dynamics

    CERN Document Server

    Peixoto, Tiago P

    2009-01-01

    We investigated the properties of Boolean networks that follow a given reliable trajectory in state space. A reliable trajectory is defined as a sequence of states which is independent of the order in which the nodes are updated. We explored numerically the topology, the update functions, and the state space structure of these networks, which we constructed using a minimum number of links and the simplest update functions. We found that the clustering coefficient is larger than in random networks, and that the probability distribution of three-node motifs is similar to that found in gene regulation networks. Among the update functions, only a subset of all possible functions occur, and they can be classified according to their probability. More homogeneous functions occur more often, leading to a dominance of canalyzing functions. Finally, we studied the entire state space of the networks. We observed that with increasing systems size, fixed points become more dominant, moving the networks close to the frozen...

  19. Enhancing Boolean networks with fuzzy operators and edge tuning

    OpenAIRE

    Poret, Arnaud; Monteiro Sousa, Claudio; Boissel, Jean-Pierre

    2014-01-01

    Quantitative modeling in systems biology can be difficult due to the scarcity of quantitative details about biological phenomenons, especially at the subcellular scale. An alternative to escape this difficulty is qualitative modeling since it requires few to no quantitative information. Among the qualitative modeling approaches, the Boolean network formalism is one of the most popular. However, Boolean models allow variables to be valued at only true or false, which can appear too simplistic ...

  20. Representations of Boolean Functions by Perceptron Networks

    Czech Academy of Sciences Publication Activity Database

    Kůrková, Věra

    Prague : Institute of Computer Science AS CR, 2014 - (Kůrková, V.; Bajer, L.; Peška, L.; Vojtáš, R.; Holeňa, M.; Nehéz, M.), s. 68-70 ISBN 978-80-87136-19-5. [ITAT 2014. European Conference on Information Technologies - Applications and Theory /14./. Demänovská dolina (SK), 25.09.2014-29.09.2014] R&D Projects: GA MŠk(CZ) LD13002 Institutional support: RVO:67985807 Keywords : perceptron networks * model complexity * Boolean functions Subject RIV: IN - Informatics, Computer Science

  1. Forced synchronization of autonomous dynamical Boolean networks

    International Nuclear Information System (INIS)

    We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics

  2. Forced synchronization of autonomous dynamical Boolean networks

    Energy Technology Data Exchange (ETDEWEB)

    Rivera-Durón, R. R., E-mail: roberto.rivera@ipicyt.edu.mx; Campos-Cantón, E., E-mail: eric.campos@ipicyt.edu.mx [División de Matemáticas Aplicadas, Instituto Potosino de Investigación Científica y Tecnológica A. C., Camino a la Presa San José 2055, Col. Lomas 4 Sección, C.P. 78216, San Luis Potosí, S.L.P. (Mexico); Campos-Cantón, I. [Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, C.P. 78000, San Luis Potosí, S.L.P. (Mexico); Gauthier, Daniel J. [Department of Physics and Center for Nonlinear and Complex Systems, Duke University, Box 90305, Durham, North Carolina 27708 (United States)

    2015-08-15

    We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.

  3. Model Checking of Boolean Process Models

    OpenAIRE

    Schneider, Christoph; Wehler, Joachim

    2011-01-01

    In the field of Business Process Management formal models for the control flow of business processes have been designed since more than 15 years. Which methods are best suited to verify the bulk of these models? The first step is to select a formal language which fixes the semantics of the models. We adopt the language of Boolean systems as reference language for Boolean process models. Boolean systems form a simple subclass of coloured Petri nets. Their characteristics are low tokens to mode...

  4. The Influence of Canalization on the Robustness of Boolean Networks

    CERN Document Server

    Kadelka, Claus; Laubenbacher, Reinhard

    2016-01-01

    Time- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on networks governed by $k$-canalizing functions, a recently introduced class of Boolean functions that contains the well-studied class of nested canalizing functions. The activities and sensitivity of a function quantify the impact of input changes on the function output. This paper generalizes the latter concept to $c$-sensitivity and provides formulas for the activities and $c$-sensitivity of general $k$-canalizing functions as well as canalizing functions with more precisely defined structure. A popular measure for the robustness of a network, the Derrida value, can be expressed as a weighted sum of the $c$-sensitivities of the governing canalizing functions, and can also be calculated for a stochastic extension of Boolean networks. These findings provide a computationally eff...

  5. Comparison of Control Approaches in Genetic Regulatory Networks by Using Stochastic Master Equation Models, Probabilistic Boolean Network Models and Differential Equation Models and Estimated Error Analyzes

    Science.gov (United States)

    Caglar, Mehmet Umut; Pal, Ranadip

    2011-03-01

    Central dogma of molecular biology states that ``information cannot be transferred back from protein to either protein or nucleic acid''. However, this assumption is not exactly correct in most of the cases. There are a lot of feedback loops and interactions between different levels of systems. These types of interactions are hard to analyze due to the lack of cell level data and probabilistic - nonlinear nature of interactions. Several models widely used to analyze and simulate these types of nonlinear interactions. Stochastic Master Equation (SME) models give probabilistic nature of the interactions in a detailed manner, with a high calculation cost. On the other hand Probabilistic Boolean Network (PBN) models give a coarse scale picture of the stochastic processes, with a less calculation cost. Differential Equation (DE) models give the time evolution of mean values of processes in a highly cost effective way. The understanding of the relations between the predictions of these models is important to understand the reliability of the simulations of genetic regulatory networks. In this work the success of the mapping between SME, PBN and DE models is analyzed and the accuracy and affectivity of the control policies generated by using PBN and DE models is compared.

  6. Boolean Factor Analysis by Attractor Neural Network

    Czech Academy of Sciences Publication Activity Database

    Frolov, A. A.; Húsek, Dušan; Muraviev, I. P.; Polyakov, P.Y.

    2007-01-01

    Roč. 18, č. 3 (2007), s. 698-707. ISSN 1045-9227 R&D Projects: GA AV ČR 1ET100300419; GA ČR GA201/05/0079 Institutional research plan: CEZ:AV0Z10300504 Keywords : recurrent neural network * Hopfield-like neural network * associative memory * unsupervised learning * neural network architecture * neural network application * statistics * Boolean factor analysis * dimensionality reduction * features clustering * concepts search * information retrieval Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 2.769, year: 2007

  7. Boolean network representation of contagion dynamics during a financial crisis

    Science.gov (United States)

    Caetano, Marco Antonio Leonel; Yoneyama, Takashi

    2015-01-01

    This work presents a network model for representation of the evolution of certain patterns of economic behavior. More specifically, after representing the agents as points in a space in which each dimension associated to a relevant economic variable, their relative "motions" that can be either stationary or discordant, are coded into a boolean network. Patterns with stationary averages indicate the maintenance of status quo, whereas discordant patterns represent aggregation of new agent into the cluster or departure from the former policies. The changing patterns can be embedded into a network representation, particularly using the concept of autocatalytic boolean networks. As a case study, the economic tendencies of the BRIC countries + Argentina were studied. Although Argentina is not included in the cluster formed by BRIC countries, it tends to follow the BRIC members because of strong commercial ties.

  8. Algorithms for Finding Small Attractors in Boolean Networks

    Directory of Open Access Journals (Sweden)

    Hayashida Morihiro

    2007-01-01

    Full Text Available A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.

  9. Neural Network Boolean Factor Analysis and Applications

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Frolov, A.; Polyakov, P.Y.; Snášel, V.

    -: WSEAS Press, 2007 - (Katehakis, M.; And ina, D.; Mastorakis, M.), s. 30-35. (Electrical and Computer Engineering Series). ISBN 978-960-6766-21-3. [CIMMACS'07. WSEAS International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics. Tenerife (ES), 14.12.2007-16.12.2007] R&D Projects: GA MŠk 1M0567; GA AV ČR 1ET100300414; GA ČR GA201/05/0079 Institutional research plan: CEZ:AV0Z10300504 Keywords : Hopfield neural network * boolean factor analysis * unsupervised learning * dimension reduction * data mining Subject RIV: BB - Applied Statistics, Operational Research

  10. Solving the Satisfiability Problem Through Boolean Networks

    OpenAIRE

    Roli, Andrea; Milano, Michela

    2011-01-01

    In this paper we present a new approach to solve the satisfiability problem (SAT), based on boolean networks (BN). We define a mapping between a SAT instance and a BN, and we solve SAT problem by simulating the BN dynamics. We prove that BN fixed points correspond to the SAT solutions. The mapping presented allows to develop a new class of algorithms to solve SAT. Moreover, this new approach suggests new ways to combine symbolic and connectionist computation and provides a general framework f...

  11. Solving the Satisfiability Problem Through Boolean Networks

    CERN Document Server

    Roli, Andrea

    2011-01-01

    In this paper we present a new approach to solve the satisfiability problem (SAT), based on boolean networks (BN). We define a mapping between a SAT instance and a BN, and we solve SAT problem by simulating the BN dynamics. We prove that BN fixed points correspond to the SAT solutions. The mapping presented allows to develop a new class of algorithms to solve SAT. Moreover, this new approach suggests new ways to combine symbolic and connectionist computation and provides a general framework for local search algorithms.

  12. Densities of mixed volumes for Boolean models

    OpenAIRE

    Weil, Wolfgang

    2001-01-01

    In generalization of the well-known formulae for quermass densities of stationary and isotropic Boolean models, we prove corresponding results for densities of mixed volumes in the stationary situation and show how they can be used to determine the intensity of non-isotropic Boolean models Z in d-dimensional space for d = 2, 3, 4. We then consider non-stationary Boolean models and extend results of Fallert on quermass densities to densities of mixed volumes. In particular, we present explicit...

  13. A more robust Boolean model describing inhibitor binding

    Institute of Scientific and Technical Information of China (English)

    Zhaoqian Steven XIE; Chao TANG

    2008-01-01

    From the first application of the Boolean model to the cell cycle regulation network of budding yeast, new regulative pathways have been discovered, par-ticularly in the G1/S transition circuit. This discovery called for finer modeling to study the essential biology, and the resulting outcomes are first introduced in the ar-ticle. A traditional Boolean network model set up for the new G1/S transition circuit shows that it cannot correctly simulate real biology unless the model parameters are fine tuned. The deficiency is caused by an overly coarse-grained description of the inhibitor binding process, which shall be overcome by a two-vector model proposed whose robustness is surveyed using random perturba-tions. Simulations show that the proposed two-vector model is much more robust in describing inhibitor binding processes within the Boolean framework.

  14. ON REDUCED SCALAR EQUATIONS FOR SYNCHRONOUS BOOLEAN NETWORKS

    OpenAIRE

    Ali Muhammad Ali Rushdi; Adnan Ahmad Alsogati

    2013-01-01

    A total description of a synchronous Boolean network is typically achieved by a matrix recurrence relation. A simpler alternative is to use a scalar equation which is a possibly nonlinear equation that involves two or more instances of a single scalar variable and some Boolean operator(s). Further simplification is possible in terms of a linear reduced scalar equation which is the simplest two-term scalar equation that includes no Boolean operators and equates the value of a scalar variable a...

  15. A SAT-based algorithm for finding attractors in synchronous Boolean networks.

    Science.gov (United States)

    Dubrova, Elena; Teslenko, Maxim

    2011-01-01

    This paper addresses the problem of finding attractors in synchronous Boolean networks. The existing Boolean decision diagram-based algorithms have limited capacity due to the excessive memory requirements of decision diagrams. The simulation-based algorithms can be applied to larger networks, however, they are incomplete. We present an algorithm, which uses a SAT-based bounded model checking to find all attractors in a Boolean network. The efficiency of the presented algorithm is evaluated by analyzing seven networks models of real biological processes, as well as 150,000 randomly generated Boolean networks of sizes between 100 and 7,000. The results show that our approach has a potential to handle an order of magnitude larger models than currently possible. PMID:21778527

  16. Consistent stabilizability of switched Boolean networks.

    Science.gov (United States)

    Li, Haitao; Wang, Yuzhen

    2013-10-01

    This paper investigates the consistent stabilizability of switched Boolean networks (SBNs) by using the semi-tensor product method, and presents a number of new results. First, an algebraic expression of SBNs is obtained by the semi-tensor product, based on which the consistent stabilizability is then studied for SBNs and some necessary and sufficient conditions are presented for the design of free-form and state-feedback switching signals, respectively. Finally, the consistent stabilizability of SBNs with state constraints is considered and some necessary and sufficient conditions are proposed. The study of illustrative examples shows that the new results obtained in this paper are very effective in designing switching signals for the consistent stabilizability of SBNs. PMID:23787170

  17. The value of less connected agents in Boolean networks

    Science.gov (United States)

    Epstein, Daniel; Bazzan, Ana L. C.

    2013-11-01

    In multiagent systems, agents often face binary decisions where one seeks to take either the minority or the majority side. Examples are minority and congestion games in general, i.e., situations that require coordination among the agents in order to depict efficient decisions. In minority games such as the El Farol Bar Problem, previous works have shown that agents may reach appropriate levels of coordination, mostly by looking at the history of past decisions. Not many works consider any kind of structure of the social network, i.e., how agents are connected. Moreover, when structure is indeed considered, it assumes some kind of random network with a given, fixed connectivity degree. The present paper departs from the conventional approach in some ways. First, it considers more realistic network topologies, based on preferential attachments. This is especially useful in social networks. Second, the formalism of random Boolean networks is used to help agents to make decisions given their attachments (for example acquaintances). This is coupled with a reinforcement learning mechanism that allows agents to select strategies that are locally and globally efficient. Third, we use agent-based modeling and simulation, a microscopic approach, which allows us to draw conclusions about individuals and/or classes of individuals. Finally, for the sake of illustration we use two different scenarios, namely the El Farol Bar Problem and a binary route choice scenario. With this approach we target systems that adapt dynamically to changes in the environment, including other adaptive decision-makers. Our results using preferential attachments and random Boolean networks are threefold. First we show that an efficient equilibrium can be achieved, provided agents do experimentation. Second, microscopic analysis show that influential agents tend to consider few inputs in their Boolean functions. Third, we have also conducted measurements related to network clustering and centrality

  18. Self-organized networks of competing boolean agents

    Science.gov (United States)

    Paczuski; Bassler; Corral

    2000-04-01

    A model of Boolean agents competing in a market is presented where each agent bases his action on information obtained from a small group of other agents. The agents play a competitive game that rewards those in the minority. After a long time interval, the poorest player's strategy is changed randomly, and the process is repeated. Eventually the network evolves to a stationary but intermittent state where random mutation of the worst strategy can change the behavior of the entire network, often causing a switch in the dynamics between attractors of vastly different lengths. PMID:11019043

  19. Towards a theory of modelling with Boolean automata networks - I. Theorisation and observations

    CERN Document Server

    Noual, Mathilde

    2011-01-01

    Although models are built on the basis of some observations of reality, the concepts that derive theoretically from their definitions as well as from their characteristics and properties are not necessarily direct consequences of these initial observations. Indeed, many of them rather follow from chains of theoretical inferences that are only based on the precise model definitions and rely strongly, in addition, on some consequential working hypotheses. Thus, it is important to address the question of which features of a model effectively carry some modelling meaning and which only result from the task of formalising observations of reality into a mathematical language. In this article, we address this question with a theoretical point view that sets our discussion strictly between the two stages of the modelling process that require knowledge of real systems, that is, between the initial stage that chooses a global theoretical framework to build the model and the final stage that exploits its formal predicti...

  20. Propagation of external regulation and asynchronous dynamics in random Boolean networks

    OpenAIRE

    Mahmoudi, Hamed; Pagnani, Andrea; Weigt, Martin; Zecchina, Riccardo

    2007-01-01

    Boolean Networks and their dynamics are of great interest as abstract modeling schemes in various disciplines, ranging from biology to computer science. Whereas parallel update schemes have been studied extensively in past years, the level of understanding of asynchronous updates schemes is still very poor. In this paper we study the propagation of external information given by regulatory input variables into a random Boolean network. We compute both analytically and numerically the time evol...

  1. Measuring Mutual Information in Random Boolean Networks

    CERN Document Server

    Luque, B; Luque, Bartolo; Ferrera, Antonio

    1999-01-01

    During the last few years an area of active research in the field of complex systems is that of their information storing and processing abilities. Common opinion has it that the most interesting beaviour of these systems is found ``at the edge of chaos'', which would seem to suggest that complex systems may have inherently non-trivial information proccesing abilities in the vicinity of sharp phase transitions. A comprenhensive, quantitative understanding of why this is the case is however still lacking. Indeed, even ``experimental'' (i.e., often numerical) evidence that this is so has been questioned for a number of systems. In this paper we will investigate, both numerically and analitically, the behavior of Random Boolean Networks (RBN's) as they undergo their order-disorder phase transition. We will use a simple mean field approximation to treat the problem, and without lack of generality we will concentrate on a particular value for the connectivity of the system. In spite of the simplicity of our argume...

  2. Evolution and Controllability of Cancer Networks: A Boolean Perspective.

    Science.gov (United States)

    Srihari, Sriganesh; Raman, Venkatesh; Leong, Hon Wai; Ragan, Mark A

    2014-01-01

    Cancer forms a robust system capable of maintaining stable functioning (cell sustenance and proliferation) despite perturbations. Cancer progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to understand cancer progression and to develop effective anti-cancer therapies. In this work, we propose a novel model for the `cancer system' as a Boolean state space in which a Boolean network, built from protein-interaction and gene-expression data from different stages of cancer, transits between Boolean satisfiability states by "editing" interactions and "flipping" genes. Edits reflect rewiring of the PPI network while flipping of genes reflect activation or silencing of genes between stages. We formulate a minimization problem min flip to identify these genes driving the transitions. The application of our model (called BoolSpace) on three case studies-pancreatic and breast tumours in human and post spinal-cord injury (SCI) in rats-reveals valuable insights into the phenomenon of cancer progression: (i) interactions involved in core cell-cycle and DNA-damage repair pathways are significantly rewired in tumours, indicating significant impact to key genome-stabilizing mechanisms; (ii) several of the genes flipped are serine/threonine kinases which act as biological switches, reflecting cellular switching mechanisms between stages; and (iii) different sets of genes are flipped during the initial and final stages indicating a pattern to tumour progression. Based on these results, we hypothesize that robustness of cancer partly stems from "passing of the baton" between genes at different stages-genes from different biological processes and/or cellular components are involved in different stages of tumour progression thereby allowing tumour cells to evade targeted therapy, and therefore an effective therapy should target a "cover set" of

  3. IMS Algorithm for Learning Representations in Boolean Neural Networks

    OpenAIRE

    Biswas, Nripendra N; Murthy, TVMK; Chandrasekhar, M.

    1991-01-01

    A new algorithm for learning representations in Boolean neural networks, where the inputs and outputs are binary bits, is presented. The algorithm has become feasible because of a newly discovered theorem which states that any non-linearly separable Boolean function can be expressed as a convergent series of linearly separable functions connected by the logical OR (+) and the logical INHIBIT (-) operators. The formation of the series is carried out by many important properties exhibited by th...

  4. Polynomial-Time Algorithm for Controllability Test of a Class of Boolean Biological Networks

    Directory of Open Access Journals (Sweden)

    Koichi Kobayashi

    2010-01-01

    Full Text Available In recent years, Boolean-network-model-based approaches to dynamical analysis of complex biological networks such as gene regulatory networks have been extensively studied. One of the fundamental problems in control theory of such networks is the problem of determining whether a given substance quantity can be arbitrarily controlled by operating the other substance quantities, which we call the controllability problem. This paper proposes a polynomial-time algorithm for solving this problem. Although the algorithm is based on a sufficient condition for controllability, it is easily computable for a wider class of large-scale biological networks compared with the existing approaches. A key to this success in our approach is to give up computing Boolean operations in a rigorous way and to exploit an adjacency matrix of a directed graph induced by a Boolean network. By applying the proposed approach to a neurotransmitter signaling pathway, it is shown that it is effective.

  5. Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling

    OpenAIRE

    Cho Kwang-Hyun; Choi Sun; Kwon Yung-Keun

    2007-01-01

    Abstract Background A number of studies on biological networks have been carried out to unravel the topological characteristics that can explain the functional importance of network nodes. For instance, connectivity, clustering coefficient, and shortest path length were previously proposed for this purpose. However, there is still a pressing need to investigate another topological measure that can better describe the functional importance of network nodes. In this respect, we considered a fee...

  6. Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

    Directory of Open Access Journals (Sweden)

    Shah Imran

    2011-07-01

    Full Text Available Abstract Background With increasing knowledge about the potential mechanisms underlying cellular functions, it is becoming feasible to predict the response of biological systems to genetic and environmental perturbations. Due to the lack of homogeneity in living tissues it is difficult to estimate the physiological effect of chemicals, including potential toxicity. Here we investigate a biologically motivated model for estimating tissue level responses by aggregating the behavior of a cell population. We assume that the molecular state of individual cells is independently governed by discrete non-deterministic signaling mechanisms. This results in noisy but highly reproducible aggregate level responses that are consistent with experimental data. Results We developed an asynchronous threshold Boolean network simulation algorithm to model signal transduction in a single cell, and then used an ensemble of these models to estimate the aggregate response across a cell population. Using published data, we derived a putative crosstalk network involving growth factors and cytokines - i.e., Epidermal Growth Factor, Insulin, Insulin like Growth Factor Type 1, and Tumor Necrosis Factor α - to describe early signaling events in cell proliferation signal transduction. Reproducibility of the modeling technique across ensembles of Boolean networks representing cell populations is investigated. Furthermore, we compare our simulation results to experimental observations of hepatocytes reported in the literature. Conclusion A systematic analysis of the results following differential stimulation of this model by growth factors and cytokines suggests that: (a using Boolean network ensembles with asynchronous updating provides biologically plausible noisy individual cellular responses with reproducible mean behavior for large cell populations, and (b with sufficient data our model can estimate the response to different concentrations of extracellular ligands. Our

  7. Boolean modeling in systems biology: an overview of methodology and applications

    International Nuclear Information System (INIS)

    Mathematical modeling of biological processes provides deep insights into complex cellular systems. While quantitative and continuous models such as differential equations have been widely used, their use is obstructed in systems wherein the knowledge of mechanistic details and kinetic parameters is scarce. On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the experimental literature and high-throughput technologies, making qualitative approaches such as Boolean network modeling extremely useful. In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models. We finally demonstrate how Boolean models can be applied to perform the structural analysis of cellular networks. This overview aims to acquaint life science researchers with the basic steps of Boolean modeling and its applications in several areas of systems biology. (paper)

  8. Boolean Models of Biological Processes Explain Cascade-Like Behavior.

    Science.gov (United States)

    Chen, Hao; Wang, Guanyu; Simha, Rahul; Du, Chenghang; Zeng, Chen

    2016-01-01

    Biological networks play a key role in determining biological function and therefore, an understanding of their structure and dynamics is of central interest in systems biology. In Boolean models of such networks, the status of each molecule is either "on" or "off" and along with the molecules interact with each other, their individual status changes from "on" to "off" or vice-versa and the system of molecules in the network collectively go through a sequence of changes in state. This sequence of changes is termed a biological process. In this paper, we examine the common perception that events in biomolecular networks occur sequentially, in a cascade-like manner, and ask whether this is likely to be an inherent property. In further investigations of the budding and fission yeast cell-cycle, we identify two generic dynamical rules. A Boolean system that complies with these rules will automatically have a certain robustness. By considering the biological requirements in robustness and designability, we show that those Boolean dynamical systems, compared to an arbitrary dynamical system, statistically present the characteristics of cascadeness and sequentiality, as observed in the budding and fission yeast cell- cycle. These results suggest that cascade-like behavior might be an intrinsic property of biological processes. PMID:26821940

  9. Binary higher order neural networks for realizing Boolean functions.

    Science.gov (United States)

    Zhang, Chao; Yang, Jie; Wu, Wei

    2011-05-01

    In order to more efficiently realize Boolean functions by using neural networks, we propose a binary product-unit neural network (BPUNN) and a binary π-ς neural network (BPSNN). The network weights can be determined by one-step training. It is shown that the addition " σ," the multiplication " π," and two kinds of special weighting operations in BPUNN and BPSNN can implement the logical operators " ∨," " ∧," and " ¬" on Boolean algebra 〈Z(2),∨,∧,¬,0,1〉 (Z(2)={0,1}), respectively. The proposed two neural networks enjoy the following advantages over the existing networks: 1) for a complete truth table of N variables with both truth and false assignments, the corresponding Boolean function can be realized by accordingly choosing a BPUNN or a BPSNN such that at most 2(N-1) hidden nodes are needed, while O(2(N)), precisely 2(N) or at most 2(N), hidden nodes are needed by existing networks; 2) a new network BPUPS based on a collaboration of BPUNN and BPSNN can be defined to deal with incomplete truth tables, while the existing networks can only deal with complete truth tables; and 3) the values of the weights are all simply -1 or 1, while the weights of all the existing networks are real numbers. Supporting numerical experiments are provided as well. Finally, we present the risk bounds of BPUNN, BPSNN, and BPUPS, and then analyze their probably approximately correct learnability. PMID:21427020

  10. ON REDUCED SCALAR EQUATIONS FOR SYNCHRONOUS BOOLEAN NETWORKS

    Directory of Open Access Journals (Sweden)

    Ali Muhammad Ali Rushdi

    2013-01-01

    Full Text Available A total description of a synchronous Boolean network is typically achieved by a matrix recurrence relation. A simpler alternative is to use a scalar equation which is a possibly nonlinear equation that involves two or more instances of a single scalar variable and some Boolean operator(s. Further simplification is possible in terms of a linear reduced scalar equation which is the simplest two-term scalar equation that includes no Boolean operators and equates the value of a scalar variable at a latter instance t2 to its value at an earlier instance t1. This equation remains valid when the times t1 and t2 are both augmented by any integral multiple of the underlying time period. In other words, there are infinitely many versions of a reduced scalar equation, any of which is useful for deducing information about the cyclic behavior of the network. However, to obtain correct information about the transient behavior of the network, one must find the true reduced scalar equation for which instances t1 and t2 are minimal. This study investigates the nature, derivation and utilization of reduced scalar equations. It relies on Boolean-algebraic manipulations for the derivation of such equations and suggests that this derivation can be facilitated by seeking certain orthogonality relations among certain successive (albeit not necessarily consecutive instances of the same scalar variable. We demonstrate, contrary to previously published assumptions or assertions, that there is typically no common reduced scalar equation for all the scalar variables. Each variable usually satisfies its own distinct reduced scalar equation. We also demonstrate that the derivation of a reduced scalar equation is achieved not only by proving it but also by disproving an immediately preceding version of it when such a version might exist. We also demonstrate that, despite the useful insight supplied by the reduced scalar equations, they do not provide a total solution like the

  11. Optimal Computation of Symmetric Boolean Functions in Collocated Networks

    CERN Document Server

    Kowshik, Hemant

    2011-01-01

    We consider collocated wireless sensor networks, where each node has a Boolean measurement and the goal is to compute a given Boolean function of these measurements. We first consider the worst case setting and study optimal block computation strategies for computing symmetric Boolean functions. We study three classes of functions: threshold functions, delta functions and interval functions. We provide exactly optimal strategies for the first two classes, and a scaling law order-optimal strategy with optimal preconstant for interval functions. We also extend the results to the case of integer measurements and certain integer-valued functions. We use lower bounds from communication complexity theory, and provide an achievable scheme using information theoretic tools. Next, we consider the case where nodes measurements are random and drawn from independent Bernoulli distributions. We address the problem of optimal function computation so as to minimize the expected total number of bits that are transmitted. In ...

  12. Boolean Models of Biosurfactants Production in Pseudomonas fluorescens

    Science.gov (United States)

    Richard, Adrien; Rossignol, Gaelle; Comet, Jean-Paul; Bernot, Gilles; Guespin-Michel, Jannine; Merieau, Annabelle

    2012-01-01

    Cyclolipopeptides (CLPs) are biosurfactants produced by numerous Pseudomonas fluorescens strains. CLP production is known to be regulated at least by the GacA/GacS two-component pathway, but the full regulatory network is yet largely unknown. In the clinical strain MFN1032, CLP production is abolished by a mutation in the phospholipase C gene () and not restored by complementation. Their production is also subject to phenotypic variation. We used a modelling approach with Boolean networks, which takes into account all these observations concerning CLP production without any assumption on the topology of the considered network. Intensive computation yielded numerous models that satisfy these properties. All models minimizing the number of components point to a bistability in CLP production, which requires the presence of a yet unknown key self-inducible regulator. Furthermore, all suggest that a set of yet unexplained phenotypic variants might also be due to this epigenetic switch. The simplest of these Boolean networks was used to propose a biological regulatory network for CLP production. This modelling approach has allowed a possible regulation to be unravelled and an unusual behaviour of CLP production in P. fluorescens to be explained. PMID:22303435

  13. Robust Boolean Operation for Sculptured Models

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    To enhance the ability of current modeling system, an uniformed representation is designed to represent wire-frame, solid, surface models. We present an algorithm for Boolean operation between the models under this representation. Accuracy, efficiency and robustness are the main consideration. The geometric information is represented with trimmed parametric patches and trimmed parametric splines. The topological information is represented with an extended half-edge data structure. In the process of intersection calculation, hierarchy intersection method is applied for unified classification. Tracing the intersection curve to overcome degenerate cases that occur frequently in practice. The algorithm has been implemented as the modeling kernel of a feature based modeling system named GS-CAD98, which was developed on Windows/NT platform.

  14. Comparison of Two Neural Networks Approaches to Boolean Matrix Factorization

    Czech Academy of Sciences Publication Activity Database

    Polyakov, P.Y.; Frolov, A. A.; Húsek, Dušan

    Los Alamitos: IEEE Computer Society, 2009 - (Snášel, V.; Pokorný, J.; Pichappan, P.; El-Qawasmeh, E.), s. 316-321 ISBN 978-1-4244-4614-8. [NDT 2009. International Conference on Networked Digital Technologies /1./. Ostrava (CZ), 29.07.2009-31.07.2009] R&D Projects: GA ČR GA205/09/1079; GA MŠk(CZ) 1M0567 Institutional research plan: CEZ:AV0Z10300504 Keywords : data mining * artificial inteligence * neural networks * multivariate statistics * Boolean factor analysis * Hopfield-like neural networks * feed forward neural network Subject RIV: BB - Applied Statistics, Operational Research

  15. Neural Network Based Boolean Factor Analysis of Parliament Voting

    Czech Academy of Sciences Publication Activity Database

    Frolov, A. A.; Polyakov, P.Y.; Húsek, Dušan; Řezanková, H.

    Heidelberg : Springer, 2006 - (Rizzi, A.; Vichi, M.), s. 861-868 ISBN 3-7908-1708-2. [COMPSTAT 2006. Symposium /17./. Rome (IN), 28.08.2006-01.09.2006] R&D Projects: GA AV ČR 1ET100300419; GA ČR GA201/05/0079 Grant ostatní: RFBR(RU) 05-07-90049 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * neural networks * social networks Subject RIV: BB - Applied Statistics, Operational Research

  16. Chaos synchronization of two stochastically coupled random Boolean networks

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Y.-C. [Department of Physics, National Sun Yat-sen University, Kaohsiung, Taiwan (China) and Nonlinear Science Group, Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)]. E-mail: d9123801@student.nsysu.edu.tw; Ho, M.-C. [Nonlinear Science Group, Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)]. E-mail: t1603@nknucc.nknu.edu.tw; Lih, J.-S. [Department of Physics and Geoscience, National Pingtung University of Education, Pingtung, Taiwan (China); Nonlinear Science Group, Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China); Jiang, I-M. [Department of Physics, National Sun Yat-sen University, Kaohsiung, Taiwan (China); Nonlinear Science Group, Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)

    2006-07-24

    In this Letter, we study the chaos synchronization of two stochastically coupled random Boolean networks (RBNs). Instead of using the 'site-by-site and all-to-all' coupling, the coupling mechanism we consider here is that: the nth cell in a network is linked by an arbitrarily chosen cell in the other network with probability {rho}, and it possesses no links with probability 1-{rho}. The mechanism is useful to investigate the coevolution of biological species via horizontal genetic exchange. We show that the density evolution of networks can be described by two deterministic coupled polynomial maps. The complete synchronization occurs when the coupling parameter exceeds a critical value. Moreover, the reverse bifurcations in inhomogeneous condition are observed and under our discussion.

  17. Evolution of a designless nanoparticle network into reconfigurable Boolean logic

    Science.gov (United States)

    Bose, S. K.; Lawrence, C. P.; Liu, Z.; Makarenko, K. S.; van Damme, R. M. J.; Broersma, H. J.; van der Wiel, W. G.

    2015-12-01

    Natural computers exploit the emergent properties and massive parallelism of interconnected networks of locally active components. Evolution has resulted in systems that compute quickly and that use energy efficiently, utilizing whatever physical properties are exploitable. Man-made computers, on the other hand, are based on circuits of functional units that follow given design rules. Hence, potentially exploitable physical processes, such as capacitive crosstalk, to solve a problem are left out. Until now, designless nanoscale networks of inanimate matter that exhibit robust computational functionality had not been realized. Here we artificially evolve the electrical properties of a disordered nanomaterials system (by optimizing the values of control voltages using a genetic algorithm) to perform computational tasks reconfigurably. We exploit the rich behaviour that emerges from interconnected metal nanoparticles, which act as strongly nonlinear single-electron transistors, and find that this nanoscale architecture can be configured in situ into any Boolean logic gate. This universal, reconfigurable gate would require about ten transistors in a conventional circuit. Our system meets the criteria for the physical realization of (cellular) neural networks: universality (arbitrary Boolean functions), compactness, robustness and evolvability, which implies scalability to perform more advanced tasks. Our evolutionary approach works around device-to-device variations and the accompanying uncertainties in performance. Moreover, it bears a great potential for more energy-efficient computation, and for solving problems that are very hard to tackle in conventional architectures.

  18. Harmonic Analysis of Boolean Networks: Determinative Power and Perturbations

    CERN Document Server

    Heckel, Reinhard; Bossert, Martin

    2011-01-01

    Consider a large Boolean network with a feed forward structure. Given a probability distribution for the inputs, can one find-possibly small-collections of input nodes that determine the states of most other nodes in the network? To identify these nodes, a notion that quantifies the determinative power of an input over states in the network is needed. We argue that the mutual information (MI) between a subset of the inputs X = {X_1, ..., X_n} of node i and the function f_i(X)$ associated with node i quantifies the determinative power of this subset of inputs over node i. To study the relation of determinative power to sensitivity to perturbations, we relate the MI to measures of perturbations, such as the influence of a variable, in terms of inequalities. The result shows that, maybe surprisingly, an input that has large influence does not necessarily have large determinative power. The main tool for the analysis is Fourier analysis of Boolean functions. Whether a function is sensitive to perturbations or not...

  19. Evolution of a designless nanoparticle network into reconfigurable Boolean logic.

    Science.gov (United States)

    Bose, S K; Lawrence, C P; Liu, Z; Makarenko, K S; van Damme, R M J; Broersma, H J; van der Wiel, W G

    2015-12-01

    Natural computers exploit the emergent properties and massive parallelism of interconnected networks of locally active components. Evolution has resulted in systems that compute quickly and that use energy efficiently, utilizing whatever physical properties are exploitable. Man-made computers, on the other hand, are based on circuits of functional units that follow given design rules. Hence, potentially exploitable physical processes, such as capacitive crosstalk, to solve a problem are left out. Until now, designless nanoscale networks of inanimate matter that exhibit robust computational functionality had not been realized. Here we artificially evolve the electrical properties of a disordered nanomaterials system (by optimizing the values of control voltages using a genetic algorithm) to perform computational tasks reconfigurably. We exploit the rich behaviour that emerges from interconnected metal nanoparticles, which act as strongly nonlinear single-electron transistors, and find that this nanoscale architecture can be configured in situ into any Boolean logic gate. This universal, reconfigurable gate would require about ten transistors in a conventional circuit. Our system meets the criteria for the physical realization of (cellular) neural networks: universality (arbitrary Boolean functions), compactness, robustness and evolvability, which implies scalability to perform more advanced tasks. Our evolutionary approach works around device-to-device variations and the accompanying uncertainties in performance. Moreover, it bears a great potential for more energy-efficient computation, and for solving problems that are very hard to tackle in conventional architectures. PMID:26389658

  20. Coevolution of Information Processing and Topology in Hierarchical Adaptive Random Boolean Networks

    CERN Document Server

    Gorski, Piotr J; Holyst, Janusz A

    2015-01-01

    Random Boolean networks (RBNs) are frequently employed for modelling complex systems driven by information processing, e.g. for gene regulatory networks (GRNs). Here we propose a hierarchical adaptive RBN (HARBN) as a system consisting of distinct adaptive RBNs - subnetworks - connected by a set of permanent interlinks. Information measures and internal subnetworks topology of HARBN coevolve and reach steady-states that are specific for a given network structure. We investigate mean node information, mean edge information as well as a mean node degree as functions of model parameters and demonstrate HARBN's ability to describe complex hierarchical systems.

  1. A Boolean Approach to Airline Business Model Innovation

    DEFF Research Database (Denmark)

    Hvass, Kristian Anders

    Research in business model innovation has identified its significance in creating a sustainable competitive advantage for a firm, yet there are few empirical studies identifying which combination of business model activities lead to success and therefore deserve innovative attention. This study...... analyzes the business models of North America low-cost carriers from 2001 to 2010 using a Boolean minimization algorithm to identify which combinations of business model activities lead to operational profitability. The research aim is threefold: complement airline literature in the realm of business model...... innovation, introduce Boolean minimization methods to the field, and propose alternative business model activities to North American carriers striving for positive operating results....

  2. Detecting small attractors of large Boolean networks by function-reduction-based strategy.

    Science.gov (United States)

    Zheng, Qiben; Shen, Liangzhong; Shang, Xuequn; Liu, Wenbin

    2016-04-01

    Boolean networks (BNs) are widely used to model gene regulatory networks and to design therapeutic intervention strategies to affect the long-term behaviour of systems. A central aim of Boolean-network analysis is to find attractors that correspond to various cellular states, such as cell types or the stage of cell differentiation. This problem is NP-hard and various algorithms have been used to tackle it with considerable success. The idea is that a singleton attractor corresponds to n consistent subsequences in the truth table. To find these subsequences, the authors gradually reduce the entire truth table of Boolean functions by extending a partial gene activity profile (GAP). Not only does this process delete inconsistent subsequences in truth tables, it also directly determines values for some nodes not extended, which means it can abandon the partial GAPs that cannot lead to an attractor as early as possible. The results of simulation show that the proposed algorithm can detect small attractors with length p = 4 in BNs of up to 200 nodes with average indegree K = 2. PMID:26997659

  3. Complementing ODE-Based System Analysis Using Boolean Networks Derived from an Euler-Like Transformation.

    Directory of Open Access Journals (Sweden)

    Claudia Stötzel

    Full Text Available In this paper, we present a systematic transition scheme for a large class of ordinary differential equations (ODEs into Boolean networks. Our transition scheme can be applied to any system of ODEs whose right hand sides can be written as sums and products of monotone functions. It performs an Euler-like step which uses the signs of the right hand sides to obtain the Boolean update functions for every variable of the corresponding discrete model. The discrete model can, on one hand, be considered as another representation of the biological system or, alternatively, it can be used to further the analysis of the original ODE model. Since the generic transformation method does not guarantee any property conservation, a subsequent validation step is required. Depending on the purpose of the model this step can be based on experimental data or ODE simulations and characteristics. Analysis of the resulting Boolean model, both on its own and in comparison with the ODE model, then allows to investigate system properties not accessible in a purely continuous setting. The method is exemplarily applied to a previously published model of the bovine estrous cycle, which leads to new insights regarding the regulation among the components, and also indicates strongly that the system is tailored to generate stable oscillations.

  4. Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks

    Directory of Open Access Journals (Sweden)

    Wai-Ki Ching

    2008-09-01

    Full Text Available A Boolean network (BN is a mathematical model of genetic networks. We propose several algorithms for control of singleton attractors in BN. We theoretically estimate the average-case time complexities of the proposed algorithms, and confirm them by computer experiments. The results suggest the importance of gene ordering. Especially, setting internal nodes ahead yields shorter computational time than setting external nodes ahead in various types of algorithms. We also present a heuristic algorithm which does not look for the optimal solution but for the solution whose computational time is shorter than that of the exact algorithms.

  5. "Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis

    Directory of Open Access Journals (Sweden)

    Arellano Gustavo

    2011-12-01

    Full Text Available Abstract Background In Thomas' formalism for modeling gene regulatory networks (GRNs, branching time, where a state can have more than one possible future, plays a prominent role. By representing a certain degree of unpredictability, branching time can model several important phenomena, such as (a asynchrony, (b incompletely specified behavior, and (c interaction with the environment. Introducing more than one possible future for a state, however, creates a difficulty for ordinary simulators, because infinitely many paths may appear, limiting ordinary simulators to statistical conclusions. Model checkers for branching time, by contrast, are able to prove properties in the presence of infinitely many paths. Results We have developed Antelope ("Analysis of Networks through TEmporal-LOgic sPEcifications", http://turing.iimas.unam.mx:8080/AntelopeWEB/, a model checker for analyzing and constructing Boolean GRNs. Currently, software systems for Boolean GRNs use branching time almost exclusively for asynchrony. Antelope, by contrast, also uses branching time for incompletely specified behavior and environment interaction. We show the usefulness of modeling these two phenomena in the development of a Boolean GRN of the Arabidopsis thaliana root stem cell niche. There are two obstacles to a direct approach when applying model checking to Boolean GRN analysis. First, ordinary model checkers normally only verify whether or not a given set of model states has a given property. In comparison, a model checker for Boolean GRNs is preferable if it reports the set of states having a desired property. Second, for efficiency, the expressiveness of many model checkers is limited, resulting in the inability to express some interesting properties of Boolean GRNs. Antelope tries to overcome these two drawbacks: Apart from reporting the set of all states having a given property, our model checker can express, at the expense of efficiency, some properties that ordinary

  6. Characterizing short-term stability for Boolean networks over any distribution of transfer functions

    Science.gov (United States)

    Seshadhri, C.; Smith, Andrew M.; Vorobeychik, Yevgeniy; Mayo, Jackson R.; Armstrong, Robert C.

    2016-07-01

    We present a characterization of short-term stability of Kauffman's N K (random) Boolean networks under arbitrary distributions of transfer functions. Given such a Boolean network where each transfer function is drawn from the same distribution, we present a formula that determines whether short-term chaos (damage spreading) will happen. Our main technical tool which enables the formal proof of this formula is the Fourier analysis of Boolean functions, which describes such functions as multilinear polynomials over the inputs. Numerical simulations on mixtures of threshold functions and nested canalyzing functions demonstrate the formula's correctness.

  7. Critical line in undirected Kauffman Boolean networks - the role of percolation

    International Nuclear Information System (INIS)

    We show that to describe correctly the position of the critical line in Kauffman random Boolean networks one must take into account percolation phenomena underlying the process of damage spreading. For this reason, since the issue of percolation transition is much simpler in random undirected networks than in the directed ones, we study the Kauffman model in undirected networks. We derive the mean field formula for the critical line in the giant components of these networks, and show that the critical line characterizing the whole network results from the fact that the ordered behavior of small clusters shields the chaotic behavior of the giant component. We also show a possible attitude towards the analytical description of the shielding effect. The theoretical derivations given in this paper very much tally with the numerical simulations done for classical random graphs

  8. SAT-based Distributed Reactive Control Protocol Synthesis for Boolean Networks

    OpenAIRE

    Sahin, Yunus Emre; Ozay, Necmiye

    2016-01-01

    This paper considers the synthesis of distributed reactive control protocols for a Boolean network in a distributed manner. We start with a directed acyclic graph representing a network of Boolean subsystems and a global contract, given as an assumption-guarantee pair. Assumption captures the environment behavior, and guarantee is the requirements to be satisfied by the system. Local assumption-guarantee contracts, together with local control protocols ensuring these local contracts, are comp...

  9. A Boolean Approach to Airline Business Model Innovation

    OpenAIRE

    Hvass, Kristian

    2012-01-01

    Research in business model innovation has identified its significance in creating a sustainable competitive advantage for a firm, yet there are few empirical studies identifying which combination of business model activities lead to success and therefore deserve innovative attention. This study analyzes the business models of North America low-cost carriers from 2001 to 2010 using a Boolean minimization algorithm to identify which combinations of business model activities le...

  10. Damage spreading in spatial and small-world random boolean networks

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Qiming [Los Alamos National Laboratory; Teuscher, Christof [Los Alamos National Laboratory

    2008-01-01

    Random Boolean Networks (RBNs) are often used as generic models for certain dynamics of complex systems, ranging from social networks, neural networks, to gene or protein interaction networks. Traditionally, RBNs are interconnected randomly and without considering any spatial arrangement of the links and nodes. However, most real-world networks are spatially extended and arranged with regular, small-world, or other non-random connections. Here we explore the RBN network topology between extreme local connections, random small-world, and random networks, and study the damage spreading with small perturbations. We find that spatially local connections change the scaling of the relevant component at very low connectivities ({bar K} << 1) and that the critical connectivity of stability K{sub s} changes compared to random networks. At higher {bar K}, this scaling remains unchanged. We also show that the relevant component of spatially local networks scales with a power-law as the system size N increases, but with a different exponent for local and small-world networks. The scaling behaviors are obtained by finite-size scaling. We further investigate the wiring cost of the networks. From an engineering perspective, our new findings provide the key trade-offs between damage spreading (robustness), the network wiring cost, and the network's communication characteristics.

  11. Damage spreading in spatial and small-world random Boolean networks

    Science.gov (United States)

    Lu, Qiming; Teuscher, Christof

    2014-02-01

    The study of the response of complex dynamical social, biological, or technological networks to external perturbations has numerous applications. Random Boolean networks (RBNs) are commonly used as a simple generic model for certain dynamics of complex systems. Traditionally, RBNs are interconnected randomly and without considering any spatial extension and arrangement of the links and nodes. However, most real-world networks are spatially extended and arranged with regular, power-law, small-world, or other nonrandom connections. Here we explore the RBN network topology between extreme local connections, random small-world, and pure random networks, and study the damage spreading with small perturbations. We find that spatially local connections change the scaling of the Hamming distance at very low connectivities (K¯≪1) and that the critical connectivity of stability Ks changes compared to random networks. At higher K¯, this scaling remains unchanged. We also show that the Hamming distance of spatially local networks scales with a power law as the system size N increases, but with a different exponent for local and small-world networks. The scaling arguments for small-world networks are obtained with respect to the system sizes and strength of spatially local connections. We further investigate the wiring cost of the networks. From an engineering perspective, our new findings provide the key design trade-offs between damage spreading (robustness), the network's wiring cost, and the network's communication characteristics.

  12. Boolean model of Yeast Apoptosis as a tool to study yeast and human apoptotic regulations

    Directory of Open Access Journals (Sweden)

    MarijaCvijovic

    2012-12-01

    Full Text Available Programmed cell death (PCD is an essential cellular mechanism that is evolutionary conserved, mediated through various pathways and acts by integrating different stimuli. Many diseases such as neurodegenerative diseases and cancers are found to be caused by, or associated with, regulations in the cell death pathways. Yeast Saccharomyces cerevisiae, is a unicellular eukaryotic organism that shares with human cells components and pathways of the PCD and is therefore used as a model organism. Boolean modelling is becoming promising approach to capture qualitative behaviour and describe essential properties of such complex networks. Here we present large literature-based and to our knowledge first Boolean model that combines pathways leading to apoptosis (a type of PCD in yeast. Analysis of the yeast model confirmed experimental findings of anti-apoptotic role of Bir1p and pro-apoptotic role of Stm1p and revealed activation of the stress protein kinase Hog proposing the maximal level of activation upon heat stress. In addition we extended the yeast model and created an in silico humanized yeast in which human pro- and anti-apoptotic regulators Bcl-2 family and Valosin-contain protein (VCP are included in the model. We showed that accumulation of Bax in in silico humanized yeast shows apoptotic markers and that VCP is essential target of Akt Signaling. The presented Boolean model provides comprehensive description of yeast apoptosis network behaviour. Extended model of humanized yeast gives new insights of how complex human disease like neurodegenration can initially be tested.

  13. Damage Spreading in Spatial and Small-world Random Boolean Networks

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Qiming [Fermilab; Teuscher, Christof [Portland State U.

    2014-02-18

    The study of the response of complex dynamical social, biological, or technological networks to external perturbations has numerous applications. Random Boolean Networks (RBNs) are commonly used a simple generic model for certain dynamics of complex systems. Traditionally, RBNs are interconnected randomly and without considering any spatial extension and arrangement of the links and nodes. However, most real-world networks are spatially extended and arranged with regular, power-law, small-world, or other non-random connections. Here we explore the RBN network topology between extreme local connections, random small-world, and pure random networks, and study the damage spreading with small perturbations. We find that spatially local connections change the scaling of the relevant component at very low connectivities ($\\bar{K} \\ll 1$) and that the critical connectivity of stability $K_s$ changes compared to random networks. At higher $\\bar{K}$, this scaling remains unchanged. We also show that the relevant component of spatially local networks scales with a power-law as the system size N increases, but with a different exponent for local and small-world networks. The scaling behaviors are obtained by finite-size scaling. We further investigate the wiring cost of the networks. From an engineering perspective, our new findings provide the key design trade-offs between damage spreading (robustness), the network's wiring cost, and the network's communication characteristics.

  14. Decisional Processes with Boolean Neural Network: the Emergence of Mental Schemes

    CERN Document Server

    Barnabei, Graziano; Conversano, Ciro; Lensi, Elena

    2010-01-01

    Human decisional processes result from the employment of selected quantities of relevant information, generally synthesized from environmental incoming data and stored memories. Their main goal is the production of an appropriate and adaptive response to a cognitive or behavioral task. Different strategies of response production can be adopted, among which haphazard trials, formation of mental schemes and heuristics. In this paper, we propose a model of Boolean neural network that incorporates these strategies by recurring to global optimization strategies during the learning session. The model characterizes as well the passage from an unstructured/chaotic attractor neural network typical of data-driven processes to a faster one, forward-only and representative of schema-driven processes. Moreover, a simplified version of the Iowa Gambling Task (IGT) is introduced in order to test the model. Our results match with experimental data and point out some relevant knowledge coming from psychological domain.

  15. Decisional Processes with Boolean Neural Network: The Emergence of Mental Schemes

    International Nuclear Information System (INIS)

    Human decisional processes result from the employment of selected quantities of relevant information, generally synthesized from environmental incoming data and stored memories. Their main goal is the production of an appropriate and adaptive response to a cognitive or behavioral task. Different strategies of response production can be adopted, among which haphazard trials, formation of mental schemes and heuristics. In this paper, we propose a model of Boolean neural network that incorporates these strategies by recurring to global optimization strategies during the learning session. The model characterizes as well the passage from an unstructured/chaotic attractor neural network typical of data-driven processes to a faster one, forward-only and representative of schema-driven processes. Moreover, a simplified version of the Iowa Gambling Task (IGT) is introduced in order to test the model. Our results match with experimental data and point out some relevant knowledge coming from psychological domain. (authors)

  16. MILES FORMULAE FOR BOOLEAN MODELS OBSERVED ON LATTICES

    Directory of Open Access Journals (Sweden)

    Joachim Ohser

    2011-05-01

    Full Text Available The densities of the intrinsic volumes – in 3D the volume density, surface density, the density of the integral of the mean curvature and the density of the Euler number – are a very useful collection of geometric characteristics of random sets. Combining integral and digital geometry we develop a method for efficient and simultaneous calculation of the intrinsic volumes of random sets observed in binary images in arbitrary dimensions. We consider isotropic and reflection invariant Boolean models sampled on homogeneous lattices and compute the expectations of the estimators of the intrinsic volumes. It turns out that the estimator for the surface density is proved to be asymptotically unbiased and thusmultigrid convergent for Boolean models with convex grains. The asymptotic bias of the estimators for the densities of the integral of the mean curvature and of the Euler number is assessed for Boolean models of balls of random diameters. Miles formulae with corresponding correction terms are derived for the 3D case.

  17. Direct relations between morphology and transport in Boolean models.

    Science.gov (United States)

    Scholz, Christian; Wirner, Frank; Klatt, Michael A; Hirneise, Daniel; Schröder-Turk, Gerd E; Mecke, Klaus; Bechinger, Clemens

    2015-10-01

    We study the relation of permeability and morphology for porous structures composed of randomly placed overlapping circular or elliptical grains, so-called Boolean models. Microfluidic experiments and lattice Boltzmann simulations allow us to evaluate a power-law relation between the Euler characteristic of the conducting phase and its permeability. Moreover, this relation is so far only directly applicable to structures composed of overlapping grains where the grain density is known a priori. We develop a generalization to arbitrary structures modeled by Boolean models and characterized by Minkowski functionals. This generalization works well for the permeability of the void phase in systems with overlapping grains, but systematic deviations are found if the grain phase is transporting the fluid. In the latter case our analysis reveals a significant dependence on the spatial discretization of the porous structure, in particular the occurrence of single isolated pixels. To link the results to percolation theory we performed Monte Carlo simulations of the Euler characteristic of the open cluster, which reveals different regimes of applicability for our permeability-morphology relations close to and far away from the percolation threshold. PMID:26565348

  18. Direct relations between morphology and transport in Boolean models

    Science.gov (United States)

    Scholz, Christian; Wirner, Frank; Klatt, Michael A.; Hirneise, Daniel; Schröder-Turk, Gerd E.; Mecke, Klaus; Bechinger, Clemens

    2015-10-01

    We study the relation of permeability and morphology for porous structures composed of randomly placed overlapping circular or elliptical grains, so-called Boolean models. Microfluidic experiments and lattice Boltzmann simulations allow us to evaluate a power-law relation between the Euler characteristic of the conducting phase and its permeability. Moreover, this relation is so far only directly applicable to structures composed of overlapping grains where the grain density is known a priori. We develop a generalization to arbitrary structures modeled by Boolean models and characterized by Minkowski functionals. This generalization works well for the permeability of the void phase in systems with overlapping grains, but systematic deviations are found if the grain phase is transporting the fluid. In the latter case our analysis reveals a significant dependence on the spatial discretization of the porous structure, in particular the occurrence of single isolated pixels. To link the results to percolation theory we performed Monte Carlo simulations of the Euler characteristic of the open cluster, which reveals different regimes of applicability for our permeability-morphology relations close to and far away from the percolation threshold.

  19. Learning and Unlearning in Hopfield-Like Neural Network Performing Boolean Factor Analysis

    Czech Academy of Sciences Publication Activity Database

    Frolov, A. A.; Húsek, Dušan; Muraviev, I. P.; Polyakov, P.Y.

    Berlin : Springer, 2010 - (Koronacki, J.; Ras, Z.; Wierzchon, S.; Kacprzyk, J.), s. 501-518 ISBN 978-3-642-05176-0. - (Studies in Computational Intelligence. 262) Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * Hopfield-like neural network * spurious attractors * statistics * bingy data Subject RIV: IN - Informatics, Computer Science

  20. Analysis and control of Boolean networks a semi-tensor product approach

    CERN Document Server

    Cheng, Daizhan; Li, Zhiqiang

    2010-01-01

    This book presents a new approach to the investigation of Boolean control networks, using the semi-tensor product (STP), which can express a logical function as a conventional discrete-time linear system. This makes it possible to analyze basic control problems.

  1. Cytoskeletal logic: a model for molecular computation via Boolean operations in microtubules and microtubule-associated proteins.

    Science.gov (United States)

    Lahoz-Beltra, R; Hameroff, S R; Dayhoff, J E

    1993-01-01

    Adaptive behaviors and dynamic activities within living cells are organized by the cytoskeleton: intracellular networks of interconnected protein polymers which include microtubules (MTs), actin, intermediate filaments, microtubule associated proteins (MAPs) and other protein structures. Cooperative interactions among cytoskeletal protein subunit conformational states have been used to model signal transmission and information processing. In the present work we present a theoretical model for molecular computing in which Boolean logic is implemented in parallel networks of individual MTs interconnected by MAPs. Conformational signals propagate on MTs as in data buses and in the model MAPs are considered as Boolean operators, either as bit-lines (like MTs) where a signal can be transported unchanged between MTs ('BUS-MAP'), or as bit-lines where a Boolean operation is performed in one of the two MAP-MT attachments ('LOGIC-MAP'). Three logic MAPs have been defined ('NOT-MAP, 'AND-MAP', 'XOR-MAP') and used to demonstrate addition, subtraction and other arithmetic operations. Although our choice of Boolean logic is arbitrary, the simulations demonstrate symbolic manipulation in a connectionist system and suggest that MT-MAP networks can perform computation in living cells and are candidates for future molecular computing devices. PMID:8318677

  2. A Boolean delay equation model of ENSO variability

    Science.gov (United States)

    Saunders, Amira; Ghil, Michael

    2001-12-01

    Boolean delay equations (BDEs) provide a mathematical framework to formulate and analyze conceptual models of complex multi-component systems. This framework is used here to construct a simple conceptual model for the El-Niño/Southern Oscillation (ENSO) phenomenon. ENSO involves the coupling of atmospheric and oceanic processes that are far from being completely understood. Our BDE model uses Boolean variables to represent key atmospheric and oceanic quantities and equations that involve logical operators to describe their evolution. Two distinct time-delay parameters, one for the local atmosphere-ocean coupling effects and the other for oceanic wave propagation, are introduced. Over a range of physically relevant delay values, this truly minimal model captures two essential features of ENSO’s interannual variability - its regularity and its tendency to phase-lock to the annual cycle. Oscillations with average cycle length that is an integer multiple of the seasonal cycle are prevalent and range from 2 to 7 years. Transition zones - where the average period lengths are noninteger rational multiples of the forcing period - exhibit Devil’s staircases, a signature of the quasi-periodic (QP) route to chaos. Our BDE model thus validates results from previous studies of the interaction of the seasonal cycle with ENSO’s “delayed oscillator”. It gives therewith support to the view that the observed irregularity results predominantly from low-order chaotic processes rather than from stochastic weather noise. Moreover, in the transition zone between the two integer periodicities of 2 and 3 years, a heretofore unsuspected, self-similar “fractal sunburst” pattern emerges in phase-parameter space. This pattern provides a distinct and more complex scenario than the QP route to chaos found in earlier, more detailed ENSO models. Period selection in this 2-3-year transitional region seems to play a key role in ENSO’s irregularity, as well as in the appearance of

  3. Combinatorics of Boolean automata circuits dynamics

    OpenAIRE

    Demongeot, Jacques; Noual, Mathilde; Sené, Sylvain

    2012-01-01

    International audience In line with fields of theoretical computer science and biology that study Boolean automata networks to model regulation networks, we present some results concerning the dynamics of networks whose underlying structures are oriented cycles, that is, Boolean automata circuits. In the context of biological regulation, former studies have highlighted the importance of circuits on the asymptotic dynamical behaviour of the biological networks that contain them. Our work fo...

  4. Improving the User Query for the Boolean Model Using Genetic Algorithms

    CERN Document Server

    Nassar, Mohammad Othman; Mashagba, Eman Al

    2011-01-01

    The Use of genetic algorithms in the Information retrieval (IR) area, especially in optimizing a user query in Arabic data collections is presented in this paper. Very little research has been carried out on Arabic text collections. Boolean model have been used in this research. To optimize the query using GA we used different fitness functions, different mutation strategies to find which is the best strategy and fitness function that can be used with Boolean model when the data collection is the Arabic language. Our results show that the best GA strategy for the Boolean model is the GA (M2, Precision) method.

  5. Improving the User Query for the Boolean Model UsingGenetic Algorithms

    Directory of Open Access Journals (Sweden)

    Mohammad Othman Nassar

    2011-09-01

    Full Text Available The Use of genetic algorithms in the Information retrieval (IR area, especially in optimizing a user query in Arabic data collections is presented in this paper. Very little research has been carried out on Arabic text collections. Boolean model have been used in this research. To optimize the query using GA we used different fitness functions, different mutation strategies to find which is the best strategy and fitness function that can be used with Boolean model when the data collection is the Arabic language. Our results show that the best GA strategy for the Boolean model is the GA (M2, Precision method.

  6. Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms

    Science.gov (United States)

    Tamura, Takeyuki; Akutsu, Tatsuya

    The Boolean network (BN) is a mathematical model of genetic networks. It is known that detecting a singleton attractor, which is also called a fixed point, is NP-hard even for AND/OR BNs (i.e., BNs consisting of AND/OR nodes), where singleton attractors correspond to steady states. Though a naive algorithm can detect a singleton attractor for an AND/OR BN in O(n 2n) time, no O((2-ε)n) (ε > 0) time algorithm was known even for an AND/OR BN with non-restricted indegree, where n is the number of nodes in a BN. In this paper, we present an O(1.787n) time algorithm for detecting a singleton attractor of a given AND/OR BN, along with related results. We also show that detection of a singleton attractor in a BN with maximum indegree two is NP-hard and can be polynomially reduced to a satisfiability problem.

  7. Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection

    Directory of Open Access Journals (Sweden)

    Christopher S. Anderson

    2016-01-01

    Full Text Available Systems virology integrates host-directed approaches with molecular profiling to understand viral pathogenesis. Self-contained statistical approaches that combine expression profiles of genes with the available databases defining the genes involved in the pathways (gene-sets have allowed characterization of predictive gene-signatures associated with outcome of the influenza virus (IV infection. However, such enrichment techniques do not take into account interactions among pathways that are responsible for the IV infection pathogenesis. We investigate dendritic cell response to seasonal H1N1 influenza A/New Caledonia/20/1999 (NC infection and infer the Boolean logic rules underlying the interaction network of ligand induced signaling pathways and transcription factors. The model reveals several novel regulatory modes and provides insights into mechanism of cross talk between NFκB and IRF mediated signaling. Additionally, the logic rule underlying the regulation of IL2 pathway that was predicted by the Boolean model was experimentally validated. Thus, the model developed in this paper integrates pathway analysis tools with the dynamic modeling approaches to reveal the regulation between signaling pathways and transcription factors using genome-wide transcriptional profiles measured upon influenza infection.

  8. Random Boolean Networks and Attractors of their Intersecting Circuits

    OpenAIRE

    Demongeot, Jacques; Elena, Adrien; Noual, Mathilde; Sené, Sylvain

    2011-01-01

    International audience The multi-scale strategy in studying biological regulatory networks analysis is based on two level of analysis. The first level is structural and consists in examining the architecture of the interaction graph underlying the network and the second level is functional and analyse the regulatory properties of the network. We apply this dual approach to the "immunetworks" involved in the control of the immune system. As a result, we show that the small number of attract...

  9. HSP70 mediates survival in apoptotic cells – Boolean network prediction and experimental validation

    Directory of Open Access Journals (Sweden)

    Suhas Vasaikar

    2015-08-01

    Full Text Available Neuronal stress or injury results in the activation of proteins, which regulate the balance between survival and apoptosis. However, the complex mechanism of cell signalling involving cell death and survival, activated in response to cellular stress is not yet completely understood. To bring more clarity about these mechanisms, a Boolean network was constructed that represented the apoptotic pathway in neuronal cells. FasL and neurotrophic growth factor (NGF were considered as inputs in the absence and presence of heat shock proteins known to shift the balance towards survival by rescuing pro-apoptotic cells. The probabilities of survival, DNA repair and apoptosis as cellular fates, in the presence of either the growth factor or FasL, revealed a survival bias encoded in the network. Boolean predictions tested by measuring the mRNA expression level of caspase-3, caspase-8 and BAX in neuronal Neuro2a (N2a cell line with NGF and FasL as external input, showed positive correlation with the observed experimental results for survival and apoptotic states. It was observed that HSP70 contributed more towards rescuing cells from apoptosis in comparison to HSP27, HSP40 and HSP90. Overexpression of HSP70 in N2a transfected cells showed reversal of cellular fate from FasL-induced apoptosis to survival. Further, the pro-survival role of the proteins BCL2, IAP, cFLIP and NFκB determined by vertex perturbation analysis was experimentally validated through protein inhibition experiments using EM20-25, Embelin and Wedelolactone, which resulted in 1.27-fold, 1.26-fold and 1.46-fold increase in apoptosis of N2a cells. The existence of a one-to-one correspondence between cellular fates and attractor states shows that Boolean networks may be employed with confidence in qualitative analytical studies of biological networks.

  10. The behavior of noise-resilient Boolean networks with diverse topologies

    International Nuclear Information System (INIS)

    The dynamics of noise-resilient Boolean networks with majority functions and diverse topologies is investigated. A wide class of possible topological configurations is parametrized as a stochastic blockmodel. For this class of networks, the dynamics always undergoes a phase transition from a non-ergodic regime, where a memory of its past states is preserved, to an ergodic regime, where no such memory exists and every microstate is equally probable. Both the average error on the network and the critical value of noise where the transition occurs are investigated analytically, and compared to numerical simulations. The results for 'partially dense' networks, comprising relatively few, but dynamically important nodes, which have a number of inputs that greatly exceeds the average for the entire network, give very general upper bounds on the maximum resilience against noise attainable on globally sparse systems

  11. Variances as order parameter and complexity measure for random Boolean networks

    Energy Technology Data Exchange (ETDEWEB)

    Luque, Bartolo [Departamento de Matematica Aplicada y EstadIstica, Escuela Superior de Ingenieros Aeronauticos, Universidad Politecnica de Madrid, Plaza Cardenal Cisneros 3, Madrid 28040 (Spain); Ballesteros, Fernando J [Observatori Astronomic, Universitat de Valencia, Ed. Instituts d' Investigacio, Pol. La Coma s/n, E-46980 Paterna, Valencia (Spain); Fernandez, Manuel [Departamento de Matematica Aplicada y EstadIstica, Escuela Superior de Ingenieros Aeronauticos, Universidad Politecnica de Madrid, Plaza Cardenal Cisneros 3, Madrid 28040 (Spain)

    2005-02-04

    Several order parameters have been considered to predict and characterize the transition between ordered and disordered phases in random Boolean networks, such as the Hamming distance between replicas or the stable core, which have been successfully used. In this work, we propose a natural and clear new order parameter: the temporal variance. We compute its value analytically and compare it with the results of numerical experiments. Finally, we propose a complexity measure based on the compromise between temporal and spatial variances. This new order parameter and its related complexity measure can be easily applied to other complex systems.

  12. Application of Neural Network Boolean Factor Analysis Procedure to Automatic Conference Papers Categorization

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Frolov, A. A.; Polyakov, P.Y.; Řezanková, H.; Snášel, V.

    Lisabon : Instituto Nacional de Estatística, 2008 - (Gomes, M.; Pinto Martins, J.; Silva, J.), s. 3739-3742 ISBN 978-972-673-992-0. [ISI 2007. Session of the International Statistical Institute /56./. Lisboa (PT), 22.08.2007-29.08.2007] R&D Projects: GA AV ČR 1ET100300414 Grant ostatní: RFBR(RU) 05-07-90049 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * document classification * automatic concepts search * unsupervised learning * neural network Subject RIV: BB - Applied Statistics, Operational Research

  13. Neural Network Based Boolean Factor Analysis: Efficient Tool for Automated Topics Search.

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Frolov, A. A.; Polyakov, P.Y.; Řezanková, H.

    Amman: Applied Science Private University, 2006 - (Issa, G.; El-Qawasmeh, E.; Raho, G.), s. 321-327 ISBN 9957-8592-0-X. [CSIT 2006. International Multiconference on Computer Science and Information Technology /4./. Amman (JO), 05.04.2006-07.04.2006] R&D Projects: GA AV ČR 1ET100300419 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * neural networks * associative memory * clustering * web searching * semantic web * information retrieval * document indexing * document classification * document processing * data mining * machine learning Subject RIV: BB - Applied Statistics, Operational Research

  14. 高阶布尔网络的结构%Structure of higher order Boolean networks*

    Institute of Scientific and Technical Information of China (English)

    李志强; 赵寅; 程代展

    2011-01-01

    The higher order Boolean (control) network is introduced and its topological structure is studied.Using semi-tensor product of matrices,its dynamics is converted into two algebraic forms,which are standard discrete-time dynamic systems.The one-to-one correspondence of the network dynamics and its first algebraic form is proved,and certain topological structures,including fixed points,cycles,and transient time,of higher order Boolean (control) networks are revealed.The relationship between the original system and its second algebraic form is also studied.%介绍高阶布尔(控制)网络,并研究了其拓扑结构.以矩阵的半张量积作为工具,把高阶布尔网络的动态过程转化为2种标准离散事件动态系统的代数形式.证明了高阶布尔网络和第1代数形式的一一对应关系,并由此得到其拓扑结构(不动点、极限圈以及暂态期等).还研究了高阶布尔网络系统与它第2代数形式的关系.

  15. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord.

    KAUST Repository

    Lovrics, Anna

    2014-11-14

    We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks.

  16. Local digital estimators of intrinsic volumes for Boolean models and in the design based setting

    DEFF Research Database (Denmark)

    Svane, Anne Marie

    In order to estimate the specific intrinsic volumes of a planar Boolean model from a binary image, we consider local digital algorithms based on weigted sums of 2×2 configuration counts. For Boolean models with balls as grains, explicit formulas for the bias of such algorithms are derived......, resulting in a set of linear equations that the weights must satisfy in order to minimize the bias in high resolution. These results generalize to larger classes of random sets, as well as to the design based situation, where a fixed set is observed on a stationary isotropic lattice. Finally, the formulas...... for the bias obtained for Boolean models are applied to existing algorithms in order to compare their accuracy....

  17. On the number of attractors of Boolean automata circuits

    OpenAIRE

    Demongeot, Jacques; Noual, Mathilde; Sené, Sylvain

    2009-01-01

    In line with fields of theoretical computer science and biology that study Boolean automata networks often seen as models of regulation networks, we present some results concerning the dynamics of networks whose underlying interaction graphs are circuits, that is Boolean automata circuits. In the context of biological regulation, former studies have highlighted the importance of circuits on the asymptotic dynamical behaviour of the biological networks that contain them. Our work focuses on th...

  18. Attractor Neural Network Combined with Likelihood Maximization Algorithm for Boolean Factor Analysis

    Czech Academy of Sciences Publication Activity Database

    Frolov, A.; Húsek, Dušan; Polyakov, P.Y.

    Vol. 1. Berlin: Springer, 2012 - (Wang, J.; Yen, G.; Polycarpou, M.), s. 1-10. (Lecture Notes in Computer Science. 7367). ISBN 978-3-642-31345-5. ISSN 0302-9743. [ISNN 2012. International Symposium on Neural Networks /9./. Shenyang (CN), 11.07.2012-14.07.2012] R&D Projects: GA ČR GAP202/10/0262 Grant ostatní: GA MŠk(CZ) ED1.1.00/02.0070 Institutional research plan: CEZ:AV0Z10300504 Keywords : Associative Neural Network * Likelihood Maximization * Boolean Factor Analysis * Binary Matrix factorization * Noise XOR Mixing * Plato Problem * Information Gain * Bars problem * Data Mining * Dimension Reduction * Hebbian Learning * Anti-Hebbian Learning Subject RIV: IN - Informatics, Computer Science

  19. Boolean nested canalizing functions: a comprehensive analysis

    CERN Document Server

    Li, Yuan; Murrugarra, David; Aguilar, Boris; Laubenbacher, Reinhard

    2012-01-01

    Boolean network models of molecular regulatory networks have been used successfully in computational systems biology. The Boolean functions that appear in published models tend to have special properties, in particular the property of being nested canalizing, a property inspired by the concept of canalization in evolutionary biology. It has been shown that networks comprised of nested canalizing functions have dynamic properties that make them suitable for modeling molecular regulatory networks, namely a small number of (large) attractors, as well as relatively short limit cycles. This paper contains a detailed analysis of this class of functions, based on a novel normal form as polynomial functions over the Boolean field. The concept of layer is introduced that stratifies variables into different classes depending on their level of dominance. Using this layer concept a closed form formula is derived for the number of nested canalizing functions with a given number of variables. Additional metrics analyzed in...

  20. Application of fuzzy logic to Boolean models for digital soil assessment

    NARCIS (Netherlands)

    Gruijter, de J.J.; Walvoort, D.J.J.; Bragato, G.

    2011-01-01

    Boolean models based on expert knowledge are often used to classify soils into a limited number of classes of a difficult-to-measure soil attribute. Although the primary data used for these classifications contain information on whether the soil is a typical class member or a boundary case between t

  1. Applying Boolean discrete methods in the production of a real-valued probabilistic programming model

    OpenAIRE

    Nix, Jonathan Darren

    2016-01-01

    In this paper we explore the application of some notable Boolean methods, namely the Disjunctive Normal Form representation of logic table expansions, and apply them to a real-valued logic model which utilizes quantities on the range [0,1] to produce a probabilistic programming of a game character's logic in mathematical form.

  2. On a Boolean-valued Model of the Strict Implication System(Continuous)

    Institute of Scientific and Technical Information of China (English)

    LI Na; LIU Hua-ke

    2004-01-01

    The reference [4] proved the consistency of S 1 and S 2 among Lewis'five strict implicationsystems in the modal logic by using the method of the Boolean-valued model. But, in this method, the consistency of S 3 , S 4 and S 5 in Lewis'five strictimplication systems is not decided. This paper makes use of the properties : (1) the equivalence of the modal systems S 3 andP 3 , S 4 and P 4 ; (2) the modal systems P 3 and P 4 all contained the modal axiom T(□p) ; (3) the modal axiom T is correspondence to the reflexiveproperty in VB . Hence, the paper proves: (a) |A S 31|=1 ; (b) |A S 41|=1 ;(c) |A S 51|=1 in the model (where B is a complete Boolean algebra, R is reflexive property in VB ). Therefore, the paper finallyproves that the Boolean-valued model VB of the ZFC axiomsystem in set theory is also a Boolean-valued model of Lewis'the strict implication system S 3 , S 4 and S 5 .

  3. Robust Template Decomposition without Weight Restriction for Cellular Neural Networks Implementing Arbitrary Boolean Functions Using Support Vector Classifiers

    Directory of Open Access Journals (Sweden)

    Yih-Lon Lin

    2013-01-01

    Full Text Available If the given Boolean function is linearly separable, a robust uncoupled cellular neural network can be designed as a maximal margin classifier. On the other hand, if the given Boolean function is linearly separable but has a small geometric margin or it is not linearly separable, a popular approach is to find a sequence of robust uncoupled cellular neural networks implementing the given Boolean function. In the past research works using this approach, the control template parameters and thresholds are restricted to assume only a given finite set of integers, and this is certainly unnecessary for the template design. In this study, we try to remove this restriction. Minterm- and maxterm-based decomposition algorithms utilizing the soft margin and maximal margin support vector classifiers are proposed to design a sequence of robust templates implementing an arbitrary Boolean function. Several illustrative examples are simulated to demonstrate the efficiency of the proposed method by comparing our results with those produced by other decomposition methods with restricted weights.

  4. Modeling bidirectional reflectance of forests and woodlands using Boolean models and geometric optics

    Science.gov (United States)

    Strahler, Alan H.; Jupp, David L. B.

    1990-01-01

    Geometric-optical discrete-element mathematical models for forest canopies have been developed using the Boolean logic and models of Serra. The geometric-optical approach is considered to be particularly well suited to describing the bidirectional reflectance of forest woodland canopies, where the concentration of leaf material within crowns and the resulting between-tree gaps make plane-parallel, radiative-transfer models inappropriate. The approach leads to invertible formulations, in which the spatial and directional variance provides the means for remote estimation of tree crown size, shape, and total cover from remotedly sensed imagery.

  5. Stratification and enumeration of Boolean functions by canalizing depth

    Science.gov (United States)

    He, Qijun; Macauley, Matthew

    2016-01-01

    Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The canalizing depth of a function describes how many canalizing variables can be recursively "picked off", until a non-canalizing function remains. In this paper, we show how every Boolean function has a unique algebraic form involving extended monomial layers and a well-defined core polynomial. This generalizes recent work on the algebraic structure of nested canalizing functions, and it yields a stratification of all Boolean functions by their canalizing depth. As a result, we obtain closed formulas for the number of n-variable Boolean functions with depth k, which simultaneously generalizes enumeration formulas for canalizing, and nested canalizing functions.

  6. Stratification and enumeration of Boolean functions by canalizing depth

    CERN Document Server

    He, Qijun

    2015-01-01

    Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The canalizing depth of a function describes how many canalizing variables can be recursively picked off, until a non-canalizing function remains. In this paper, we show how every Boolean function has a unique algebraic form involving extended monomial layers and a well-defined core polynomial. This generalizes recent work on the algebraic structure of nested canalizing functions, and it yields a stratification of all Boolean functions by their canalizing depth. As a result, we obtain closed formulas for the number of n-variable Boolean functions with depth k, which simultaneously generalizes enumeration formulas for canalizing, and nested canalizing functions.

  7. An efficient algorithm to identify the optimal one-bit perturbation based on the basin-of-state size of Boolean networks.

    Science.gov (United States)

    Hu, Mingxiao; Shen, Liangzhong; Zan, Xiangzhen; Shang, Xuequn; Liu, Wenbin

    2016-01-01

    Boolean networks are widely used to model gene regulatory networks and to design therapeutic intervention strategies to affect the long-term behavior of systems. In this paper, we investigate the less-studied one-bit perturbation, which falls under the category of structural intervention. Previous works focused on finding the optimal one-bit perturbation to maximally alter the steady-state distribution (SSD) of undesirable states through matrix perturbation theory. However, the application of the SSD is limited to Boolean networks with about ten genes. In 2007, Xiao et al. proposed to search the optimal one-bit perturbation by altering the sizes of the basin of attractions (BOAs). However, their algorithm requires close observation of the state-transition diagram. In this paper, we propose an algorithm that efficiently determines the BOA size after a perturbation. Our idea is that, if we construct the basin of states for all states, then the size of the BOA of perturbed networks can be obtained just by updating the paths of the states whose transitions have been affected. Results from both synthetic and real biological networks show that the proposed algorithm performs better than the exhaustive SSD-based algorithm and can be applied to networks with about 25 genes. PMID:27196530

  8. Boolean modeling of neural systems with point-process inputs and outputs.

    Science.gov (United States)

    Marmarelis, Vasilis Z; Zanos, Theodoros P; Courellis, Spiros H; Berger, Theodore W

    2006-01-01

    This paper presents a novel modeling approach for neural systems with point-process inputs and outputs (binary time-series of 0's and 1's) that utilizes Boolean operators of modulo-2 multiplication and addition, corresponding to the logical AND and OR operations respectively. The form of the employed mathematical model is akin to a "Boolean-Volterra" model that contains the product terms of all relevant input lags in a hierarchical order, where terms of order higher than first represent nonlinear interactions among the various lagged values of each input point-process or among lagged values of various inputs (if multiple inputs exist) as they reflect on the output. The coefficients of this Boolean model are also binary variables that indicate the presence or absence of the respective term in each specific model/system. Simulations are used to explore the properties of such models and the feasibility of accurate estimation of such models from short data-records in the presence of noise (i.e. spurious spikes). The results demonstrate the feasibility of obtaining reliable estimates of such models, even in the presence of considerable noise in the input and/or output, thus making the proposed approach an attractive candidate for modeling neural systems in a practical context. PMID:17946091

  9. Modeling boolean decision rules applied to multiple-observer decision strategies.

    Science.gov (United States)

    Maguire, W

    1996-01-01

    A model that derives multiple-observer decision strategy ROC curves for boolean decision rules applied to binary decisions of two or three observers is presented. It is assumed that covert decision variables consistent with ROC models of observer performance underlie decisions and that readers' decision criteria are in a fixed relationship. The specific parameters of individual ROC curves and the correlational structure that describes interobserver agreement have dramatic effects upon the relative benefits to be derived from different boolean strategies. A common strategy employed in clinical practice, in which the overall decision is positive if any observer makes a positive decision, is most effective when the readers are of similar ability, when they adopt similar decision criteria, when interreader agreement is greater for negative than for positive cases, and when the individual ROC slope is observer decision strategies can be evaluated using the model equations. A bootstrap method for testing model-associated hypotheses is described. PMID:8717599

  10. Boolean decision problems with competing interactions on scale-free networks: equilibrium and nonequilibrium behavior in an external bias.

    Science.gov (United States)

    Zhu, Zheng; Andresen, Juan Carlos; Moore, M A; Katzgraber, Helmut G

    2014-02-01

    We study the equilibrium and nonequilibrium properties of Boolean decision problems with competing interactions on scale-free networks in an external bias (magnetic field). Previous studies at zero field have shown a remarkable equilibrium stability of Boolean variables (Ising spins) with competing interactions (spin glasses) on scale-free networks. When the exponent that describes the power-law decay of the connectivity of the network is strictly larger than 3, the system undergoes a spin-glass transition. However, when the exponent is equal to or less than 3, the glass phase is stable for all temperatures. First, we perform finite-temperature Monte Carlo simulations in a field to test the robustness of the spin-glass phase and show that the system has a spin-glass phase in a field, i.e., exhibits a de Almeida-Thouless line. Furthermore, we study avalanche distributions when the system is driven by a field at zero temperature to test if the system displays self-organized criticality. Numerical results suggest that avalanches (damage) can spread across the whole system with nonzero probability when the decay exponent of the interaction degree is less than or equal to 2, i.e., that Boolean decision problems on scale-free networks with competing interactions can be fragile when not in thermal equilibrium. PMID:25353433

  11. Origin and Elimination of Two Global Spurious Attractors in Hopfield-Like Neural Network Performing Boolean Factor Analysis

    Czech Academy of Sciences Publication Activity Database

    Frolov, A. A.; Húsek, Dušan; Muraviev, I. P.; Polyakov, P.Y.

    2010-01-01

    Roč. 73, č. 7-9 (2010), s. 1394-1404. ISSN 0925-2312 R&D Projects: GA ČR GA205/09/1079; GA MŠk(CZ) 1M0567 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * Hopfield neural Network * unsupervised learning * dimension reduction * data mining Subject RIV: IN - Informatics, Computer Science Impact factor: 1.429, year: 2010

  12. PARAMETER ESTIMATION IN NON-HOMOGENEOUS BOOLEAN MODELS: AN APPLICATION TO PLANT DEFENSE RESPONSE

    Directory of Open Access Journals (Sweden)

    Maria Angeles Gallego

    2014-11-01

    Full Text Available Many medical and biological problems require to extract information from microscopical images. Boolean models have been extensively used to analyze binary images of random clumps in many scientific fields. In this paper, a particular type of Boolean model with an underlying non-stationary point process is considered. The intensity of the underlying point process is formulated as a fixed function of the distance to a region of interest. A method to estimate the parameters of this Boolean model is introduced, and its performance is checked in two different settings. Firstly, a comparative study with other existent methods is done using simulated data. Secondly, the method is applied to analyze the longleaf data set, which is a very popular data set in the context of point processes included in the R package spatstat. Obtained results show that the new method provides as accurate estimates as those obtained with more complex methods developed for the general case. Finally, to illustrate the application of this model and this method, a particular type of phytopathological images are analyzed. These images show callose depositions in leaves of Arabidopsis plants. The analysis of callose depositions, is very popular in the phytopathological literature to quantify activity of plant immunity.

  13. Computational complexity of Boolean functions

    International Nuclear Information System (INIS)

    Boolean functions are among the fundamental objects of discrete mathematics, especially in those of its subdisciplines which fall under mathematical logic and mathematical cybernetics. The language of Boolean functions is convenient for describing the operation of many discrete systems such as contact networks, Boolean circuits, branching programs, and some others. An important parameter of discrete systems of this kind is their complexity. This characteristic has been actively investigated starting from Shannon's works. There is a large body of scientific literature presenting many fundamental results. The purpose of this survey is to give an account of the main results over the last sixty years related to the complexity of computation (realization) of Boolean functions by contact networks, Boolean circuits, and Boolean circuits without branching. Bibliography: 165 titles.

  14. Techniques for solving Boolean equation systems

    OpenAIRE

    Keinänen, Misa

    2006-01-01

    Boolean equation systems are ordered sequences of Boolean equations decorated with least and greatest fixpoint operators. Boolean equation systems provide a useful framework for formal verification because various specification and verification problems, for instance, μ-calculus model checking can be represented as the problem of solving Boolean equation systems. The general problem of solving a Boolean equation system is a computationally hard task, and no polynomial time solution technique ...

  15. Parameter Learning of Boolean Bayesian Networks%布尔型贝叶斯网络参数学习

    Institute of Scientific and Technical Information of China (English)

    吴永广; 周兴旺

    2015-01-01

    布尔型贝叶斯网络是一类由布尔型变量组成的网络,它能够以线性多变量函数描述,使计算和处理上灵活高效。通过运用连接树算法对络进行分块化处理的方法,可以提高算法的效率,然后以传统的最大似然估计方法对布尔型网络的参数进行学习。服从同一分布律的贝叶斯网络参数学习算法发展比较成熟,这类以狄利克雷或者高斯分布为基础的算法在应用领域中难以发挥其应有的价值。相比之下,基于布尔型贝叶斯网络下的参数学习更贴近于应用,在人工智能和数据挖掘等领域有很好的发展前景。%Boolean Bayesian network is a class of Bayesian networks which are made up of Boolean varia-bles. The method to describe the network with a multi-linear function is flexible and efficient to compute and process variables. By introducing Junction Tree algorithm,the network can be divided into blocks which can make it easy to calculate. Then the traditional maximum likelihood estimation method was used for learning Boolean networks. Parameter learning algorithm following the same distribution is more ma-ture,but this kind of algorithm based on Dirichlet or Gaussian distribution is difficult to play its proper val-ue in practice. In contrast,parameter learning based on Boolean networks gets close to applications. It has good prospects for development in areas such as artificial intelligence and data mining.

  16. A Boolean Analysis Predicting Industry Change: Innovation, Imitation & Business Models

    OpenAIRE

    Hvass, Kristian Anders

    2008-01-01

    The deregulated scheduled passenger airline industry is in a constant state of motion as managers continually adapt their business models to meet the challenging market environment. Such adaptation has led to a variety of airlines populating the industry; from the birth of low-cost carriers to the transformation of state-owned behemoths to lean and successful carriers. These dynamics challenge airline managers to continuously acclimate their business models and to understand industry evolu...

  17. On the Number of Attractors of Positive and Negative Boolean Automata Circuits.

    OpenAIRE

    Demongeot, Jacques; Noual, Mathilde; Sené, Sylvain

    2010-01-01

    International audience In line with fields of theoretical computer science and biology that study Boolean automata networks often seen as models of regulation networks, we present some results concerning the dynamics of networks whose underlying interaction graphs are circuits, that is, Boolean automata circuits. In the context of biological regulation, former studies have highlighted the importance of circuits on the asymptotic dynamical behaviour of the biological networks that contain t...

  18. Comparison of Neural Network Boolean Factor Analysis Method with Some Other Dimension Reduction Methods on Bars Problem

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Moravec, P.; Snášel, V.; Frolov, A.; Řezanková, H.; Polyakov, P.Y.

    Berlin : Springer, 2007 - (Ghosh, A.; De, R.), s. 235-243 ISBN 978-3-540-77045-9. - (Lecture Notes in Computer Science. 4815). [PReMI 2007. International Conference /2./. Kolkata (IN), 18.12.2007-22.12.2007] R&D Projects: GA MŠk(CZ) 1M0567; GA AV ČR 1ET100300419 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * neural network * dimension reduction * cluster analysis Subject RIV: BB - Applied Statistics, Operational Research

  19. Boolean implication networks derived from large scale, whole genome microarray datasets

    OpenAIRE

    Sahoo, Debashis; Dill, David L.; Gentles, Andrew J.; Tibshirani, Robert; Plevritis, Sylvia K.

    2008-01-01

    We describe a method for extracting Boolean implications (if-then relationships) in very large amounts of gene expression microarray data. A meta-analysis of data from thousands of microarrays for humans, mice, and fruit flies finds millions of implication relationships between genes that would be missed by other methods. These relationships capture gender differences, tissue differences, development, and differentiation. New relationships are discovered that are preserved across all three sp...

  20. A solution to the surface intersection problem. [Boolean functions in geometric modeling

    Science.gov (United States)

    Timer, H. G.

    1977-01-01

    An application-independent geometric model within a data base framework should support the use of Boolean operators which allow the user to construct a complex model by appropriately combining a series of simple models. The use of these operators leads to the concept of implicitly and explicitly defined surfaces. With an explicitly defined model, the surface area may be computed by simply summing the surface areas of the bounding surfaces. For an implicitly defined model, the surface area computation must deal with active and inactive regions. Because the surface intersection problem involves four unknowns and its solution is a space curve, the parametric coordinates of each surface must be determined as a function of the arc length. Various subproblems involved in the general intersection problem are discussed, and the mathematical basis for their solution is presented along with a program written in FORTRAN IV for implementation on the IBM 370 TSO system.

  1. Boolean Differential Operators

    OpenAIRE

    Catumba, Jorge; Diaz, Rafael

    2012-01-01

    We consider four combinatorial interpretations for the algebra of Boolean differential operators. We show that each interpretation yields an explicit matrix representation for Boolean differential operators.

  2. Boolean modeling of neural systems with point-process inputs and outputs. Part I: theory and simulations.

    Science.gov (United States)

    Marmarelis, Vasilis Z; Zanos, Theodoros P; Berger, Theodore W

    2009-08-01

    This paper presents a new modeling approach for neural systems with point-process (spike) inputs and outputs that utilizes Boolean operators (i.e. modulo 2 multiplication and addition that correspond to the logical AND and OR operations respectively, as well as the AND_NOT logical operation representing inhibitory effects). The form of the employed mathematical models is akin to a "Boolean-Volterra" model that contains the product terms of all relevant input lags in a hierarchical order, where terms of order higher than first represent nonlinear interactions among the various lagged values of each input point-process or among lagged values of various inputs (if multiple inputs exist) as they reflect on the output. The coefficients of this Boolean-Volterra model are also binary variables that indicate the presence or absence of the respective term in each specific model/system. Simulations are used to explore the properties of such models and the feasibility of their accurate estimation from short data-records in the presence of noise (i.e. spurious spikes). The results demonstrate the feasibility of obtaining reliable estimates of such models, with excitatory and inhibitory terms, in the presence of considerable noise (spurious spikes) in the outputs and/or the inputs in a computationally efficient manner. A pilot application of this approach to an actual neural system is presented in the companion paper (Part II). PMID:19517238

  3. Memory-Based Boolean Game and Self-Organized Phenomena on Networks

    Institute of Scientific and Technical Information of China (English)

    HUANG Zi-Gang; WU Zhi-Xi; GUAN Jian-Yue; WANG Ying-Hai

    2006-01-01

    @@ We study a memory-based Boolean game (MBBG) taking place on a regular ring, wherein each agent acts according to its local optimal states of the last M time steps recorded in memory, and the agents in the minority are rewarded. One free parameter p between 0 and 1 is introduced to denote the strength of the agent willing to make a decision according to its memory. It is found that giving proper willing strength p, the MBBG system can spontaneously evolve to a state of performance better than the random game; while for larger p, the herd behaviour emerges to reduce the system profit. By analysing the dependence of dynamics of the system on the memory capacity M, we find that a higher memory capacity favours the emergence of the better performance state, and effectively restrains the herd behaviour, thus increases the system profit. Considering the high cost of long-time memory, the enhancement of memory capacity for restraining the herd behaviour is also discussed,and M = 5 is suggested to be a good choice.

  4. Boolean operations of STL models based on edge-facet intersection

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    For the data processing of the Rapid Prototyping Manufacturing, Boolean operation can offer a versatile tool for editing or modifying the STL model, adding the artificial construction, and creating the complex assistant support structure to meet the special technical requests. The topological structure of STL models was built firstly in order to obtain the neighborhood relationship among the triangular facets. The intersection test between every edge of one solid and every facet of another solid Was taken to get the intersection points. According to the matching relationship of the triangle index recorded in the data structure of the intersection points, the intersection segments array and the intersection loop were traced out. Each intersected triangle was subdivided by the Constrained Delaunay Triangulations. The intersected surfaces were divided into several surface patches along the intersection loops. The inclusion prediction between the surface patch and the other solid was taken by testing whether the candidate point Was inside or outside the solid region of the slice. Detecting the loops for determination of the valid intersection lines greatly increases the efficiency and the reliability of the process.

  5. APPLICATION OF THE OVERLAY WEIGHTED MODEL AND BOOLEAN LOGIC TO DETERMINE THE BEST LOCATIONS FOR ARTIFICIAL RECHARGE OF GROUNDWATER

    Directory of Open Access Journals (Sweden)

    Max Billib

    2011-12-01

    Full Text Available With population increase, lack of conventional fresh water resources and uncertainties due to climate change, there is growing interest in the arid and semi-arid areas to increase groundwater recharge with recycled water. Finding the best locations for artificial recharge of groundwater in such areas is one of the most crucial design steps to guarantee the long life and the sustainability of these projects. This study presents two ways to go about performing analysis; creating a suitability map to find out the suitability of every location on the map and another way is querying the created data sets to obtain a Boolean result of true or false map. These techniques have been applied on Sadat Industrial City which is located in a semi arid area in the western desert fringes of The Nile delta in the north west of Egypt. Thematic layers for number of parameters were prepared from some maps and satellite images and they have been classified, weighted and integrated in ArcGIS environment. By the means of the overlay weighted model in ArcGIS a suitability map which is classified into number of priority zones was obtained and it could be compared with the obtained true-false map of Boolean logic. Both methods suggested mostly the northern parts of the city for groundwater recharge; however the weighted model could give more accurate suitability map while Boolean logic suggested wider ranges of areas. This study recommends Boolean logic as a first estimator for locating the best locations as it is easier and not time consuming, while the overlay weighted model for more accurate results.

  6. Fault Tolerant Boolean Satisfiability

    CERN Document Server

    Roy, A

    2011-01-01

    A delta-model is a satisfying assignment of a Boolean formula for which any small alteration, such as a single bit flip, can be repaired by flips to some small number of other bits, yielding a new satisfying assignment. These satisfying assignments represent robust solutions to optimization problems (e.g., scheduling) where it is possible to recover from unforeseen events (e.g., a resource becoming unavailable). The concept of delta-models was introduced by Ginsberg, Parkes and Roy (AAAI 1998), where it was proved that finding delta-models for general Boolean formulas is NP-complete. In this paper, we extend that result by studying the complexity of finding delta-models for classes of Boolean formulas which are known to have polynomial time satisfiability solvers. In particular, we examine 2-SAT, Horn-SAT, Affine-SAT, dual-Horn-SAT, 0-valid and 1-valid SAT. We see a wide variation in the complexity of finding delta-models, e.g., while 2-SAT and Affine-SAT have polynomial time tests for delta-models, testing w...

  7. Boolean gates on actin filaments

    Science.gov (United States)

    Siccardi, Stefano; Tuszynski, Jack A.; Adamatzky, Andrew

    2016-01-01

    Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications.

  8. Investigating Boolean Matrix Factorization

    Czech Academy of Sciences Publication Activity Database

    Snášel, V.; Platoš, J.; Krömer, P.; Húsek, Dušan; Neruda, Roman; Frolov, A. A.

    - : ACM, 2008 - (Ding, C.; Li, T.; Zhu, S.), s. 18-25 ISBN 978-1-60558-307-5. [DMMT'08. Workshop in Conjunction with SIGKDD 2008 /14./. Las Vegas (US), 24.08.2008-24.08.2008] Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * nonnegative matrix factorization * neural networks * information retrieval * data mining * binary data Subject RIV: BB - Applied Statistics, Operational Research http://users.cs.fiu.edu/~taoli/kdd08-workshop/DMMT08-Proceedings.pdf

  9. Quantum boolean functions

    OpenAIRE

    Montanaro, Ashley; Osborne, Tobias J.

    2008-01-01

    In this paper we introduce the study of quantum boolean functions, which are unitary operators f whose square is the identity: f^2 = I. We describe several generalisations of well-known results in the theory of boolean functions, including quantum property testing; a quantum version of the Goldreich-Levin algorithm for finding the large Fourier coefficients of boolean functions; and two quantum versions of a theorem of Friedgut, Kalai and Naor on the Fourier spectra of boolean functions. In o...

  10. Boolean reasoning the logic of boolean equations

    CERN Document Server

    Brown, Frank Markham

    2012-01-01

    A systematic treatment of Boolean reasoning, this concise, newly revised edition combines the works of early logicians with recent investigations, including previously unpublished research results. Brown begins with an overview of elementary mathematical concepts and outlines the theory of Boolean algebras. Two concluding chapters deal with applications. 1990 edition.

  11. Boolean Expression Diagrams

    DEFF Research Database (Denmark)

    Andersen, Henrik Reif; Hulgaard, Henrik

    2002-01-01

    This paper presents a new data structure called boolean expression diagrams (BEDs) for representing and manipulating Boolean functions. BEDs are a generalization of binary decision diagrams (BDDs) which can represent any Boolean circuit in linear space. Two algorithms are described for transforming...

  12. 布尔表达式的化简与并行排序网络验证%Boolean expression simplification and parallel sort network validation

    Institute of Scientific and Technical Information of China (English)

    王德才; 徐建国; 吴哲辉; 罗永亮; 王传民

    2009-01-01

    To design an effective tool that can be used to verify the correctness of a parallel sorting network, a Boolean expression sim-plification algorithm based on the [0,1] theory and Boolean function of the characteristics and the nature is put forward, based on this algorithm a validation tool is designed. The characteristics and the nature of [0,1] theory and Boolean function are discussed and the natures that are helpful to simplify of the operation are pointed out. The tool can be used for the design of parallel sorting networks based on the parameters of the network graphics, and it can automatically generate the Boolean expressions and simplify it. The tool's output will be helpful to analyze the network, and it can also be used to design and optimize the sort network. Finally, the validity of the tool is demonstrated by the application.%为设计出能够验证并行排序网络正确性的有效工具,根据[0,1]原理和布尔函数的特点和性质,提出一种布尔表达式的化简算法,并根据此算法设计出验证工具.对[0,1]原理和布尔函数的特点和性质进行了讨论,指出有利于化简操作的性质.设计出的工具能够根据并行排序网络的参数显示网络图形、自动生成布尔表达式并实现化简验证,工具的输出有利于对排序网络的分析,也可以用于辅助排序网络的设计和优化.实验结果表明了该工具的有效性.

  13. Fault Tolerant Boolean Satisfiability

    OpenAIRE

    Roy, A

    2011-01-01

    A delta-model is a satisfying assignment of a Boolean formula for which any small alteration, such as a single bit flip, can be repaired by flips to some small number of other bits, yielding a new satisfying assignment. These satisfying assignments represent robust solutions to optimization problems (e.g., scheduling) where it is possible to recover from unforeseen events (e.g., a resource becoming unavailable). The concept of delta-models was introduced by Ginsberg, Parkes and Roy (AAAI 1998...

  14. Controllability and observability of Boolean control networks%布尔控制网络的能控性与能观性

    Institute of Scientific and Technical Information of China (English)

    李志强; 宋金利

    2013-01-01

    Using the semi-tensor product,we convert the Boolean control network to its algebraic form.From the structure matrix of Boolean control network,the controllability and observability of the Boolean control network are discussed.A novel necessary and sufficient condition for controllability,which improves the recent results,is given.The new controllability condition eliminates the redundant computation of controllability matrix.The highest power of matrix is reduced from 2m+n to 2 n.Also,a sufficient condition for observability is obtained,which can be computed easily.A numerical example is presented to show the applicability of our controllability and observability condition.%利用矩阵的半张量积,布尔控制网络被转化为离散时间系统.本文从离散时间系统的结构矩阵出发,讨论了逻辑控制系统的能控能观性条件,得到了一个新的能控性条件.新的条件简化了原有能控性矩阵的计算复杂性,矩阵的最高阶数由原来的2m+n降到了2n.另外,还得到了检验布尔控制网络能观性的条件.与原有条件相比,新的条件更容易计算检验.最后,给出一个实例,检验给出的能控能观性判断条件的正确性.

  15. Boolean algebra essentials

    CERN Document Server

    Solomon, Alan D

    2012-01-01

    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Boolean Algebra includes set theory, sentential calculus, fundamental ideas of Boolean algebras, lattices, rings and Boolean algebras, the structure of a Boolean algebra, and Boolean

  16. Fast Gr\\"obner Basis Computation for Boolean Polynomials

    CERN Document Server

    Hinkelmann, Franziska

    2010-01-01

    We introduce the Macaulay2 package BooleanGB, which computes a Gr\\"obner basis for Boolean polynomials using a binary representation rather than symbolic. We compare the runtime of several Boolean models from systems in biology and give an application to Sudoku.

  17. "Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis

    OpenAIRE

    Arellano Gustavo; Argil Julián; Azpeitia Eugenio; Benítez Mariana; Carrillo Miguel; Góngora Pedro; Rosenblueth David A.; Alvarez-Buylla Elena R

    2011-01-01

    Abstract Background In Thomas' formalism for modeling gene regulatory networks (GRNs), branching time, where a state can have more than one possible future, plays a prominent role. By representing a certain degree of unpredictability, branching time can model several important phenomena, such as (a) asynchrony, (b) incompletely specified behavior, and (c) interaction with the environment. Introducing more than one possible future for a state, however, creates a difficulty for ordinary simulat...

  18. Monotone Boolean functions

    International Nuclear Information System (INIS)

    Monotone Boolean functions are an important object in discrete mathematics and mathematical cybernetics. Topics related to these functions have been actively studied for several decades. Many results have been obtained, and many papers published. However, until now there has been no sufficiently complete monograph or survey of results of investigations concerning monotone Boolean functions. The object of this survey is to present the main results on monotone Boolean functions obtained during the last 50 years

  19. Boolean integral calculus

    Science.gov (United States)

    Tucker, Jerry H.; Tapia, Moiez A.; Bennett, A. Wayne

    1988-01-01

    The concept of Boolean integration is developed, and different Boolean integral operators are introduced. Given the changes in a desired function in terms of the changes in its arguments, the ways of 'integrating' (i.e. realizing) such a function, if it exists, are presented. The necessary and sufficient conditions for integrating, in different senses, the expression specifying the changes are obtained. Boolean calculus has applications in the design of logic circuits and in fault analysis.

  20. Boolean Expression Diagrams

    DEFF Research Database (Denmark)

    Andersen, Henrik Reif; Hulgaard, Henrik

    This paper presents a new data structure called Boolean Expression Diagrams (BEDs) for representing and manipulating Boolean functions. BEDs are a generalization of Binary Decision Diagrams (BDDs) which can represent any Boolean circuit in linear space and still maintain many of the desirable...... properties of BDDs. Two algorithms are described for transforming a BED into a reduced ordered BDD. One closely mimics the BDD apply-operator while the other can exploit the structural information of the Boolean expression. The efficacy of the BED representation is demonstrated by verifying that the...

  1. INCLUSION RATIO BASED ESTIMATOR FOR THE MEAN LENGTH OF THE BOOLEAN LINE SEGMENT MODEL WITH AN APPLICATION TO NANOCRYSTALLINE CELLULOSE

    Directory of Open Access Journals (Sweden)

    Mikko Niilo-Rämä

    2014-06-01

    Full Text Available A novel estimator for estimating the mean length of fibres is proposed for censored data observed in square shaped windows. Instead of observing the fibre lengths, we observe the ratio between the intensity estimates of minus-sampling and plus-sampling. It is well-known that both intensity estimators are biased. In the current work, we derive the ratio of these biases as a function of the mean length assuming a Boolean line segment model with exponentially distributed lengths and uniformly distributed directions. Having the observed ratio of the intensity estimators, the inverse of the derived function is suggested as a new estimator for the mean length. For this estimator, an approximation of its variance is derived. The accuracies of the approximations are evaluated by means of simulation experiments. The novel method is compared to other methods and applied to real-world industrial data from nanocellulose crystalline.

  2. Analysis and Control of Boolean Networks:A Semi-tensor Product Approach%布尔网络的分析与控制-矩阵半张量积方法

    Institute of Scientific and Technical Information of China (English)

    程代展; 齐洪胜; 赵寅

    2011-01-01

    布尔网络是描述基因调控网络的一个有力工具.由于系统生物学的发展,布尔网络的分析与控制成为生物学与系统控制学科的交叉热点.本文综述作者用其原创的矩阵半张量积方法在布尔网络的分析与控制中得到的一系列结果.内容包括:布尔网络的拓扑结构,布尔控制网络的能控、能观性与实现,布尔网络的稳定性和布尔控制网络的镇定,布尔控制网络的干扰解耦,布尔(控制)网络的辨识,以及布尔网络的最优控制等.%Boolean network is a powerful tool for describing gene regulatory network. With the development of the systems biology, the analysis and control of Boolean networks become a hot topic for multidisciplinary research. This paper surveys some recent results obtained in the analysis and control of Boolean networks using semi-tensor product of matrices. The contents of this paper include the topological structure of Boolean networks, the controllability and observability, realization, stability and stabilization, disturbance decoupling, identification, and optimal control of Boolean (control) networks.

  3. Image Restoration Research Based on Boolean Cloud Model Algorithm%基于布尔云模型算法的图像修复研究

    Institute of Scientific and Technical Information of China (English)

    王宝红; 郭水旺; 季钢

    2013-01-01

    Aiming at the deficiencies of the existing image restoration algorithm,Boolean cloud model algorithm is used.First the cloud model is constructed,cloud entropy to determine cloud Boolean relations,clouds appear,Boolean logic to calculate each cloud droplet collection of mutual information entropy,entropy of different results to determine value.Followed by the input and Boolean cloud state function determines the cloud model decision by input Boolean function can produce new clouds again,optimize cloud states choose different cloud entropy dynamic changes.Finally,the algorithm processes.simulation results show operator to connect natural repair image,smoothness,to maintain the overall continuous,and PSNR value.%针对现有图像修复算法的不足,采用布尔云模型算法.首先构造云模型,利用云熵确定云布尔关系.不同的云团值出现时,布尔逻辑计算每个云滴集合的互信息熵.通过比较熵的不同来确定结果值;接着在受输入和布尔函数决定后产生云态,云模型在受输入和布尔函数决定后,可以再次产生新的云团.对云态进行选择优化,其不同的云熵动态变化,最后给出了算法流程.仿真结果显示算法对修复图像连接自然,有光滑性,保持了整体连续,并且PSNR值较大.

  4. New Measure of Boolean Factor Analysis Quality

    Czech Academy of Sciences Publication Activity Database

    Frolov, A. A.; Húsek, Dušan; Polyakov, P.Y.

    Vol. 1. Heidelberg: Springer, 2011 - (Dobnikar, A.; Lotrič, U.; Šter, B.), s. 100-109. (Lecture Notes in Computer Science. 6593). ISBN 978-3-642-20281-0. ISSN 0302-9743. [ICANNGA'2011. International Conference /10./. Ljubljana (SI), 14.04.2011-16.04.2011] R&D Projects: GA ČR GAP202/10/0262; GA ČR GA205/09/1079 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * information gain * expectation-maximization * associative memory * neural network application * Boolean matrix factorization * bars problem * Hopfield neural network Subject RIV: IN - Informatics, Computer Science

  5. Boolean filters of distributive lattices

    Directory of Open Access Journals (Sweden)

    M. Sambasiva Rao

    2013-07-01

    Full Text Available In this paper we introduce the notion of Boolean filters in a pseudo-complemented distributive lattice and characterize the class of all Boolean filters. Further a set of equivalent conditions are derived for a proper filter to become a prime Boolean filter. Also a set of equivalent conditions is derived for a pseudo-complemented distributive lattice to become a Boolean algebra. Finally, a Boolean filter is characterized in terms of congruences.

  6. An autocatalytic network model for stock markets

    Science.gov (United States)

    Caetano, Marco Antonio Leonel; Yoneyama, Takashi

    2015-02-01

    The stock prices of companies with businesses that are closely related within a specific sector of economy might exhibit movement patterns and correlations in their dynamics. The idea in this work is to use the concept of autocatalytic network to model such correlations and patterns in the trends exhibited by the expected returns. The trends are expressed in terms of positive or negative returns within each fixed time interval. The time series derived from these trends is then used to represent the movement patterns by a probabilistic boolean network with transitions modeled as an autocatalytic network. The proposed method might be of value in short term forecasting and identification of dependencies. The method is illustrated with a case study based on four stocks of companies in the field of natural resource and technology.

  7. Two Expectation-Maximization Algorithms for Boolean Factor Analysis

    Czech Academy of Sciences Publication Activity Database

    Frolov, A. A.; Húsek, Dušan; Polyakov, P.Y.

    2014-01-01

    Roč. 130, 23 April (2014), s. 83-97. ISSN 0925-2312 R&D Projects: GA ČR GAP202/10/0262 Grant ostatní: GA MŠk(CZ) ED1.1.00/02.0070; GA MŠk(CZ) EE.2.3.20.0073 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean Factor analysis * Binary Matrix factorization * Neural networks * Binary data model * Dimension reduction * Bars problem Subject RIV: IN - Informatics, Computer Science Impact factor: 2.083, year: 2014

  8. Collaborative networks: Reference modeling

    NARCIS (Netherlands)

    L.M. Camarinha-Matos; H. Afsarmanesh

    2008-01-01

    Collaborative Networks: Reference Modeling works to establish a theoretical foundation for Collaborative Networks. Particular emphasis is put on modeling multiple facets of collaborative networks and establishing a comprehensive modeling framework that captures and structures diverse perspectives of

  9. Inadmissible Class of Boolean Functions under Stuck-at Faults

    OpenAIRE

    Das, Debesh K.; Chowdhury, Debabani; Bhattacharya, Bhargab B; Sasao, Tsutomu

    2013-01-01

    Many underlying structural and functional factors that determine the fault behavior of a combinational network, are not yet fully understood. In this paper, we show that there exists a large class of Boolean functions, called root functions, which can never appear as faulty response in irredundant two-level circuits even when any arbitrary multiple stuck-at faults are injected. Conversely, we show that any other Boolean function can appear as a faulty response from an irredundant realization ...

  10. Geometric Operators on Boolean Functions

    OpenAIRE

    Frisvad, Jeppe Revall; Falster, Peter

    2007-01-01

    In truth-functional propositional logic, any propositional formula represents a Boolean function (according to some valuation of the formula). We describe operators based on Decartes' concept of constructing coordinate systems, for translation of a propositional formula to the image of a Boolean function. With this image of a Boolean function corresponding to a propositional formula, we prove that the orthogonal projection operator leads to a theorem describing all rules of inference in propo...

  11. Algorithms for Weighted Boolean Optimization

    OpenAIRE

    Manquinho, Vasco; Marques-Silva, Joao; Planes Cid, Jordi

    2009-01-01

    The Pseudo-Boolean Optimization (PBO) and Maximum Satisfiability (MaxSAT) problems are natural optimization extensions of Boolean Satisfiability (SAT). In the recent past, different algorithms have been proposed for PBO and for MaxSAT, despite the existence of straightforward mappings from PBO to MaxSAT and viceversa. This papers proposes Weighted Boolean Optimization (WBO), a new uni- fied framework that aggregates and extends PBO and MaxSAT. In addition, the paper proposes...

  12. Boolean Delay Equations: A Simple Way of Looking at Interactions and Extreme Events

    Science.gov (United States)

    Ghil, Michael

    2013-04-01

    Boolean Delay Equations (BDEs) are semi-discrete dynamical models with Boolean-valued variables that evolve in continuous time. Systems of BDEs can be classified into conservative or dissipative, in a manner that parallels the classification of ordinary or partial differential equations. Solutions to certain conservative BDEs exhibit growth of complexity in time; such BDEs can be seen therefore as metaphors for biological evolution or human history. Dissipative BDEs are structurally stable and exhibit multiple equilibria and limit cycles, as well as more complex, fractal solution sets, such as Devil's staircases and ``fractal sunbursts.'' BDE systems have been used as highly idealized models of climate change on several time scales, as well as in earthquake modeling and prediction, and in genetics. BDEs with an infinite number of variables on a regular spatial grid have been called "partial BDEs" and we discuss connections with other types of discrete dynamical systems, including cellular automata and Boolean networks. We present recent BDE work on damage propagation in networks, with an emphasis on production-chain models. This formalism turns out to be well adapted to investigating propagation of an initial damage due to a climatic or other natural disaster. It thus serves to study economic impacts of extreme events, as well as extreme disruption of a network of interactions.

  13. 基于布尔语义的Gentzen推导模型%Gentzen Deduction Model Based on Boolean Logic Semantics

    Institute of Scientific and Technical Information of China (English)

    陈博; 眭跃飞

    2015-01-01

    Deduction systems are important arts of searching technology. This paper gives a new correspondence between the propositional logic and Boolean algebra, where an inequation is corresponding to a Gentzen sequent, so that the inequation is true in every Boolean algebra if and only if the Gentzen sequent is provable. In information retrieval, the information inference can effectively turn into the operation on poset. Precisely, the logical language for the propositional logic contains operators Ø'Ù'Ú;the terms instead of formulas are defined (a|Øt|t1 Ù t2|t1 Ú t2 , where a is an element) and used to represent elements in Boolean algebra. This paper defines an assignment v using Boolean algebra as its domain, and assigns the terms to be the element in Boolean algebra. The sequence ΓÞΔ is satisfied if tv £tv. Finally, this paper gives a Gentzen system to prove the soundness and completeness theorem.%布尔模型是信息检索系统的一种基础模型。给出了命题逻辑和布尔代数间的一种新的对应关系,其中布尔代数中的不等式对应Gentzen系统中的矢列式,使得当一个不等式在任意布尔代数中为真,当且仅当它所对应的矢列式是可证的。并且使得在信息检索中,针对信息的推理可以有效地转为偏序集上的运算。讨论的命题逻辑语言的运算符为Ø、Ù、Ú;并且定义了项(a|Øt|t1Ù t2|t1Ú t2'其中a是一个元素)来替代原先的公式和表示布尔代数中的元素。此外,定义了以布尔代数为论域的赋值v,将命题逻辑中的项赋值为布尔代数中的元素,并且如果tv £t v ,则矢列式ΓÞ D为真。最后给出了Gentzen系统下的可靠性和完备性定理的证明。tÎΓtÎΔ

  14. Social Network Modelling

    OpenAIRE

    Pugacheva, E

    2015-01-01

    In the offered review some key issues of social network analysis are discussed. This is a brief summary of social network characteristics, models of network formation, and the network perspective. The aim of this overview is to contribute to interdisciplinary dialogue among researchers in physics, mathematics, sociology, who share a common interest in understanding the network phenomena.

  15. 硬件加速的渐进式多边形模型布尔运算%GPU-Accelerated Progressive Boolean Operations on Polygonal Models

    Institute of Scientific and Technical Information of China (English)

    赵汉理; 孟庆如; 金小刚; 黄辉; 王明

    2015-01-01

    多边形模型的布尔运算中包含复杂的求交计算以及多边形重建过程,精度控制和处理效率是其中的关键。为了降低布尔运算复杂度,提出一种适合硬件加速的基于渐进式布尔运算的多层次细节网格模型生成方法。该方法采用分层深度图像来近似表示多边形实体的封闭边界,将多边形的求交计算简化为坐标轴平行的采样点的实体内外部判断;为了免去各层次细节模型的重复采样过程,渐进式地将边界采样点归并到低分辨率下的立方体中;运用特征保持的多边形重建算法将相同立方体内的边界采样点转换成多边形顶点,根据邻接关系生成网格模型。上述算法使用支持图形硬件加速的CUDA编程并行实现。实验结果表明了算法的可行性。%Boolean operations on polygonal models involve the complex intersection calculations and po-lygonal reconstruction, where the precision control and processing efficiency are two key problems. To re-duce the Boolean operation complexity, this paper proposes a progressive and GPU accelerated Boolean op-eration approach to generate levels-of-detail polygonal models. Layered depth images are employed to ap-proximate the enclosed boundaries of polygons and the intersection calculations are performed as the in/out classification of axis-aligned sampling points. To avoid the additional sampling process for levels-of-detail models, the boundary points are progressively merged into low-resolution cubes. The feature-preserving dual contouring algorithm is adopted to convert boundary points into a mesh model. The proposed algorithm can be implementation in parallel on GPU with the hardware-supported CUDA. Finally, experimental results show the feasibility of the proposed approach.

  16. Symmetry in Boolean Satisfiability

    Directory of Open Access Journals (Sweden)

    Fadi A. Aloul

    2010-06-01

    Full Text Available This paper reviews recent approaches on how to accelerate Boolean Satisfiability (SAT search by exploiting symmetries in the problem space. SAT search algorithms traverse an exponentially large search space looking for an assignment that satisfies a set of constraints. The presence of symmetries in the search space induces equivalence classes on the set of truth assignments. The goal is to use symmetries to avoid traversing all assignments by constraining the search to visit a few representative assignments in each equivalence class. This can lead to a significant reduction in search runtime without affecting the completeness of the search.

  17. Boolean Orthogonalizing Combination Methods

    Directory of Open Access Journals (Sweden)

    Yavuz Can

    2015-05-01

    Full Text Available In this paper a new logical operation method called “ presented. It is used to calculate the difference, but also the complement of a function as well as the EXOR and EXNOR of two minterms respectively two ternary respectively two ternary-vector logical operation method called “orthogonal OR advantages of both methods are their results, which are already available form that has an essential advantage for continuing calculations. Since it applies, an orthogonal disjunctive normal form is equal to orthogonal antivalence normal form, subsequent Boolean differential calculus will be simplified.

  18. Approximate Reasoning with Fuzzy Booleans

    NARCIS (Netherlands)

    Broek, van den P.M.; Noppen, J.A.R.

    2004-01-01

    This paper introduces, in analogy to the concept of fuzzy numbers, the concept of fuzzy booleans, and examines approximate reasoning with the compositional rule of inference using fuzzy booleans. It is shown that each set of fuzzy rules is equivalent to a set of fuzzy rules with singleton crisp ante

  19. Geometric Operators on Boolean Functions

    DEFF Research Database (Denmark)

    Frisvad, Jeppe Revall; Falster, Peter

    of a few geometric operators working on the images of Boolean functions. The operators we describe, arise from the niche area of array-based logic and have previously been tightly bound to an array-based representation of Boolean functions. We redefine the operators in an abstract form to make them...

  20. Linear Programming Formulation of the Boolean Satisfiability Problem

    CERN Document Server

    Diaby, Moustapha

    2008-01-01

    In this paper, we present a new, graph-based modeling approach and a polynomial-sized linear programming (LP) formulation of the Boolean satisfiability problem (SAT). The approach is illustrated with a numerical example.

  1. Cryptographic Boolean functions and applications

    CERN Document Server

    Cusick, Thomas W

    2009-01-01

    Boolean functions are the building blocks of symmetric cryptographic systems. Symmetrical cryptographic algorithms are fundamental tools in the design of all types of digital security systems (i.e. communications, financial and e-commerce).Cryptographic Boolean Functions and Applications is a concise reference that shows how Boolean functions are used in cryptography. Currently, practitioners who need to apply Boolean functions in the design of cryptographic algorithms and protocols need to patch together needed information from a variety of resources (books, journal articles and other sources). This book compiles the key essential information in one easy to use, step-by-step reference. Beginning with the basics of the necessary theory the book goes on to examine more technical topics, some of which are at the frontier of current research.-Serves as a complete resource for the successful design or implementation of cryptographic algorithms or protocols using Boolean functions -Provides engineers and scient...

  2. Cardinal invariants on Boolean algebras

    CERN Document Server

    Monk, J Donald

    2014-01-01

    This book is concerned with cardinal number valued functions defined for any Boolean algebra. Examples of such functions are independence, which assigns to each Boolean algebra the supremum of the cardinalities of its free subalgebras, and cellularity, which gives the supremum of cardinalities of sets of pairwise disjoint elements. Twenty-one such functions are studied in detail, and many more in passing. The questions considered are the behaviour of these functions under algebraic operations such as products, free products, ultraproducts, and their relationships to one another. Assuming familiarity with only the basics of Boolean algebras and set theory, through simple infinite combinatorics and forcing, the book reviews current knowledge about these functions, giving complete proofs for most facts. A special feature of the book is the attention given to open problems, of which 185 are formulated. Based on Cardinal Functions on Boolean Algebras (1990) and Cardinal Invariants on Boolean Algebras (1996) by the...

  3. Boolean delay equations: A simple way of looking at complex systems

    Science.gov (United States)

    Ghil, Michael; Zaliapin, Ilya; Coluzzi, Barbara

    2008-12-01

    Boolean Delay Equations (BDEs) are semi-discrete dynamical models with Boolean-valued variables that evolve in continuous time. Systems of BDEs can be classified into conservative or dissipative, in a manner that parallels the classification of ordinary or partial differential equations. Solutions to certain conservative BDEs exhibit growth of complexity in time; such BDEs can be seen therefore as metaphors for biological evolution or human history. Dissipative BDEs are structurally stable and exhibit multiple equilibria and limit cycles, as well as more complex, fractal solution sets, such as Devil’s staircases and “fractal sunbursts.” All known solutions of dissipative BDEs have stationary variance. BDE systems of this type, both free and forced, have been used as highly idealized models of climate change on interannual, interdecadal and paleoclimatic time scales. BDEs are also being used as flexible, highly efficient models of colliding cascades of loading and failure in earthquake modeling and prediction, as well as in genetics. In this paper we review the theory of systems of BDEs and illustrate their applications to climatic and solid-earth problems. The former have used small systems of BDEs, while the latter have used large hierarchical networks of BDEs. We moreover introduce BDEs with an infinite number of variables distributed in space (“partial BDEs”) and discuss connections with other types of discrete dynamical systems, including cellular automata and Boolean networks. This research-and-review paper concludes with a set of open questions.

  4. 语义特征建模系统中布尔算法的研究%Research on Boolean Operation in Semantic Feature Modeling System

    Institute of Scientific and Technical Information of China (English)

    金瑛浩; 孙立镌

    2012-01-01

    To improve the efficiency of boolean operations in semantic feature modeling system,a semantic representation based method was proposed. It represents feature models with semantic representation, manages feature elements by cellular model,improves detect efficiency of features interaction and builds new the feature entity by splitting inter-sectant cells and semantic faces. This method can not only build the boolean entity rapidly and exactly, but also avoid errors such as holes and losing geometry faces. Experiments on computer show that this new method is more adaptable and practicable.%为了提高语义特征建模系统中布尔操作的运行效率,提出了一种基于语义表示法的布尔操作算法.该算法用语义表示法表示特征模型,用细胞元模型组织和管理特征元素,用语义面替代几何面来提高特征的交互检测效率,通过细胞分裂和语义面分解来生成新实体.该算法不仅可以快速准确地生成布尔实体,还可以避免几何面的丢失及“孔洞”等错误的发生.实验证明,该算法具有广泛的使用前景和实用价值.

  5. A unified biological modeling and simulation system for analyzing biological reaction networks

    Science.gov (United States)

    Yu, Seok Jong; Tung, Thai Quang; Park, Junho; Lim, Jongtae; Yoo, Jaesoo

    2013-12-01

    In order to understand the biological response in a cell, a researcher has to create a biological network and design an experiment to prove it. Although biological knowledge has been accumulated, we still don't have enough biological models to explain complex biological phenomena. If a new biological network is to be created, integrated modeling software supporting various biological models is required. In this research, we design and implement a unified biological modeling and simulation system, called ezBioNet, for analyzing biological reaction networks. ezBioNet designs kinetic and Boolean network models and simulates the biological networks using a server-side simulation system with Object Oriented Parallel Accelerator Library framework. The main advantage of ezBioNet is that a user can create a biological network by using unified modeling canvas of kinetic and Boolean models and perform massive simulations, including Ordinary Differential Equation analyses, sensitivity analyses, parameter estimates and Boolean network analysis. ezBioNet integrates useful biological databases, including the BioModels database, by connecting European Bioinformatics Institute servers through Web services Application Programming Interfaces. In addition, we employ Eclipse Rich Client Platform, which is a powerful modularity framework to allow various functional expansions. ezBioNet is intended to be an easy-to-use modeling tool and a simulation system for understanding the control mechanism by monitoring the change of each component in a biological network. The simulation result can be managed and visualized on ezBioNet, which is available free of charge at http://ezbionet.sourceforge.net or http://ezbionet.cbnu.ac.kr.

  6. Boolean Equi-propagation for Optimized SAT Encoding

    CERN Document Server

    Metodi, Amit; Lagoon, Vitaly; Stuckey, Peter J

    2011-01-01

    We present an approach to propagation based solving, Boolean equi-propagation, where constraints are modelled as propagators of information about equalities between Boolean literals. Propagation based solving applies this information as a form of partial evaluation resulting in optimized SAT encodings. We demonstrate for a variety of benchmarks that our approach results in smaller CNF encodings and leads to speed-ups in solving times.

  7. On Kolmogorov's superpositions and Boolean functions

    Energy Technology Data Exchange (ETDEWEB)

    Beiu, V.

    1998-12-31

    The paper overviews results dealing with the approximation capabilities of neural networks, as well as bounds on the size of threshold gate circuits. Based on an explicit numerical (i.e., constructive) algorithm for Kolmogorov's superpositions they will show that for obtaining minimum size neutral networks for implementing any Boolean function, the activation function of the neurons is the identity function. Because classical AND-OR implementations, as well as threshold gate implementations require exponential size (in the worst case), it will follow that size-optimal solutions for implementing arbitrary Boolean functions require analog circuitry. Conclusions and several comments on the required precision are ending the paper.

  8. A Note on the Inversion Complexity of Boolean Functions in Boolean Formulas

    OpenAIRE

    Morizumi, Hiroki

    2008-01-01

    In this note, we consider the minimum number of NOT operators in a Boolean formula representing a Boolean function. In circuit complexity theory, the minimum number of NOT gates in a Boolean circuit computing a Boolean function $f$ is called the inversion complexity of $f$. In 1958, Markov determined the inversion complexity of every Boolean function and particularly proved that $\\lceil \\log_2(n+1) \\rceil$ NOT gates are sufficient to compute any Boolean function on $n$ variables. As far as we...

  9. Boolean Factor Analysis by Expectation-Maximization Method

    Czech Academy of Sciences Publication Activity Database

    Frolov, A. A.; Húsek, Dušan; Polyakov, P.Y.

    Heidelberg : Springer, 2013 - (Kudělka, M.; Pokorný, J.; Snášel, V.; Abraham, A.), s. 243-254 ISBN 978-3-642-31602-9. ISSN 2194-5357. - (Advances in Intelligent Systems and Computing. 179). [IHCI 2011. International Conference on Intelligent Human Computer Interaction /3./. Prague (CZ), 29.08.2011-31.08.2011] R&D Projects: GA ČR GAP202/10/0262; GA ČR GA205/09/1079 Grant ostatní: GA MŠk(CZ) ED1.1.00/02.0070 Institutional research plan: CEZ:AV0Z10300504 Keywords : neural networks * hidden pattern search * Boolean factor analysis * generative model * information redundancy * exceptation-maximization Subject RIV: IN - Informatics, Computer Science

  10. Brain Network Modelling

    DEFF Research Database (Denmark)

    Andersen, Kasper Winther

    Three main topics are presented in this thesis. The first and largest topic concerns network modelling of functional Magnetic Resonance Imaging (fMRI) and Diffusion Weighted Imaging (DWI). In particular nonparametric Bayesian methods are used to model brain networks derived from resting state f...... for their ability to reproduce node clustering and predict unseen data. Comparing the models on whole brain networks, BCD and IRM showed better reproducibility and predictability than IDM, suggesting that resting state networks exhibit community structure. This also points to the importance of using models, which...... allow for complex interactions between all pairs of clusters. In addition, it is demonstrated how the IRM can be used for segmenting brain structures into functionally coherent clusters. A new nonparametric Bayesian network model is presented. The model builds upon the IRM and can be used to infer...

  11. Modeling Epidemic Network Failures

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Fagertun, Anna Manolova

    2013-01-01

    This paper presents the implementation of a failure propagation model for transport networks when multiple failures occur resulting in an epidemic. We model the Susceptible Infected Disabled (SID) epidemic model and validate it by comparing it to analytical solutions. Furthermore, we evaluate...... the SID model’s behavior and impact on the network performance, as well as the severity of the infection spreading. The simulations are carried out in OPNET Modeler. The model provides an important input to epidemic connection recovery mechanisms, and can due to its flexibility and versatility be used...... to evaluate multiple epidemic scenarios in various network types....

  12. Artificial neural network modelling

    CERN Document Server

    Samarasinghe, Sandhya

    2016-01-01

    This book covers theoretical aspects as well as recent innovative applications of Artificial Neural networks (ANNs) in natural, environmental, biological, social, industrial and automated systems. It presents recent results of ANNs in modelling small, large and complex systems under three categories, namely, 1) Networks, Structure Optimisation, Robustness and Stochasticity 2) Advances in Modelling Biological and Environmental Systems and 3) Advances in Modelling Social and Economic Systems. The book aims at serving undergraduates, postgraduates and researchers in ANN computational modelling. .

  13. Generalized join-hemimorphisms on Boolean algebras

    OpenAIRE

    Sergio Celani

    2003-01-01

    We introduce the notions of generalized join-hemimorphism and generalized Boolean relation as an extension of the notions of join-hemimorphism and Boolean relation, respectively. We prove a duality between these two notions. We will also define a generalization of the notion of Boolean algebra with operators by considering a finite family of Boolean algebras endowed with a generalized join-hemimorphism. Finally, we define suitable notions of subalgebra, congruences, Boole...

  14. Boolean Operations on Conic Polygons

    Institute of Scientific and Technical Information of China (English)

    Yong-Xi Gong; Yu Liu; Lun Wu; Yu-Bo Xie

    2009-01-01

    An algorithm for Boolean operations on conic polygons is proposed. Conic polygons are polygons consisting of conic segments or bounded conics with directions. Preliminaries of Boolean operations on general polygons are presented. In our algorithm, the intersection points and the topological relationships between two conic polygons are computed. Boundaries are obtained by tracking path and selecting uncrossed boundaries following rule tables to build resulting conic polygons.We define a set of rules for the intersection, union, and subtraction operations on conic polygons. The algorithm considers degeneration cases such as homology, complement, interior, and exterior. The algorithm is also evaluated and implemented.

  15. Cardinal invariants on Boolean algebras

    CERN Document Server

    Monk, J Donald

    2009-01-01

    Deals with cardinal number valued functions defined for any Boolean algebra. This title considers the behavior of these functions under algebraic operations such as products, free products, ultraproducts, and their relationships to one another. It covers topics such as ultraproducts and Fedorchukis theorem

  16. Boolean-Valued Belief Functions

    Czech Academy of Sciences Publication Activity Database

    Kramosil, Ivan

    2002-01-01

    Roč. 31, č. 2 (2002), s. 153-181. ISSN 0308-1079 R&D Projects: GA AV ČR IAA1030803 Institutional research plan: AV0Z1030915 Keywords : Dempster-Schafer theory * Boolean algebra Subject RIV: BA - General Mathematics Impact factor: 0.241, year: 2002

  17. Evolutionary Design of Boolean Functions

    Institute of Scientific and Technical Information of China (English)

    WANG Zhang-yi; ZHANG Huan-guo; QIN Zhong-ping; MENG Qing-shu

    2005-01-01

    We use evolutionary computing to synthesize Boolean functions randomly. By using specific crossover and mutation operator in evolving process and modifying search space and fitness function, we get some high non-linearity functions which have other good cryptography characteristics such as autocorrelation etc. Comparing to other heuristic search techniques, evolutionary computing approach is more effective because of global search strategy and implicit parallelism.

  18. Ordered Boolean List (OBL): reducing the footprint for evaluating Boolean expressions.

    Science.gov (United States)

    Rossignac, Jaroslaw Jarek

    2011-09-01

    An Expanded Boolean Expression (EBE) does not contain any XOR or EQUAL operators. The occurrence of each variable is a different literal. We provide a linear time algorithm that converts an EBE of n literals into a logically equivalent Ordered Boolean List (OBL) and show how to use the OBL to evaluate the EBE in n steps and O(log log n) space, if the values of the literals are each read once in the order prescribed by the OBL. (An evaluation workspace of 5 bits suffices for all EBEs of up to six billion literals.) The primary application is the SIMD architecture, where the same EBE is evaluated in parallel for different input vectors when rendering solid models on the GPU directly from their Constructive Solid Geometry (CSG) representation. We compare OBL to the Reduced Ordered Binary Decision Diagram (ROBDD) and suggest possible applications of OBL to logic verification and to circuit design. PMID:21737862

  19. Method of Boolean operation based on 3D grid model%三维网格模型的布尔运算方法

    Institute of Scientific and Technical Information of China (English)

    陈学工; 杨兰; 黄伟; 季兴

    2011-01-01

    提出了一种基于三维网格模型的布尔运算方法.首先通过基于方向包围盒(OBB)层次包围盒树的碰撞检测算法,得到实体的相交三角形对;接下来求出两相交三角形之间的交线,建立与三角形的交线拓扑关系;通过分类处理三种交线类型来对相交三角形进行区域划分,得到一系列多边形,并对多边形进行三角剖分形成结果区域;最后根据体的包含关系构建关系邻接表,判断多边形区域的相对于其他实体的内外关系并通过网格模型的拓扑关系,定位表面三角网格区域;同时根据交、并、差等布尔操作,对结果区域进行取舍,得到最终结果.实验结果表明相交部分的岩性与实体的岩性相吻合,验证了该算法的正确性以及可行性.%A kind of Boolean operational method based on a three-dimensional grid model was proposed. Firstly, through collision detection algorithm based on hierarchical bounding box tree of Oriented Bounding Box (ORB), the intersecting triangles could be got. Through the intersection test of the triangles, the intersecting lines could be obtained and the intersecting lines topology relations with the triangles could be established. Secondly, a regional division for the intersecting triangles was made through processing the three types of intersecting lines, so as to get a series of polygons, and carry out Delaunay triangulations for polygon to get the result area. Lastly, relation adjacency list was constructed based on solid containing relations, the polygon's internal relation and external relation with other entities were judged, and the triangles were located according to the mesh model topology relations. Simultaneously, according to such Boolean operations as the intersection, union, and differences, according to the grid model topology relations were judged, the position of the triangles were judged and then the final results could be obtained. Experimental results show that this

  20. Implementing Boolean Matrix Factorization

    Czech Academy of Sciences Publication Activity Database

    Neruda, Roman; Snášel, V.; Platoš, J.; Krömer, P.; Húsek, Dušan; Frolov, A. A.

    Vol. Part I. Berlin : Springer, 2008 - (Kůrková, V.; Neruda, R.; Koutník, J.), s. 543-552 ISBN 978-3-540-87535-2. - (Lecture Notes in Computer Science. 5163). [ICANN 2008. International Conference on Artificial Neural Network s /18./. Prague (CZ), 03.09.2008-06.09.2008] Institutional research plan: CEZ:AV0Z10300504 Keywords : factor analysis * genetic algorithm * neural network s Subject RIV: IN - Informatics, Computer Science

  1. Learning Boolean functions with concentrated spectra

    Science.gov (United States)

    Mixon, Dustin G.; Peterson, Jesse

    2015-08-01

    This paper discusses the theory and application of learning Boolean functions that are concentrated in the Fourier domain. We first estimate the VC dimension of this function class in order to establish a small sample complexity of learning in this case. Next, we propose a computationally efficient method of empirical risk minimization, and we apply this method to the MNIST database of handwritten digits. These results demonstrate the effectiveness of our model for modern classification tasks. We conclude with a list of open problems for future investigation.

  2. Network Reliability Algorithm Based on Pathset Matrix and Boolean Operation%基于路集矩阵与布尔运算的网络可靠度算法

    Institute of Scientific and Technical Information of China (English)

    高会生; 展敬宇; 王博颖; 李潇睿

    2012-01-01

    This paper analyzes the network reliability algorithm based on pathset matrix, and there exists a serious combination explosion problem in this algorithm. Aiming at this problem, it proposes a network reliability algorithm based on pathset matrix and boolean operation. The concept of bit vector is introduced. In addition, the pre-process of special pathsets and count of all-one bit vectors are also implied. Experimental results show that it not only increases the memory utilization, reduce the redundancy but also relieve the combination explosion problem in some degree.%分析基于路集矩阵与布尔运算的网络可靠度算法,指出其存在组合爆炸问题.为此,提出一种改进算法,引入位矢量以减少内存需求,对特殊路集进行预处理并统计全1位矢量.实验结果表明,改进算法可提高内存利用率、减少冗余运算,能在一定程度上缓解组合爆炸问题.

  3. Exploiting Surroundedness for Saliency Detection: A Boolean Map Approach.

    Science.gov (United States)

    Zhang, Jianming; Sclaroff, Stan

    2016-05-01

    We demonstrate the usefulness of surroundedness for eye fixation prediction by proposing a Boolean Map based Saliency model (BMS). In our formulation, an image is characterized by a set of binary images, which are generated by randomly thresholding the image's feature maps in a whitened feature space. Based on a Gestalt principle of figure-ground segregation, BMS computes a saliency map by discovering surrounded regions via topological analysis of Boolean maps. Furthermore, we draw a connection between BMS and the Minimum Barrier Distance to provide insight into why and how BMS can properly captures the surroundedness cue via Boolean maps. The strength of BMS is verified by its simplicity, efficiency and superior performance compared with 10 state-of-the-art methods on seven eye tracking benchmark datasets. PMID:26336114

  4. Terse Integer Linear Programs for Boolean Optimization

    Directory of Open Access Journals (Sweden)

    Christoph Buchheim

    2009-05-01

    Full Text Available We present a new polyhedral approach to nonlinear Boolean optimization. Compared to other methods, it produces much smaller integer programming models, making it more efficient from a practical point of view. We mainly obtain this by two different ideas: first, we do not require the objective function to be in any normal form. The transformation into a normal form usually leads to the introduction of many additional variables or constraints. Second, we reduce the problem to the degree-two case in a very efficient way, by slightly extending the dimension of the original variable space. The resulting model turns out to be closely related to the maximum cut problem; we show that the corresponding polytope is a face of a suitable cut polytope in most cases. In particular, our separation problem reduces to the one for the maximum cut problem. In practice, the approach appears to be very competitive for unconstrained Boolean optimization problems. First experimental results, which have been obtained for some particularly hard instances of the Max-SAT Evaluation 2007, show that our very general implementation can outperform even special-purpose Max-SAT solvers. The software is accessible online under “we.logoptimize.it”.

  5. Cost-Optimal Execution of Trees of Boolean Operators with Shared Streams

    OpenAIRE

    Casanova, Henri; Lim, Lipyeow; Robert, Yves; Vivien, Frédéric; Zaidouni, Dounia

    2013-01-01

    The processing of queries expressed as trees of boolean operators applied to predicates on sensor data streams has several applications in mobile computing. Sensor data must be retrieved from the sensors to a query processing device, such as a smartphone, over one or more network interfaces. Retrieving a data item incurs a cost, e.g., an energy expense that depletes the smartphone's battery. Since the query tree contains boolean operators, part of the tree can be shortcircuited depending on t...

  6. A Network-of-Networks Model for Electrical Infrastructure Networks

    CERN Document Server

    Halappanavar, Mahantesh; Hogan, Emilie; Duncan, Daniel; Zhenyu,; Huang,; Hines, Paul D H

    2015-01-01

    Modeling power transmission networks is an important area of research with applications such as vulnerability analysis, study of cascading failures, and location of measurement devices. Graph-theoretic approaches have been widely used to solve these problems, but are subject to several limitations. One of the limitations is the ability to model a heterogeneous system in a consistent manner using the standard graph-theoretic formulation. In this paper, we propose a {\\em network-of-networks} approach for modeling power transmission networks in order to explicitly incorporate heterogeneity in the model. This model distinguishes between different components of the network that operate at different voltage ratings, and also captures the intra and inter-network connectivity patterns. By building the graph in this fashion we present a novel, and fundamentally different, perspective of power transmission networks. Consequently, this novel approach will have a significant impact on the graph-theoretic modeling of powe...

  7. Neural Network Model For Fast Learning And Retrieval

    Science.gov (United States)

    Arsenault, Henri H.; Macukow, Bohdan

    1989-05-01

    An approach to learning in a multilayer neural network is presented. The proposed network learns by creating interconnections between the input layer and the intermediate layer. In one of the new storage prescriptions proposed, interconnections are excitatory (positive) only and the weights depend on the stored patterns. In the intermediate layer each mother cell is responsible for one stored pattern. Mutually interconnected neurons in the intermediate layer perform a winner-take-all operation, taking into account correlations between stored vectors. The performance of networks using this interconnection prescription is compared with two previously proposed schemes, one using inhibitory connections at the output and one using all-or-nothing interconnections. The network can be used as a content-addressable memory or as a symbolic substitution system that yields an arbitrarily defined output for any input. The training of a model to perform Boolean logical operations is also described. Computer simulations using the network as an autoassociative content-addressable memory show the model to be efficient. Content-addressable associative memories and neural logic modules can be combined to perform logic operations on highly corrupted data.

  8. A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks

    Science.gov (United States)

    Laomettachit, Teeraphan; Chen, Katherine C.; Baumann, William T.

    2016-01-01

    To understand the molecular mechanisms that regulate cell cycle progression in eukaryotes, a variety of mathematical modeling approaches have been employed, ranging from Boolean networks and differential equations to stochastic simulations. Each approach has its own characteristic strengths and weaknesses. In this paper, we propose a “standard component” modeling strategy that combines advantageous features of Boolean networks, differential equations and stochastic simulations in a framework that acknowledges the typical sorts of reactions found in protein regulatory networks. Applying this strategy to a comprehensive mechanism of the budding yeast cell cycle, we illustrate the potential value of standard component modeling. The deterministic version of our model reproduces the phenotypic properties of wild-type cells and of 125 mutant strains. The stochastic version of our model reproduces the cell-to-cell variability of wild-type cells and the partial viability of the CLB2-dbΔ clb5Δ mutant strain. Our simulations show that mathematical modeling with “standard components” can capture in quantitative detail many essential properties of cell cycle control in budding yeast. PMID:27187804

  9. A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks.

    Directory of Open Access Journals (Sweden)

    Teeraphan Laomettachit

    Full Text Available To understand the molecular mechanisms that regulate cell cycle progression in eukaryotes, a variety of mathematical modeling approaches have been employed, ranging from Boolean networks and differential equations to stochastic simulations. Each approach has its own characteristic strengths and weaknesses. In this paper, we propose a "standard component" modeling strategy that combines advantageous features of Boolean networks, differential equations and stochastic simulations in a framework that acknowledges the typical sorts of reactions found in protein regulatory networks. Applying this strategy to a comprehensive mechanism of the budding yeast cell cycle, we illustrate the potential value of standard component modeling. The deterministic version of our model reproduces the phenotypic properties of wild-type cells and of 125 mutant strains. The stochastic version of our model reproduces the cell-to-cell variability of wild-type cells and the partial viability of the CLB2-dbΔ clb5Δ mutant strain. Our simulations show that mathematical modeling with "standard components" can capture in quantitative detail many essential properties of cell cycle control in budding yeast.

  10. A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks.

    Science.gov (United States)

    Laomettachit, Teeraphan; Chen, Katherine C; Baumann, William T; Tyson, John J

    2016-01-01

    To understand the molecular mechanisms that regulate cell cycle progression in eukaryotes, a variety of mathematical modeling approaches have been employed, ranging from Boolean networks and differential equations to stochastic simulations. Each approach has its own characteristic strengths and weaknesses. In this paper, we propose a "standard component" modeling strategy that combines advantageous features of Boolean networks, differential equations and stochastic simulations in a framework that acknowledges the typical sorts of reactions found in protein regulatory networks. Applying this strategy to a comprehensive mechanism of the budding yeast cell cycle, we illustrate the potential value of standard component modeling. The deterministic version of our model reproduces the phenotypic properties of wild-type cells and of 125 mutant strains. The stochastic version of our model reproduces the cell-to-cell variability of wild-type cells and the partial viability of the CLB2-dbΔ clb5Δ mutant strain. Our simulations show that mathematical modeling with "standard components" can capture in quantitative detail many essential properties of cell cycle control in budding yeast. PMID:27187804

  11. Quantum algorithms for testing Boolean functions

    Directory of Open Access Journals (Sweden)

    Erika Andersson

    2010-06-01

    Full Text Available We discuss quantum algorithms, based on the Bernstein-Vazirani algorithm, for finding which variables a Boolean function depends on. There are 2^n possible linear Boolean functions of n variables; given a linear Boolean function, the Bernstein-Vazirani quantum algorithm can deterministically identify which one of these Boolean functions we are given using just one single function query. The same quantum algorithm can also be used to learn which input variables other types of Boolean functions depend on, with a success probability that depends on the form of the Boolean function that is tested, but does not depend on the total number of input variables. We also outline a procedure to futher amplify the success probability, based on another quantum algorithm, the Grover search.

  12. Boolean Reasoning with Graphs of Partitions

    OpenAIRE

    Goossens, Daniel

    2010-01-01

    version longue du papier court "A Dynamic Boolean Knowledge Base" accepté à ICTAI 2010. This paper presents an implemented architecture for easy learning, reorganizing and navigation into a Boolean knowledge base. As the base grows with new definitions and constraints, it is normalized by the closure of a completion operator. This normalization allows arbitrary formats for Boolean expressions. It ensures basic reasoning abilities and spontaneously organizes intermingled taxonomies of conce...

  13. Inverse fracture network modelling

    International Nuclear Information System (INIS)

    The basic problem in analyzing flow and transport in fractured rock is that the flow may be largely governed by a poorly connected network of fractures. Flow in such a system cannot be modeled with traditional modelling techniques. Fracture network models also have a limitation, in that they are based on geological data on fracture geometry even though it is known that only a small portion of fractures observed is hydraulically active. This paper discusses a new technique developed for treating the problem as well as presents a modelling example carried out to apply it. The approach is developed in Lawrence Berkeley Laboratory and it treats the fracture zone as an 'equivalent discontinuum'. The discontinuous nature of the problem is represented through flow on a partially filled lattice. An equivalent discontinuum model is constructed by adding and removing conductive elements through a statistical inverse technique called 'simulated annealing'. The fracture network model is 'annealed' until the modified systems behaves like the observed. The further development of the approach continues at LBL and in a joint LBL/VTT collaboration project the possibilities to apply the technique in Finnish conditions are investigated

  14. Estimation of Boolean Factor Analysis Performance by Informational Gain

    Czech Academy of Sciences Publication Activity Database

    Frolov, A.; Húsek, Dušan; Polyakov, P.Y.

    Berlin : Springer, 2010 - (Snášel, V.; Szczepaniak, P.; Abraham, A.; Kacprzyk, J.), s. 83-94 ISBN 978-3-642-10686-6. - (Advances in Intelligent and Soft Computing. 67). [AWIC 2009. Atlantic Web Intelligence Conference /6./. Prague (CZ), 09.09.2009-11.09.2009] Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * informational gain * Hopfield-like network Subject RIV: IN - Informatics, Computer Science

  15. Progress in Applications of Boolean Functions

    CERN Document Server

    Sasao, Tsutomu

    2010-01-01

    This book brings together five topics on the application of Boolean functions. They are 1. Equivalence classes of Boolean functions: The number of n-variable functions is large, even for values as small as n = 6, and there has been much research on classifying functions. There are many classifications, each with their own distinct merit. 2. Boolean functions for cryptography: The process of encrypting/decrypting plain text messages often depends on Boolean functions with specific properties. For example, highly nonlinear functions are valued because they are less susceptible to linear attacks.

  16. Limitations of Lower-Bound Methods for the Wire Complexity of Boolean Operators

    OpenAIRE

    Drucker, Andrew

    2012-01-01

    We study the circuit complexity of Boolean operators, i.e., collections of Boolean functions defined over a common input. Our focus is the well-studied model in which arbitrary Boolean functions are allowed as gates, and in which a circuit's complexity is measured by its depth and number of wires. We show sharp limitations of several existing lower-bound methods for this model. First, we study an information-theoretic lower-bound method due to Cherukhin, that yields bounds of form $\\Omega_d(n...

  17. Duality methods in networks, computer science models, and disordered condensed matter systems

    Science.gov (United States)

    Mitchell, Joseph Dan

    In this thesis, I explore lattice independent duality and systems to which it can be applied. I first demonstrate classical duality on models in an external field, including the Ising, Potts, and x -- y models, showing in particular how this modifies duality to be lattice independent and applicable to networks. I then present a novel application of duality on the boolean satsifiability problem, one of the most important problems in computational complexity, through mapping to a low temperature Ising model. This establishes the equivalence between boolean satisfiability and a problem of enumerating the positive solutions to a Diophantine system of equations. I continue by combining duality with a prominent tool for models on networks, belief propagation, deriving a new message passing procedure, dual belief propagation. In the final part of my thesis, I shift to propose and examine a semiclassical model, the two-component Coulomb glass model, which can explain the giant magnetoresistance peak present in disordered films near a superconductor-insulator transition as the effect of competition between single particle and localized pair transport. I numerically analyze the density of states and transport properties of this model.

  18. Boolean Search: Current State and Perspectives.

    Science.gov (United States)

    Frants, Valery I.; Shapiro, Jacob; Taksa, Isak; Voiskunskii, Vladimir G.

    1999-01-01

    Discusses the use of Boolean logic in information-retrieval systems and analyzes existing criticisms of operational systems. Considers users' ability to use and understand Boolean operators, ranking, the quality of query formulations, and negative effects of criticism; and concludes that criticism is directed at the methodology employed in…

  19. Version Spaces and Generalized Monotone Boolean Functions

    NARCIS (Netherlands)

    J.C. Bioch (Cor); T. Ibaraki

    2002-01-01

    textabstractWe consider generalized monotone functions f: X --> {0,1} defined for an arbitrary binary relation <= on X by the property x <= y implies f(x) <= f(y). These include the standard monotone (or positive) Boolean functions, regular Boolean functions and other interesting functions as speci

  20. Coevolutionary modeling in network formation

    KAUST Repository

    Al-Shyoukh, Ibrahim

    2014-12-03

    Network coevolution, the process of network topology evolution in feedback with dynamical processes over the network nodes, is a common feature of many engineered and natural networks. In such settings, the change in network topology occurs at a comparable time scale to nodal dynamics. Coevolutionary modeling offers the possibility to better understand how and why network structures emerge. For example, social networks can exhibit a variety of structures, ranging from almost uniform to scale-free degree distributions. While current models of network formation can reproduce these structures, coevolutionary modeling can offer a better understanding of the underlying dynamics. This paper presents an overview of recent work on coevolutionary models of network formation, with an emphasis on the following three settings: (i) dynamic flow of benefits and costs, (ii) transient link establishment costs, and (iii) latent preferential attachment.

  1. Modelling Citation Networks

    CERN Document Server

    Goldberg, S R; Evans, T S

    2014-01-01

    The distribution of the number of academic publications as a function of citation count for a given year is remarkably similar from year to year. We measure this similarity as a width of the distribution and find it to be approximately constant from year to year. We show that simple citation models fail to capture this behaviour. We then provide a simple three parameter citation network model using a mixture of local and global search processes which can reproduce the correct distribution over time. We use the citation network of papers from the hep-th section of arXiv to test our model. For this data, around 20% of citations use global information to reference recently published papers, while the remaining 80% are found using local searches. We note that this is consistent with other studies though our motivation is very different from previous work. Finally, we also find that the fluctuations in the size of an academic publication's bibliography is important for the model. This is not addressed in most mode...

  2. A Network Synthesis Model for Generating Protein Interaction Network Families

    OpenAIRE

    Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon

    2012-01-01

    In this work, we introduce a novel network synthesis model that can generate families of evolutionarily related synthetic protein-protein interaction (PPI) networks. Given an ancestral network, the proposed model generates the network family according to a hypothetical phylogenetic tree, where the descendant networks are obtained through duplication and divergence of their ancestors, followed by network growth using network evolution models. We demonstrate that this network synthesis model ca...

  3. Network model with structured nodes

    Science.gov (United States)

    Frisco, Pierluigi

    2011-08-01

    We present a network model in which words over a specific alphabet, called structures, are associated to each node and undirected edges are added depending on some distance measure between different structures. This model shifts the underlying principle of network generation from a purely mathematical one to an information-based one. It is shown how this model differs from the Barábasi-Albert and duplication models and how it can generate networks with topological features similar to biological networks: power law degree distribution, low average path length, clustering coefficient independent from the network size, etc. Two biological networks: S. cerevisiae gene network and E. coli protein-protein interaction network, are replicated using this model.

  4. Expectation-Maximization Approach to Boolean Factor Analysis

    Czech Academy of Sciences Publication Activity Database

    Frolov, A. A.; Húsek, Dušan; Polyakov, P.Y.

    Piscataway: IEEE, 2011, s. 559-566. ISBN 978-1-4244-9636-5. [IJCNN 2011. International Joint Conference on Neural Networks. San Jose (US), 31.07.2011-05.08.2011] R&D Projects: GA ČR GAP202/10/0262; GA ČR GA205/09/1079; GA MŠk(CZ) 1M0567 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * bars problem * dendritic inhibition * expectation-maximization * neural network application * statistics Subject RIV: IN - Informatics, Computer Science

  5. A neighbourhood evolving network model

    International Nuclear Information System (INIS)

    Many social, technological, biological and economical systems are best described by evolved network models. In this short Letter, we propose and study a new evolving network model. The model is based on the new concept of neighbourhood connectivity, which exists in many physical complex networks. The statistical properties and dynamics of the proposed model is analytically studied and compared with those of Barabasi-Albert scale-free model. Numerical simulations indicate that this network model yields a transition between power-law and exponential scaling, while the Barabasi-Albert scale-free model is only one of its special (limiting) cases. Particularly, this model can be used to enhance the evolving mechanism of complex networks in the real world, such as some social networks development

  6. Mining and modeling character networks

    CERN Document Server

    Bonato, Anthony; Elenberg, Ethan R; Gleich, David F; Hou, Yangyang

    2016-01-01

    We investigate social networks of characters found in cultural works such as novels and films. These character networks exhibit many of the properties of complex networks such as skewed degree distribution and community structure, but may be of relatively small order with a high multiplicity of edges. Building on recent work of beveridge, we consider graph extraction, visualization, and network statistics for three novels: Twilight by Stephanie Meyer, Steven King's The Stand, and J.K. Rowling's Harry Potter and the Goblet of Fire. Coupling with 800 character networks from films found in the http://moviegalaxies.com/ database, we compare the data sets to simulations from various stochastic complex networks models including random graphs with given expected degrees (also known as the Chung-Lu model), the configuration model, and the preferential attachment model. Using machine learning techniques based on motif (or small subgraph) counts, we determine that the Chung-Lu model best fits character networks and we ...

  7. Mining TCGA data using Boolean implications.

    Directory of Open Access Journals (Sweden)

    Subarna Sinha

    Full Text Available Boolean implications (if-then rules provide a conceptually simple, uniform and highly scalable way to find associations between pairs of random variables. In this paper, we propose to use Boolean implications to find relationships between variables of different data types (mutation, copy number alteration, DNA methylation and gene expression from the glioblastoma (GBM and ovarian serous cystadenoma (OV data sets from The Cancer Genome Atlas (TCGA. We find hundreds of thousands of Boolean implications from these data sets. A direct comparison of the relationships found by Boolean implications and those found by commonly used methods for mining associations show that existing methods would miss relationships found by Boolean implications. Furthermore, many relationships exposed by Boolean implications reflect important aspects of cancer biology. Examples of our findings include cis relationships between copy number alteration, DNA methylation and expression of genes, a new hierarchy of mutations and recurrent copy number alterations, loss-of-heterozygosity of well-known tumor suppressors, and the hypermethylation phenotype associated with IDH1 mutations in GBM. The Boolean implication results used in the paper can be accessed at http://crookneck.stanford.edu/microarray/TCGANetworks/.

  8. Generalizing Boolean Satisfiability II: Theory

    CERN Document Server

    Dixon, H E; Luks, E M; Parkes, A J; 10.1613/jair.1555

    2011-01-01

    This is the second of three planned papers describing ZAP, a satisfiability engine that substantially generalizes existing tools while retaining the performance characteristics of modern high performance solvers. The fundamental idea underlying ZAP is that many problems passed to such engines contain rich internal structure that is obscured by the Boolean representation used; our goal is to define a representation in which this structure is apparent and can easily be exploited to improve computational performance. This paper presents the theoretical basis for the ideas underlying ZAP, arguing that existing ideas in this area exploit a single, recurring structure in that multiple database axioms can be obtained by operating on a single axiom using a subgroup of the group of permutations on the literals in the problem. We argue that the group structure precisely captures the general structure at which earlier approaches hinted, and give numerous examples of its use. We go on to extend the Davis-Putnam-Logemann-...

  9. Local Correction of Boolean Functions

    CERN Document Server

    Alon, Noga

    2011-01-01

    A Boolean function f over n variables is said to be q-locally correctable if, given a black-box access to a function g which is "close" to an isomorphism f_sigma of f, we can compute f_sigma(x) for any x in Z_2^n with good probability using q queries to g. We observe that any k-junta, that is, any function which depends only on k of its input variables, is O(2^k)-locally correctable. Moreover, we show that there are examples where this is essentially best possible, and locally correcting some k-juntas requires a number of queries which is exponential in k. These examples, however, are far from being typical, and indeed we prove that for almost every k-junta, O(k log k) queries suffice.

  10. Boolean Delay Equations: A simple way of looking at complex systems

    OpenAIRE

    Ghil, Michael; Zaliapin, Ilya; Coluzzi, Barbara

    2006-01-01

    Boolean Delay Equations (BDEs) are semi-discrete dynamical models with Boolean-valued variables that evolve in continuous time. Systems of BDEs can be classified into conservative or dissipative, in a manner that parallels the classification of ordinary or partial differential equations. Solutions to certain conservative BDEs exhibit growth of complexity in time. They represent therewith metaphors for biological evolution or human history. Dissipative BDEs are structurally stable and exhibit ...

  11. Analysis of Boolean Functions based on Interaction Graphs and their influence in System Biology

    OpenAIRE

    Das, Jayanta Kumar; Rout, Ranjeet Kumar; Choudhury, Pabitra Pal

    2014-01-01

    Interaction graphs provide an important qualitative modeling approach for System Biology. This paper presents a novel approach for construction of interaction graph with the help of Boolean function decomposition. Each decomposition part (Consisting of 2-bits) of the Boolean functions has some important significance. In the dynamics of a biological system, each variable or node is nothing but gene or protein. Their regulation has been explored in terms of interaction graphs which are generate...

  12. Translating Pseudo-Boolean Constraints into CNF

    CERN Document Server

    Aavani, Amir

    2011-01-01

    A Pseudo-Boolean constraint is a linear constraint over Boolean variables. This kind of constraints has been widely used in expressing NP-complete problems. This paper introduces a new algorithm for translating Pseudo-Boolean constraints into CNF clauses. The CNF produced by the proposed encoding has small size, and we also characterize the constraints for which one can expect the SAT solvers to perform well on the produced CNF. We show that there are many constraints for which the proposed encoding has a good performance.

  13. Modeling Dynamics of Information Networks

    OpenAIRE

    Rosvall, Martin; Sneppen, Kim

    2003-01-01

    We propose an information-based model for network dynamics in which imperfect information leads to networks where the different vertices have widely different number of edges to other vertices, and where the topology has hierarchical features. The possibility to observe scale free networks is linked to a minimally connected system where hubs remain dynamic.

  14. Boolean Logic with Fault Tolerant Coding

    OpenAIRE

    Alagoz, B. Baykant

    2009-01-01

    Error detectable and error correctable coding in Hamming space was researched to discover possible fault tolerant coding constellations, which can implement Boolean logic with fault tolerant property. Basic logic operators of the Boolean algebra were developed to apply fault tolerant coding in the logic circuits. It was shown that application of three-bit fault tolerant codes have provided the digital system skill of auto-recovery without need for designing additional-fault tolerance mechanisms.

  15. Sensitivity versus block sensitivity of Boolean functions

    CERN Document Server

    Virza, Madars

    2010-01-01

    Determining relationship between sensitivity and block sensitivity of Boolean functions is of interest for computational complexity theory. We construct a sequence of Boolean functions with bs(f) = 1/2 (s(f))^2+ 1/2 s(f). The best known separation previously was bs(f) = 1/2 (s(f))^2 due to Rubinstein (1995). We also report results of computer search for functions with at most 12 variables.

  16. Developing Personal Network Business Models

    DEFF Research Database (Denmark)

    Saugstrup, Dan; Henten, Anders

    2006-01-01

    The aim of the paper is to examine the issue of business modeling in relation to personal networks, PNs. The paper builds on research performed on business models in the EU 1ST MAGNET1 project (My personal Adaptive Global NET). The paper presents the Personal Network concept and briefly reports on...

  17. Complex Networks in Psychological Models

    Science.gov (United States)

    Wedemann, R. S.; Carvalho, L. S. A. V. D.; Donangelo, R.

    We develop schematic, self-organizing, neural-network models to describe mechanisms associated with mental processes, by a neurocomputational substrate. These models are examples of real world complex networks with interesting general topological structures. Considering dopaminergic signal-to-noise neuronal modulation in the central nervous system, we propose neural network models to explain development of cortical map structure and dynamics of memory access, and unify different mental processes into a single neurocomputational substrate. Based on our neural network models, neurotic behavior may be understood as an associative memory process in the brain, and the linguistic, symbolic associative process involved in psychoanalytic working-through can be mapped onto a corresponding process of reconfiguration of the neural network. The models are illustrated through computer simulations, where we varied dopaminergic modulation and observed the self-organizing emergent patterns at the resulting semantic map, interpreting them as different manifestations of mental functioning, from psychotic through to normal and neurotic behavior, and creativity.

  18. Internet Network Resource Information Model

    Institute of Scientific and Technical Information of China (English)

    陈传峰; 李增智; 唐亚哲; 刘康平

    2002-01-01

    The foundation of any network management systens is a database that con-tains information about the network resources relevant to the management tasks. A networkinformation model is an abstraction of network resources, including both managed resources andmanaging resources. In the SNMP-based management framework, management information isdefined almost exclusively from a "device" viewpoint, namely, managing a network is equiva-lent to managing a collection of individual nodes. Aiming at making use of recent advances indistributed computing and in object-oriented analysis and design, the Internet management ar-chitecture can also be based on the Open Distributed Processing Reference Model (RM-ODP).The purpose of this article is to provide an Internet Network Resource Information Model.First, a layered management information architecture will be discussed. Then the Internetnetwork resource information model is presented. The information model is specified usingObject-Z.

  19. Telecommunications network modelling, planning and design

    CERN Document Server

    Evans, Sharon

    2003-01-01

    Telecommunication Network Modelling, Planning and Design addresses sophisticated modelling techniques from the perspective of the communications industry and covers some of the major issues facing telecommunications network engineers and managers today. Topics covered include network planning for transmission systems, modelling of SDH transport network structures and telecommunications network design and performance modelling, as well as network costs and ROI modelling and QoS in 3G networks.

  20. Modeling of fluctuating reaction networks

    International Nuclear Information System (INIS)

    Full Text:Various dynamical systems are organized as reaction networks, where the population size of one component affects the populations of all its neighbors. Such networks can be found in interstellar surface chemistry, cell biology, thin film growth and other systems. I cases where the populations of reactive species are large, the network can be modeled by rate equations which provide all reaction rates within mean field approximation. However, in small systems that are partitioned into sub-micron size, these populations strongly fluctuate. Under these conditions rate equations fail and the master equation is needed for modeling these reactions. However, the number of equations in the master equation grows exponentially with the number of reactive species, severely limiting its feasibility for complex networks. Here we present a method which dramatically reduces the number of equations, thus enabling the incorporation of the master equation in complex reaction networks. The method is examplified in the context of reaction network on dust grains. Its applicability for genetic networks will be discussed. 1. Efficient simulations of gas-grain chemistry in interstellar clouds. Azi Lipshtat and Ofer Biham, Phys. Rev. Lett. 93 (2004), 170601. 2. Modeling of negative autoregulated genetic networks in single cells. Azi Lipshtat, Hagai B. Perets, Nathalie Q. Balaban and Ofer Biham, Gene: evolutionary genomics (2004), In press

  1. Neural network modeling of emotion

    Science.gov (United States)

    Levine, Daniel S.

    2007-03-01

    This article reviews the history and development of computational neural network modeling of cognitive and behavioral processes that involve emotion. The exposition starts with models of classical conditioning dating from the early 1970s. Then it proceeds toward models of interactions between emotion and attention. Then models of emotional influences on decision making are reviewed, including some speculative (not and not yet simulated) models of the evolution of decision rules. Through the late 1980s, the neural networks developed to model emotional processes were mainly embodiments of significant functional principles motivated by psychological data. In the last two decades, network models of these processes have become much more detailed in their incorporation of known physiological properties of specific brain regions, while preserving many of the psychological principles from the earlier models. Most network models of emotional processes so far have dealt with positive and negative emotion in general, rather than specific emotions such as fear, joy, sadness, and anger. But a later section of this article reviews a few models relevant to specific emotions: one family of models of auditory fear conditioning in rats, and one model of induced pleasure enhancing creativity in humans. Then models of emotional disorders are reviewed. The article concludes with philosophical statements about the essential contributions of emotion to intelligent behavior and the importance of quantitative theories and models to the interdisciplinary enterprise of understanding the interactions of emotion, cognition, and behavior.

  2. Duality theories for Boolean algebras with operators

    CERN Document Server

    Givant, Steven

    2014-01-01

    In this new text, Steven Givant—the author of several acclaimed books, including works co-authored with Paul Halmos and Alfred Tarski—develops three theories of duality for Boolean algebras with operators. Givant addresses the two most recognized dualities (one algebraic and the other topological) and introduces a third duality, best understood as a hybrid of the first two. This text will be of interest to graduate students and researchers in the fields of mathematics, computer science, logic, and philosophy who are interested in exploring special or general classes of Boolean algebras with operators. Readers should be familiar with the basic arithmetic and theory of Boolean algebras, as well as the fundamentals of point-set topology.

  3. Algorithms for Boolean Function Query Properties

    OpenAIRE

    Aaronson, Scott

    2001-01-01

    We present new algorithms to compute fundamental properties of a Boolean function given in truth-table form. Specifically, we give an O(N^2.322 log N) algorithm for block sensitivity, an O(N^1.585 log N) algorithm for `tree decomposition,' and an O(N) algorithm for `quasisymmetry.' These algorithms are based on new insights into the structure of Boolean functions that may be of independent interest. We also give a subexponential-time algorithm for the space-bounded quantum query complexity of...

  4. A finite alternation result for reversible boolean circuits

    OpenAIRE

    Selinger, Peter

    2016-01-01

    We say that a reversible boolean function on n bits has alternation depth d if it can be written as the sequential composition of d reversible boolean functions, each of which acts only on the top n-1 bits or on the bottom n-1 bits. We show that every reversible boolean function of n >= 4 bits has alternation depth 9.

  5. Simplified models of biological networks.

    Science.gov (United States)

    Sneppen, Kim; Krishna, Sandeep; Semsey, Szabolcs

    2010-01-01

    The function of living cells is controlled by complex regulatory networks that are built of a wide diversity of interacting molecular components. The sheer size and intricacy of molecular networks of even the simplest organisms are obstacles toward understanding network functionality. This review discusses the achievements and promise of a bottom-up approach that uses well-characterized subnetworks as model systems for understanding larger networks. It highlights the interplay between the structure, logic, and function of various types of small regulatory circuits. The bottom-up approach advocates understanding regulatory networks as a collection of entangled motifs. We therefore emphasize the potential of negative and positive feedback, as well as their combinations, to generate robust homeostasis, epigenetics, and oscillations. PMID:20192769

  6. Advances in theoretical models of network science

    Institute of Scientific and Technical Information of China (English)

    FANG Jin-qing; BI Qiao; LI Yong

    2007-01-01

    In this review article, we will summarize the main advances in network science investigated by the CIAE Group of Complex Network in this field. Several theoretical models of network science were proposed and their topological and dynamical properties are reviewed and compared with the other models. Our models mainly include a harmonious unifying hybrid preferential model, a large unifying hybrid network model, a quantum interference network, a hexagonal nanowire network, and a small-world network with the same degree. The models above reveal some new phenomena and findings, which are useful for deeply understanding and investigating complex networks and their applications.

  7. Security models for heterogeneous networking.

    OpenAIRE

    Mapp, Glenford E.; Aiash, Mahdi; Lasebae, Aboubaker; Phan, Raphael

    2010-01-01

    Security for Next Generation Networks (NGNs) is an attractive topic for many research groups. The Y-Comm security group believes that a new security approach is needed to address the security challenges in 4G networks. This paper sheds light on our approach of providing security for the Y-Comm architecture as an example of 4G communication frameworks. Our approach proposes a four-layer security integrated module to protect data and three targeted security models to protect different network e...

  8. Comparison of Seven Methods for Boolean Factor Analysis and Their Evaluation by Information Gain

    Czech Academy of Sciences Publication Activity Database

    Frolov, A.; Húsek, Dušan; Polyakov, P.Y.

    2016-01-01

    Roč. 27, č. 3 (2016), s. 538-550. ISSN 2162-237X R&D Projects: GA MŠk ED1.1.00/02.0070 Institutional support: RVO:67985807 Keywords : associative memory * bars problem (BP) * Boolean factor analysis (BFA) * data mining * dimension reduction * Hebbian learning rule * information gain * likelihood maximization (LM) * neural network application * recurrent neural network * statistics Subject RIV: IN - Informatics, Computer Science Impact factor: 4.291, year: 2014

  9. A Multilayer Model of Computer Networks

    OpenAIRE

    Shchurov, Andrey A.

    2015-01-01

    The fundamental concept of applying the system methodology to network analysis declares that network architecture should take into account services and applications which this network provides and supports. This work introduces a formal model of computer networks on the basis of the hierarchical multilayer networks. In turn, individual layers are represented as multiplex networks. The concept of layered networks provides conditions of top-down consistency of the model. Next, we determined the...

  10. Some Aspects of Boolean Valued Analysis

    OpenAIRE

    Kusraev, A. G.; Kutateladze, S. S.

    2015-01-01

    This is a survey of some recent applications of Boolean valued analysis to operator theory and harmonic analysis. Under consideration are pseudoembedding operators, the noncommutative Wickstead problem, the Radon-Nikodym Theorem for JB-algebras, and the Bochner Theorem for lattice-valued positive definite mappings on locally compact groups.

  11. Demonstrating Boolean Logic Using Simple Electrical Circuits

    Science.gov (United States)

    McElhaney, Kevin W.

    2004-01-01

    While exploring the subject of geometric proofs, boolean logic operators AND and OR can be used to allow students to visualize their true-or-false patterns. An activity in the form of constructing electrical circuits is illustrated to explain the concept.

  12. Boolean Queries Optimization by Genetic Algorithms

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Owais, S.S.J.; Krömer, P.; Snášel, Václav

    2005-01-01

    Roč. 15, - (2005), s. 395-409. ISSN 1210-0552 R&D Projects: GA AV ČR 1ET100300414 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary algorithms * genetic algorithms * genetic programming * information retrieval * Boolean query Subject RIV: BB - Applied Statistics, Operational Research

  13. Evolutionary Algorithms for Boolean Queries Optimization

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Snášel, Václav; Neruda, Roman; Owais, S.S.J.; Krömer, P.

    2006-01-01

    Roč. 3, č. 1 (2006), s. 15-20. ISSN 1790-0832 R&D Projects: GA AV ČR 1ET100300414 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary algorithms * genetic algorithms * information retrieval * Boolean query Subject RIV: BA - General Mathematics

  14. A complexity theory based on Boolean algebra

    DEFF Research Database (Denmark)

    Skyum, Sven; Valiant, Leslie

    1985-01-01

    A projection of a Boolean function is a function obtained by substituting for each of its variables a variable, the negation of a variable, or a constant. Reducibilities among computational problems under this relation of projection are considered. It is shown that much of what is of everyday rel...

  15. A Boolean Map Theory of Visual Attention

    Science.gov (United States)

    Huang, Liqiang; Pashler, Harold

    2007-01-01

    A theory is presented that attempts to answer two questions. What visual contents can an observer consciously access at one moment? Answer: only one feature value (e.g., green) per dimension, but those feature values can be associated (as a group) with multiple spatially precise locations (comprising a single labeled Boolean map). How can an…

  16. Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET.

    Science.gov (United States)

    Rodriguez, Ana; Crespo, Isaac; Androsova, Ganna; del Sol, Antonio

    2015-01-01

    High-throughput technologies have led to the generation of an increasing amount of data in different areas of biology. Datasets capturing the cell's response to its intra- and extra-cellular microenvironment allows such data to be incorporated as signed and directed graphs or influence networks. These prior knowledge networks (PKNs) represent our current knowledge of the causality of cellular signal transduction. New signalling data is often examined and interpreted in conjunction with PKNs. However, different biological contexts, such as cell type or disease states, may have distinct variants of signalling pathways, resulting in the misinterpretation of new data. The identification of inconsistencies between measured data and signalling topologies, as well as the training of PKNs using context specific datasets (PKN contextualization), are necessary conditions to construct reliable, predictive models, which are current challenges in the systems biology of cell signalling. Here we present PRUNET, a user-friendly software tool designed to address the contextualization of a PKNs to specific experimental conditions. As the input, the algorithm takes a PKN and the expression profile of two given stable steady states or cellular phenotypes. The PKN is iteratively pruned using an evolutionary algorithm to perform an optimization process. This optimization rests in a match between predicted attractors in a discrete logic model (Boolean) and a Booleanized representation of the phenotypes, within a population of alternative subnetworks that evolves iteratively. We validated the algorithm applying PRUNET to four biological examples and using the resulting contextualized networks to predict missing expression values and to simulate well-characterized perturbations. PRUNET constitutes a tool for the automatic curation of a PKN to make it suitable for describing biological processes under particular experimental conditions. The general applicability of the implemented algorithm

  17. Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET.

    Directory of Open Access Journals (Sweden)

    Ana Rodriguez

    Full Text Available High-throughput technologies have led to the generation of an increasing amount of data in different areas of biology. Datasets capturing the cell's response to its intra- and extra-cellular microenvironment allows such data to be incorporated as signed and directed graphs or influence networks. These prior knowledge networks (PKNs represent our current knowledge of the causality of cellular signal transduction. New signalling data is often examined and interpreted in conjunction with PKNs. However, different biological contexts, such as cell type or disease states, may have distinct variants of signalling pathways, resulting in the misinterpretation of new data. The identification of inconsistencies between measured data and signalling topologies, as well as the training of PKNs using context specific datasets (PKN contextualization, are necessary conditions to construct reliable, predictive models, which are current challenges in the systems biology of cell signalling. Here we present PRUNET, a user-friendly software tool designed to address the contextualization of a PKNs to specific experimental conditions. As the input, the algorithm takes a PKN and the expression profile of two given stable steady states or cellular phenotypes. The PKN is iteratively pruned using an evolutionary algorithm to perform an optimization process. This optimization rests in a match between predicted attractors in a discrete logic model (Boolean and a Booleanized representation of the phenotypes, within a population of alternative subnetworks that evolves iteratively. We validated the algorithm applying PRUNET to four biological examples and using the resulting contextualized networks to predict missing expression values and to simulate well-characterized perturbations. PRUNET constitutes a tool for the automatic curation of a PKN to make it suitable for describing biological processes under particular experimental conditions. The general applicability of the

  18. Target-Centric Network Modeling

    DEFF Research Database (Denmark)

    Mitchell, Dr. William L.; Clark, Dr. Robert M.

    In Target-Centric Network Modeling: Case Studies in Analyzing Complex Intelligence Issues, authors Robert Clark and William Mitchell take an entirely new approach to teaching intelligence analysis. Unlike any other book on the market, it offers case study scenarios using actual intelligence...... reporting formats, along with a tested process that facilitates the production of a wide range of analytical products for civilian, military, and hybrid intelligence environments. Readers will learn how to perform the specific actions of problem definition modeling, target network modeling, and...... collaborative sharing in the process of creating a high-quality, actionable intelligence product. The case studies reflect the complexity of twenty-first century intelligence issues by dealing with multi-layered target networks that cut across political, economic, social, technological, and military issues...

  19. Hydraulic Modeling: Pipe Network Analysis

    OpenAIRE

    Datwyler, Trevor T.

    2012-01-01

    Water modeling is becoming an increasingly important part of hydraulic engineering. One application of hydraulic modeling is pipe network analysis. Using programmed algorithms to repeatedly solve continuity and energy equations, computer software can greatly reduce the amount of time required to analyze a closed conduit system. Such hydraulic models can become a valuable tool for cities to maintain their water systems and plan for future growth. The Utah Division of Drinking Water regulations...

  20. Spatial Models for Virtual Networks

    Science.gov (United States)

    Janssen, Jeannette

    This paper discusses the use of spatial graph models for the analysis of networks that do not have a direct spatial reality, such as web graphs, on-line social networks, or citation graphs. In a spatial graph model, nodes are embedded in a metric space, and link formation depends on the relative position of nodes in the space. It is argued that spatial models form a good basis for link mining: assuming a spatial model, the link information can be used to infer the spatial position of the nodes, and this information can then be used for clustering and recognition of node similarity. This paper gives a survey of spatial graph models, and discusses their suitability for link mining.

  1. Ising model for distribution networks

    CERN Document Server

    Hooyberghs, H; Giuraniuc, C; Van Schaeybroeck, B; Indekeu, J O

    2012-01-01

    An elementary Ising spin model is proposed for demonstrating cascading failures (break-downs, blackouts, collapses, avalanches, ...) that can occur in realistic networks for distribution and delivery by suppliers to consumers. A ferromagnetic Hamiltonian with quenched random fields results from policies that maximize the gap between demand and delivery. Such policies can arise in a competitive market where firms artificially create new demand, or in a solidary environment where too high a demand cannot reasonably be met. Network failure in the context of a policy of solidarity is possible when an initially active state becomes metastable and decays to a stable inactive state. We explore the characteristics of the demand and delivery, as well as the topological properties, which make the distribution network susceptible of failure. An effective temperature is defined, which governs the strength of the activity fluctuations which can induce a collapse. Numerical results, obtained by Monte Carlo simulations of t...

  2. Boolean representations of simplicial complexes and matroids

    CERN Document Server

    Rhodes, John

    2015-01-01

    This self-contained monograph explores a new theory centered around boolean representations of simplicial complexes leading to a new class of complexes featuring matroids as central to the theory. The book illustrates these new tools to study the classical theory of matroids as well as their important geometric connections. Moreover, many geometric and topological features of the theory of matroids find their counterparts in this extended context.   Graduate students and researchers working in the areas of combinatorics, geometry, topology, algebra and lattice theory will find this monograph appealing due to the wide range of new problems raised by the theory. Combinatorialists will find this extension of the theory of matroids useful as it opens new lines of research within and beyond matroids. The geometric features and geometric/topological applications will appeal to geometers. Topologists who desire to perform algebraic topology computations will appreciate the algorithmic potential of boolean represent...

  3. Fast Vertical Mining Using Boolean Algebra

    Directory of Open Access Journals (Sweden)

    Hosny M. Ibrahim

    2015-01-01

    Full Text Available The vertical association rules mining algorithm is an efficient mining method, which makes use of support sets of frequent itemsets to calculate the support of candidate itemsets. It overcomes the disadvantage of scanning database many times like Apriori algorithm. In vertical mining, frequent itemsets can be represented as a set of bit vectors in memory, which enables for fast computation. The sizes of bit vectors for itemsets are the main space expense of the algorithm that restricts its expansibility. Therefore, in this paper, a proposed algorithm that compresses the bit vectors of frequent itemsets will be presented. The new bit vector schema presented here depends on Boolean algebra rules to compute the intersection of two compressed bit vectors without making any costly decompression operation. The experimental results show that the proposed algorithm, Vertical Boolean Mining (VBM algorithm is better than both Apriori algorithm and the classical vertical association rule mining algorithm in the mining time and the memory usage.

  4. Iterative Radial Basis Functions Neural Networks as Metamodels of Stochastic Simulations of the Quality of Search Engines in the World Wide Web.

    Science.gov (United States)

    Meghabghab, George

    2001-01-01

    Discusses the evaluation of search engines and uses neural networks in stochastic simulation of the number of rejected Web pages per search query. Topics include the iterative radial basis functions (RBF) neural network; precision; response time; coverage; Boolean logic; regression models; crawling algorithms; and implications for search engine…

  5. Efficient Analog Circuits for Boolean Satisfiability

    OpenAIRE

    Yin, Xunzhao; Sedighi, Behnam; Varga, Melinda; Ercsey-Ravasz, Maria; Toroczkai, Zoltan; Hu, Xiaobo Sharon

    2016-01-01

    Efficient solutions to NP-complete problems would significantly benefit both science and industry. However, such problems are intractable on digital computers based on the von Neumann architecture, thus creating the need for alternative solutions to tackle such problems. Recently, a deterministic, continuous-time dynamical system (CTDS) was proposed (Nature Physics, 7(12), 966 (2011)) to solve a representative NP-complete problem, Boolean Satisfiability (SAT). This solver shows polynomial ana...

  6. Using Genetic Algorithms for Boolean Queries Optimization

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Snášel, Václav; Owais, S.S.J.; Krömer, P.

    Calgary: ACTA Press, 2005 - (Hamza, M.), s. 178-184 ISBN 0-88986-510-8. [IASTED International Conference on Internet and Multimedia Systems and Applications /9./. Honolulu (US), 15.08.2005-17.08.2005] R&D Projects: GA AV ČR 1ET100300419 Institutional research plan: CEZ:AV0Z10300504 Keywords : genetic algorithms * information retrieval * Boolean query * genetic programming Subject RIV: BA - General Mathematics

  7. On the Implementation of Boolean Matrix Factorization

    Czech Academy of Sciences Publication Activity Database

    Snášel, V.; Krömer, P.; Platoš, J.; Húsek, Dušan

    Los Alamitos: IEEE, 2008, s. 554-558. ISBN 978-0-7695-3299-8. [ETID '08. International Workshop on Evolutionary Techniques /2./, in collocation with DEXA 2008 International Conference /19./. Turin (IT), 01.09.2008-05.09.2008] Institutional research plan: CEZ:AV0Z10300504 Keywords : data mining * genetic algorithms * Boolean factorization * binary data * machine learning * feature extraction Subject RIV: IN - Informatics, Computer Science

  8. Nonparametric Bayesian Modeling of Complex Networks

    DEFF Research Database (Denmark)

    Schmidt, Mikkel Nørgaard; Mørup, Morten

    2013-01-01

    Modeling structure in complex networks using Bayesian nonparametrics makes it possible to specify flexible model structures and infer the adequate model complexity from the observed data. This article provides a gentle introduction to nonparametric Bayesian modeling of complex networks: Using...... for complex networks can be derived and point out relevant literature....

  9. Research on the model of home networking

    Science.gov (United States)

    Yun, Xiang; Feng, Xiancheng

    2007-11-01

    It is the research hotspot of current broadband network to combine voice service, data service and broadband audio-video service by IP protocol to transport various real time and mutual services to terminal users (home). Home Networking is a new kind of network and application technology which can provide various services. Home networking is called as Digital Home Network. It means that PC, home entertainment equipment, home appliances, Home wirings, security, illumination system were communicated with each other by some composing network technology, constitute a networking internal home, and connect with WAN by home gateway. It is a new network technology and application technology, and can provide many kinds of services inside home or between homes. Currently, home networking can be divided into three kinds: Information equipment, Home appliances, Communication equipment. Equipment inside home networking can exchange information with outer networking by home gateway, this information communication is bidirectional, user can get information and service which provided by public networking by using home networking internal equipment through home gateway connecting public network, meantime, also can get information and resource to control the internal equipment which provided by home networking internal equipment. Based on the general network model of home networking, there are four functional entities inside home networking: HA, HB, HC, and HD. (1) HA (Home Access) - home networking connects function entity; (2) HB (Home Bridge) Home networking bridge connects function entity; (3) HC (Home Client) - Home networking client function entity; (4) HD (Home Device) - decoder function entity. There are many physical ways to implement four function entities. Based on theses four functional entities, there are reference model of physical layer, reference model of link layer, reference model of IP layer and application reference model of high layer. In the future home network

  10. Mathematical Modelling Plant Signalling Networks

    KAUST Repository

    Muraro, D.

    2013-01-01

    During the last two decades, molecular genetic studies and the completion of the sequencing of the Arabidopsis thaliana genome have increased knowledge of hormonal regulation in plants. These signal transduction pathways act in concert through gene regulatory and signalling networks whose main components have begun to be elucidated. Our understanding of the resulting cellular processes is hindered by the complex, and sometimes counter-intuitive, dynamics of the networks, which may be interconnected through feedback controls and cross-regulation. Mathematical modelling provides a valuable tool to investigate such dynamics and to perform in silico experiments that may not be easily carried out in a laboratory. In this article, we firstly review general methods for modelling gene and signalling networks and their application in plants. We then describe specific models of hormonal perception and cross-talk in plants. This mathematical analysis of sub-cellular molecular mechanisms paves the way for more comprehensive modelling studies of hormonal transport and signalling in a multi-scale setting. © EDP Sciences, 2013.

  11. Probabilistic logic modeling of network reliability for hybrid network architectures

    Energy Technology Data Exchange (ETDEWEB)

    Wyss, G.D.; Schriner, H.K.; Gaylor, T.R.

    1996-10-01

    Sandia National Laboratories has found that the reliability and failure modes of current-generation network technologies can be effectively modeled using fault tree-based probabilistic logic modeling (PLM) techniques. We have developed fault tree models that include various hierarchical networking technologies and classes of components interconnected in a wide variety of typical and atypical configurations. In this paper we discuss the types of results that can be obtained from PLMs and why these results are of great practical value to network designers and analysts. After providing some mathematical background, we describe the `plug-and-play` fault tree analysis methodology that we have developed for modeling connectivity and the provision of network services in several current- generation network architectures. Finally, we demonstrate the flexibility of the method by modeling the reliability of a hybrid example network that contains several interconnected ethernet, FDDI, and token ring segments. 11 refs., 3 figs., 1 tab.

  12. Energy modelling in sensor networks

    Directory of Open Access Journals (Sweden)

    D. Schmidt

    2007-06-01

    Full Text Available Wireless sensor networks are one of the key enabling technologies for the vision of ambient intelligence. Energy resources for sensor nodes are very scarce. A key challenge is the design of energy efficient communication protocols. Models of the energy consumption are needed to accurately simulate the efficiency of a protocol or application design, and can also be used for automatic energy optimizations in a model driven design process. We propose a novel methodology to create models for sensor nodes based on few simple measurements. In a case study the methodology was used to create models for MICAz nodes. The models were integrated in a simulation environment as well as in a SDL runtime framework of a model driven design process. Measurements on a test application that was created automatically from an SDL specification showed an 80% reduction in energy consumption compared to an implementation without power saving strategies.

  13. Plant Growth Models Using Artificial Neural Networks

    Science.gov (United States)

    Bubenheim, David

    1997-01-01

    In this paper, we descrive our motivation and approach to devloping models and the neural network architecture. Initial use of the artificial neural network for modeling the single plant process of transpiration is presented.

  14. Boolean Logic Optimization in Majority-Inverter Graphs

    OpenAIRE

    Amarù, Luca; Gaillardon, Pierre-Emmanuel; De Micheli, Giovanni

    2015-01-01

    We present a Boolean logic optimization framework based on Majority-Inverter Graph (MIG). An MIG is a directed acyclic graph consisting of three-input majority nodes and regular/complemented edges. Current MIG optimization is supported by a consistent algebraic framework. However, when algebraic methods cannot improve a result quality, stronger Boolean methods are needed to attain further optimization. For this purpose, we propose MIG Boolean methods exploiting the error masking property of m...

  15. Using Boolean Constraint Propagation for Sub-clause Deduction

    OpenAIRE

    Darras, Sylvain; Dequen, Gilles; Devendeville, Laure; Mazure, Bertrand; Ostrowski, Richard; Sais, Lahkdar

    2005-01-01

    Boolean Constraint Propagation (BCP) is recognized as one of the most use- ful technique for efficient satisfiability checking. In this paper a new extension of the scope of boolean constraint propagation is proposed. It makes an original use of BCP to achieve further reduction of boolean formulas. Considering the impli- cation graph generated by the constraint propagation process as a resolution tree, sub-clauses from the original formula can be deduced. Then, we show how such extension can ...

  16. Modelling of biochemical reaction networks

    OpenAIRE

    Gloppen Jørgensen, Arne Gunnar

    2011-01-01

    This report investigates signalling in reaction kinetic networks. The main topic is signalling between a substance being controlled by another substance and how this can be related to control theory. Different types of so-called natural controllers are compared and certain properties are investigated. Natural controllers are models on how a catalyst enzyme controls, for example the concentration, of a substance. There are sixteen different combinations of signalling between these substanc...

  17. Asymptotic properties of wireless multi-hop networks

    OpenAIRE

    Dousse, Olivier; Thiran, Patrick

    2007-01-01

    In this dissertation, we consider wireless multi-hop networks, where the nodes are randomly placed. We are particularly interested in their asymptotic properties when the number of nodes tends to infinity. We use percolation theory as our main tool of analysis. As a first model, we assume that nodes have a fixed connectivity range, and can establish wireless links to all nodes within this range, but no other (Boolean model). We compute for one-dimensional networks the probability that two nod...

  18. Hierarchical Models for Independence Structures of Networks

    OpenAIRE

    Sadeghi, Kayvan; Rinaldo, Alessandro

    2016-01-01

    We introduce a new family of network models, called hierarchical network models, that allow to represent in an explicit manner the stochastic dependence among the edges. In particular, each member of this family can be associated with a graphical model defining conditional independence clauses among the edges of the network, called the dependency graph. Every network model of dyadic independence assumption can be generalized to construct members of this new family. Using this new framework, w...

  19. Stabilizing gene regulatory networks through feedforward loops

    Science.gov (United States)

    Kadelka, C.; Murrugarra, D.; Laubenbacher, R.

    2013-06-01

    The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has been identified as the action of so-called microRNAs that operate via feedforward loops. We present results of a computational study, using the modeling framework of stochastic Boolean networks, which explores the role that such network motifs play in stabilizing global dynamics. The paper introduces a new measure for the stability of stochastic networks. The results show that certain types of feedforward loops do indeed buffer the network against stochastic effects.

  20. An evolving network model with community structure

    International Nuclear Information System (INIS)

    Many social and biological networks consist of communities-groups of nodes within which connections are dense, but between which connections are sparser. Recently, there has been considerable interest in designing algorithms for detecting community structures in real-world complex networks. In this paper, we propose an evolving network model which exhibits community structure. The network model is based on the inner-community preferential attachment and inter-community preferential attachment mechanisms. The degree distributions of this network model are analysed based on a mean-field method. Theoretical results and numerical simulations indicate that this network model has community structure and scale-free properties

  1. Brand Marketing Model on Social Networks

    Directory of Open Access Journals (Sweden)

    Jolita Jezukevičiūtė

    2014-04-01

    Full Text Available The paper analyzes the brand and its marketing solutions onsocial networks. This analysis led to the creation of improvedbrand marketing model on social networks, which will contributeto the rapid and cheap organization brand recognition, increasecompetitive advantage and enhance consumer loyalty. Therefore,the brand and a variety of social networks are becoming a hotresearch area for brand marketing model on social networks.The world‘s most successful brand marketing models exploratoryanalysis of a single case study revealed a brand marketingsocial networking tools that affect consumers the most. Basedon information analysis and methodological studies, develop abrand marketing model on social networks.

  2. Combinational Logic-Level Verification using Boolean Expression Diagrams

    DEFF Research Database (Denmark)

    Hulgaard, Henrik; Williams, Poul Frederick; Andersen, Henrik Reif

    1997-01-01

    Boolean Expression Diagrams (BEDs) is a new data structure for representing and manipulating Boolean functions. BEDs are a generalization of Binary Decision Diagrams (BDDs) that are capable of representing any Boolean circuit in linear space and still maintain many of the desirable properties of...... BDDs. This paper demonstrates that BEDs are well suited for solving the combinational logic-level verification problem which is, given two combinational circuits, to determine whether they implement the same Boolean functions. Based on all combinational circuits in the ISCAS 85 and LGSynth 91...

  3. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

    Directory of Open Access Journals (Sweden)

    Jensen Paul A

    2011-09-01

    Full Text Available Abstract Background Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model. Results We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae. Conclusion The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.

  4. Modeling the Dynamics of Compromised Networks

    Energy Technology Data Exchange (ETDEWEB)

    Soper, B; Merl, D M

    2011-09-12

    Accurate predictive models of compromised networks would contribute greatly to improving the effectiveness and efficiency of the detection and control of network attacks. Compartmental epidemiological models have been applied to modeling attack vectors such as viruses and worms. We extend the application of these models to capture a wider class of dynamics applicable to cyber security. By making basic assumptions regarding network topology we use multi-group epidemiological models and reaction rate kinetics to model the stochastic evolution of a compromised network. The Gillespie Algorithm is used to run simulations under a worst case scenario in which the intruder follows the basic connection rates of network traffic as a method of obfuscation.

  5. RMBNToolbox: random models for biochemical networks

    Directory of Open Access Journals (Sweden)

    Niemi Jari

    2007-05-01

    Full Text Available Abstract Background There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model sizes remain limited. The lack of kinetic information is usually the limiting factor for the construction of detailed simulation models. Results We present a computational toolbox for generating random biochemical network models which mimic real biochemical networks. The toolbox is called Random Models for Biochemical Networks. The toolbox works in the Matlab environment, and it makes it possible to generate various network structures, stoichiometries, kinetic laws for reactions, and parameters therein. The generation can be based on statistical rules and distributions, and more detailed information of real biochemical networks can be used in situations where it is known. The toolbox can be easily extended. The resulting network models can be exported in the format of Systems Biology Markup Language. Conclusion While more information is accumulating on biochemical networks, random networks can be used as an intermediate step towards their better understanding. Random networks make it possible to study the effects of various network characteristics to the overall behavior of the network. Moreover, the construction of artificial network models provides the ground truth data needed in the validation of various computational methods in the fields of parameter estimation and data analysis.

  6. Information Network Model Query Processing

    Science.gov (United States)

    Song, Xiaopu

    Information Networking Model (INM) [31] is a novel database model for real world objects and relationships management. It naturally and directly supports various kinds of static and dynamic relationships between objects. In INM, objects are networked through various natural and complex relationships. INM Query Language (INM-QL) [30] is designed to explore such information network, retrieve information about schema, instance, their attributes, relationships, and context-dependent information, and process query results in the user specified form. INM database management system has been implemented using Berkeley DB, and it supports INM-QL. This thesis is mainly focused on the implementation of the subsystem that is able to effectively and efficiently process INM-QL. The subsystem provides a lexical and syntactical analyzer of INM-QL, and it is able to choose appropriate evaluation strategies and index mechanism to process queries in INM-QL without the user's intervention. It also uses intermediate result structure to hold intermediate query result and other helping structures to reduce complexity of query processing.

  7. Complete Boolean Satisfiability Solving Algorithms Based on Local Search

    Institute of Scientific and Technical Information of China (English)

    Wen-Sheng Guo; Guo-Wu Yang; William N.N.Hung; Xiaoyu Song

    2013-01-01

    Boolean satisfiability (SAT) is a well-known problem in computer science,artificial intelligence,and operations research.This paper focuses on the satisfiability problem of Model RB structure that is similar to graph coloring problems and others.We propose a translation method and three effective complete SAT solving algorithms based on the characterization of Model RB structure.We translate clauses into a graph with exclusive sets and relative sets.In order to reduce search depth,we determine search order using vertex weights and clique in the graph.The results show that our algorithms are much more effective than the best SAT solvers in numerous Model RB benchmarks,especially in those large benchmark instances.

  8. Boolean and brain-inspired computing using spin-transfer torque devices

    Science.gov (United States)

    Fan, Deliang

    Several completely new approaches (such as spintronic, carbon nanotube, graphene, TFETs, etc.) to information processing and data storage technologies are emerging to address the time frame beyond current Complementary Metal-Oxide-Semiconductor (CMOS) roadmap. The high speed magnetization switching of a nano-magnet due to current induced spin-transfer torque (STT) have been demonstrated in recent experiments. Such STT devices can be explored in compact, low power memory and logic design. In order to truly leverage STT devices based computing, researchers require a re-think of circuit, architecture, and computing model, since the STT devices are unlikely to be drop-in replacements for CMOS. The potential of STT devices based computing will be best realized by considering new computing models that are inherently suited to the characteristics of STT devices, and new applications that are enabled by their unique capabilities, thereby attaining performance that CMOS cannot achieve. The goal of this research is to conduct synergistic exploration in architecture, circuit and device levels for Boolean and brain-inspired computing using nanoscale STT devices. Specifically, we first show that the non-volatile STT devices can be used in designing configurable Boolean logic blocks. We propose a spin-memristor threshold logic (SMTL) gate design, where memristive cross-bar array is used to perform current mode summation of binary inputs and the low power current mode spintronic threshold device carries out the energy efficient threshold operation. Next, for brain-inspired computing, we have exploited different spin-transfer torque device structures that can implement the hard-limiting and soft-limiting artificial neuron transfer functions respectively. We apply such STT based neuron (or 'spin-neuron') in various neural network architectures, such as hierarchical temporal memory and feed-forward neural network, for performing "human-like" cognitive computing, which show more than

  9. Multilayer weighted social network model

    Science.gov (United States)

    Murase, Yohsuke; Török, János; Jo, Hang-Hyun; Kaski, Kimmo; Kertész, János

    2014-11-01

    Recent empirical studies using large-scale data sets have validated the Granovetter hypothesis on the structure of the society in that there are strongly wired communities connected by weak ties. However, as interaction between individuals takes place in diverse contexts, these communities turn out to be overlapping. This implies that the society has a multilayered structure, where the layers represent the different contexts. To model this structure we begin with a single-layer weighted social network (WSN) model showing the Granovetterian structure. We find that when merging such WSN models, a sufficient amount of interlayer correlation is needed to maintain the relationship between topology and link weights, while these correlations destroy the enhancement in the community overlap due to multiple layers. To resolve this, we devise a geographic multilayer WSN model, where the indirect interlayer correlations due to the geographic constraints of individuals enhance the overlaps between the communities and, at the same time, the Granovetterian structure is preserved.

  10. Brand Marketing Model on Social Networks

    OpenAIRE

    Jolita Jezukevičiūtė; Vida Davidavičienė

    2014-01-01

    The paper analyzes the brand and its marketing solutions onsocial networks. This analysis led to the creation of improvedbrand marketing model on social networks, which will contributeto the rapid and cheap organization brand recognition, increasecompetitive advantage and enhance consumer loyalty. Therefore,the brand and a variety of social networks are becoming a hotresearch area for brand marketing model on social networks.The world‘s most successful brand marketing models exploratoryanalys...

  11. Qualitative networks: a symbolic approach to analyze biological signaling networks

    Directory of Open Access Journals (Sweden)

    Henzinger Thomas A

    2007-01-01

    Full Text Available Abstract Background A central goal of Systems Biology is to model and analyze biological signaling pathways that interact with one another to form complex networks. Here we introduce Qualitative networks, an extension of Boolean networks. With this framework, we use formal verification methods to check whether a model is consistent with the laboratory experimental observations on which it is based. If the model does not conform to the data, we suggest a revised model and the new hypotheses are tested in-silico. Results We consider networks in which elements range over a small finite domain allowing more flexibility than Boolean values, and add target functions that allow to model a rich set of behaviors. We propose a symbolic algorithm for analyzing the steady state of these networks, allowing us to scale up to a system consisting of 144 elements and state spaces of approximately 1086 states. We illustrate the usefulness of this approach through a model of the interaction between the Notch and the Wnt signaling pathways in mammalian skin, and its extensive analysis. Conclusion We introduce an approach for constructing computational models of biological systems that extends the framework of Boolean networks and uses formal verification methods for the analysis of the model. This approach can scale to multicellular models of complex pathways, and is therefore a useful tool for the analysis of complex biological systems. The hypotheses formulated during in-silico testing suggest new avenues to explore experimentally. Hence, this approach has the potential to efficiently complement experimental studies in biology.

  12. Network Bandwidth Utilization Forecast Model on High Bandwidth Network

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Wucherl; Sim, Alex

    2014-07-07

    With the increasing number of geographically distributed scientific collaborations and the scale of the data size growth, it has become more challenging for users to achieve the best possible network performance on a shared network. We have developed a forecast model to predict expected bandwidth utilization for high-bandwidth wide area network. The forecast model can improve the efficiency of resource utilization and scheduling data movements on high-bandwidth network to accommodate ever increasing data volume for large-scale scientific data applications. Univariate model is developed with STL and ARIMA on SNMP path utilization data. Compared with traditional approach such as Box-Jenkins methodology, our forecast model reduces computation time by 83.2percent. It also shows resilience against abrupt network usage change. The accuracy of the forecast model is within the standard deviation of the monitored measurements.

  13. Modelling delay propagation within an airport network

    NARCIS (Netherlands)

    Pyrgiotis, N.; Malone, K.M.; Odoni, A.

    2013-01-01

    We describe an analytical queuing and network decomposition model developed to study the complex phenomenon of the propagation of delays within a large network of major airports. The Approximate Network Delays (AND) model computes the delays due to local congestion at individual airports and capture

  14. An acoustical model based monitoring network

    NARCIS (Netherlands)

    Wessels, P.W.; Basten, T.G.H.; Eerden, F.J.M. van der

    2010-01-01

    In this paper the approach for an acoustical model based monitoring network is demonstrated. This network is capable of reconstructing a noise map, based on the combination of measured sound levels and an acoustic model of the area. By pre-calculating the sound attenuation within the network the noi

  15. Analysis by fracture network modelling

    International Nuclear Information System (INIS)

    This report describes the Fracture Network Modelling and Performance Assessment Support performed by Golder Associates Inc. during the Heisei-11 (1999-2000) fiscal year. The primary objective of the Golder Associates work scope during HY-11 was to provide theoretical and review support to the JNC HY-12 Performance assessment effort. In addition, Golder Associates provided technical support to JNC for the Aespoe Project. Major efforts for performance assessment support included analysis of PAWorks pathways and software documentation, verification, and performance assessment visualization. Support for the Aespoe project including 'Task 4' predictive modelling of sorbing tracer transport in TRUE-1 rock block, and integrated hydrogeological and geochemical modelling of Aespoe island for 'Task 5'. Technical information about Golder Associates HY-11 support to JNC is provided in the appendices to this report. (author)

  16. Towards boolean operations with thermal photons

    CERN Document Server

    Ben-Abdallah, Philippe

    2016-01-01

    The Boolean algebra is the natural theoretical framework for a classical information treatment. The basic logical operations are usually performed using logic gates. In this Letter we demonstrate that NOT, OR and AND gates can be realized exploiting the near-field radiative interaction in N-body systems with phase change materials. With the recent development of a photon thermal transistor and thermal memory, this result paves the way for a full information treatment and smart solutions for active thermal management at nanoscale with photons.

  17. Constructions of vector output Boolean functions with high generalized nonlinearity

    Institute of Scientific and Technical Information of China (English)

    KE Pin-hui; ZHANG Sheng-yuan

    2008-01-01

    Carlet et al. recently introduced generalized nonlinearity to measure the ability to resist the improved correlation attack of a vector output Boolean function. This article presents a construction of vector output Boolean functions with high generalized nonlinearity using the sample space. The relation between the resilient order and generalized nonlinearity is also discussed.

  18. E-Referencer: Transforming Boolean OPACs to Web Search Engines.

    Science.gov (United States)

    Khoo, Christopher S. G.; Poo, Danny C. C.; Toh, Teck-Kang; Hong, Glenn

    E-Referencer is an expert intermediary system for searching library online public access catalogs (OPACs) on the World Wide Web. It is implemented as a proxy server that mediates the interaction between the user and Boolean OPACs. It transforms a Boolean OPAC into a retrieval system with many of the search capabilities of Web search engines.…

  19. An evolutionary model of social networks

    Science.gov (United States)

    Ludwig, M.; Abell, P.

    2007-07-01

    Social networks in communities, markets, and societies self-organise through the interactions of many individuals. In this paper we use a well-known mechanism of social interactions — the balance of sentiment in triadic relations — to describe the development of social networks. Our model contrasts with many existing network models, in that people not only establish but also break up relations whilst the network evolves. The procedure generates several interesting network features such as a variety of degree distributions and degree correlations. The resulting network converges under certain conditions to a steady critical state where temporal disruptions in triangles follow a power-law distribution.

  20. Introducing Synchronisation in Deterministic Network Models

    DEFF Research Database (Denmark)

    Schiøler, Henrik; Jessen, Jan Jakob; Nielsen, Jens Frederik D.;

    2006-01-01

    The paper addresses performance analysis for distributed real time systems through deterministic network modelling. Its main contribution is the introduction and analysis of models for synchronisation between tasks and/or network elements. Typical patterns of synchronisation are presented leading...... to the suggestion of suitable network models. An existing model for flow control is presented and an inherent weakness is revealed and remedied. Examples are given and numerically analysed through deterministic network modelling. Results are presented to highlight the properties of the suggested models...

  1. Graph Annotations in Modeling Complex Network Topologies

    CERN Document Server

    Dimitropoulos, Xenofontas; Vahdat, Amin; Riley, George

    2007-01-01

    The coarsest approximation of the structure of a complex network, such as the Internet, is a simple undirected unweighted graph. This approximation, however, loses too much detail. In reality, objects represented by vertices and edges in such a graph possess some non-trivial internal structure that varies across and differentiates among distinct types of links or nodes. In this work, we abstract such additional information as network annotations. We introduce a network topology modeling framework that treats annotations as an extended correlation profile of a network. Assuming we have this profile measured for a given network, we present an algorithm to rescale it in order to construct networks of varying size that still reproduce the original measured annotation profile. Using this methodology, we accurately capture the network properties essential for realistic simulations of network applications and protocols, or any other simulations involving complex network topologies, including modeling and simulation ...

  2. Hybrid modeling of communication networks using Modelica

    OpenAIRE

    Färnqvist, Daniel; Strandemar, Katrin; Johansson, Karl Henrik; Hespanha, João Pedro

    2002-01-01

    Modeling and simulation of communication networks using the modeling language Modelica are discussed. Congestion control in packet-switched networks, such as the Internet, is today mainly analyzed through time-consuming simulations of individual packets. We show, by developing a model library based on a recent hybrid systems model, that Modelica provides an efficient platform for the analysis of communication networks. As an example, a comparison between the two congestion control protocols i...

  3. Hierarchical relational models for document networks

    OpenAIRE

    Chang, Jonathan; Blei, David M.

    2009-01-01

    We develop the relational topic model (RTM), a hierarchical model of both network structure and node attributes. We focus on document networks, where the attributes of each document are its words, that is, discrete observations taken from a fixed vocabulary. For each pair of documents, the RTM models their link as a binary random variable that is conditioned on their contents. The model can be used to summarize a network of documents, predict links between them, and predi...

  4. Multiscaling in the YX model of networks

    CERN Document Server

    Holme, Petter; Minnhagen, Petter

    2009-01-01

    We investigate a Hamiltonian model of networks. The model is a mirror formulation of the XY model (hence the name) -- instead letting the XY spins vary, keeping the coupling topology static, we keep the spins conserved and sample different underlying networks. Our numerical simulations show complex scaling behaviors, but no finite-temperature critical behavior. The ground state and low-order excitations for sparse, finite graphs is a fragmented set of isolated network clusters. Configurations of higher energy are typically more connected. The connected networks of lowest energy are stretched out giving the network large average distances. For the finite sizes we investigate there are three regions -- a low-energy regime of fragmented networks, and intermediate regime of stretched-out networks, and a high-energy regime of compact, disordered topologies. Scaling up the system size, the borders between these regimes approach zero temperature algebraically, but different network structural quantities approach the...

  5. Network model of bilateral power markets based on complex networks

    Science.gov (United States)

    Wu, Yang; Liu, Junyong; Li, Furong; Yan, Zhanxin; Zhang, Li

    2014-06-01

    The bilateral power transaction (BPT) mode becomes a typical market organization with the restructuring of electric power industry, the proper model which could capture its characteristics is in urgent need. However, the model is lacking because of this market organization's complexity. As a promising approach to modeling complex systems, complex networks could provide a sound theoretical framework for developing proper simulation model. In this paper, a complex network model of the BPT market is proposed. In this model, price advantage mechanism is a precondition. Unlike other general commodity transactions, both of the financial layer and the physical layer are considered in the model. Through simulation analysis, the feasibility and validity of the model are verified. At same time, some typical statistical features of BPT network are identified. Namely, the degree distribution follows the power law, the clustering coefficient is low and the average path length is a bit long. Moreover, the topological stability of the BPT network is tested. The results show that the network displays a topological robustness to random market member's failures while it is fragile against deliberate attacks, and the network could resist cascading failure to some extent. These features are helpful for making decisions and risk management in BPT markets.

  6. How to model wireless mesh networks topology

    International Nuclear Information System (INIS)

    The specification of network connectivity model or topology is the beginning of design and analysis in Computer Network researches. Wireless Mesh Networks is an autonomic network that is dynamically self-organised, self-configured while the mesh nodes establish automatic connectivity with the adjacent nodes in the relay network of wireless backbone routers. Researches in Wireless Mesh Networks range from node deployment to internetworking issues with sensor, Internet and cellular networks. These researches require modelling of relationships and interactions among nodes including technical characteristics of the links while satisfying the architectural requirements of the physical network. However, the existing topology generators model geographic topologies which constitute different architectures, thus may not be suitable in Wireless Mesh Networks scenarios. The existing methods of topology generation are explored, analysed and parameters for their characterisation are identified. Furthermore, an algorithm for the design of Wireless Mesh Networks topology based on square grid model is proposed in this paper. The performance of the topology generated is also evaluated. This research is particularly important in the generation of a close-to-real topology for ensuring relevance of design to the intended network and validity of results obtained in Wireless Mesh Networks researches

  7. Model Of Neural Network With Creative Dynamics

    Science.gov (United States)

    Zak, Michail; Barhen, Jacob

    1993-01-01

    Paper presents analysis of mathematical model of one-neuron/one-synapse neural network featuring coupled activation and learning dynamics and parametrical periodic excitation. Demonstrates self-programming, partly random behavior of suitable designed neural network; believed to be related to spontaneity and creativity of biological neural networks.

  8. Magneto-electric network models in electromagnetism

    OpenAIRE

    Demenko, A.; Sykulski, J. K.

    2006-01-01

    Purpose – The aim of this paper is to develop network models of an electromagnetic field containing both eddy and displacement currents. The proposed network models provide good physical insight, help understanding of complicated electromagnetic phenomena and aid explanation of methods of analysis of electromagnetic systems. Design/methodology/approach – The models consist of magnetic and electric networks coupled via sources. The analogy between the finite element method and the loop and nod...

  9. CIMS Network Protocol and Its Net Models

    Institute of Scientific and Technical Information of China (English)

    罗军舟; 顾冠群

    1997-01-01

    Computer communication network architectures for cims are based on the OSI Reference Model.In this paper,CIMS network protocol model is set up on the basis of the corresqonding service model.Then the authors present a formal specification of transport protocols by using an extended Predicate/Transition net system that is briefly introduced in the third part.Finally,the general methods for the Petri nets based formal specification of CIMS network protocols are outlined.

  10. An approach to 3D NURBS modeling of complex fault network considering its historic tectonics

    Institute of Scientific and Technical Information of China (English)

    ZHONG Denghua; LIU Jie; LI Mingchao

    2006-01-01

    Fault disposal is a research area that presents difficulties in 3D geological modeling and visualization. In this paper, we propose an integrated approach to reconstructing a complex fault network (CFN). Based on the non-uniform rational B-spline (NURBS)techniques, fault surface was constructed, reflecting the regulation of its spatial tendency, and correlative surfaces were enclosed to form a fault body model. Based on these models and considering their historic tectonics, a method was put forward to settle the 3D modeling problem when the intersection of two faults in CFN induced the change of their relative positions. First, according to the relationships of intersection obtained from geological interpretation, we introduced the topological sort to determine the order of fault body construction and rebuilt fault bodies in terms of the order; then, with the disposal method of two intersectant faults in 3D modeling and applying the Boolean operation, we investigated the characteristic of faults at the intersectant part. An example of its application in hydropower engineering project was proposed. Its results show that this modeling approach can increase the computing efficiency while less computer memory is required, and it can also factually and objectively reproduce the CFN in the engineering region, which establishes a theoretical basis for 3D modeling and analysis of complex engineering geology.

  11. Agent-based modeling and network dynamics

    CERN Document Server

    Namatame, Akira

    2016-01-01

    The book integrates agent-based modeling and network science. It is divided into three parts, namely, foundations, primary dynamics on and of social networks, and applications. The book begins with the network origin of agent-based models, known as cellular automata, and introduce a number of classic models, such as Schelling’s segregation model and Axelrod’s spatial game. The essence of the foundation part is the network-based agent-based models in which agents follow network-based decision rules. Under the influence of the substantial progress in network science in late 1990s, these models have been extended from using lattices into using small-world networks, scale-free networks, etc. The book also shows that the modern network science mainly driven by game-theorists and sociophysicists has inspired agent-based social scientists to develop alternative formation algorithms, known as agent-based social networks. The book reviews a number of pioneering and representative models in this family. Upon the gi...

  12. Oligopoly Model of a Debit Card Network

    OpenAIRE

    Manchev, Peter

    2006-01-01

    The paper builds an oligopoly model of a debit card network. It examines the competition between debit card issuers. We show that there is an optimal pricing for the debit card network, which maximizes all issuer's revenues. The paper also shows that establishing a link between debit card networks averages the costs provided that there is no growth in the customer's usage of the networks, resulting from the link.

  13. Edge exchangeable models for network data

    CERN Document Server

    Crane, Harry

    2016-01-01

    Exchangeable models for vertex labeled graphs cannot replicate the large sample behaviors of sparsity and power law degree distributions observed in many network datasets. Out of this mathematical impossibility emerges the question of how network data can be modeled in a way that reflects known empirical behaviors and respects basic statistical principles. We address this question by observing that edges, not vertices, act as the statistical units in most network datasets, making a theory of edge labeled networks more natural for most applications. Within this context we introduce the new invariance principle of {\\em edge exchangeability}, which unlike its vertex exchangeable counterpart can produce networks with sparse and/or power law structure. We characterize the class of all edge exchangeable network models and identify a particular two parameter family of models with suitable theoretical properties for statistical inference. We discuss issues of estimation from edge exchangeable models and compare our a...

  14. Modeling data throughput on communication networks

    Energy Technology Data Exchange (ETDEWEB)

    Eldridge, J.M.

    1993-11-01

    New challenges in high performance computing and communications are driving the need for fast, geographically distributed networks. Applications such as modeling physical phenomena, interactive visualization, large data set transfers, and distributed supercomputing require high performance networking [St89][Ra92][Ca92]. One measure of a communication network`s performance is the time it takes to complete a task -- such as transferring a data file or displaying a graphics image on a remote monitor. Throughput, defined as the ratio of the number of useful data bits transmitted per the time required to transmit those bits, is a useful gauge of how well a communication system meets this performance measure. This paper develops and describes an analytical model of throughput. The model is a tool network designers can use to predict network throughput. It also provides insight into those parts of the network that act as a performance bottleneck.

  15. Queuing theory models for computer networks

    Science.gov (United States)

    Galant, David C.

    1989-01-01

    A set of simple queuing theory models which can model the average response of a network of computers to a given traffic load has been implemented using a spreadsheet. The impact of variations in traffic patterns and intensities, channel capacities, and message protocols can be assessed using them because of the lack of fine detail in the network traffic rates, traffic patterns, and the hardware used to implement the networks. A sample use of the models applied to a realistic problem is included in appendix A. Appendix B provides a glossary of terms used in this paper. This Ames Research Center computer communication network is an evolving network of local area networks (LANs) connected via gateways and high-speed backbone communication channels. Intelligent planning of expansion and improvement requires understanding the behavior of the individual LANs as well as the collection of networks as a whole.

  16. A language for real time simulation of processes with boolean inputs and outputs

    OpenAIRE

    Fernández Camacho, Eduardo; García Franquelo, Leopoldo; Lozano, J.

    1983-01-01

    This paper deals with the problem of real time simulation of processes with boolean inputs and outputs. A language for this purpose and the programs that processes it is presented. The language allows the description of processes with simultaneous evolutions as a timed petri net type of description is used. Random failures can also be Introduced in the behaviour of the model. The language allows the control of a semlgraphic CRT in order to facilitate the task of following the model behaviour.

  17. A Conceptual Model of Learning Networks

    Science.gov (United States)

    Koper, Rob

    In the TENCompetence project a set of UML models (Booch et al. 1999) have been developed to specify the core concepts for Learning Networks Services that support professional competence development. The three most important, high-level models are (a) the use case model, (b) the conceptual model, and (c) the domain model. The first model identifies the primary use cases we need in order to support professional competence development. The second model describes the concept of competence and competence development from a theoretical point of view. What is a competence? How does it relate to the cognitive system of an actor? How are competences developed? The third model is a UML Domain Model that defines, among other things, the components of a Learning Network, defines the concepts and relationships between the concepts in a Learning Network and provides a starting point for the design of the overall architecture for Learning Network Services, including the data model.

  18. Polynomial threshold functions and Boolean threshold circuits

    DEFF Research Database (Denmark)

    Hansen, Kristoffer Arnsfelt; Podolskii, Vladimir V.

    2013-01-01

    secondary interest. We show that PTFs on general Boolean domains are tightly connected to depth two threshold circuits. Our main results in regard to this connection are: PTFs of polynomial length and polynomial degree compute exactly the functions computed by THRMAJ circuits. An exponential length lower...... bound for PTFs that holds regardless of degree, thereby extending known lower bounds for THRMAJ circuits. We generalize two-party unbounded error communication complexity to the multi-party number-on-the-forehead setting, and show that communication lower bounds for 3-player protocols would yield size...... lower bounds for THRTHR circuits. We obtain several other results about PTFs. These include relationships between weight and degree of PTFs, and a degree lower bound for PTFs of constant length. We also consider a variant of PTFs over the max-plus algebra. We show that they are connected to PTFs over...

  19. Representing Boolean Functions by Decision Trees

    KAUST Repository

    Chikalov, Igor

    2011-01-01

    A Boolean or discrete function can be represented by a decision tree. A compact form of decision tree named binary decision diagram or branching program is widely known in logic design [2, 40]. This representation is equivalent to other forms, and in some cases it is more compact than values table or even the formula [44]. Representing a function in the form of decision tree allows applying graph algorithms for various transformations [10]. Decision trees and branching programs are used for effective hardware [15] and software [5] implementation of functions. For the implementation to be effective, the function representation should have minimal time and space complexity. The average depth of decision tree characterizes the expected computing time, and the number of nodes in branching program characterizes the number of functional elements required for implementation. Often these two criteria are incompatible, i.e. there is no solution that is optimal on both time and space complexity. © Springer-Verlag Berlin Heidelberg 2011.

  20. Random graph models for dynamic networks

    CERN Document Server

    Zhang, Xiao; Newman, M E J

    2016-01-01

    We propose generalizations of a number of standard network models, including the classic random graph, the configuration model, and the stochastic block model, to the case of time-varying networks. We assume that the presence and absence of edges are governed by continuous-time Markov processes with rate parameters that can depend on properties of the nodes. In addition to computing equilibrium properties of these models, we demonstrate their use in data analysis and statistical inference, giving efficient algorithms for fitting them to observed network data. This allows us, for instance, to estimate the time constants of network evolution or infer community structure from temporal network data using cues embedded both in the probabilities over time that node pairs are connected by edges and in the characteristic dynamics of edge appearance and disappearance. We illustrate our methods with a selection of applications, both to computer-generated test networks and real-world examples.

  1. Exponential-family Random Network Models

    OpenAIRE

    Fellows, I; Handcock, MS

    2012-01-01

    Random graphs, where the connections between nodes are considered random variables, have wide applicability in the social sciences. Exponential-family Random Graph Models (ERGM) have shown themselves to be a useful class of models for representing com- plex social phenomena. We generalize ERGM by also modeling nodal attributes as random variates, thus creating a random model of the full network, which we call Exponential-family Random Network Models (ERNM). We demonstrate how this framework a...

  2. Diverse Embedding Neural Network Language Models

    OpenAIRE

    Audhkhasi, Kartik; Sethy, Abhinav; Ramabhadran, Bhuvana

    2014-01-01

    We propose Diverse Embedding Neural Network (DENN), a novel architecture for language models (LMs). A DENNLM projects the input word history vector onto multiple diverse low-dimensional sub-spaces instead of a single higher-dimensional sub-space as in conventional feed-forward neural network LMs. We encourage these sub-spaces to be diverse during network training through an augmented loss function. Our language modeling experiments on the Penn Treebank data set show the performance benefit of...

  3. Monochromaticity in Neutral Evolutionary Network Models

    OpenAIRE

    Halu, Arda; Bianconi, Ginestra

    2012-01-01

    Recent studies on epistatic networks of model organisms have unveiled a certain type of modular property called monochromaticity in which the networks are clusterable into functional modules that interact with each other through the same type of epistasis. Here we propose and study three epistatic network models that are inspired by the Duplication-Divergence mechanism to gain insight into the evolutionary basis of monochromaticity and to test if it can be explained as the outcome of a neutra...

  4. Neutral Mutations and Punctuated Equilibrium in Evolving Genetic Networks

    OpenAIRE

    Bornholdt, Stefan; Sneppen, Kim

    1997-01-01

    Boolean networks may be viewed as idealizations of biological genetic networks, where each node is represented by an on-off switch which is a function of the binary output from some other nodes. We evolve connectivity in a single Boolean network, and demonstrate how the sole requirement of sequential matching of attractors may open for an evolution that exhibits punctuated equilibrium.

  5. Performance modeling of network data services

    Energy Technology Data Exchange (ETDEWEB)

    Haynes, R.A.; Pierson, L.G.

    1997-01-01

    Networks at major computational organizations are becoming increasingly complex. The introduction of large massively parallel computers and supercomputers with gigabyte memories are requiring greater and greater bandwidth for network data transfers to widely dispersed clients. For networks to provide adequate data transfer services to high performance computers and remote users connected to them, the networking components must be optimized from a combination of internal and external performance criteria. This paper describes research done at Sandia National Laboratories to model network data services and to visualize the flow of data from source to sink when using the data services.

  6. Unified Hybrid Network Theoretical Model Trilogy

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The first of the unified hybrid network theoretical model trilogy (UHNTF) is the harmonious unification hybrid preferential model (HUHPM), seen in the inner loop of Fig. 1, the unified hybrid ratio is defined.

  7. Modeling information flow in biological networks

    International Nuclear Information System (INIS)

    Large-scale molecular interaction networks are being increasingly used to provide a system level view of cellular processes. Modeling communications between nodes in such huge networks as information flows is useful for dissecting dynamical dependences between individual network components. In the information flow model, individual nodes are assumed to communicate with each other by propagating the signals through intermediate nodes in the network. In this paper, we first provide an overview of the state of the art of research in the network analysis based on information flow models. In the second part, we describe our computational method underlying our recent work on discovering dysregulated pathways in glioma. Motivated by applications to inferring information flow from genotype to phenotype in a very large human interaction network, we generalized previous approaches to compute information flows for a large number of instances and also provided a formal proof for the method

  8. Network models in economics and finance

    CERN Document Server

    Pardalos, Panos; Rassias, Themistocles

    2014-01-01

    Using network models to investigate the interconnectivity in modern economic systems allows researchers to better understand and explain some economic phenomena. This volume presents contributions by known experts and active researchers in economic and financial network modeling. Readers are provided with an understanding of the latest advances in network analysis as applied to economics, finance, corporate governance, and investments. Moreover, recent advances in market network analysis  that focus on influential techniques for market graph analysis are also examined. Young researchers will find this volume particularly useful in facilitating their introduction to this new and fascinating field. Professionals in economics, financial management, various technologies, and network analysis, will find the network models presented in this book beneficial in analyzing the interconnectivity in modern economic systems.

  9. Strategic games on a hierarchical network model

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Among complex network models, the hierarchical network model is the one most close to such real networks as world trade web, metabolic network, WWW, actor network, and so on. It has not only the property of power-law degree distribution, but growth based on growth and preferential attachment, showing the scale-free degree distribution property. In this paper, we study the evolution of cooperation on a hierarchical network model, adopting the prisoner's dilemma (PD) game and snowdrift game (SG) as metaphors of the interplay between connected nodes. BA model provides a unifying framework for the emergence of cooperation. But interestingly, we found that on hierarchical model, there is no sign of cooperation for PD game, while the frequency of cooperation decreases as the common benefit decreases for SG. By comparing the scaling clustering coefficient properties of the hierarchical network model with that of BA model, we found that the former amplifies the effect of hubs. Considering different performances of PD game and SG on complex network, we also found that common benefit leads to cooperation in the evolution. Thus our study may shed light on the emergence of cooperation in both natural and social environments.

  10. Evaluation of EOR Processes Using Network Models

    DEFF Research Database (Denmark)

    Larsen, Jens Kjell; Krogsbøll, Anette

    1998-01-01

    The report consists of the following parts: 1) Studies of wetting properties of model fluids and fluid mixtures aimed at an optimal selection of candidates for micromodel experiments. 2) Experimental studies of multiphase transport properties using physical models of porous networks (micromodels......) including estimation of their "petrophysical" properties (e.g. absolute permeability). 3) Mathematical modelling and computer studies of multiphase transport through pore space using mathematical network models. 4) Investigation of link between pore-scale and macroscopic recovery mechanisms....

  11. On a hierarchy of Boolean functions hard to compute in constant depth

    OpenAIRE

    Bernasconi, Anna

    2001-01-01

    Any attempt to find connections between mathematical properties and complexity has a strong relevance to the field of Complexity Theory. This is due to the lack of mathematical techniques to prove lower bounds for general models of computation.\\par This work represents a step in this direction: we define a combinatorial property that makes Boolean functions ''\\emphhard'' to compute in constant depth and show how the harmonic analysis on the hypercube can be applied to derive new lower bounds ...

  12. Closure Properties of Classes of Spatio-Temporal Objects for Boolean Set Operations

    OpenAIRE

    Haesevoets, Sofie; Kuijpers, Bart

    2000-01-01

    We study a model for spatio-temporal objects, introduced by Chomicki and Revesz, in which spatio-temporal data is specified by a spatial reference object together with a geometric transformation that determines the movement of the reference object in time. We give complete results concerning closure under Boolean set operators for the different classes of spatio-temporal objects introduced by these authors (In particular, we also answer a conjecture by Chomicki and Revesz negatively). Since o...

  13. Approximate Counting for Complex-Weighted Boolean Constraint Satisfaction Problems

    CERN Document Server

    Yamakami, Tomoyuki

    2010-01-01

    Constraint satisfaction problems (or CSPs) have been extensively studied in AI, database theory, graph theory, etc. From an approximation viewpoint, it has been important to approximate the total number of assignments that satisfy all given Boolean constraints. There is a trichotomy theorem for such approximate counting for (non-weighted) Boolean CSPs; namely, all such counting problems are neatly classified into three categories under polynomial-time approximation-preserving reductions [Dyer, Goldberg, and Jerrum, 2010]. We extend this result to approximate counting for complex-weighted Boolean CSPs, provided that all arity-1 constraints are freely available to use. This makes a significant progress in the quest for the approximation classification of all counting Boolean CSPs in the most general form. To deal with complex weights, we employ proof techniques along the line of solving Holant problems [Valiant, 2002, 2008]. Our result also gives an approximation version of the dichotomy theorem of the complexi...

  14. Automatic Ranked Output from Boolean Searches in SIRE

    Science.gov (United States)

    Noreault, Terry; And Others

    1977-01-01

    This study examined the effectiveness using an automatic algorithm to rank the results of Boolean searches of an inverted file design document retrieval system. Relevant documents were ranked significantly higher than nonrelevant documents on output lists. (Author/KP)

  15. Boolean Burritos: How the Faculty Ate Up Keyword Searching.

    Science.gov (United States)

    York, Sherry

    1999-01-01

    Describes an activity that librarians can use to acquaint teachers with keyword searching and Boolean operators to more successfully use the library's online catalog. Uses food ingredients to represent various possible combinations. (LRW)

  16. Boolean functions with a vertex-transitive group of automorphisms

    Czech Academy of Sciences Publication Activity Database

    Savický, Petr

    -, submitted 2015 (2016) R&D Projects: GA ČR GAP202/10/1333 Institutional support: RVO:67985807 Keywords : Boolean Functions * hypercube * isometric transformation * vertex-transitive group of automorphisms Subject RIV: BA - General Mathematics

  17. Modelling the structure of complex networks

    DEFF Research Database (Denmark)

    Herlau, Tue

    A complex network is a systems in which a discrete set of units interact in a quantifiable manner. Representing systems as complex networks have become increasingly popular in a variety of scientific fields including biology, social sciences and economics. Parallel to this development complex...... next chapters will treat some of the various symmetries, representer theorems and probabilistic structures often deployed in the modelling complex networks, the construction of sampling methods and various network models. The introductory chapters will serve to provide context for the included written...

  18. Towards reproducible descriptions of neuronal network models.

    Directory of Open Access Journals (Sweden)

    Eilen Nordlie

    2009-08-01

    Full Text Available Progress in science depends on the effective exchange of ideas among scientists. New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely. This applies to simulation studies as well as to experiments and theories. But after more than 50 years of neuronal network simulations, we still lack a clear and common understanding of the role of computational models in neuroscience as well as established practices for describing network models in publications. This hinders the critical evaluation of network models as well as their re-use. We analyze here 14 research papers proposing neuronal network models of different complexity and find widely varying approaches to model descriptions, with regard to both the means of description and the ordering and placement of material. We further observe great variation in the graphical representation of networks and the notation used in equations. Based on our observations, we propose a good model description practice, composed of guidelines for the organization of publications, a checklist for model descriptions, templates for tables presenting model structure, and guidelines for diagrams of networks. The main purpose of this good practice is to trigger a debate about the communication of neuronal network models in a manner comprehensible to humans, as opposed to machine-readable model description languages. We believe that the good model description practice proposed here, together with a number of other recent initiatives on data-, model-, and software-sharing, may lead to a deeper and more fruitful exchange of ideas among computational neuroscientists in years to come. We further hope that work on standardized ways of describing--and thinking about--complex neuronal networks will lead the scientific community to a clearer understanding of high-level concepts in network dynamics, and will thus lead to deeper insights into the function of the brain.

  19. Symbolic regression of generative network models

    CERN Document Server

    Menezes, Telmo

    2014-01-01

    Networks are a powerful abstraction with applicability to a variety of scientific fields. Models explaining their morphology and growth processes permit a wide range of phenomena to be more systematically analysed and understood. At the same time, creating such models is often challenging and requires insights that may be counter-intuitive. Yet there currently exists no general method to arrive at better models. We have developed an approach to automatically detect realistic decentralised network growth models from empirical data, employing a machine learning technique inspired by natural selection and defining a unified formalism to describe such models as computer programs. As the proposed method is completely general and does not assume any pre-existing models, it can be applied "out of the box" to any given network. To validate our approach empirically, we systematically rediscover pre-defined growth laws underlying several canonical network generation models and credible laws for diverse real-world netwo...

  20. Quantifying and Analyzing the Network Basis of Genetic Complexity

    OpenAIRE

    Thompson, Ethan G.; Galitski, Timothy

    2012-01-01

    Genotype-to-phenotype maps exhibit complexity. This genetic complexity is mentioned frequently in the literature, but a consistent and quantitative definition is lacking. Here, we derive such a definition and investigate its consequences for model genetic systems. The definition equates genetic complexity with a surplus of genotypic diversity over phenotypic diversity. Applying this definition to ensembles of Boolean network models, we found that the in-degree distribution and the number of p...

  1. Integrating Boolean and Mathematical Solving: Foundations, Basic Algorithms and Requirements

    OpenAIRE

    Audemard, Gilles; Bertoli, Piergiorgio; Cimatti, Alessandro; Kornilowicz, Artur; Sebastiani, Roberto

    2002-01-01

    In the last years we have witnessed an impressive advance in the efficiency of boolean solving techniques, which has brought large previously intractable problems at the reach of state-of-the-art solvers. Unfortunately, simple boolean expressions are not expressive enough for representing many real-world problems, which require handling also integer or real values and operators. On the other hand, mathematical solvers, like computer-algebra systems or constraint solvers, cannot handle efficie...

  2. Complex networks analysis in socioeconomic models

    CERN Document Server

    Varela, Luis M; Ausloos, Marcel; Carrete, Jesus

    2014-01-01

    This chapter aims at reviewing complex networks models and methods that were either developed for or applied to socioeconomic issues, and pertinent to the theme of New Economic Geography. After an introduction to the foundations of the field of complex networks, the present summary adds insights on the statistical mechanical approach, and on the most relevant computational aspects for the treatment of these systems. As the most frequently used model for interacting agent-based systems, a brief description of the statistical mechanics of the classical Ising model on regular lattices, together with recent extensions of the same model on small-world Watts-Strogatz and scale-free Albert-Barabasi complex networks is included. Other sections of the chapter are devoted to applications of complex networks to economics, finance, spreading of innovations, and regional trade and developments. The chapter also reviews results involving applications of complex networks to other relevant socioeconomic issues, including res...

  3. Implementing network constraints in the EMPS model

    Energy Technology Data Exchange (ETDEWEB)

    Helseth, Arild; Warland, Geir; Mo, Birger; Fosso, Olav B.

    2010-02-15

    This report concerns the coupling of detailed market and network models for long-term hydro-thermal scheduling. Currently, the EPF model (Samlast) is the only tool available for this task for actors in the Nordic market. A new prototype for solving the coupled market and network problem has been developed. The prototype is based on the EMPS model (Samkjoeringsmodellen). Results from the market model are distributed to a detailed network model, where a DC load flow detects if there are overloads on monitored lines or intersections. In case of overloads, network constraints are generated and added to the market problem. Theoretical and implementation details for the new prototype are elaborated in this report. The performance of the prototype is tested against the EPF model on a 20-area Nordic dataset. (Author)

  4. Modelling and control of road traffic networks

    OpenAIRE

    Haut, Bertrand

    2007-01-01

    Road traffic networks offer a particularly challenging research subject to the control community. The traffic congestion around big cities is constantly increasing and is now becoming a major problem. However, the dynamics of a road network exhibit some complex behaviours such as nonlinearities, delays and saturation effects that prevent the use of some classical control algorithms. This thesis presents different models and control algorithms used for road traffic networks. The dynamics ar...

  5. Delivery Time Reliability Model of Logistics Network

    OpenAIRE

    Liusan Wu; Qingmei Tan; Yuehui Zhang

    2013-01-01

    Natural disasters like earthquake and flood will surely destroy the existing traffic network, usually accompanied by delivery delay or even network collapse. A logistics-network-related delivery time reliability model defined by a shortest-time entropy is proposed as a means to estimate the actual delivery time reliability. The less the entropy is, the stronger the delivery time reliability remains, and vice versa. The shortest delivery time is computed separately based on two different assum...

  6. Modelling Microwave Devices Using Artificial Neural Networks

    Directory of Open Access Journals (Sweden)

    Andrius Katkevičius

    2012-04-01

    Full Text Available Artificial neural networks (ANN have recently gained attention as fast and flexible equipment for modelling and designing microwave devices. The paper reviews the opportunities to use them for undertaking the tasks on the analysis and synthesis. The article focuses on what tasks might be solved using neural networks, what challenges might rise when using artificial neural networks for carrying out tasks on microwave devices and discusses problem-solving techniques for microwave devices with intermittent characteristics.Article in Lithuanian

  7. Measuring and modeling switched Ethernet networks

    OpenAIRE

    2003-01-01

    Switched Ethernet is a dominating technology in local area networks, and a strong contender in system area networks. This thesis describes measurements on switched Ethernets, in the context of high speed system area networks with real time requirements. One such system is the ATLAS level 2 trigger, which formed the basis of the measurements. Further on the thesis describes the design, implementation and results from a simulation model of the measured devic...

  8. Modeling Evolution of Weighted Clique Networks

    International Nuclear Information System (INIS)

    We propose a weighted clique network evolution model, which expands continuously by the addition of a new clique (maximal complete sub-graph) at each time step. And the cliques in the network overlap with each other. The structural expansion of the weighted clique network is combined with the edges' weight and vertices' strengths dynamical evolution. The model is based on a weight-driven dynamics and a weights' enhancement mechanism combining with the network growth. We study the network properties, which include the distribution of vertices' strength and the distribution of edges' weight, and find that both the distributions follow the scale-free distribution. At the same time, we also find that the relationship between strength and degree of a vertex are linear correlation during the growth of the network. On the basis of mean-field theory, we study the weighted network model and prove that both vertices' strength and edges' weight of this model follow the scale-free distribution. And we exploit an algorithm to forecast the network dynamics, which can be used to reckon the distributions and the corresponding scaling exponents. Furthermore, we observe that mean-field based theoretic results are consistent with the statistical data of the model, which denotes the theoretical result in this paper is effective. (interdisciplinary physics and related areas of science and technology)

  9. Modeling Evolution of Weighted Clique Networks

    Science.gov (United States)

    Yang, Xu-Hua; Jiang, Feng-Ling; Chen, Sheng-Yong; Wang, Wan-Liang

    2011-11-01

    We propose a weighted clique network evolution model, which expands continuously by the addition of a new clique (maximal complete sub-graph) at each time step. And the cliques in the network overlap with each other. The structural expansion of the weighted clique network is combined with the edges' weight and vertices' strengths dynamical evolution. The model is based on a weight-driven dynamics and a weights' enhancement mechanism combining with the network growth. We study the network properties, which include the distribution of vertices' strength and the distribution of edges' weight, and find that both the distributions follow the scale-free distribution. At the same time, we also find that the relationship between strength and degree of a vertex are linear correlation during the growth of the network. On the basis of mean-field theory, we study the weighted network model and prove that both vertices' strength and edges' weight of this model follow the scale-free distribution. And we exploit an algorithm to forecast the network dynamics, which can be used to reckon the distributions and the corresponding scaling exponents. Furthermore, we observe that mean-field based theoretic results are consistent with the statistical data of the model, which denotes the theoretical result in this paper is effective.

  10. Homophyly/Kinship Model: Naturally Evolving Networks

    Science.gov (United States)

    Li, Angsheng; Li, Jiankou; Pan, Yicheng; Yin, Xianchen; Yong, Xi

    2015-10-01

    It has been a challenge to understand the formation and roles of social groups or natural communities in the evolution of species, societies and real world networks. Here, we propose the hypothesis that homophyly/kinship is the intrinsic mechanism of natural communities, introduce the notion of the affinity exponent and propose the homophyly/kinship model of networks. We demonstrate that the networks of our model satisfy a number of topological, probabilistic and combinatorial properties and, in particular, that the robustness and stability of natural communities increase as the affinity exponent increases and that the reciprocity of the networks in our model decreases as the affinity exponent increases. We show that both homophyly/kinship and reciprocity are essential to the emergence of cooperation in evolutionary games and that the homophyly/kinship and reciprocity determined by the appropriate affinity exponent guarantee the emergence of cooperation in evolutionary games, verifying Darwin’s proposal that kinship and reciprocity are the means of individual fitness. We propose the new principle of structure entropy minimisation for detecting natural communities of networks and verify the functional module property and characteristic properties by a healthy tissue cell network, a citation network, some metabolic networks and a protein interaction network.

  11. Network Development And Mobilisation Through 'Network Latency' - An Alternative To Stage Models Of Network Developments

    OpenAIRE

    Fairhead, J.; O'Sullivan, D.

    1996-01-01

    How and why do some networks develop rapidly and effectively, and others not? This paper draws from two contrasting project case-studies to help us discuss this question. The first case shows a pattern of network development that is highly projectspecific and can best be described by a conventional, essentially linear, 'stages' development model. In such a model, network effectiveness is believed to be a product of repeated social interactions that ultimately result in a high degree of social...

  12. Evaluating Network Models: A Likelihood Analysis

    CERN Document Server

    Wang, Wen-Qiang; Zhou, Tao

    2011-01-01

    Many models are put forward to mimic the evolution of real networked systems. A well-accepted way to judge the validity is to compare the modeling results with real networks subject to several structural features. Even for a specific real network, we cannot fairly evaluate the goodness of different models since there are too many structural features while there is no criterion to select and assign weights on them. Motivated by the studies on link prediction algorithms, we propose a unified method to evaluate the network models via the comparison of the likelihoods of the currently observed network driven by different models, with an assumption that the higher the likelihood is, the better the model is. We test our method on the real Internet at the Autonomous System (AS) level, and the results suggest that the Generalized Linear Preferential (GLP) model outperforms the Tel Aviv Network Generator (Tang), while both two models are better than the Barab\\'asi-Albert (BA) and Erd\\"os-R\\'enyi (ER) models. Our metho...

  13. Designing Network-based Business Model Ontology

    DEFF Research Database (Denmark)

    Hashemi Nekoo, Ali Reza; Ashourizadeh, Shayegheh; Zarei, Behrouz

    2015-01-01

    is going to propose e-business model ontology from the network point of view and its application in real world. The suggested ontology for network-based businesses is composed of individuals` characteristics and what kind of resources they own. also, their connections and pre-conceptions of connections...... such as shared-mental model and trust. However, it mostly covers previous business model elements. To confirm the applicability of this ontology, it has been implemented in business angel network and showed how it works....

  14. An endogenous model of the credit network

    Science.gov (United States)

    He, Jianmin; Sui, Xin; Li, Shouwei

    2016-01-01

    In this paper, an endogenous credit network model of firm-bank agents is constructed. The model describes the endogenous formation of firm-firm, firm-bank and bank-bank credit relationships. By means of simulations, the model is capable of showing some obvious similarities with empirical evidence found by other scholars: the upper-tail of firm size distribution can be well fitted with a power-law; the bank size distribution can be lognormally distributed with a power-law tail; the bank in-degrees of the interbank credit network as well as the firm-bank credit network fall into two-power-law distributions.

  15. Modelling and designing electric energy networks

    International Nuclear Information System (INIS)

    The author gives an overview of his research works in the field of electric network modelling. After a brief overview of technological evolutions from the telegraph to the all-electric fly-by-wire aircraft, he reports and describes various works dealing with a simplified modelling of electric systems and with fractal simulation. Then, he outlines the challenges for the design of electric networks, proposes a design process, gives an overview of various design models, methods and tools, and reports an application in the design of electric networks for future jumbo jets

  16. Characterization and Modeling of Network Traffic

    DEFF Research Database (Denmark)

    Shawky, Ahmed; Bergheim, Hans; Ragnarsson, Olafur;

    2011-01-01

    This paper attempts to characterize and model backbone network traffic, using a small number of statistics. In order to reduce cost and processing power associated with traffic analysis. The parameters affecting the behaviour of network traffic are investigated and the choice is that inter......-arrival time, IP addresses, port numbers and transport protocol are the only necessary parameters to model network traffic behaviour. In order to recreate this behaviour, a complex model is needed which is able to recreate traffic behaviour based on a set of statistics calculated from the parameters values...

  17. Multiscaling in an YX model of networks

    Science.gov (United States)

    Holme, Petter; Wu, Zhi-Xi; Minnhagen, Petter

    2009-09-01

    We investigate a Hamiltonian model of networks. The model is a mirror formulation of the XY model (hence the name)—instead of letting the XY spins vary, keeping the coupling topology static, we keep the spins conserved and sample different underlying networks. Our numerical simulations show complex scaling behaviors with various exponents as the system grows and temperature approaches zero, but no finite-temperature universal critical behavior. The ground-state and low-order excitations for sparse, finite graphs are a fragmented set of isolated network clusters. Configurations of higher energy are typically more connected. The connected networks of lowest energy are stretched out giving the network large average distances. For the finite sizes we investigate, there are three regions—a low-energy regime of fragmented networks, an intermediate regime of stretched-out networks, and a high-energy regime of compact, disordered topologies. Scaling up the system size, the borders between these regimes approach zero temperature algebraically, but different network-structural quantities approach their T=0 values with different exponents. We argue this is a, perhaps rare, example of a statistical-physics model where finite sizes show a more interesting behavior than the thermodynamic limit.

  18. Cyber threat model for tactical radio networks

    Science.gov (United States)

    Kurdziel, Michael T.

    2014-05-01

    The shift to a full information-centric paradigm in the battlefield has allowed ConOps to be developed that are only possible using modern network communications systems. Securing these Tactical Networks without impacting their capabilities has been a challenge. Tactical networks with fixed infrastructure have similar vulnerabilities to their commercial counterparts (although they need to be secure against adversaries with greater capabilities, resources and motivation). However, networks with mobile infrastructure components and Mobile Ad hoc Networks (MANets) have additional unique vulnerabilities that must be considered. It is useful to examine Tactical Network based ConOps and use them to construct a threat model and baseline cyber security requirements for Tactical Networks with fixed infrastructure, mobile infrastructure and/or ad hoc modes of operation. This paper will present an introduction to threat model assessment. A definition and detailed discussion of a Tactical Network threat model is also presented. Finally, the model is used to derive baseline requirements that can be used to design or evaluate a cyber security solution that can be scaled and adapted to the needs of specific deployments.

  19. Modeling GMPLS and Optical MPLS Networks

    DEFF Research Database (Denmark)

    Christiansen, Henrik Lehrmann; Wessing, Henrik

    2003-01-01

    . The MPLS concept is attractive because it can work as a unifying control structure. covering all technologies. This paper describes how a novel scheme for optical MPLS and circuit switched GMPLS based networks can incorporated in such multi-domain, MPLS-based scenarios and how it could be modeled. Network...

  20. Stochastic discrete model of karstic networks

    Science.gov (United States)

    Jaquet, O.; Siegel, P.; Klubertanz, G.; Benabderrhamane, H.

    Karst aquifers are characterised by an extreme spatial heterogeneity that strongly influences their hydraulic behaviour and the transport of pollutants. These aquifers are particularly vulnerable to contamination because of their highly permeable networks of conduits. A stochastic model is proposed for the simulation of the geometry of karstic networks at a regional scale. The model integrates the relevant physical processes governing the formation of karstic networks. The discrete simulation of karstic networks is performed with a modified lattice-gas cellular automaton for a representative description of the karstic aquifer geometry. Consequently, more reliable modelling results can be obtained for the management and the protection of karst aquifers. The stochastic model was applied jointly with groundwater modelling techniques to a regional karst aquifer in France for the purpose of resolving surface pollution issues.

  1. Efficient Analog Circuits for Boolean Satisfiability

    CERN Document Server

    Yin, Xunzhao; Varga, Melinda; Ercsey-Ravasz, Maria; Toroczkai, Zoltan; Hu, Xiaobo Sharon

    2016-01-01

    Efficient solutions to NP-complete problems would significantly benefit both science and industry. However, such problems are intractable on digital computers based on the von Neumann architecture, thus creating the need for alternative solutions to tackle such problems. Recently, a deterministic, continuous-time dynamical system (CTDS) was proposed (Nature Physics, 7(12), 966 (2011)) to solve a representative NP-complete problem, Boolean Satisfiability (SAT). This solver shows polynomial analog time-complexity on even the hardest benchmark $k$-SAT ($k \\geq 3$) formulas, but at an energy cost through exponentially driven auxiliary variables. With some modifications to the CTDS equations, here we present a novel analog hardware SAT solver, AC-SAT, implementing the CTDS. AC-SAT is intended to be used as a co-processor, and with its modular design can be readily extended to different problem sizes. The circuit is designed and simulated based on a 32nm CMOS technology. SPICE simulation results show speedup factor...

  2. Model-based control of networked systems

    CERN Document Server

    Garcia, Eloy; Montestruque, Luis A

    2014-01-01

    This monograph introduces a class of networked control systems (NCS) called model-based networked control systems (MB-NCS) and presents various architectures and control strategies designed to improve the performance of NCS. The overall performance of NCS considers the appropriate use of network resources, particularly network bandwidth, in conjunction with the desired response of the system being controlled.   The book begins with a detailed description of the basic MB-NCS architecture that provides stability conditions in terms of state feedback updates . It also covers typical problems in NCS such as network delays, network scheduling, and data quantization, as well as more general control problems such as output feedback control, nonlinear systems stabilization, and tracking control.   Key features and topics include: Time-triggered and event-triggered feedback updates Stabilization of uncertain systems subject to time delays, quantization, and extended absence of feedback Optimal control analysis and ...

  3. Dynamic regimes of random fuzzy logic networks

    International Nuclear Information System (INIS)

    Random multistate networks, generalizations of the Boolean Kauffman networks, are generic models for complex systems of interacting agents. Depending on their mean connectivity, these networks exhibit ordered as well as chaotic behavior with a critical boundary separating both regimes. Typically, the nodes of these networks are assigned single discrete states. Here, we describe nodes by fuzzy numbers, i.e. vectors of degree-of-membership (DOM) functions specifying the degree to which the nodes are in each of their discrete states. This allows our models to deal with imprecision and uncertainties. Compatible update rules are constructed by expressing the update rules of the multistate network in terms of Boolean operators and generalizing them to fuzzy logic (FL) operators. The standard choice for these generalizations is the Goedel FL, where AND and OR are replaced by the minimum and maximum of two DOMs, respectively. In mean-field approximations we are able to analytically describe the percolation and asymptotic distribution of DOMs in random Goedel FL networks. This allows us to characterize the different dynamic regimes of random multistate networks in terms of FL. In a low-dimensional example, we provide explicit computations and validate our mean-field results by showing that they agree well with network simulations.

  4. Dynamic regimes of random fuzzy logic networks

    Science.gov (United States)

    Wittmann, Dominik M.; Theis, Fabian J.

    2011-01-01

    Random multistate networks, generalizations of the Boolean Kauffman networks, are generic models for complex systems of interacting agents. Depending on their mean connectivity, these networks exhibit ordered as well as chaotic behavior with a critical boundary separating both regimes. Typically, the nodes of these networks are assigned single discrete states. Here, we describe nodes by fuzzy numbers, i.e. vectors of degree-of-membership (DOM) functions specifying the degree to which the nodes are in each of their discrete states. This allows our models to deal with imprecision and uncertainties. Compatible update rules are constructed by expressing the update rules of the multistate network in terms of Boolean operators and generalizing them to fuzzy logic (FL) operators. The standard choice for these generalizations is the Gödel FL, where AND and OR are replaced by the minimum and maximum of two DOMs, respectively. In mean-field approximations we are able to analytically describe the percolation and asymptotic distribution of DOMs in random Gödel FL networks. This allows us to characterize the different dynamic regimes of random multistate networks in terms of FL. In a low-dimensional example, we provide explicit computations and validate our mean-field results by showing that they agree well with network simulations.

  5. Modeling trust context in networks

    CERN Document Server

    Adali, Sibel

    2013-01-01

    We make complex decisions every day, requiring trust in many different entities for different reasons. These decisions are not made by combining many isolated trust evaluations. Many interlocking factors play a role, each dynamically impacting the others.? In this brief, 'trust context' is defined as the system level description of how the trust evaluation process unfolds.Networks today are part of almost all human activity, supporting and shaping it. Applications increasingly incorporate new interdependencies and new trust contexts. Social networks connect people and organizations throughout

  6. Graphical Model Theory for Wireless Sensor Networks

    International Nuclear Information System (INIS)

    Information processing in sensor networks, with many small processors, demands a theory of computation that allows the minimization of processing effort, and the distribution of this effort throughout the network. Graphical model theory provides a probabilistic theory of computation that explicitly addresses complexity and decentralization for optimizing network computation. The junction tree algorithm, for decentralized inference on graphical probability models, can be instantiated in a variety of applications useful for wireless sensor networks, including: sensor validation and fusion; data compression and channel coding; expert systems, with decentralized data structures, and efficient local queries; pattern classification, and machine learning. Graphical models for these applications are sketched, and a model of dynamic sensor validation and fusion is presented in more depth, to illustrate the junction tree algorithm

  7. Graphical Model Theory for Wireless Sensor Networks

    Energy Technology Data Exchange (ETDEWEB)

    Davis, William B.

    2002-12-08

    Information processing in sensor networks, with many small processors, demands a theory of computation that allows the minimization of processing effort, and the distribution of this effort throughout the network. Graphical model theory provides a probabilistic theory of computation that explicitly addresses complexity and decentralization for optimizing network computation. The junction tree algorithm, for decentralized inference on graphical probability models, can be instantiated in a variety of applications useful for wireless sensor networks, including: sensor validation and fusion; data compression and channel coding; expert systems, with decentralized data structures, and efficient local queries; pattern classification, and machine learning. Graphical models for these applications are sketched, and a model of dynamic sensor validation and fusion is presented in more depth, to illustrate the junction tree algorithm.

  8. Monochromaticity in neutral evolutionary network models.

    Science.gov (United States)

    Halu, Arda; Bianconi, Ginestra

    2012-12-01

    Recent studies on epistatic networks of model organisms have unveiled a certain type of modular property called monochromaticity in which the networks are clustered into functional modules that interact with each other through the same type of epistasis. Here, we propose and study three epistatic network models that are inspired by the duplication-divergence mechanism to gain insight into the evolutionary basis of monochromaticity and to test if it can be explained as the outcome of a neutral evolutionary hypothesis. We show that the epistatic networks formed by these stochastic evolutionary models have monochromaticity conflict distributions that are centered close to zero and are statistically significantly different from their randomized counterparts. In particular, the last model we propose yields a strictly monochromatic solution. Our results agree with the monochromaticity findings in real organisms and point toward the possible role of a neutral mechanism in the evolution of this phenomenon. PMID:23367998

  9. Modeling Network Traffic in Wavelet Domain

    Directory of Open Access Journals (Sweden)

    Sheng Ma

    2004-12-01

    Full Text Available This work discovers that although network traffic has the complicated short- and long-range temporal dependence, the corresponding wavelet coefficients are no longer long-range dependent. Therefore, a "short-range" dependent process can be used to model network traffic in the wavelet domain. Both independent and Markov models are investigated. Theoretical analysis shows that the independent wavelet model is sufficiently accurate in terms of the buffer overflow probability for Fractional Gaussian Noise traffic. Any model, which captures additional correlations in the wavelet domain, only improves the performance marginally. The independent wavelet model is then used as a unified approach to model network traffic including VBR MPEG video and Ethernet data. The computational complexity is O(N for developing such wavelet models and generating synthesized traffic of length N, which is among the lowest attained.

  10. Fracture network modelling and performance assessment support

    International Nuclear Information System (INIS)

    This report describes the Fracture Network Modelling and Performance Assessment Support performed by Golder Associates Inc. during the Heisei-12 (2000-2001) fiscal year. The primary objective of the work described in this report was to assist JNC in research related to characterization of solute transport pathways in fracture networks by the discrete fracture network (DFN) and channel network (CN) approaches. In addition, Golder supported JNC participation in the Aespoe Modeling Task Force on of Groundwater Flow and Transport (AMTF). Golder carried out extensive analyses of flow and transport for a 5 meter scale fracture network pathway for AMTF Task 4, and assisted in development of AMTF Task 6 which will address the integration of site characterization and repository safety assessment. Technical information about Golder Associates HY-12 support to JNC/Tokai is provided in the appendices to this report. (author)

  11. Modelling subtle growth of linguistic networks

    CERN Document Server

    Kulig, Andrzej; Kwapien, Jaroslaw; Oswiecimka, Pawel

    2014-01-01

    We investigate properties of evolving linguistic networks defined by the word-adjacency relation. Such networks belong to the category of networks with accelerated growth but their shortest path length appears to reveal the network size dependence of different functional form than the ones known so far. We thus compare the networks created from literary texts with their artificial substitutes based on different variants of the Dorogovtsev-Mendes model and observe that none of them is able to properly simulate the novel asymptotics of the shortest path length. Then, we identify grammar induced local chain-like linear growth as a missing element in this model and extend it by incorporating such effects. It is in this way that a satisfactory agreement with the empirical result is obtained.

  12. Sparsity in Model Gene Regulatory Networks

    International Nuclear Information System (INIS)

    We propose a gene regulatory network model which incorporates the microscopic interactions between genes and transcription factors. In particular the gene's expression level is determined by deterministic synchronous dynamics with contribution from excitatory interactions. We study the structure of networks that have a particular '' function '' and are subject to the natural selection pressure. The question of network robustness against point mutations is addressed, and we conclude that only a small part of connections defined as '' essential '' for cell's existence is fragile. Additionally, the obtained networks are sparse with narrow in-degree and broad out-degree, properties well known from experimental study of biological regulatory networks. Furthermore, during sampling procedure we observe that significantly different genotypes can emerge under mutation-selection balance. All the preceding features hold for the model parameters which lay in the experimentally relevant range. (author)

  13. Energy-oriented models for WDM networks

    OpenAIRE

    Ricciardi, Sergio; Careglio, Davide; Palmieri, Francesco; Fiore, Ugo; Santos Boada, Germán; Solé Pareta, Josep

    2010-01-01

    A realistic energy-oriented model is necessary to formally characterize the energy consumption and the consequent carbon footprint of actual and future high-capacity WDM networks. The energy model describes the energy consumption of the various network elements (NE) and predicts their energy consumption behavior under different traffic loads and for the diverse traffic types, including all optical and electronic traffic, O/E/O conversions, 3R regenerations, add/drop multiplexing, etc. Besi...

  14. Survey of propagation Model in wireless Network

    OpenAIRE

    Hemant Kumar Sharma; Sanjeev Sharma; Krishna Kumar Pandey

    2011-01-01

    To implementation of mobile ad hoc network wave propagation models are necessary to determine propagation characteristic through a medium. Wireless mobile ad hoc networks are self creating and self organizing entity. Propagation study provides an estimation of signal characteristics. Accurate prediction of radio propagation behaviour for MANET is becoming a difficult task. This paper presents investigation of propagation model. Radio wave propagation mechanisms are absorption, reflection, ref...

  15. Clustered model reduction of positive directed networks

    OpenAIRE

    Ishizaki, Takayuki; Kashima, Kenji; Girard, Antoine; Imura, Jun-ichi; Chen, Luonan; Aihara, Kazuyuki

    2015-01-01

    This paper proposes a clustered model reduction method for semistable positive linear systems evolving over directed networks. In this method, we construct a set of clusters, i.e., disjoint sets of state variables, based on a notion of cluster reducibility, defined as the uncontrollability of local states. By aggregating the reducible clusters with aggregation coefficients associated with the Frobenius eigenvector, we obtain an approximate model that preserves not only a network structure amo...

  16. IP Network Management Model Based on NGOSS

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jin-yu; LI Hong-hui; LIU Feng

    2004-01-01

    This paper addresses a management model for IP network based on Next Generation Operation Support System (NGOSS). It makes the network management on the base of all the operation actions of ISP, It provides QoS to user service through the whole path by providing end-to-end Service Level Agreements (SLA) management through whole path. Based on web and coordination technology, this paper gives an implement architecture of this model.

  17. Model-Based Clustering of Large Networks

    CERN Document Server

    Vu, Duy Quang; Schweinberger, Michael

    2012-01-01

    We describe a network clustering framework, based on finite mixture models, that can be applied to discrete-valued networks with hundreds of thousands of nodes and billions of edge variables. Relative to other recent model-based clustering work for networks, we introduce a more flexible modeling framework, improve the variational-approximation estimation algorithm, discuss and implement standard error estimation via a parametric bootstrap approach, and apply these methods to much larger datasets than those seen elsewhere in the literature. The more flexible modeling framework is achieved through introducing novel parameterizations of the model, giving varying degrees of parsimony, using exponential family models whose structure may be exploited in various theoretical and algorithmic ways. The algorithms, which we show how to adapt to the more complicated optimization requirements introduced by the constraints imposed by the novel parameterizations we propose, are based on variational generalized EM algorithms...

  18. A simple model for studying interacting networks

    Science.gov (United States)

    Liu, Wenjia; Jolad, Shivakumar; Schmittmann, Beate; Zia, R. K. P.

    2011-03-01

    Many specific physical networks (e.g., internet, power grid, interstates), have been characterized in considerable detail, but in isolation from each other. Yet, each of these networks supports the functions of the others, and so far, little is known about how their interactions affect their structure and functionality. To address this issue, we consider two coupled model networks. Each network is relatively simple, with a fixed set of nodes, but dynamically generated set of links which has a preferred degree, κ . In the stationary state, the degree distribution has exponential tails (far from κ), an attribute which we can explain. Next, we consider two such networks with different κ 's, reminiscent of two social groups, e.g., extroverts and introverts. Finally, we let these networks interact by establishing a controllable fraction of cross links. The resulting distribution of links, both within and across the two model networks, is investigated and discussed, along with some potential consequences for real networks. Supported in part by NSF-DMR-0705152 and 1005417.

  19. A survey of statistical network models

    CERN Document Server

    Goldenberg, Anna; Fienberg, Stephen E; Airoldi, Edoardo M

    2009-01-01

    Networks are ubiquitous in science and have become a focal point for discussion in everyday life. Formal statistical models for the analysis of network data have emerged as a major topic of interest in diverse areas of study, and most of these involve a form of graphical representation. Probability models on graphs date back to 1959. Along with empirical studies in social psychology and sociology from the 1960s, these early works generated an active network community and a substantial literature in the 1970s. This effort moved into the statistical literature in the late 1970s and 1980s, and the past decade has seen a burgeoning network literature in statistical physics and computer science. The growth of the World Wide Web and the emergence of online networking communities such as Facebook, MySpace, and LinkedIn, and a host of more specialized professional network communities has intensified interest in the study of networks and network data. Our goal in this review is to provide the reader with an entry poin...

  20. The Network Performance Assessment Model - Regulation with a Reference Network

    International Nuclear Information System (INIS)

    A new model - the Network Performance Assessment Model - has been developed gradually since 1998, in order to evaluate and benchmark local electricity grids. The model is intended to be a regulation tool for the Swedish local electricity networks, used by the Swedish Energy Agency. At spring 2004 the Network Performance Assessment Model will run into operation, based on the companies' results for 2003. The mission of the Network Performance Assessment Model is to evaluate the networks from a costumers' point of view and establish a fair price level. In order to do that, the performance of the operator is evaluated. The performances are assessed in correspondence to a price level that the consumer is considered to accept, can agree to as fair and is prepared to pay. This price level is based on an average cost, based on the cost of an efficient grid that will be built today, with already known technology. The performances are accounted in Customer Values. Those Customer Values are what can be created by someone but can't be created better by someone else. The starting point is to look upon the companies from a customers' point of view. The factors that can't be influenced by the companies are evaluated by fixed rules, valid to all companies. The rules reflect the differences. The cost for a connection is evaluated from the actual facts, i.e. the distances between the subscribers and the demanded capacity by the subscriber. This is done by the creation of a reference network, with a capacity to fulfill the demand from the subscriber. This is an efficient grid with no spare capacity and no excess capacity. The companies' existing grid are without importance, as well as holds for dimensioning as technology. Those factors which the company can influence, for an example connection reliability, are evaluated from a customer perspective by measuring the actual reliability, measured as the number and length of the interruption. When implemented to the regulation the Network

  1. MODEL FOR NETWORKED BUSINESS: Case study of Application Service Provider's network

    OpenAIRE

    Pesonen, Tero

    2011-01-01

    MODEL FOR NETWORKED BUSINESS Case study of Application Service Provider's network The aim of the research was to create a network business model to optimise benefits for a business network in the area of software industry. The main research questions were: ? What kind of network business models can be found? ? What are the value creation mechanisms as well as advantages and disadvantages of different models? ? How to use former frameworks to develop a network business mode...

  2. Research on Context Aware Network Security Model

    Directory of Open Access Journals (Sweden)

    XiaoHui Guo

    2013-08-01

    Full Text Available According to high development of internet and mobile internet technologies, more and more services and applications are researched and are becoming more and more important in people’s life. At the same time, there are still many risks that virus attack from internet. Network security is facing more challenges than before, such as attack method becoming more diversify, attack times are increasing rapidly, and attack behavior are becoming a system to damage network security. What’s more, application data is more changeable that before, which makes it more difficult to judge which behavior is attack and response to the attack. Current network security system can’t prevent a system level attack, what’s more, can’t response to the attack quickly and effectively. Therefore, this paper designed a new context aware network security model to prevent various attack effectively, present the context declaim algorithm to judge network attack, and then designed a data share mechanism to share attack information with peer machine, which can decrease the response time deeply. Finally, this paper designed a set experiment to validate the quality and performance of context based network security model, the result shows this model can prevent network attack effectively and more memory saving in changeable application.

  3. Performance modeling, stochastic networks, and statistical multiplexing

    CERN Document Server

    Mazumdar, Ravi R

    2013-01-01

    This monograph presents a concise mathematical approach for modeling and analyzing the performance of communication networks with the aim of introducing an appropriate mathematical framework for modeling and analysis as well as understanding the phenomenon of statistical multiplexing. The models, techniques, and results presented form the core of traffic engineering methods used to design, control and allocate resources in communication networks.The novelty of the monograph is the fresh approach and insights provided by a sample-path methodology for queueing models that highlights the importan

  4. Modeling, Optimization & Control of Hydraulic Networks

    DEFF Research Database (Denmark)

    Tahavori, Maryamsadat

    2014-01-01

    . The nonlinear network model is derived based on the circuit theory. A suitable projection is used to reduce the state vector and to express the model in standard state-space form. Then, the controllability of nonlinear nonaffine hydraulic networks is studied. The Lie algebra-based controllability matrix is used...... to solve nonlinear optimal control problems. In the water supply system model, the hydraulic resistance of the valve is estimated by real data and it is considered to be a disturbance. The disturbance in our system is updated every 24 hours based on the amount of water usage by consumers every day. Model...

  5. Second moment method for a family of boolean CSP

    CERN Document Server

    Boufkhad, Yacine

    2011-01-01

    The estimation of phase transitions in random boolean Constraint Satisfaction Problems (CSP) is based on two fundamental tools: the first and second moment methods. While the first moment method on the number of solutions permits to compute upper bounds on any boolean CSP, the second moment method used for computing lower bounds proves to be more tricky and in most cases gives only the trivial lower bound 0. In this paper, we define a subclass of boolean CSP covering the monotone versions of many known NP-Complete boolean CSPs. We give a method for computing non trivial lower bounds for any member of this subclass. This is achieved thanks to an application of the second moment method to some selected solutions called characteristic solutions that depend on the boolean CSP considered. We apply, as an example, this method to establish that the threshold r_{k} of monotone 1-in-k-SAT is \\log k/k\\leq r_{k}\\leq\\log^{2}k/k

  6. Efficient Algorithms for Membership in Boolean Hierarchies of Regular Languages

    CERN Document Server

    Glasser, Christian; Selivanov, Victor

    2008-01-01

    The purpose of this paper is to provide efficient algorithms that decide membership for classes of several Boolean hierarchies for which efficiency (or even decidability) were previously not known. We develop new forbidden-chain characterizations for the single levels of these hierarchies and obtain the following results: - The classes of the Boolean hierarchy over level $\\Sigma_1$ of the dot-depth hierarchy are decidable in $NL$ (previously only the decidability was known). The same remains true if predicates mod $d$ for fixed $d$ are allowed. - If modular predicates for arbitrary $d$ are allowed, then the classes of the Boolean hierarchy over level $\\Sigma_1$ are decidable. - For the restricted case of a two-letter alphabet, the classes of the Boolean hierarchy over level $\\Sigma_2$ of the Straubing-Th\\'erien hierarchy are decidable in $NL$. This is the first decidability result for this hierarchy. - The membership problems for all mentioned Boolean-hierarchy classes are logspace many-one hard for $NL$. - T...

  7. Modeling acquaintance networks based on balance theory

    Directory of Open Access Journals (Sweden)

    Vukašinović Vida

    2014-09-01

    Full Text Available An acquaintance network is a social structure made up of a set of actors and the ties between them. These ties change dynamically as a consequence of incessant interactions between the actors. In this paper we introduce a social network model called the Interaction-Based (IB model that involves well-known sociological principles. The connections between the actors and the strength of the connections are influenced by the continuous positive and negative interactions between the actors and, vice versa, the future interactions are more likely to happen between the actors that are connected with stronger ties. The model is also inspired by the social behavior of animal species, particularly that of ants in their colony. A model evaluation showed that the IB model turned out to be sparse. The model has a small diameter and an average path length that grows in proportion to the logarithm of the number of vertices. The clustering coefficient is relatively high, and its value stabilizes in larger networks. The degree distributions are slightly right-skewed. In the mature phase of the IB model, i.e., when the number of edges does not change significantly, most of the network properties do not change significantly either. The IB model was found to be the best of all the compared models in simulating the e-mail URV (University Rovira i Virgili of Tarragona network because the properties of the IB model more closely matched those of the e-mail URV network than the other models

  8. Optimal transportation networks models and theory

    CERN Document Server

    Bernot, Marc; Morel, Jean-Michel

    2009-01-01

    The transportation problem can be formalized as the problem of finding the optimal way to transport a given measure into another with the same mass. In contrast to the Monge-Kantorovitch problem, recent approaches model the branched structure of such supply networks as minima of an energy functional whose essential feature is to favour wide roads. Such a branched structure is observable in ground transportation networks, in draining and irrigation systems, in electrical power supply systems and in natural counterparts such as blood vessels or the branches of trees. These lectures provide mathematical proof of several existence, structure and regularity properties empirically observed in transportation networks. The link with previous discrete physical models of irrigation and erosion models in geomorphology and with discrete telecommunication and transportation models is discussed. It will be mathematically proven that the majority fit in the simple model sketched in this volume.

  9. Modeling Emergence in Neuroprotective Regulatory Networks

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Haack, Jereme N.; McDermott, Jason E.; Stevens, S.L.; Stenzel-Poore, Mary

    2013-01-05

    The use of predictive modeling in the analysis of gene expression data can greatly accelerate the pace of scientific discovery in biomedical research by enabling in silico experimentation to test disease triggers and potential drug therapies. Techniques that focus on modeling emergence, such as agent-based modeling and multi-agent simulations, are of particular interest as they support the discovery of pathways that may have never been observed in the past. Thus far, these techniques have been primarily applied at the multi-cellular level, or have focused on signaling and metabolic networks. We present an approach where emergence modeling is extended to regulatory networks and demonstrate its application to the discovery of neuroprotective pathways. An initial evaluation of the approach indicates that emergence modeling provides novel insights for the analysis of regulatory networks that can advance the discovery of acute treatments for stroke and other diseases.

  10. International migration network: Topology and modeling

    Science.gov (United States)

    Fagiolo, Giorgio; Mastrorillo, Marina

    2013-07-01

    This paper studies international migration from a complex-network perspective. We define the international migration network (IMN) as the weighted-directed graph where nodes are world countries and links account for the stock of migrants originated in a given country and living in another country at a given point in time. We characterize the binary and weighted architecture of the network and its evolution over time in the period 1960-2000. We find that the IMN is organized around a modular structure with a small-world binary pattern displaying disassortativity and high clustering, with power-law distributed weighted-network statistics. We also show that a parsimonious gravity model of migration can account for most of observed IMN topological structure. Overall, our results suggest that socioeconomic, geographical, and political factors are more important than local-network properties in shaping the structure of the IMN.

  11. Modeling of urban traffic networks with lattice Boltzmann model

    Science.gov (United States)

    Meng, Jian-ping; Qian, Yue-hong; Dai, Shi-qiang

    2008-02-01

    It is of great importance to uncover the characteristics of traffic networks. However, there have been few researches concerning kinetics models for urban traffic networks. In this work, a lattice Boltzmann model (LBM) for urban traffic networks is proposed by incorporating the ideas of the Biham-Middleton-Levine (BML) model into the LBM for road traffic. In the present model, situations at intersections with the red and green traffic signals are treated as a kind of boundary conditions varying with time. Thus, the urban traffic network could be described in the mesoscopic level. By performing numerical simulations under the periodic boundary conditions, the behavior of average velocity is investigated in detail. The numerical results agree quite well with those given by the Chowdhury-Schadschneider (ChSch) model (Chowdhury D. and Schadschneider A., Phys. Rev. E, 59 (1999) R1311). Furthermore, the statistical noise is reduced in this discrete kinetics model, thus, the present model has considerably high computational efficiency.

  12. Metanetworks of artificially evolved regulatory networks

    CERN Document Server

    Danacı, Burçin

    2014-01-01

    We study metanetworks arising in genotype and phenotype spaces, in the context of a model population of Boolean graphs evolved under selection for short dynamical attractors. We define the adjacency matrix of a graph as its genotype, which gets mutated in the course of evolution, while its phenotype is its set of dynamical attractors. Metanetworks in the genotype and phenotype spaces are formed, respectively, by genetic proximity and by phenotypic similarity, the latter weighted by the sizes of the basins of attraction of the shared attractors. We find that populations of evolved networks form giant clusters in genotype space, have Poissonian degree distributions but exhibit hierarchically organized $k$-core decompositions, while random populations of Boolean graphs are typically so far removed from each other genetically that they cannot form a metanetwork. In phenotype space, the metanetworks of evolved populations are super robust both under the elimination of weak connections and random removal of nodes. ...

  13. An evolving network model with modular growth

    Institute of Scientific and Technical Information of China (English)

    Zou Zhi-Yun; Liu Peng; Lei Li; Gao Jian-Zhi

    2012-01-01

    In this paper,we propose an evolving network model growing fast in units of module,according to the analysis of the evolution characteristics in real complex networks.Each module is a small-world network containing several interconnected nodes and the nodes between the modules are linked by preferential attachment on degree of nodes.We study the modularity measure of the proposed model,which can be adjusted by changing the ratio of the number of innermodule edges and the number of inter-module edges.In view of the mean-field theory,we develop an analytical function of the degree distribution,which is verified by a numerical example and indicates that the degree distribution shows characteristics of the small-world network and the scale-free network distinctly at different segments.The clustering coefficient and the average path length of the network are simulated numerically,indicating that the network shows the small-world property and is affected little by the randomness of the new module.

  14. An evolving network model with modular growth

    International Nuclear Information System (INIS)

    In this paper, we propose an evolving network model growing fast in units of module, according to the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected nodes and the nodes between the modules are linked by preferential attachment on degree of nodes. We study the modularity measure of the proposed model, which can be adjusted by changing the ratio of the number of inner-module edges and the number of inter-module edges. In view of the mean-field theory, we develop an analytical function of the degree distribution, which is verified by a numerical example and indicates that the degree distribution shows characteristics of the small-world network and the scale-free network distinctly at different segments. The clustering coefficient and the average path length of the network are simulated numerically, indicating that the network shows the small-world property and is affected little by the randomness of the new module. (interdisciplinary physics and related areas of science and technology)

  15. Hybrid neural network models of transducers

    International Nuclear Information System (INIS)

    A hybrid neural network (NN) approach is proposed and applied to modeling of transducers in the paper. The modeling procedures are also presented in detail. First, the simulated studies on the modeling of single input–single output and multi input–multi output transducers are conducted respectively by use of the developed hybrid NN scheme. Secondly, the hybrid NN modeling approach is utilized to characterize a six-axis force sensor prototype based on the measured data. The results show that the hybrid NN approach can significantly improve modeling precision in comparison with the conventional modeling method. In addition, the method is superior to NN black-box modeling because the former possesses smaller network scale, higher convergence speed, higher model precision and better generalization performance

  16. Modelling complex networks by random hierarchical graphs

    Directory of Open Access Journals (Sweden)

    M.Wróbel

    2008-06-01

    Full Text Available Numerous complex networks contain special patterns, called network motifs. These are specific subgraphs, which occur oftener than in randomized networks of Erdős-Rényi type. We choose one of them, the triangle, and build a family of random hierarchical graphs, being Sierpiński gasket-based graphs with random "decorations". We calculate the important characteristics of these graphs - average degree, average shortest path length, small-world graph family characteristics. They depend on probability of decorations. We analyze the Ising model on our graphs and describe its critical properties using a renormalization-group technique.

  17. Grid architecture model of network centric warfare

    Institute of Scientific and Technical Information of China (English)

    Yan Tihua; Wang Baoshu

    2006-01-01

    NCW(network centric warfare) is an information warfare concentrating on network. A global network-centric warfare architecture with OGSA grid technology is put forward, which is a four levels system including the user level, the application level, the grid middleware layer and the resource level. In grid middleware layer, based on virtual hosting environment, a BEPL4WS grid service composition method is introduced. In addition, the NCW grid service model is built with the help of Eclipse-SDK-3.0.1 and Bpws4j.

  18. Enhanced Gravity Model of trade: reconciling macroeconomic and network models

    CERN Document Server

    Almog, Assaf; Garlaschelli, Diego

    2015-01-01

    The bilateral trade relations between world countries form a complex network, the International Trade Network (ITN), which is involved in an increasing number of worldwide economic processes, including globalization, integration, industrial production, and the propagation of shocks and instabilities. Characterizing the ITN via a simple yet accurate model is an open problem. The classical Gravity Model of trade successfully reproduces the volume of trade between two connected countries using known macroeconomic properties such as GDP and geographic distance. However, it generates a network with an unrealistically homogeneous topology, thus failing to reproduce the highly heterogeneous structure of the real ITN. On the other hand, network models successfully reproduce the complex topology of the ITN, but provide no information about trade volumes. Therefore macroeconomic and network models of trade suffer from complementary limitations but are still largely incompatible. Here, we make an important step forward ...

  19. The International Trade Network: weighted network analysis and modelling

    International Nuclear Information System (INIS)

    Tools of the theory of critical phenomena, namely the scaling analysis and universality, are argued to be applicable to large complex web-like network structures. Using a detailed analysis of the real data of the International Trade Network we argue that the scaled link weight distribution has an approximate log-normal distribution which remains robust over a period of 53 years. Another universal feature is observed in the power-law growth of the trade strength with gross domestic product, the exponent being similar for all countries. Using the 'rich-club' coefficient measure of the weighted networks it has been shown that the size of the rich-club controlling half of the world's trade is actually shrinking. While the gravity law is known to describe well the social interactions in the static networks of population migration, international trade, etc, here for the first time we studied a non-conservative dynamical model based on the gravity law which excellently reproduced many empirical features of the ITN

  20. A Network Model of Credit Risk Contagion

    OpenAIRE

    Ting-Qiang Chen; Jian-Min He

    2012-01-01

    A network model of credit risk contagion is presented, in which the effect of behaviors of credit risk holders and the financial market regulators and the network structure are considered. By introducing the stochastic dominance theory, we discussed, respectively, the effect mechanisms of the degree of individual relationship, individual attitude to credit risk contagion, the individual ability to resist credit risk contagion, the monitoring strength of the financial market regulators, and th...

  1. Non-nequilibrium model on Apollonian networks

    CERN Document Server

    Lima, F W S; Araújo, Ascânio D

    2012-01-01

    We investigate the Majority-Vote Model with two states ($-1,+1$) and a noise $q$ on Apollonian networks. The main result found here is the presence of the phase transition as a function of the noise parameter $q$. We also studies de effect of redirecting a fraction $p$ of the links of the network. By means of Monte Carlo simulations, we obtained the exponent ratio $\\gamma/\

  2. Stochastic modeling and analysis of telecoms networks

    CERN Document Server

    Decreusefond, Laurent

    2012-01-01

    This book addresses the stochastic modeling of telecommunication networks, introducing the main mathematical tools for that purpose, such as Markov processes, real and spatial point processes and stochastic recursions, and presenting a wide list of results on stability, performances and comparison of systems.The authors propose a comprehensive mathematical construction of the foundations of stochastic network theory: Markov chains, continuous time Markov chains are extensively studied using an original martingale-based approach. A complete presentation of stochastic recursions from an

  3. Keystone Business Models for Network Security Processors

    OpenAIRE

    Arthur Low; Steven Muegge

    2013-01-01

    Network security processors are critical components of high-performance systems built for cybersecurity. Development of a network security processor requires multi-domain experience in semiconductors and complex software security applications, and multiple iterations of both software and hardware implementations. Limited by the business models in use today, such an arduous task can be undertaken only by large incumbent companies and government organizations. Neither the “fabless semiconductor...

  4. Decomposed Implicit Models of Piecewise - Linear Networks

    Directory of Open Access Journals (Sweden)

    J. Brzobohaty

    1992-05-01

    Full Text Available The general matrix form of the implicit description of a piecewise-linear (PWL network and the symbolic block diagram of the corresponding circuit model are proposed. Their decomposed forms enable us to determine quite separately the existence of the individual breakpoints of the resultant PWL characteristic and their coordinates using independent network parameters. For the two-diode and three-diode cases all the attainable types of the PWL characteristic are introduced.

  5. Bus Network Modeling Using Ant Algorithms

    OpenAIRE

    Sepideh Eshragh; Shahriar Afandizadeh Zargari; Ardeshir Faghri; Earl Rusty Lee

    2010-01-01

    Bus transit network modeling is a complex and combinatorial problem. The main purpose of this paper is to apply a contemporary method for designing a bus transit network with the objective of achieving optimum results. The method is called Ant Algorithms, a Meta Heuristic method, which has been applied to optimization problems in transportation with noticeable success. The description of the algorithm, as well as the main methodology and computations, is presented in this paper. Furthermore, ...

  6. Dynamic Modeling of the Electric Transportation Network

    CERN Document Server

    Scir`e, A; Eguiluz, V M; Scir\\`{e}, Alessandro; Tuval, Id\\'an

    2005-01-01

    We introduce a model for the dynamic self-organization of the electric grid. The model is characterized by a conserved magnitude, energy, that can travel following the links of the network to satisfy nodes' load. The load fluctuates in time causing local overloads that drive the dynamic evolution of the network topology. Our model displays a transition from a fully connected network to a configuration with a non-trivial topology and where global failures are suppressed. The most efficient topology is characterized by an exponential degree distribution, in agreement with the topology of the real electric grid. The model intrinsically presents self-induced break-down events, which can be thought as representative of real black-outs.

  7. Modeling Computations in a Semantic Network

    CERN Document Server

    Rodriguez, Marko A

    2007-01-01

    Semantic network research has seen a resurgence from its early history in the cognitive sciences with the inception of the Semantic Web initiative. The Semantic Web effort has brought forth an array of technologies that support the encoding, storage, and querying of the semantic network data structure at the world stage. Currently, the popular conception of the Semantic Web is that of a data modeling medium where real and conceptual entities are related in semantically meaningful ways. However, new models have emerged that explicitly encode procedural information within the semantic network substrate. With these new technologies, the Semantic Web has evolved from a data modeling medium to a computational medium. This article provides a classification of existing computational modeling efforts and the requirements of supporting technologies that will aid in the further growth of this burgeoning domain.

  8. Network Design Models for Container Shipping

    DEFF Research Database (Denmark)

    Reinhardt, Line Blander; Kallehauge, Brian; Nielsen, Anders Nørrelund;

    included in the calculation of the capacity and that a inhomogeneous fleet is modeled. The model also includes the cost of transshipment which is one of the major cost for the shipping companies. The concept of pseudo simple routes is introduced to expand the set of feasible routes. The linearization of......This paper presents a study of the network design problem in container shipping. The paper combines the network design and fleet assignment problem into a mixed integer linear programming model minimizing the overall cost. The major contributions of this paper is that the time of a vessel route is...

  9. Empirical generalization assessment of neural network models

    DEFF Research Database (Denmark)

    Larsen, Jan; Hansen, Lars Kai

    1995-01-01

    This paper addresses the assessment of generalization performance of neural network models by use of empirical techniques. We suggest to use the cross-validation scheme combined with a resampling technique to obtain an estimate of the generalization performance distribution of a specific model...

  10. Nonconsensus opinion model on directed networks

    Science.gov (United States)

    Qu, Bo; Li, Qian; Havlin, Shlomo; Stanley, H. Eugene; Wang, Huijuan

    2014-11-01

    Dynamic social opinion models have been widely studied on undirected networks, and most of them are based on spin interaction models that produce a consensus. In reality, however, many networks such as Twitter and the World Wide Web are directed and are composed of both unidirectional and bidirectional links. Moreover, from choosing a coffee brand to deciding who to vote for in an election, two or more competing opinions often coexist. In response to this ubiquity of directed networks and the coexistence of two or more opinions in decision-making situations, we study a nonconsensus opinion model introduced by Shao et al. [Phys. Rev. Lett. 103, 018701 (2009), 10.1103/PhysRevLett.103.018701] on directed networks. We define directionality ξ as the percentage of unidirectional links in a network, and we use the linear correlation coefficient ρ between the in-degree and out-degree of a node to quantify the relation between the in-degree and out-degree. We introduce two degree-preserving rewiring approaches which allow us to construct directed networks that can have a broad range of possible combinations of directionality ξ and linear correlation coefficient ρ and to study how ξ and ρ impact opinion competitions. We find that, as the directionality ξ or the in-degree and out-degree correlation ρ increases, the majority opinion becomes more dominant and the minority opinion's ability to survive is lowered.

  11. Dual modeling of political opinion networks

    Science.gov (United States)

    Wang, R.; A. Wang, Q.

    2011-09-01

    We present the result of a dual modeling of opinion networks. The model complements the agent-based opinion models by attaching to the social agent (voters) network a political opinion (party) network having its own intrinsic mechanisms of evolution. These two subnetworks form a global network, which can be either isolated from, or dependent on, the external influence. Basically, the evolution of the agent network includes link adding and deleting, with the opinion changes influenced by social validation, the political climate, the attractivity of the parties, and the interaction between them. The opinion network is initially composed of numerous nodes representing opinions or parties that are located on a one dimensional axis according to their political positions. The mechanism of evolution includes union, splitting, change of position, and attractivity, taking into account the pairwise node interaction decaying with node distance in power law. The global evolution ends in a stable distribution of the social agents over a quasistable and fluctuating stationary number of remaining parties. Empirical study on the lifetime distribution of numerous parties and vote results is carried out to verify numerical results.

  12. Experimental Comparison of Schemes for Interpreting Boolean Queries

    OpenAIRE

    Lee, Whay C.; Edward A Fox

    1988-01-01

    The standard interpretation of the logical operators in a Boolean retrieval system is in general too strict. A standard Boolean query rarely comes close to retrieving all and only those documents which are relevant to the user. An AND query is often too narrow and an OR query is often too broad. The choice of the AND results in retrieving on the left end of a typical average recall-precision graph, while the choice of the OR results in retrieving on the right end, implying a tradeoff between ...

  13. Some Properties of Inclusions of Multisets and Contractive Boolean Operators

    OpenAIRE

    Hyvernat, Pierre

    2011-01-01

    10 pages, including appendix Consider the following curious puzzle: call an n-tuple X=(X_1, ..., X_n) of sets smaller than another n-tuple Y if it has fewer //unordered sections//. We show that equivalence classes for this preorder are very easy to describe and characterize the preorder in terms of the simpler pointwise inclusion and the existence of a special increasing boolean operator f:B^n -> B^n. We also show that contrary to increasing boolean operators, the relevant operators are no...

  14. Constant-Overhead Secure Computation of Boolean Circuits using Preprocessing

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre; Zakarias, Sarah Nouhad Haddad

    We present a protocol for securely computing a Boolean circuit $C$ in presence of a dishonest and malicious majority. The protocol is unconditionally secure, assuming access to a preprocessing functionality that is not given the inputs to compute on. For a large number of players the work done by...... each player is the same as the work needed to compute the circuit in the clear, up to a constant factor. Our protocol is the first to obtain these properties for Boolean circuits. On the technical side, we develop new homomorphic authentication schemes based on asymptotically good codes with an...

  15. Boolean Logic: An Aid for Searching Computer Databases in Special Education and Rehabilitation.

    Science.gov (United States)

    Summers, Edward G.

    1989-01-01

    The article discusses using Boolean logic as a tool for searching computerized information retrieval systems in special education and rehabilitation technology. It includes discussion of the Boolean search operators AND, OR, and NOT; Venn diagrams; and disambiguating parentheses. Six suggestions are offered for development of good Boolean logic…

  16. Cellular automata modelling of biomolecular networks dynamics.

    Science.gov (United States)

    Bonchev, D; Thomas, S; Apte, A; Kier, L B

    2010-01-01

    The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215

  17. Modelling Users` Trust in Online Social Networks

    Directory of Open Access Journals (Sweden)

    Iacob Cătoiu

    2014-02-01

    Full Text Available Previous studies (McKnight, Lankton and Tripp, 2011; Liao, Lui and Chen, 2011 have shown the crucial role of trust when choosing to disclose sensitive information online. This is the case of online social networks users, who must disclose a certain amount of personal data in order to gain access to these online services. Taking into account privacy calculus model and the risk/benefit ratio, we propose a model of users’ trust in online social networks with four variables. We have adapted metrics for the purpose of our study and we have assessed their reliability and validity. We use a Partial Least Squares (PLS based structural equation modelling analysis, which validated all our initial assumptions, indicating that our three predictors (privacy concerns, perceived benefits and perceived risks explain 48% of the variation of users’ trust in online social networks, the resulting variable of our study. We also discuss the implications and further research opportunities of our study.

  18. The Kuramoto model in complex networks

    CERN Document Server

    Rodrigues, Francisco A; Ji, Peng; Kurths, Jürgen

    2016-01-01

    Synchronization of an ensemble of oscillators is an emergent phenomenon present in several complex systems, ranging from social and physical to biological and technological systems. The most successful approach to describe how coherent behavior emerges in these complex systems is given by the paradigmatic Kuramoto model. This model has been traditionally studied in complete graphs. However, besides being intrinsically dynamical, complex systems present very heterogeneous structure, which can be represented as complex networks. This report is dedicated to review main contributions in the field of synchronization in networks of Kuramoto oscillators. In particular, we provide an overview of the impact of network patterns on the local and global dynamics of coupled phase oscillators. We cover many relevant topics, which encompass a description of the most used analytical approaches and the analysis of several numerical results. Furthermore, we discuss recent developments on variations of the Kuramoto model in net...

  19. Ripple-Spreading Network Model Optimization by Genetic Algorithm

    OpenAIRE

    Xiao-Bing Hu; Ming Wang; Mark S. Leeson

    2013-01-01

    Small-world and scale-free properties are widely acknowledged in many real-world complex network systems, and many network models have been developed to capture these network properties. The ripple-spreading network model (RSNM) is a newly reported complex network model, which is inspired by the natural ripple-spreading phenomenon on clam water surface. The RSNM exhibits good potential for describing both spatial and temporal features in the development of many real-world networks where the i...

  20. A quantum speedup in machine learning: finding an N-bit Boolean function for a classification

    International Nuclear Information System (INIS)

    We compare quantum and classical machines designed for learning an N-bit Boolean function in order to address how a quantum system improves the machine learning behavior. The machines of the two types consist of the same number of operations and control parameters, but only the quantum machines utilize the quantum coherence naturally induced by unitary operators. We show that quantum superposition enables quantum learning that is faster than classical learning by expanding the approximate solution regions, i.e., the acceptable regions. This is also demonstrated by means of numerical simulations with a standard feedback model, namely random search, and a practical model, namely differential evolution. (paper)

  1. A quantum speedup in machine learning: finding an N-bit Boolean function for a classification

    Science.gov (United States)

    Yoo, Seokwon; Bang, Jeongho; Lee, Changhyoup; Lee, Jinhyoung

    2014-10-01

    We compare quantum and classical machines designed for learning an N-bit Boolean function in order to address how a quantum system improves the machine learning behavior. The machines of the two types consist of the same number of operations and control parameters, but only the quantum machines utilize the quantum coherence naturally induced by unitary operators. We show that quantum superposition enables quantum learning that is faster than classical learning by expanding the approximate solution regions, i.e., the acceptable regions. This is also demonstrated by means of numerical simulations with a standard feedback model, namely random search, and a practical model, namely differential evolution.

  2. Boolean network model for GPR142 against Type 2 diabetes and relative dynamic change ratio analysis using systems and biological circuits approach

    OpenAIRE

    Kaushik, Aman Chandra; Sahi, Shakti

    2015-01-01

    Systems biology addresses challenges in the analysis of genomics data, especially for complex genes and protein interactions using Meta data approach on various signaling pathways. In this paper, we report systems biology and biological circuits approach to construct pathway and identify early gene and protein interactions for predicting GPR142 responses in Type 2 diabetes. The information regarding genes, proteins and other molecules involved in Type 2 diabetes were retrieved from literature...

  3. Boolean network model for GPR142 against Type 2 diabetes and relative dynamic change ratio analysis using systems and biological circuits approach.

    Science.gov (United States)

    Kaushik, Aman Chandra; Sahi, Shakti

    2015-06-01

    Systems biology addresses challenges in the analysis of genomics data, especially for complex genes and protein interactions using Meta data approach on various signaling pathways. In this paper, we report systems biology and biological circuits approach to construct pathway and identify early gene and protein interactions for predicting GPR142 responses in Type 2 diabetes. The information regarding genes, proteins and other molecules involved in Type 2 diabetes were retrieved from literature and kinetic simulation of GPR142 was carried out in order to determine the dynamic interactions. The major objective of this work was to design a GPR142 biochemical pathway using both systems biology as well as biological circuits synthetically. The term 'synthetically' refers to building biological circuits for cell signaling pathway especially for hormonal pathway disease. The focus of the paper is on logical components and logical circuits whereby using these applications users can create complex virtual circuits. Logic gates process represents only true or false and investigates whether biological regulatory circuits are active or inactive. The basic gates used are AND, NAND, OR, XOR and NOT gates and Integrated circuit composition of many such basic gates and some derived gates. Biological circuits may have a futuristic application in biomedical sciences which may involve placing a micro chip in human cells to modulate the down or up regulation of hormonal disease. PMID:25972988

  4. Features and heterogeneities in growing network models

    Science.gov (United States)

    Ferretti, Luca; Cortelezzi, Michele; Yang, Bin; Marmorini, Giacomo; Bianconi, Ginestra

    2012-06-01

    Many complex networks from the World Wide Web to biological networks grow taking into account the heterogeneous features of the nodes. The feature of a node might be a discrete quantity such as a classification of a URL document such as personal page, thematic website, news, blog, search engine, social network, etc., or the classification of a gene in a functional module. Moreover the feature of a node can be a continuous variable such as the position of a node in the embedding space. In order to account for these properties, in this paper we provide a generalization of growing network models with preferential attachment that includes the effect of heterogeneous features of the nodes. The main effect of heterogeneity is the emergence of an “effective fitness” for each class of nodes, determining the rate at which nodes acquire new links. The degree distribution exhibits a multiscaling behavior analogous to the the fitness model. This property is robust with respect to variations in the model, as long as links are assigned through effective preferential attachment. Beyond the degree distribution, in this paper we give a full characterization of the other relevant properties of the model. We evaluate the clustering coefficient and show that it disappears for large network size, a property shared with the Barabási-Albert model. Negative degree correlations are also present in this class of models, along with nontrivial mixing patterns among features. We therefore conclude that both small clustering coefficients and disassortative mixing are outcomes of the preferential attachment mechanism in general growing networks.

  5. String networks with junctions in competition models

    CERN Document Server

    Avelino, P P; Losano, L; Menezes, J; de Oliveira, B F

    2016-01-01

    In this work we give specific examples of competition models, with six and eight species, whose three-dimensional dynamics naturally leads to the formation of string networks with junctions, associated with regions that have a high concentration of enemy species. We study the two- and three-dimensional evolution of such networks, both using stochastic network and mean field theory simulations. If the predation, reproduction and mobility probabilities do not vary in space and time, we find that the networks attain scaling regimes with a characteristic length roughly proportional to $t^{1/2}$, where $t$ is the physical time, thus showing that the presence of junctions, on its own, does not have a significant impact on their scaling properties.

  6. Extracting protein regulatory networks with graphical models.

    Science.gov (United States)

    Grzegorczyk, Marco

    2007-09-01

    During the last decade the development of high-throughput biotechnologies has resulted in the production of exponentially expanding quantities of biological data, such as genomic and proteomic expression data. One fundamental problem in systems biology is to learn the architecture of biochemical pathways and regulatory networks in an inferential way from such postgenomic data. Along with the increasing amount of available data, a lot of novel statistical methods have been developed and proposed in the literature. This article gives a non-mathematical overview of three widely used reverse engineering methods, namely relevance networks, graphical Gaussian models, and Bayesian networks, whereby the focus is on their relative merits and shortcomings. In addition the reverse engineering results of these graphical methods on cytometric protein data from the RAF-signalling network are cross-compared via AUROC scatter plots. PMID:17893851

  7. Mobility Models for Next Generation Wireless Networks Ad Hoc, Vehicular and Mesh Networks

    CERN Document Server

    Santi, Paolo

    2012-01-01

    Mobility Models for Next Generation Wireless Networks: Ad Hoc, Vehicular and Mesh Networks provides the reader with an overview of mobility modelling, encompassing both theoretical and practical aspects related to the challenging mobility modelling task. It also: Provides up-to-date coverage of mobility models for next generation wireless networksOffers an in-depth discussion of the most representative mobility models for major next generation wireless network application scenarios, including WLAN/mesh networks, vehicular networks, wireless sensor networks, and

  8. Unsupervised model compression for multilayer bootstrap networks

    OpenAIRE

    ZHANG, XIAO-LEI

    2015-01-01

    Recently, multilayer bootstrap network (MBN) has demonstrated promising performance in unsupervised dimensionality reduction. It can learn compact representations in standard data sets, i.e. MNIST and RCV1. However, as a bootstrap method, the prediction complexity of MBN is high. In this paper, we propose an unsupervised model compression framework for this general problem of unsupervised bootstrap methods. The framework compresses a large unsupervised bootstrap model into a small model by ta...

  9. A Model for Telestrok Network Evaluation

    DEFF Research Database (Denmark)

    Storm, Anna; Günzel, Franziska; Theiss, Stephan

    2011-01-01

    analysis lacking, current telestroke reimbursement by third-party payers is limited to special contracts and not included in the regular billing system. Based on a systematic literature review and expert interviews with health care economists, third-party payers and neurologists, a Markov model was...... developed from the third-party payer perspective. In principle, it enables telestroke networks to conduct cost-effectiveness studies, because the majority of the required data can be extracted from health insurance companies’ databases and the telestroke network itself. The model presents a basis for...

  10. Mathematical Modelling of Network Traffic

    OpenAIRE

    Li, Yu

    2015-01-01

    ncreasing access to the Internet is producing profound influence around the World. More and more people are taking advantage of the Internet to obtain information, communicate with each other far away and enjoy various recreations. This largely increased demand for the Internet requires better and more effective models. During the 1990s, a number of studies show that due to a different nature from telephonic traffic, in particular a bursty nature, traditional queuing models are not applicable...

  11. The noisy voter model on complex networks

    Science.gov (United States)

    Carro, Adrián; Toral, Raúl; San Miguel, Maxi

    2016-04-01

    We propose a new analytical method to study stochastic, binary-state models on complex networks. Moving beyond the usual mean-field theories, this alternative approach is based on the introduction of an annealed approximation for uncorrelated networks, allowing to deal with the network structure as parametric heterogeneity. As an illustration, we study the noisy voter model, a modification of the original voter model including random changes of state. The proposed method is able to unfold the dependence of the model not only on the mean degree (the mean-field prediction) but also on more complex averages over the degree distribution. In particular, we find that the degree heterogeneity—variance of the underlying degree distribution—has a strong influence on the location of the critical point of a noise-induced, finite-size transition occurring in the model, on the local ordering of the system, and on the functional form of its temporal correlations. Finally, we show how this latter point opens the possibility of inferring the degree heterogeneity of the underlying network by observing only the aggregate behavior of the system as a whole, an issue of interest for systems where only macroscopic, population level variables can be measured.

  12. An evolving model of online bipartite networks

    Science.gov (United States)

    Zhang, Chu-Xu; Zhang, Zi-Ke; Liu, Chuang

    2013-12-01

    Understanding the structure and evolution of online bipartite networks is a significant task since they play a crucial role in various e-commerce services nowadays. Recently, various attempts have been tried to propose different models, resulting in either power-law or exponential degree distributions. However, many empirical results show that the user degree distribution actually follows a shifted power-law distribution, the so-called Mandelbrot’s law, which cannot be fully described by previous models. In this paper, we propose an evolving model, considering two different user behaviors: random and preferential attachment. Extensive empirical results on two real bipartite networks, Delicious and CiteULike, show that the theoretical model can well characterize the structure of real networks for both user and object degree distributions. In addition, we introduce a structural parameter p, to demonstrate that the hybrid user behavior leads to the shifted power-law degree distribution, and the region of power-law tail will increase with the increment of p. The proposed model might shed some lights in understanding the underlying laws governing the structure of real online bipartite networks.

  13. Broadband model of the distribution network

    DEFF Research Database (Denmark)

    Jensen, Martin Høgdahl

    Due to increased interest in the power quality of the distribution network, it is necessary to have an accurate model of the distribution network. One of the commonly used components in the distribution, is the low-voltage four-wire PEX-M-AL distribution cable. There exists no model...... of this component, and it is chosen to focus on the development of such a model. Based on the electromagnetic field equations, the shunt admittance and series impedance parameters of the four-wire cable are derived. The influence of the conductance is considered negligible and is not included in the shunt...... is measured. The measurement are performed with and without the four-wire cable inserted between the transformer and load. The 10 kV test-site is modelled in EMTDC with standard components. Similarly, the non-linear load is modelled as a six-pulse diode bridge loaded with a resistor on the DC...

  14. Ising model on random networks and the canonical tensor model

    International Nuclear Information System (INIS)

    We introduce a statistical system on random networks of trivalent vertices for the purpose of studying the canonical tensor model, which is a rank-three tensor model in the canonical formalism. The partition function of the statistical system has a concise expression in terms of integrals, and has the same symmetries as the kinematical ones of the canonical tensor model. We consider the simplest non-trivial case of the statistical system corresponding to the Ising model on random networks, and find that its phase diagram agrees with what is implied by regrading the Hamiltonian vector field of the canonical tensor model with N=2 as a renormalization group flow. Along the way, we obtain an explicit exact expression of the free energy of the Ising model on random networks in the thermodynamic limit by the Laplace method. This paper provides a new example connecting a model of quantum gravity and a random statistical system

  15. Network Reconstruction with Realistic Models

    OpenAIRE

    Grzegorczyk, Marco; Aderhold, Andrej; Husmeier, Dirk

    2015-01-01

    We extend a recently proposed gradient-matching method for inferring interactions in complex systems described by differential equations in various respects: improved gradient inference, evaluation of the influence of the prior on kinetic parameters, comparative evaluation of two model selection paradigms: marginal likelihood versus DIC (divergence information criterion), comparative evaluation of different numerical procedures for computing the marginal likelihood, extension of the methodolo...

  16. International Trade: a Reinforced Urn Network Model

    CERN Document Server

    Peluso, Stefano; Muliere, Pietro; Lomi, Alessandro

    2016-01-01

    We propose a unified modelling framework that theoretically justifies the main empirical regularities characterizing the international trade network. Each country is associated to a Polya urn whose composition controls the propensity of the country to trade with other countries. The urn composition is updated through the walk of the Reinforced Urn Process of Muliere et al. (2000). The model implies a local preferential attachment scheme and a power law right tail behaviour of bilateral trade flows. Different assumptions on the urns' reinforcement parameters account for local clustering, path-shortening and sparsity. Likelihood-based estimation approaches are facilitated by feasible likelihood analytical derivation in various network settings. A simulated example and the empirical results on the international trade network are discussed.

  17. Delivery Time Reliability Model of Logistics Network

    Directory of Open Access Journals (Sweden)

    Liusan Wu

    2013-01-01

    Full Text Available Natural disasters like earthquake and flood will surely destroy the existing traffic network, usually accompanied by delivery delay or even network collapse. A logistics-network-related delivery time reliability model defined by a shortest-time entropy is proposed as a means to estimate the actual delivery time reliability. The less the entropy is, the stronger the delivery time reliability remains, and vice versa. The shortest delivery time is computed separately based on two different assumptions. If a path is concerned without capacity restriction, the shortest delivery time is positively related to the length of the shortest path, and if a path is concerned with capacity restriction, a minimax programming model is built to figure up the shortest delivery time. Finally, an example is utilized to confirm the validity and practicality of the proposed approach.

  18. Exhaustive Search for Fuzzy Gene Networks from Microarray Data

    Energy Technology Data Exchange (ETDEWEB)

    Sokhansanj, B A; Fitch, J P; Quong, J N; Quong, A A

    2003-07-07

    Recent technological advances in high-throughput data collection allow for the study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are required to interpret large and complex data sets. Rationally designed system perturbations (e.g. gene knock-outs, metabolite removal, etc) can be used to iteratively refine hypothetical models, leading to a modeling-experiment cycle for high-throughput biological system analysis. We use fuzzy logic gene network models because they have greater resolution than Boolean logic models and do not require the precise parameter measurement needed for chemical kinetics-based modeling. The fuzzy gene network approach is tested by exhaustive search for network models describing cyclin gene interactions in yeast cell cycle microarray data, with preliminary success in recovering interactions predicted by previous biological knowledge and other analysis techniques. Our goal is to further develop this method in combination with experiments we are performing on bacterial regulatory networks.

  19. Bayesian Network Based XP Process Modelling

    Directory of Open Access Journals (Sweden)

    Mohamed Abouelela

    2010-07-01

    Full Text Available A Bayesian Network based mathematical model has been used for modelling Extreme Programmingsoftware development process. The model is capable of predicting the expected finish time and theexpected defect rate for each XP release. Therefore, it can be used to determine the success/failure of anyXP Project. The model takes into account the effect of three XP practices, namely: Pair Programming,Test Driven Development and Onsite Customer practices. The model’s predictions were validated againsttwo case studies. Results show the precision of our model especially in predicting the project finish time.

  20. Modeling the Pro-inflammatory Tumor Microenvironment in Acute Lymphoblastic Leukemia Predicts a Breakdown of Hematopoietic-Mesenchymal Communication Networks

    Science.gov (United States)

    Enciso, Jennifer; Mayani, Hector; Mendoza, Luis; Pelayo, Rosana

    2016-01-01

    Lineage fate decisions of hematopoietic cells depend on intrinsic factors and extrinsic signals provided by the bone marrow microenvironment, where they reside. Abnormalities in composition and function of hematopoietic niches have been proposed as key contributors of acute lymphoblastic leukemia (ALL) progression. Our previous experimental findings strongly suggest that pro-inflammatory cues contribute to mesenchymal niche abnormalities that result in maintenance of ALL precursor cells at the expense of normal hematopoiesis. Here, we propose a molecular regulatory network interconnecting the major communication pathways between hematopoietic stem and progenitor cells (HSPCs) and mesenchymal stromal cells (MSCs) within the BM. Dynamical analysis of the network as a Boolean model reveals two stationary states that can be interpreted as the intercellular contact status. Furthermore, simulations describe the molecular patterns observed during experimental proliferation and activation. Importantly, our model predicts instability in the CXCR4/CXCL12 and VLA4/VCAM1 interactions following microenvironmental perturbation due by temporal signaling from Toll like receptors (TLRs) ligation. Therefore, aberrant expression of NF-κB induced by intrinsic or extrinsic factors may contribute to create a tumor microenvironment where a negative feedback loop inhibiting CXCR4/CXCL12 and VLA4/VCAM1 cellular communication axes allows for the maintenance of malignant cells. PMID:27594840

  1. Boolean approaches to graph embeddings related to VLSI

    Institute of Scientific and Technical Information of China (English)

    刘彦佩

    2001-01-01

    This paper discusses the development of Boolean methods in some topics on graph em-beddings which are related to VLSI. They are mainly the general theory of graph embeddability, the orientabilities of a graph and the rectilinear layout of an electronic circuit.

  2. On the Road to Genetic Boolean Matrix Factorization

    Czech Academy of Sciences Publication Activity Database

    Snášel, V.; Platoš, J.; Krömer, P.; Húsek, Dušan; Frolov, A.

    2007-01-01

    Roč. 17, č. 6 (2007), s. 675-688. ISSN 1210-0552 Institutional research plan: CEZ:AV0Z10300504 Keywords : data mining * genetic algorithms * Boolean factorization * binary data * machine learning * feature extraction Subject RIV: IN - Informatics, Computer Science Impact factor: 0.280, year: 2007

  3. On the Road to Genetic Boolean Matrix Factorization

    Czech Academy of Sciences Publication Activity Database

    Snášel, V.; Platoš, J.; Krömer, P.; Húsek, Dušan; Frolov, A.

    2007-01-01

    Roč. 17, č. 6 (2007), s. 675-688. ISSN 1210-0552 Institutional research plan: CEZ:AV0Z10300504 Keywords : data mining * genetic algorithm s * Boolean factorization * binary data * machine learning * feature extraction Subject RIV: IN - Informatics, Computer Science Impact factor: 0.280, year: 2007

  4. Boolean linear differential operators on elementary cellular automata

    Science.gov (United States)

    Martín Del Rey, Ángel

    2014-12-01

    In this paper, the notion of boolean linear differential operator (BLDO) on elementary cellular automata (ECA) is introduced and some of their more important properties are studied. Special attention is paid to those differential operators whose coefficients are the ECA with rule numbers 90 and 150.

  5. Pointwise Approximation for the Iterated Boolean Sums of Bernstein Operators

    Institute of Scientific and Technical Information of China (English)

    HUO Xiao-yan; LI Cui-xiang; YAO Qiu-mei

    2013-01-01

    In this paper,with the help of modulus of smoothness ω2r(4)(f,t),we discuss the pointwise approximation properties for the iterated Boolean sums of Bernstein operator Bnn and obtain direct and inverse theorems when 1-1/r ≤ λ ≤ 1,r ∈ N.

  6. Constant-overhead secure computation of Boolean circuits using preprocessing

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre; Zakarias, S.

    2013-01-01

    We present a protocol for securely computing a Boolean circuit C in presence of a dishonest and malicious majority. The protocol is unconditionally secure, assuming a preprocessing functionality that is not given the inputs. For a large number of players the work for each player is the same as...

  7. New Considerations for Spectral Classification of Boolean Switching Functions

    Directory of Open Access Journals (Sweden)

    J. E. Rice

    2011-01-01

    Full Text Available This paper presents some new considerations for spectral techniques for classification of Boolean functions. These considerations incorporate discussions of the feasibility of extending this classification technique beyond n=5. A new implementation is presented along with a basic analysis of the complexity of the problem. We also note a correction to results in this area that were reported in previous work.

  8. Graphical interpretation of Boolean operators for protein NMR assignments

    NARCIS (Netherlands)

    Verdegem, Dries; Dijkstra, Klaas; Hanoulle, Xavier; Lippens, Guy

    2008-01-01

    We have developed a graphics based algorithm for semi-automated protein NMR assignments. Using the basic sequential triple resonance assignment strategy, the method is inspired by the Boolean operators as it applies "AND"-, "OR"- and "NOT"-like operations on planes pulled out of the classical three-

  9. On the Prime Whales of a Boolean Algebra

    OpenAIRE

    Holland, Jason

    2013-01-01

    In this note, we introduce objects called prime whales and use them to represent a Boolean algebra as an algebra of sets in a way that is analogous to Stone's Representation Theorem. We also characterize the existence of prime whales in terms of the existence of prime ideals.

  10. Keystone Business Models for Network Security Processors

    Directory of Open Access Journals (Sweden)

    Arthur Low

    2013-07-01

    Full Text Available Network security processors are critical components of high-performance systems built for cybersecurity. Development of a network security processor requires multi-domain experience in semiconductors and complex software security applications, and multiple iterations of both software and hardware implementations. Limited by the business models in use today, such an arduous task can be undertaken only by large incumbent companies and government organizations. Neither the “fabless semiconductor” models nor the silicon intellectual-property licensing (“IP-licensing” models allow small technology companies to successfully compete. This article describes an alternative approach that produces an ongoing stream of novel network security processors for niche markets through continuous innovation by both large and small companies. This approach, referred to here as the "business ecosystem model for network security processors", includes a flexible and reconfigurable technology platform, a “keystone” business model for the company that maintains the platform architecture, and an extended ecosystem of companies that both contribute and share in the value created by innovation. New opportunities for business model innovation by participating companies are made possible by the ecosystem model. This ecosystem model builds on: i the lessons learned from the experience of the first author as a senior integrated circuit architect for providers of public-key cryptography solutions and as the owner of a semiconductor startup, and ii the latest scholarly research on technology entrepreneurship, business models, platforms, and business ecosystems. This article will be of interest to all technology entrepreneurs, but it will be of particular interest to owners of small companies that provide security solutions and to specialized security professionals seeking to launch their own companies.

  11. Psychometric Measurement Models and Artificial Neural Networks

    Science.gov (United States)

    Sese, Albert; Palmer, Alfonso L.; Montano, Juan J.

    2004-01-01

    The study of measurement models in psychometrics by means of dimensionality reduction techniques such as Principal Components Analysis (PCA) is a very common practice. In recent times, an upsurge of interest in the study of artificial neural networks apt to computing a principal component extraction has been observed. Despite this interest, the…

  12. The Kuramoto model in complex networks

    Science.gov (United States)

    Rodrigues, Francisco A.; Peron, Thomas K. DM.; Ji, Peng; Kurths, Jürgen

    2016-01-01

    Synchronization of an ensemble of oscillators is an emergent phenomenon present in several complex systems, ranging from social and physical to biological and technological systems. The most successful approach to describe how coherent behavior emerges in these complex systems is given by the paradigmatic Kuramoto model. This model has been traditionally studied in complete graphs. However, besides being intrinsically dynamical, complex systems present very heterogeneous structure, which can be represented as complex networks. This report is dedicated to review main contributions in the field of synchronization in networks of Kuramoto oscillators. In particular, we provide an overview of the impact of network patterns on the local and global dynamics of coupled phase oscillators. We cover many relevant topics, which encompass a description of the most used analytical approaches and the analysis of several numerical results. Furthermore, we discuss recent developments on variations of the Kuramoto model in networks, including the presence of noise and inertia. The rich potential for applications is discussed for special fields in engineering, neuroscience, physics and Earth science. Finally, we conclude by discussing problems that remain open after the last decade of intensive research on the Kuramoto model and point out some promising directions for future research.

  13. Green Network Planning Model for Optical Backbones

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Jensen, Michael;

    2010-01-01

    Communication networks are becoming more essential for our daily lives and critically important for industry and governments. The intense growth in the backbone traffic implies an increment of the power demands of the transmission systems. This power usage might have a significant negative effect...... an analytical model to consider environmental aspects in the planning stage of backbones design....

  14. A spatial model for social networks

    OpenAIRE

    Wong, Ling Heng; Pattison, Philippa; Robins, Garry

    2005-01-01

    We study spatial embeddings of random graphs in which nodes are randomly distributed in geographical space. We let the edge probability between any two nodes to be dependent on the spatial distance between them and demonstrate that this model captures many generic properties of social networks, including the ``small-world'' properties, skewed degree distribution, and most distinctively the existence of community structures.

  15. A Model of Mental State Transition Network

    Science.gov (United States)

    Xiang, Hua; Jiang, Peilin; Xiao, Shuang; Ren, Fuji; Kuroiwa, Shingo

    Emotion is one of the most essential and basic attributes of human intelligence. Current AI (Artificial Intelligence) research is concentrating on physical components of emotion, rarely is it carried out from the view of psychology directly(1). Study on the model of artificial psychology is the first step in the development of human-computer interaction. As affective computing remains unpredictable, creating a reasonable mental model becomes the primary task for building a hybrid system. A pragmatic mental model is also the fundament of some key topics such as recognition and synthesis of emotions. In this paper a Mental State Transition Network Model(2) is proposed to detect human emotions. By a series of psychological experiments, we present a new way to predict coming human's emotions depending on the various current emotional states under various stimuli. Besides, people in different genders and characters are taken into consideration in our investigation. According to the psychological experiments data derived from 200 questionnaires, a Mental State Transition Network Model for describing the transitions in distribution among the emotions and relationships between internal mental situations and external are concluded. Further more the coefficients of the mental transition network model were achieved. Comparing seven relative evaluating experiments, an average precision rate of 0.843 is achieved using a set of samples for the proposed model.

  16. Unified Model for Generation Complex Networks with Utility Preferential Attachment

    Institute of Scientific and Technical Information of China (English)

    WU Jian-Jun; GAO Zi-You; SUN Hui-Jun

    2006-01-01

    In this paper, based on the utility preferential attachment, we propose a new unified model to generate different network topologies such as scale-free, small-world and random networks. Moreover, a new network structure named super scale network is found, which has monopoly characteristic in our simulation experiments. Finally, the characteristics ofthis new network are given.

  17. Network Coding Capacity of Random Wireless Networks under a SINR Model

    OpenAIRE

    Kong, Zhenning; Aly, Salah A.; Soljanin, Emina; Yeh, Edmund M.; Klappenecker, Andreas

    2008-01-01

    Previous work on network coding capacity for random wired and wireless networks have focused on the case where the capacities of links in the network are independent. In this paper, we consider a more realistic model, where wireless networks are modelled by random geometric graphs with interference and noise. In this model, the capacities of links are not independent. By employing coupling and martingale methods, we show that, under mild conditions, the network coding capacity for random wire...

  18. Distributed Bayesian Networks for User Modeling

    DEFF Research Database (Denmark)

    Tedesco, Roberto; Dolog, Peter; Nejdl, Wolfgang;

    2006-01-01

    The World Wide Web is a popular platform for providing eLearning applications to a wide spectrum of users. However – as users differ in their preferences, background, requirements, and goals – applications should provide personalization mechanisms. In the Web context, user models used by such...... adaptive applications are often partial fragments of an overall user model. The fragments have then to be collected and merged into a global user profile. In this paper we investigate and present algorithms able to cope with distributed, fragmented user models – based on Bayesian Networks – in the context...... mechanism efficiently combines distributed learner models without the need to exchange internal structure of local Bayesian networks, nor local evidence between the involved platforms....

  19. Hybrid simulation models of production networks

    CERN Document Server

    Kouikoglou, Vassilis S

    2001-01-01

    This book is concerned with a most important area of industrial production, that of analysis and optimization of production lines and networks using discrete-event models and simulation. The book introduces a novel approach that combines analytic models and discrete-event simulation. Unlike conventional piece-by-piece simulation, this method observes a reduced number of events between which the evolution of the system is tracked analytically. Using this hybrid approach, several models are developed for the analysis of production lines and networks. The hybrid approach combines speed and accuracy for exceptional analysis of most practical situations. A number of optimization problems, involving buffer design, workforce planning, and production control, are solved through the use of hybrid models.

  20. Exponential Separation of Quantum and Classical One-Way Communication Complexity for a Boolean Function

    CERN Document Server

    Gavinsky, D; Kempe, J; Gavinsky, Dmitry; Kempe, Julia; Wolf, Ronald de

    2006-01-01

    We give an exponential separation between one-way quantum and classical communication complexity for a Boolean function. Earlier such a separation was known only for a relation. A very similar result was obtained earlier but independently by Kerenidis and Raz [KR06]. Our version of the result gives an example in the bounded storage model of cryptography, where the key is secure if the adversary has a certain amount of classical storage, but is completely insecure if he has a similar amount of quantum storage.

  1. XY model in small-world networks

    OpenAIRE

    Kim, Beom Jun; Hong, H.; Holme, Petter; Jeon, Gun Sang; Minnhagen, Petter; Choi, M. Y.

    2001-01-01

    The phase transition in the XY model on one-dimensional small-world networks is investigated by means of Monte-Carlo simulations. It is found that long-range order is present at finite temperatures, even for very small values of the rewiring probability, suggesting a finite-temperature transition for any nonzero rewiring probability. Nature of the phase transition is discussed in comparison with the globally-coupled XY model.

  2. Modeling Multistandard Wireless Networks in OPNET

    DEFF Research Database (Denmark)

    Zakrzewska, Anna; Berger, Michael Stübert; Ruepp, Sarah Renée

    2011-01-01

    Future wireless communication is emerging towards one heterogeneous platform. In this new environment wireless access will be provided by multiple radio technologies that are cooperating and complementing one another. The paper investigates the possibilities of developing such a multistandard...... system using OPNET Modeler. A network model consisting of LTE interworking with WLAN and WiMAX is considered from the radio resource management perspective. In particular, implementing a joint packet scheduler across multiple systems is discussed more in detail....

  3. Constructing a fish metabolic network model

    OpenAIRE

    Li, S.; Pozhitkov, A.; R. Ryan; Manning, C; Brown-Peterson, N.; Brouwer, M

    2010-01-01

    We report the construction of a genome-wide fish metabolic network model, MetaFishNet, and its application to analyzing high throughput gene expression data. This model is a stepping stone to broader applications of fish systems biology, for example by guiding study design through comparison with human metabolism and the integration of multiple data types. MetaFishNet resources, including a pathway enrichment analysis tool, are accessible at http://metafishnet.appspot.com.

  4. Distance distribution in configuration-model networks

    Science.gov (United States)

    Nitzan, Mor; Katzav, Eytan; Kühn, Reimer; Biham, Ofer

    2016-06-01

    We present analytical results for the distribution of shortest path lengths between random pairs of nodes in configuration model networks. The results, which are based on recursion equations, are shown to be in good agreement with numerical simulations for networks with degenerate, binomial, and power-law degree distributions. The mean, mode, and variance of the distribution of shortest path lengths are also evaluated. These results provide expressions for central measures and dispersion measures of the distribution of shortest path lengths in terms of moments of the degree distribution, illuminating the connection between the two distributions.

  5. Bus Network Modeling Using Ant Algorithms

    Directory of Open Access Journals (Sweden)

    Sepideh Eshragh

    2010-02-01

    Full Text Available Bus transit network modeling is a complex and combinatorial problem. The main purpose of this paper is to apply a contemporary method for designing a bus transit network with the objective of achieving optimum results. The method is called Ant Algorithms, a Meta Heuristic method, which has been applied to optimization problems in transportation with noticeable success. The description of the algorithm, as well as the main methodology and computations, is presented in this paper. Furthermore, a case study using Ant Algorithms applied to the city of Ghazvin, one of the most important suburbs of Tehran, Iran, is presented.

  6. Adaptive-network models of swarm dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Huepe, Cristian [614 N Paulina Street, Chicago, IL 60622-6062 (United States); Zschaler, Gerd; Do, Anne-Ly; Gross, Thilo, E-mail: cristian@northwestern.edu [Max-Planck-Institut fuer Physik komplexer Systeme, Noethnitzer Strasse 38, 01187 Dresden (Germany)

    2011-07-15

    We propose a simple adaptive-network model describing recent swarming experiments. Exploiting an analogy with human decision making, we capture the dynamics of the model using a low-dimensional system of equations permitting analytical investigation. We find that the model reproduces several characteristic features of swarms, including spontaneous symmetry breaking, noise- and density-driven order-disorder transitions that can be of first or second order, and intermittency. Reproducing these experimental observations using a non-spatial model suggests that spatial geometry may have less of an impact on collective motion than previously thought.

  7. Adaptive-network models of swarm dynamics

    International Nuclear Information System (INIS)

    We propose a simple adaptive-network model describing recent swarming experiments. Exploiting an analogy with human decision making, we capture the dynamics of the model using a low-dimensional system of equations permitting analytical investigation. We find that the model reproduces several characteristic features of swarms, including spontaneous symmetry breaking, noise- and density-driven order-disorder transitions that can be of first or second order, and intermittency. Reproducing these experimental observations using a non-spatial model suggests that spatial geometry may have less of an impact on collective motion than previously thought.

  8. Dynamical Analysis of Protein Regulatory Network in Budding Yeast Nucleus

    Institute of Scientific and Technical Information of China (English)

    LI Fang-Ting; JIA Xun

    2006-01-01

    @@ Recent progresses in the protein regulatory network of budding yeast Saccharomyces cerevisiae have provided a global picture of its protein network for further dynamical research. We simplify and modularize the protein regulatory networks in yeast nucleus, and study the dynamical properties of the core 37-node network by a Boolean network model, especially the evolution steps and final fixed points. Our simulation results show that the number of fixed points N(k) for a given size of the attraction basin k obeys a power-law distribution N(k)∝k-2.024. The yeast network is more similar to a scale-free network than a random network in the above dynamical properties.

  9. Channel models for wireless body area networks.

    Science.gov (United States)

    Takizawa, Kenichi; Aoyagi, Akahiro; Takada, Jun-Ichi; Katayama, Norihiko; Yekeh, Kamya; Takehiko, Yazdandoost; Kohno, Kobayashi Ryuji

    2008-01-01

    Wireless patient monitoring using wearable sensors is a promising application. This paper provides stochastic channel models for wireless body area network (WBAN) on the human body. Parameters of the channel models are extracted from measured channel transfer functions (CTFs) in a hospital room. Measured frequency bands are selected so as to include permissible bands for WBAN; ultra wideband (UWB), the industry, science and medical (ISM) bands, and wireless medical telemetry system (WMTS) bands. As channel models, both a path loss model and a power delay profile (PDP) model are considered. But, even though path loss models are derived for the all frequency bands, PDP model is only for the UWB band due to the highly frequency selectiveness of UWB channels. The parameters extracted from the measurement results are summarized for each channel model. PMID:19162968

  10. Spatial Models and Networks of Living Systems

    DEFF Research Database (Denmark)

    Juul, Jeppe Søgaard

    When studying the dynamics of living systems, insight can often be gained by developing a mathematical model that can predict future behaviour of the system or help classify system characteristics. However, in living cells, organisms, and especially groups of interacting individuals, a large number...... species. Such systems are known to be stabilized by spatial structure. Finally, I analyse data from a large mobile phone network and show that people who are topologically close in the network have similar communication patterns. This main part of the thesis is based on six different articles, which I...... have co-authored during my three year PhD at the Center for Models of Life. Apart from these, I have co-authored another six articles, which also relate to spatial models of living systems. These are included as appendixes, but not described in detail in the thesis....

  11. Higher-dimensional models of networks

    CERN Document Server

    Spivak, David I

    2009-01-01

    Networks are often studied as graphs, where the vertices stand for entities in the world and the edges stand for connections between them. While relatively easy to study, graphs are often inadequate for modeling real-world situations, especially those that include contexts of more than two entities. For these situations, one typically uses hypergraphs or simplicial complexes. In this paper, we provide a precise framework in which graphs, hypergraphs, simplicial complexes, and many other categories, all of which model higher graphs, can be studied side-by-side. We show how to transform a hypergraph into its nearest simplicial analogue, for example. Our framework includes many new categories as well, such as one that models broadcasting networks. We give several examples and applications of these ideas.

  12. KSC Centralized Index Model in Complex Network

    Directory of Open Access Journals (Sweden)

    Jian Xu

    2014-05-01

    Full Text Available To dig potential spread nodes in a complex network mainly relies on using centralized indicators such as the node degree, closeness, betweenness and K-shell to evaluate spread node, which causes that the excavation accuracy is not high and adaptability not strong and induces other shortcomings, therefore this paper proposes KSC of centering indicator model. This model not only considers the internal attributes of nodes, but also takes the external attributes of nodes into account, and it finally conducts simulation experiments on propagation through the use of SIR model. The experimental results show that: The proposed algorithm is suitable for a variety of complex networks and it finds better, more promising and more influential dissemination nodes.

  13. Design and Implementation of a Network Security Model for Cooperative Network

    OpenAIRE

    Salah Alabady

    2009-01-01

    In this paper a design and implementation of a network security model was presented, using routers and firewall.Also this paper was conducted the network security weakness in router and firewall network devices, type of threats andresponses to those threats, and the method to prevent the attacks and hackers to access the network. Also this paper provides achecklist to use in evaluating whether a network is adhering to best practices in network security and data confidentiality. Themain aim of...

  14. The noisy voter model on complex networks

    CERN Document Server

    Carro, Adrián; Miguel, Maxi San

    2016-01-01

    We propose a new analytical method to study stochastic, binary-state models on complex networks. Moving beyond the usual mean-field theories, this alternative approach is based on the introduction of an uncorrelated network approximation, allowing to deal with the network structure as parametric heterogeneity. As an illustration, we study the noisy voter model, a modification of the original voter model including random changes of state. The proposed method is able to unfold the dependence of the model not only on the mean degree (the mean-field prediction) but also on more complex averages over the degree distribution. In particular, we find that the degree heterogeneity ---variance of the underlying degree distribution--- has a strong influence on the location of the critical point of a noise-induced, finite-size transition occurring in the model, on the local ordering of the system, and on the functional form of its temporal correlations. Finally, we show how this latter point opens the possibility of infe...

  15. Classes of feedforward neural networks and their circuit complexity

    OpenAIRE

    Shawe-Taylor, John S.; Anthony, Martin H.G.; Kern, Walter

    1992-01-01

    This paper aims to place neural networks in the context of boolean circuit complexity. We define appropriate classes of feedforward neural networks with specified fan-in, accuracy of computation and depth and using techniques of communication complexity proceed to show that the classes fit into a well-studied hierarchy of boolean circuits. Results cover both classes of sigmoid activation function networks and linear threshold networks. This provides a much needed theoretical basis for the stu...

  16. Features and heterogeneities in growing network models

    CERN Document Server

    Ferretti, Luca; Yang, Bin; Marmorini, Giacomo; Bianconi, Ginestra

    2011-01-01

    Many complex networks from the World-Wide-Web to biological networks are growing taking into account the heterogeneous features of the nodes. The feature of a node might be a discrete quantity such as a classification of a URL document as personal page, thematic website, news, blog, search engine, social network, ect. or the classification of a gene in a functional module. Moreover the feature of a node can be a continuous variable such as the position of a node in the embedding space. In order to account for these properties, in this paper we provide a generalization of growing network models with preferential attachment that includes the effect of heterogeneous features of the nodes. The main effect of heterogeneity is the emergence of an "effective fitness" for each class of nodes, determining the rate at which nodes acquire new links. Beyond the degree distribution, in this paper we give a full characterization of the other relevant properties of the model. We evaluate the clustering coefficient and show ...

  17. Performance modeling, loss networks, and statistical multiplexing

    CERN Document Server

    Mazumdar, Ravi

    2009-01-01

    This monograph presents a concise mathematical approach for modeling and analyzing the performance of communication networks with the aim of understanding the phenomenon of statistical multiplexing. The novelty of the monograph is the fresh approach and insights provided by a sample-path methodology for queueing models that highlights the important ideas of Palm distributions associated with traffic models and their role in performance measures. Also presented are recent ideas of large buffer, and many sources asymptotics that play an important role in understanding statistical multiplexing. I

  18. Relativistic Computing Model Applied in Corporate Networks

    Directory of Open Access Journals (Sweden)

    Chau Sen Shia*1,

    2014-05-01

    Full Text Available Environmental computing information technology (it is one of the subjects of interest for organizations when the subject covers financial economics and return on investment for companies. This work aims to present as a contribution proposing a relativistic model of computation using the relativistic physics concepts and foundations of quantum mechanics to propose a new vision in the use of virtualization environment in corporate networks. The model was based on simulation and testing of connection with providers in virtualization environments with Datacenters and implementing the basics of relativity and quantum mechanics in communication with networks of companies, to establish alliances and resource sharing between organizations. The data were collected and then were performed calculations that demonstrate and identify connections and integrations that establish relations of cloud computing with the relativistic vision, in such a way that complement the approaches of physics and computing with the theories of the magnetic field and the propagation of light. The research is characterized as exploratory, because searches check physical connections with cloud computing, the network of companies and the adhesion of the proposed model. Were presented the relationship between the proposal and the practical application that makes it possible to describe the results of the main features, demonstrating the relativistic model integration with new technologies of virtualization of Datacenters, and optimize the resource with the propagation of light, electromagnetic waves, simultaneity, length contraction and time dilation

  19. Artificial Neural Network Model for Predicting Compressive

    Directory of Open Access Journals (Sweden)

    Salim T. Yousif

    2013-05-01

    Full Text Available   Compressive strength of concrete is a commonly used criterion in evaluating concrete. Although testing of the compressive strength of concrete specimens is done routinely, it is performed on the 28th day after concrete placement. Therefore, strength estimation of concrete at early time is highly desirable. This study presents the effort in applying neural network-based system identification techniques to predict the compressive strength of concrete based on concrete mix proportions, maximum aggregate size (MAS, and slump of fresh concrete. Back-propagation neural networks model is successively developed, trained, and tested using actual data sets of concrete mix proportions gathered from literature.    The test of the model by un-used data within the range of input parameters shows that the maximum absolute error for model is about 20% and 88% of the output results has absolute errors less than 10%. The parametric study shows that water/cement ratio (w/c is the most significant factor  affecting the output of the model.     The results showed that neural networks has strong potential as a feasible tool for predicting compressive strength of concrete.

  20. Networks in Cell Biology = Modelling cell biology with networks

    OpenAIRE

    Buchanan, Mark; Caldarelli, Guido; De Los Rios, Paolo; Rao, Francesco; Vendruscolo, M.

    2010-01-01

    The science of complex biological networks is transforming research in areas ranging from evolutionary biology to medicine. This is the first book on the subject, providing a comprehensive introduction to complex network science and its biological applications. With contributions from key leaders in both network theory and modern cell biology, this book discusses the network science that is increasingly foundational for systems biology and the quantitative understanding of living systems. It ...

  1. Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape.

    Directory of Open Access Journals (Sweden)

    Elena R Alvarez-Buylla

    Full Text Available In contrast to the classical view of development as a preprogrammed and deterministic process, recent studies have demonstrated that stochastic perturbations of highly non-linear systems may underlie the emergence and stability of biological patterns. Herein, we address the question of whether noise contributes to the generation of the stereotypical temporal pattern in gene expression during flower development. We modeled the regulatory network of organ identity genes in the Arabidopsis thaliana flower as a stochastic system. This network has previously been shown to converge to ten fixed-point attractors, each with gene expression arrays that characterize inflorescence cells and primordial cells of sepals, petals, stamens, and carpels. The network used is binary, and the logical rules that govern its dynamics are grounded in experimental evidence. We introduced different levels of uncertainty in the updating rules of the network. Interestingly, for a level of noise of around 0.5-10%, the system exhibited a sequence of transitions among attractors that mimics the sequence of gene activation configurations observed in real flowers. We also implemented the gene regulatory network as a continuous system using the Glass model of differential equations, that can be considered as a first approximation of kinetic-reaction equations, but which are not necessarily equivalent to the Boolean model. Interestingly, the Glass dynamics recover a temporal sequence of attractors, that is qualitatively similar, although not identical, to that obtained using the Boolean model. Thus, time ordering in the emergence of cell-fate patterns is not an artifact of synchronous updating in the Boolean model. Therefore, our model provides a novel explanation for the emergence and robustness of the ubiquitous temporal pattern of floral organ specification. It also constitutes a new approach to understanding morphogenesis, providing predictions on the population dynamics of

  2. Air pollution model and neural network: an integrated modelling system

    International Nuclear Information System (INIS)

    It is well known that neural networks can work as universal approximators of non-linear functions and they have become a useful tool either where any precise phenomenological model is available or when uncertainty complicates the application of deterministic modelling as, for example, in environmental systems. Usually, N N models are using as regression tool. We have developed an integrated modelling system coupling an air dispersion model with a neural network method both to simulate the influence of important parameters on air pollution models and to minimize the input neural net variables. In our approach, an optimised 3-Layer Perception is used to filter the air pollution concentrations evaluated by means of the non-Gaussian analytical model ADMD. We applied this methodology to the well known Indianapolis urban data set which deals with a release of pollutants from an elevated emission source.

  3. New Federated Collaborative Networked Organization Model (FCNOM

    Directory of Open Access Journals (Sweden)

    Morcous M. Yassa

    2012-01-01

    Full Text Available Formation of Collaborative Networked Organization (CNO usually comes upon expected business opportunities and needs huge of negotiation during its lifecycle, especially to increase the Dynamic Virtual Organization (DVO configuration automation. Decision makers need more comprehensive information about CNO system to support their decisions. Unfortunately, there is no single formal modeling, tool, approach or any comprehensive methodology that covers all perspectives. In spite of there are some approaches to model CNO have been existed, these approaches model the CNO either with respect to the technology, or business without considering organizational behavior, federation modeling, and external environments. The aim of this paper is to propose an integrated framework that combines the existed modeling perspectives, as well as, proposes new ones. Also, it provides clear CNO boundaries. By using this approach the view of CNO environment becomes clear and unified. Also, it minimizes the negotiations within CNO components during its life cycle, supports DVO configuration automation, as well as, helps decision making for DVO, and achieves harmonization between CNO partners. The proposed FCNOM utilizes CommonKADS methodology organization model for describing CNO components. Insurance Collaborative Network has been used as an example to proof the proposed FCNOM model.

  4. Modeling In-Network Aggregation in VANETs

    NARCIS (Netherlands)

    Dietzel, Stefan; Kargl, Frank; Heijenk, Geert; Schaub, Florian

    2011-01-01

    The multitude of applications envisioned for vehicular ad hoc networks requires efficient communication and dissemination mechanisms to prevent network congestion. In-network data aggregation promises to reduce bandwidth requirements and enable scalability in large vehicular networks. However, most

  5. Reliable Communication Models in Interdependent Critical Infrastructure Networks

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sangkeun (Matt) [ORNL; Chinthavali, Supriya [ORNL; Shankar, Mallikarjun [ORNL

    2016-01-01

    Modern critical infrastructure networks are becoming increasingly interdependent where the failures in one network may cascade to other dependent networks, causing severe widespread national-scale failures. A number of previous efforts have been made to analyze the resiliency and robustness of interdependent networks based on different models. However, communication network, which plays an important role in today's infrastructures to detect and handle failures, has attracted little attention in the interdependency studies, and no previous models have captured enough practical features in the critical infrastructure networks. In this paper, we study the interdependencies between communication network and other kinds of critical infrastructure networks with an aim to identify vulnerable components and design resilient communication networks. We propose several interdependency models that systematically capture various features and dynamics of failures spreading in critical infrastructure networks. We also discuss several research challenges in building reliable communication solutions to handle failures in these models.

  6. Centralized Bayesian reliability modelling with sensor networks

    Czech Academy of Sciences Publication Activity Database

    Dedecius, Kamil; Sečkárová, Vladimíra

    2013-01-01

    Roč. 19, č. 5 (2013), s. 471-482. ISSN 1387-3954 R&D Projects: GA MŠk 7D12004 Grant ostatní: GA MŠk(CZ) SVV-265315 Keywords : Bayesian modelling * Sensor network * Reliability Subject RIV: BD - Theory of Information Impact factor: 0.984, year: 2013 http://library.utia.cas.cz/separaty/2013/AS/dedecius-0392551.pdf

  7. Bayesian Network Models for Adaptive Testing

    Czech Academy of Sciences Publication Activity Database

    Plajner, Martin; Vomlel, Jiří

    Achen: Sun SITE Central Europe, 2016 - (Agosta, J.; Carvalho, R.), s. 24-33. (CEUR Workshop Proceedings. Vol 1565). ISSN 1613-0073. [The Twelfth UAI Bayesian Modeling Applications Workshop (BMAW 2015). Amsterdam (NL), 16.07.2015] R&D Projects: GA ČR GA13-20012S Institutional support: RVO:67985556 Keywords : Bayesian networks * Computerized adaptive testing Subject RIV: JD - Computer Applications, Robotics http://library.utia.cas.cz/separaty/2016/MTR/plajner-0458062.pdf

  8. The Channel Network model and field applications

    International Nuclear Information System (INIS)

    The Channel Network model describes the fluid flow and solute transport in fractured media. The model is based on field observations, which indicate that flow and transport take place in a three-dimensional network of connected channels. The channels are generated in the model from observed stochastic distributions and solute transport is modeled taking into account advection and rock interactions, such as matrix diffusion and sorption within the rock. The most important site-specific data for the Channel Network model are the conductance distribution of the channels and the flow-wetted surface. The latter is the surface area of the rock in contact with the flowing water. These parameters may be estimated from hydraulic measurements. For the Aespoe site, several borehole data sets are available, where a packer distance of 3 meters was used. Numerical experiments were performed in order to study the uncertainties in the determination of the flow-wetted surface and conductance distribution. Synthetic data were generated along a borehole and hydraulic tests with different packer distances were simulated. The model has previously been used to study the Long-term Pumping and Tracer Test (LPT2) carried out in the Aespoe Hard Rock Laboratory (HRL) in Sweden, where the distance travelled by the tracers was of the order hundreds of meters. Recently, the model has been used to simulate the tracer tests performed in the TRUE experiment at HRL, with travel distance of the order of tens of meters. Several tracer tests with non-sorbing and sorbing species have been performed

  9. A proposed "osi based" network troubles identification model

    OpenAIRE

    Murat Kayri; Ismail Kayri

    2010-01-01

    The OSI model, developed by ISO in 1984, attempts to summarize complicated network cases on layers. Moreover, network troubles are expressed by taking the model into account. However, there has been no standardization for network troubles up to now. Network troubles have only been expressed by the name of the related layer. In this paper, it is pointed out that possible troubles on the related layer vary and possible troubles on each layer are categorized for functional network administration...

  10. A proposed "osi based" network troubles identification model

    CERN Document Server

    Kayri, Murat; 10.5121/ijngn.2010.2302

    2010-01-01

    The OSI model, developed by ISO in 1984, attempts to summarize complicated network cases on layers. Moreover, network troubles are expressed by taking the model into account. However, there has been no standardization for network troubles up to now. Network troubles have only been expressed by the name of the related layer. In this paper, it is pointed out that possible troubles on the related layer vary and possible troubles on each layer are categorized for functional network administration and they are standardized in an eligible way. The proposed model for network trouble shooting was developed considering the OSI model.

  11. Nonequilibrium Zaklan model on Apollonian Networks

    CERN Document Server

    Lima, F W S

    2012-01-01

    The Zaklan model had been proposed and studied recently using the equilibrium Ising model on Square Lattices (SL) by Zaklan et al (2008), near the critical temperature of the Ising model presenting a well-defined phase transition; but on normal and modified Apollonian networks (ANs), Andrade et al. (2005, 2009) studied the equilibrium Ising model. They showed the equilibrium Ising model not to present on ANs a phase transition of the type for the 2D Ising model. Here, within the context of agent-based Monte-Carlo simulations, we study the Zaklan model using the well-known majority-vote model (MVM) with noise and apply it to tax evasion on ANs, to show that differently from the Ising model the MVM on ANs presents a well defined phase transition. To control the tax evasion in the economics model proposed by Zaklan et al, MVM is applied in the neighborhood of the critical noise $q_{c}$ to the Zaklan model. Here we show that the Zaklan model is robust because this can be studied besides using equilibrium dynamics...

  12. Electronic circuits modeling using artificial neural networks

    Directory of Open Access Journals (Sweden)

    Andrejević Miona V.

    2003-01-01

    Full Text Available In this paper artificial neural networks (ANN are applied to modeling of electronic circuits. ANNs are used for application of the black-box modeling concept in the time domain. Modeling process is described, so the topology of the ANN, the testing signal used for excitation, together with the complexity of ANN are considered. The procedure is first exemplified in modeling of resistive circuits. MOS transistor, as a four-terminal device, is modeled. Then nonlinear negative resistive characteristic is modeled in order to be used as a piece-wise linear resistor in Chua's circuit. Examples of modeling nonlinear dynamic circuits are given encompassing a variety of modeling problems. A nonlinear circuit containing quartz oscillator is considered for modeling. Verification of the concept is performed by verifying the ability of the model to generalize i.e. to create acceptable responses to excitations not used during training. Implementation of these models within a behavioral simulator is exemplified. Every model is implemented in realistic surrounding in order to show its interaction, and of course, its usage and purpose.

  13. Mathematical model for spreading dynamics of social network worms

    International Nuclear Information System (INIS)

    In this paper, a mathematical model for social network worm spreading is presented from the viewpoint of social engineering. This model consists of two submodels. Firstly, a human behavior model based on game theory is suggested for modeling and predicting the expected behaviors of a network user encountering malicious messages. The game situation models the actions of a user under the condition that the system may be infected at the time of opening a malicious message. Secondly, a social network accessing model is proposed to characterize the dynamics of network users, by which the number of online susceptible users can be determined at each time step. Several simulation experiments are carried out on artificial social networks. The results show that (1) the proposed mathematical model can well describe the spreading dynamics of social network worms; (2) weighted network topology greatly affects the spread of worms; (3) worms spread even faster on hybrid social networks

  14. Some applications of neural networks in microwave modeling

    Directory of Open Access Journals (Sweden)

    Milovanović Bratislav D.

    2003-01-01

    Full Text Available This paper presents some applications of neural networks in the microwave modeling. The applications are related to modeling of either passive or active structures and devices. Modeling is performed using not only simple multilayer perception network (MLP but also advanced knowledge based neural network (KBNN structures.

  15. borealis - A generalized global update algorithm for Boolean optimization problems

    CERN Document Server

    Zhu, Zheng; Katzgraber, Helmut G

    2016-01-01

    Optimization problems with Boolean variables that fall into the nondeterministic polynomial (NP) class are of fundamental importance in computer science, mathematics, physics and industrial applications. Most notably, solving constraint-satisfaction problems, which are related to spin-glass-like Hamiltonians in physics, remains a difficult numerical task. As such, there has been great interest in designing efficient heuristics to solve these computationally difficult problems. Inspired by parallel tempering Monte Carlo in conjunction with the rejection-free isoenergetic cluster algorithm developed for Ising spin glasses, we present a generalized global update optimization heuristic that can be applied to different NP-complete problems with Boolean variables. The global cluster updates allow for a wide-spread sampling of phase space, thus considerably speeding up optimization. By carefully tuning the pseudo-temperature (needed to randomize the configurations) of the problem, we show that the method can efficie...

  16. High Quality Test Pattern Generation and Boolean Satisfiability

    CERN Document Server

    Eggersglüß, Stephan

    2012-01-01

    This book provides an overview of automatic test pattern generation (ATPG) and introduces novel techniques to complement classical ATPG, based on Boolean Satisfiability (SAT).  A fast and highly fault efficient SAT-based ATPG framework is presented which is also able to generate high-quality delay tests such as robust path delay tests, as well as tests with long propagation paths to detect small delay defects. The aim of the techniques and methodologies presented in this book is to improve SAT-based ATPG, in order to make it applicable in industrial practice. Readers will learn to improve the performance and robustness of the overall test generation process, so that the ATPG algorithm reliably will generate test patterns for most targeted faults in acceptable run time to meet the high fault coverage demands of industry. The techniques and improvements presented in this book provide the following advantages: Provides a comprehensive introduction to test generation and Boolean Satisfiability (SAT); Describes a...

  17. Complexity of Propositional Abduction for Restricted Sets of Boolean Functions

    CERN Document Server

    Creignou, Nadia; Thomas, Michael

    2009-01-01

    Abduction is a fundamental and important form of non-monotonic reasoning. Given a knowledge base explaining how the world behaves it aims at finding an explanation for some observed manifestation. In this paper we focus on propositional abduction, where the knowledge base and the manifestation are represented by propositional formulae. The problem of deciding whether there exists an explanation has been shown to be SigmaP2-complete in general. We consider variants obtained by restricting the allowed connectives in the formulae to certain sets of Boolean functions. We give a complete classification of the complexity for all considerable sets of Boolean functions. In this way, we identify easier cases, namely NP-complete and polynomial cases; and we highlight sources of intractability. Further, we address the problem of counting the explanations and draw a complete picture for the counting complexity.

  18. Complex networks-based energy-efficient evolution model for wireless sensor networks

    International Nuclear Information System (INIS)

    Based on complex networks theory, we present two self-organized energy-efficient models for wireless sensor networks in this paper. The first model constructs the wireless sensor networks according to the connectivity and remaining energy of each sensor node, thus it can produce scale-free networks which have a performance of random error tolerance. In the second model, we not only consider the remaining energy, but also introduce the constraint of links to each node. This model can make the energy consumption of the whole network more balanced. Finally, we present the numerical experiments of the two models.

  19. A network model for Ebola spreading.

    Science.gov (United States)

    Rizzo, Alessandro; Pedalino, Biagio; Porfiri, Maurizio

    2016-04-01

    The availability of accurate models for the spreading of infectious diseases has opened a new era in management and containment of epidemics. Models are extensively used to plan for and execute vaccination campaigns, to evaluate the risk of international spreadings and the feasibility of travel bans, and to inform prophylaxis campaigns. Even when no specific therapeutical protocol is available, as for the Ebola Virus Disease (EVD), models of epidemic spreading can provide useful insight to steer interventions in the field and to forecast the trend of the epidemic. Here, we propose a novel mathematical model to describe EVD spreading based on activity driven networks (ADNs). Our approach overcomes the simplifying assumption of homogeneous mixing, which is central to most of the mathematically tractable models of EVD spreading. In our ADN-based model, each individual is not bound to contact every other, and its network of contacts varies in time as a function of an activity potential. Our model contemplates the possibility of non-ideal and time-varying intervention policies, which are critical to accurately describe EVD spreading in afflicted countries. The model is calibrated from field data of the 2014 April-to-December spreading in Liberia. We use the model as a predictive tool, to emulate the dynamics of EVD in Liberia and offer a one-year projection, until December 2015. Our predictions agree with the current vision expressed by professionals in the field, who consider EVD in Liberia at its final stage. The model is also used to perform a what-if analysis to assess the efficacy of timely intervention policies. In particular, we show that an earlier application of the same intervention policy would have greatly reduced the number of EVD cases, the duration of the outbreak, and the infrastructures needed for the implementation of the intervention. PMID:26804645

  20. Worst-Case Groundness Analysis Using Definite Boolean Functions

    OpenAIRE

    Genaim, Samir; Codish, Michael; Howe, Jacob M.

    2004-01-01

    This note illustrates theoretical worst-case scenarios for groundness analyses obtained through abstract interpretation over the abstract domains of definite (Def) and positive (Pos) Boolean functions. For Def, an example is given for which any Def-based abstract interpretation for groundness analysis follows a chain which is exponential in the number of argument positions as well as in the number of clauses but sub-exponential in the size of the program. For Pos, we strengthen a previous res...

  1. Reduction of Database Independence to Dividing in Atomless Boolean Algebras

    OpenAIRE

    Hyttinen, Tapani; Paolini, Gianluca

    2014-01-01

    We prove that the form of conditional independence at play in database theory and independence logic is reducible to the first-order dividing calculus in the theory of atomless Boolean algebras. This establishes interesting connections between independence in database theory and stochastic independence. As indeed, in light of the aforementioned reduction and recent work of Ben-Yaacov [4], the former case of independence can be seen as the discrete version of the latter.

  2. Yes/No/Maybe: A Boolean attempt at feedback

    OpenAIRE

    12130478 - Louw, Henk; 10095519 - Van Rooy, Albertus Jacobus

    2010-01-01

    This paper describes an experiment in which Boolean feedback (a kind of checklist) was used to provide feedback on the paragraph structures of first year students in an Academic Literacy course. We begin by introducing the major problems with feedback on L2 writing and establishing why a focus on paragraph structures in particular is of importance. The experiment conducted was a two-draft assignment in which three different kinds of feedback (technique A: handwritten comments, B: consciousnes...

  3. A Boolean algebra approach to the construction of snarks

    OpenAIRE

    Fiol Mora, Miquel Àngel

    1991-01-01

    This work deals with the construction of snarks, that is, cubic graphs that cannot be 3-edge-colored. A natural generalization of the concept of "color", that describes in a simple way the coloring ("0" or "1") of any set of (semi)edges, is introduced. This approach allows us to apply the Boolean logic theory to find an ample family of snarks, which includes many of the previous known constructions and also some interesting ones. Peer Reviewed

  4. Boolean logic device done with DFB laser diode

    OpenAIRE

    Hurtado Villavieja, Antonio; González Marcos, Ana; Martín Pereda, José Antonio

    2004-01-01

    We present simulation results on how power output-input characteristic Instability in Distributed FeedBack -DFB semiconductor laser diode SLA can be employed to implemented Boolean logic device. Two configurations of DFB Laser diode under external optical injection, either in the transmission or in the reflective mode of operation, is used to implement different Optical Logic Cells (OLCs), called the Q- and the P-Device OLCs. The external optical injection correspond to two inputs data plus a...

  5. Boolean Functions, Projection Operators and Quantum Error Correcting Codes

    OpenAIRE

    Aggarwal, Vaneet; Calderbank, A. Robert

    2006-01-01

    This paper describes a fundamental correspondence between Boolean functions and projection operators in Hilbert space. The correspondence is widely applicable, and it is used in this paper to provide a common mathematical framework for the design of both additive and non-additive quantum error correcting codes. The new framework leads to the construction of a variety of codes including an infinite class of codes that extend the original ((5,6,2)) code found by Rains [21]. It also extends to o...

  6. Matroids, hereditary collections and simplicial complexes having boolean representations

    OpenAIRE

    Rhodes, John; Silva, Pedro V.

    2012-01-01

    Inspired by the work of Izakhian and Rhodes, a theory of representation of hereditary collections by boolean matrices is developed. This corresponds to representation by finite $\\vee$-generated lattices. The lattice of flats, defined for hereditary collections, lattices and matrices, plays a central role in the theory. The representations constitute a lattice and the minimal and strictly join irreducible elements are studied, as well as various closure operators.

  7. Soft Rough Approximation Operators on a Complete Atomic Boolean Lattice

    OpenAIRE

    Heba I. Mustafa

    2013-01-01

    The concept of soft sets based on complete atomic Boolean lattice, which can be seen as a generalization of soft sets, is introduced. Some operations on these soft sets are discussed, and new types of soft sets such as full, keeping infimum, and keeping supremum are defined and supported by some illustrative examples. Two pairs of new soft rough approximation operators are proposed and the relationship among soft set is investigated, and their related properties are given. We show that Järvin...

  8. Boolean Functions with a Simple Certificate for CNF Complexity

    Czech Academy of Sciences Publication Activity Database

    Čepek, O.; Kučera, P.; Savický, Petr

    2012-01-01

    Roč. 160, 4-5 (2012), s. 365-382. ISSN 0166-218X R&D Projects: GA MŠk(CZ) 1M0545 Grant ostatní: GA ČR(CZ) GP201/07/P168; GA ČR(CZ) GAP202/10/1188 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean functions * CNF representations Subject RIV: BA - General Mathematics Impact factor: 0.718, year: 2012

  9. Modeling online social networks based on preferential linking

    Institute of Scientific and Technical Information of China (English)

    Hu Hai-Bo; Guo Jin-Li; Chen Jun

    2012-01-01

    We study the phenomena of preferential linking in a large-scale evolving online social network and find that the linear preference holds for preferential creation,preferential acceptance,and preferential attachment.Based on the linear preference,we propose an analyzable model,which illustrates the mechanism of network growth and reproduces the process of network evolution.Our simulations demonstrate that the degree distribution of the network produced by the model is in good agreement with that of the real network.This work provides a possible bridge between the micro-mechanisms of network growth and the macrostructures of online social networks.

  10. Modeling online social networks based on preferential linking

    International Nuclear Information System (INIS)

    We study the phenomena of preferential linking in a large-scale evolving online social network and find that the linear preference holds for preferential creation, preferential acceptance, and preferential attachment. Based on the linear preference, we propose an analyzable model, which illustrates the mechanism of network growth and reproduces the process of network evolution. Our simulations demonstrate that the degree distribution of the network produced by the model is in good agreement with that of the real network. This work provides a possible bridge between the micro-mechanisms of network growth and the macrostructures of online social networks

  11. Constant communication complexity protocols for multiparty accumulative boolean functions

    CERN Document Server

    pal, S P; Kumar, S; Das, Sima; Kumar, Somesh; pal, Sudebkumar Prasant

    2005-01-01

    Generalizing a boolean function from Cleve and Buhrman \\cite{cb:sqec}, we consider the class of {\\it accumulative boolean functions} of the form $f_B(X_1,X_2,..., X_m)=\\bigoplus_{i=1}^n t_B(x_i^1x_i^2... x_i^m)$, where $X_j=(x^j_1,x^j_2,..., x^j_n), 1\\leq j\\leq m$ and $t_B(x_i^1x_i^2... x_i^m)=1$ for input $m$-tuples $x_i^1x_i^2...x_i^m\\in B\\subseteq A\\subseteq \\{0,1\\}^n$, and 0, otherwise. Here the set $A$ is the promise set for function $f_B$. The input vectors $X_j, 1\\leq j\\leq m$ are given to the $m\\geq 2$ parties respectively, who communicate classical bits in a distributed environment so that one of them (say Alice) comes up with the value of the function. We algebraically characterize entanglement assisted LOCC protocols requiring only $m-1$ cbits of communication, for certain classes of such multiparty boolean functions for $m\\geq 2$ parties under appropriate uniform parity promise restrictions on input $m$-tuples $x_i^1x_i^2...x_i^m, 1\\leq i\\leq n$. In contrast, for certain $m$-party accumulative boo...

  12. Modeling GSM Based Network Communication in Vehicular Network

    OpenAIRE

    M. Milton Joe; Ramakrishnan, B.; R. S. Shaji

    2014-01-01

    Obviously fair communication establishment in every technology increases the efficiency. As we know well, vehicles are used in day to day life of every human being to move from one location to another location. If network communication is formed between vehicles, mobile phones and home based telephones, it will increase the safety of the passengers by communicating with one another. In this paper, we propose GSM based network communication in vehicles, which will develop reliable network comm...

  13. Towards a Realistic Model for Failure Propagation in Interdependent Networks

    CERN Document Server

    Sturaro, Agostino; Conti, Mauro; Das, Sajal K

    2015-01-01

    Modern networks are becoming increasingly interdependent. As a prominent example, the smart grid is an electrical grid controlled through a communications network, which in turn is powered by the electrical grid. Such interdependencies create new vulnerabilities and make these networks more susceptible to failures. In particular, failures can easily spread across these networks due to their interdependencies, possibly causing cascade effects with a devastating impact on their functionalities. In this paper we focus on the interdependence between the power grid and the communications network, and propose a novel realistic model, HINT (Heterogeneous Interdependent NeTworks), to study the evolution of cascading failures. Our model takes into account the heterogeneity of such networks as well as their complex interdependencies. We compare HINT with previously proposed models both on synthetic and real network topologies. Experimental results show that existing models oversimplify the failure evolution and network...

  14. An Anti-attack Model Based on Complex Network Theory in P2P networks

    CERN Document Server

    Peng, Hao; Zhao, Dandan; Zhang, Aixin; Li, Jianhua

    2011-01-01

    Complex network theory is a useful way to study many real systems. In this paper, an anti-attack model based on complex network theory is introduced. The mechanism of this model is based on dynamic compensation process and reverse percolation process in P2P networks. The main purpose of the paper is: (i) a dynamic compensation process can turn an attacked P2P network into a power-law (PL) network with exponential cutoff; (ii) a local healing process can restore the maximum degree of peers in an attacked P2P network to a normal level; (iii) a restoring process based on reverse percolation theory connects the fragmentary peers of an attacked P2P network together into a giant connected component. In this way, the model based on complex network theory can be effectively utilized for anti-attack and protection purposes in P2P networks.

  15. A hybrid neural network model for consciousness

    Institute of Scientific and Technical Information of China (English)

    蔺杰; 金小刚; 杨建刚

    2004-01-01

    A new framework for consciousness is introduced based upon traditional artificial neural network models. This framework reflects explicit connections between two parts of the brain: one global working memory and distributed modular cerebral networks relating to specific brain functions. Accordingly this framework is composed of three layers,physical mnemonic layer and abstract thinking layer,which cooperate together through a recognition layer to accomplish information storage and cognition using algorithms of how these interactions contribute to consciousness:(1)the reception process whereby cerebral subsystems group distributed signals into coherent object patterns;(2)the partial recognition process whereby patterns from particular subsystems are compared or stored as knowledge; and(3)the resonant learning process whereby global workspace stably adjusts its structure to adapt to patterns' changes. Using this framework,various sorts of human actions can be explained,leading to a general approach for analyzing brain functions.

  16. Modelling Traffic in IMS Network Nodes

    Directory of Open Access Journals (Sweden)

    BA Alassane

    2013-07-01

    Full Text Available IMS is well integrated with existing voice and data networks, while adopting many of their keycharacteristics.The Call Session Control Functions (CSCFs servers are the key part of the IMS structure. They are themain components responsible for processing and routing signalling messages.When CSCFs servers (P-CSCF, I-CSCF, S-CSCF are running on the same host, the SIP message can beinternally passed between SIP servers using a single operating system mechanism like a queue. It increasesthe reliability of the network [5], [6]. We have proposed in a last work for each type of service (between ICSCFand S-CSCF (call, data, multimedia.[23], to use less than two servers well dimensioned andrunning on the same operating system.Instead dimensioning servers, in order to increase performance, we try to model traffic on IMS nodes,particularly on entries nodes; it will provide results on separation of incoming flows, and then offer moresatisfactory service.

  17. A hybrid neural network model for consciousness

    Institute of Scientific and Technical Information of China (English)

    蔺杰; 金小刚; 杨建刚

    2004-01-01

    A new framework for consciousness is introduced based upon traditional artificial neural network models. This framework reflects explicit connections between two parts of the brain: one global working memory and distributed modular cerebral networks relating to specific brain functions. Accordingly this framework is composed of three layers, physical mnemonic layer and abstract thinking layer, which cooperate together through a recognition layer to accomplish information storage and cognition using algorithms of how these interactions contribute to consciousness: (l) the reception process whereby cerebral subsystems group distributed signals into coherent object patterns; (2) the partial recognition process whereby patterns from particular subsystems are compared or stored as knowledge; and (3) the resonant learning process whereby global workspace stably adjusts its structure to adapt to patterns' changes. Using this framework, various sorts of human actions can be explained, leading to a general approach for analyzing brain functions.

  18. Predictive Modeling of Opinion and Connectivity Dynamics in Social Networks

    OpenAIRE

    Saini, Ajay; Markuzon, Natasha

    2016-01-01

    Recent years saw an increased interest in modeling and understanding the mechanisms of opinion and innovation spread through human networks. Using analysis of real-world social data, researchers are able to gain a better understanding of the dynamics of social networks and subsequently model the changes in such networks over time. We developed a social network model that both utilizes an agent-based approach with a dynamic update of opinions and connections between agents and reflects opinion...

  19. A Proposed "OSI Based" Network Troubles Identification Model

    Directory of Open Access Journals (Sweden)

    Murat Kayri

    2010-09-01

    Full Text Available The OSI model, developed by ISO in 1984, attempts to summarize complicated network cases on layers.Moreover, network troubles are expressed by taking the model into account. However, there has been nostandardization for network troubles up to now. Network troubles have only been expressed by the name ofthe related layer. In this paper, it is pointed out that possible troubles on the related layer vary and possibletroubles on each layer are categorized for functional network administration and they are standardized inan eligible way. The proposed model for network trouble shooting was developed considering the OSImodel

  20. Towards an evolutionary model of transcription networks.

    Directory of Open Access Journals (Sweden)

    Dan Xie

    2011-06-01

    Full Text Available DNA evolution models made invaluable contributions to comparative genomics, although it seemed formidable to include non-genomic features into these models. In order to build an evolutionary model of transcription networks (TNs, we had to forfeit the substitution model used in DNA evolution and to start from modeling the evolution of the regulatory relationships. We present a quantitative evolutionary model of TNs, subjecting the phylogenetic distance and the evolutionary changes of cis-regulatory sequence, gene expression and network structure to one probabilistic framework. Using the genome sequences and gene expression data from multiple species, this model can predict regulatory relationships between a transcription factor (TF and its target genes in all species, and thus identify TN re-wiring events. Applying this model to analyze the pre-implantation development of three mammalian species, we identified the conserved and re-wired components of the TNs downstream to a set of TFs including Oct4, Gata3/4/6, cMyc and nMyc. Evolutionary events on the DNA sequence that led to turnover of TF binding sites were identified, including a birth of an Oct4 binding site by a 2nt deletion. In contrast to recent reports of large interspecies differences of TF binding sites and gene expression patterns, the interspecies difference in TF-target relationship is much smaller. The data showed increasing conservation levels from genomic sequences to TF-DNA interaction, gene expression, TN, and finally to morphology, suggesting that evolutionary changes are larger at molecular levels and smaller at functional levels. The data also showed that evolutionarily older TFs are more likely to have conserved target genes, whereas younger TFs tend to have larger re-wiring rates.