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Sample records for network rewiring models

  1. Measuring the evolutionary rewiring of biological networks.

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    Chong Shou

    Full Text Available We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of "commonplace" networks such as family trees, co-authorships and linux-kernel function dependencies.

  2. Network rewiring dynamics with convergence towards a star network.

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    Whigham, P A; Dick, G; Parry, M

    2016-10-01

    Network rewiring as a method for producing a range of structures was first introduced in 1998 by Watts & Strogatz (Nature393, 440-442. (doi:10.1038/30918)). This approach allowed a transition from regular through small-world to a random network. The subsequent interest in scale-free networks motivated a number of methods for developing rewiring approaches that converged to scale-free networks. This paper presents a rewiring algorithm (RtoS) for undirected, non-degenerate, fixed size networks that transitions from regular, through small-world and scale-free to star-like networks. Applications of the approach to models for the spread of infectious disease and fixation time for a simple genetics model are used to demonstrate the efficacy and application of the approach.

  3. Measuring partner choice in plant-pollinator networks: using null models to separate rewiring and fidelity from chance.

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    MacLeod, Molly; Genung, Mark A; Ascher, John S; Winfree, Rachael

    2016-11-01

    Recent studies of mutualistic networks show that interactions between partners change across years. Both biological mechanisms and chance could drive these patterns, but the relative importance of these factors has not been separated. We established a field experiment consisting of 102 monospecific plots of 17 native plant species, from which we collected 6713 specimens of 52 bee species over four years. We used these data and a null model to determine whether bee species' foraging choices varied more or less over time beyond the variation expected by chance. Thus we provide the first quantitative definition of rewiring and fidelity as these terms are used in the literature on interaction networks. All 52 bee species varied in plant partner choice across years, but for 27 species this variation was indistinguishable from random partner choice. Another 11 species showed rewiring, varying more across years than expected by chance, while 14 species showed fidelity, indicating that they both prefer certain plant species and are consistent in those preferences across years. Our study shows that rewiring and fidelity both exist in mutualist networks, but that once sampling effects have been accounted for, they are less common than has been reported in the ecological literature. © 2016 by the Ecological Society of America.

  4. Rewiring of neuronal networks during synaptic silencing.

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    Wrosch, Jana Katharina; Einem, Vicky von; Breininger, Katharina; Dahlmanns, Marc; Maier, Andreas; Kornhuber, Johannes; Groemer, Teja Wolfgang

    2017-09-15

    Analyzing the connectivity of neuronal networks, based on functional brain imaging data, has yielded new insight into brain circuitry, bringing functional and effective networks into the focus of interest for understanding complex neurological and psychiatric disorders. However, the analysis of network changes, based on the activity of individual neurons, is hindered by the lack of suitable meaningful and reproducible methodologies. Here, we used calcium imaging, statistical spike time analysis and a powerful classification model to reconstruct effective networks of primary rat hippocampal neurons in vitro. This method enables the calculation of network parameters, such as propagation probability, path length, and clustering behavior through the measurement of synaptic activity at the single-cell level, thus providing a fuller understanding of how changes at single synapses translate to an entire population of neurons. We demonstrate that our methodology can detect the known effects of drug-induced neuronal inactivity and can be used to investigate the extensive rewiring processes affecting population-wide connectivity patterns after periods of induced neuronal inactivity.

  5. Coevolution of Cooperation and Partner Rewiring Range in Spatial Social Networks

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    Khoo, Tommy; Pauls, Scott

    2016-01-01

    In recent years, there has been growing interest in the study of coevolutionary games on networks. Despite much progress, little attention has been paid to spatially embedded networks, where the underlying geographic distance, rather than the graph distance, is an important and relevant aspect of the partner rewiring process. It thus remains largely unclear how individual partner rewiring range preference, local vs. global, emerges and affects cooperation. Here we explicitly address this issue using a coevolutionary model of cooperation and partner rewiring range preference in spatially embedded social networks. In contrast to local rewiring, global rewiring has no distance restriction but incurs a one-time cost upon establishing any long range link. We find that under a wide range of model parameters, global partner switching preference can coevolve with cooperation. Moreover, the resulting partner network is highly degree-heterogeneous with small average shortest path length while maintaining high clusterin...

  6. Spatially constrained adaptive rewiring in cortical networks creates spatially modular small world architectures.

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    Jarman, Nicholas; Trengove, Chris; Steur, Erik; Tyukin, Ivan; van Leeuwen, Cees

    2014-12-01

    A modular small-world topology in functional and anatomical networks of the cortex is eminently suitable as an information processing architecture. This structure was shown in model studies to arise adaptively; it emerges through rewiring of network connections according to patterns of synchrony in ongoing oscillatory neural activity. However, in order to improve the applicability of such models to the cortex, spatial characteristics of cortical connectivity need to be respected, which were previously neglected. For this purpose we consider networks endowed with a metric by embedding them into a physical space. We provide an adaptive rewiring model with a spatial distance function and a corresponding spatially local rewiring bias. The spatially constrained adaptive rewiring principle is able to steer the evolving network topology to small world status, even more consistently so than without spatial constraints. Locally biased adaptive rewiring results in a spatial layout of the connectivity structure, in which topologically segregated modules correspond to spatially segregated regions, and these regions are linked by long-range connections. The principle of locally biased adaptive rewiring, thus, may explain both the topological connectivity structure and spatial distribution of connections between neuronal units in a large-scale cortical architecture.

  7. Impact of constrained rewiring on network structure and node dynamics.

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    Rattana, P; Berthouze, L; Kiss, I Z

    2014-11-01

    In this paper, we study an adaptive spatial network. We consider a susceptible-infected-susceptible (SIS) epidemic on the network, with a link or contact rewiring process constrained by spatial proximity. In particular, we assume that susceptible nodes break links with infected nodes independently of distance and reconnect at random to susceptible nodes available within a given radius. By systematically manipulating this radius we investigate the impact of rewiring on the structure of the network and characteristics of the epidemic. We adopt a step-by-step approach whereby we first study the impact of rewiring on the network structure in the absence of an epidemic, then with nodes assigned a disease status but without disease dynamics, and finally running network and epidemic dynamics simultaneously. In the case of no labeling and no epidemic dynamics, we provide both analytic and semianalytic formulas for the value of clustering achieved in the network. Our results also show that the rewiring radius and the network's initial structure have a pronounced effect on the endemic equilibrium, with increasingly large rewiring radiuses yielding smaller disease prevalence.

  8. Dynamics of the cell-cycle network under genome-rewiring perturbations.

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    Katzir, Yair; Elhanati, Yuval; Averbukh, Inna; Braun, Erez

    2013-12-01

    The cell-cycle progression is regulated by a specific network enabling its ordered dynamics. Recent experiments supported by computational models have shown that a core of genes ensures this robust cycle dynamics. However, much less is known about the direct interaction of the cell-cycle regulators with genes outside of the cell-cycle network, in particular those of the metabolic system. Following our recent experimental work, we present here a model focusing on the dynamics of the cell-cycle core network under rewiring perturbations. Rewiring is achieved by placing an essential metabolic gene exclusively under the regulation of a cell-cycle's promoter, forcing the cell-cycle network to function under a multitasking challenging condition; operating in parallel the cell-cycle progression and a metabolic essential gene. Our model relies on simple rate equations that capture the dynamics of the relevant protein-DNA and protein-protein interactions, while making a clear distinction between these two different types of processes. In particular, we treat the cell-cycle transcription factors as limited 'resources' and focus on the redistribution of resources in the network during its dynamics. This elucidates the sensitivity of its various nodes to rewiring interactions. The basic model produces the correct cycle dynamics for a wide range of parameters. The simplicity of the model enables us to study the interface between the cell-cycle regulation and other cellular processes. Rewiring a promoter of the network to regulate a foreign gene, forces a multitasking regulatory load. The higher the load on the promoter, the longer is the cell-cycle period. Moreover, in agreement with our experimental results, the model shows that different nodes of the network exhibit variable susceptibilities to the rewiring perturbations. Our model suggests that the topology of the cell-cycle core network ensures its plasticity and flexible interface with other cellular processes, without a

  9. Efficient rewirings for enhancing synchronizability of dynamical networks

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    Rad, Ali Ajdari; Jalili, Mahdi; Hasler, Martin

    2008-09-01

    In this paper, we present an algorithm for optimizing synchronizability of complex dynamical networks. Starting with an undirected and unweighted network, we end up with an undirected and unweighted network with the same number of nodes and edges having enhanced synchronizability. To this end, based on some network properties, rewirings, i.e., eliminating an edge and creating a new edge elsewhere, are performed iteratively avoiding always self-loops and multiple edges between the same nodes. We show that the method is able to enhance the synchronizability of networks of any size and topological properties in a small number of steps that scales with the network size. For numerical simulations, an optimization algorithm based on simulated annealing is used. Also, the evolution of different topological properties of the network such as distribution of node degree, node and edge betweenness centrality is tracked with the iteration steps. We use networks such as scale-free, Strogatz-Watts and random to start with and we show that regardless of the initial network, the final optimized network becomes homogeneous. In other words, in the network with high synchronizability, parameters, such as, degree, shortest distance, node, and edge betweenness centralities are almost homogeneously distributed. Also, parameters, such as, maximum node and edge betweenness centralities are small for the rewired network. Although we take the eigenratio of the Laplacian as the target function for optimization, we show that it is also possible to choose other appropriate target functions exhibiting almost the same performance. Furthermore, we show that even if the network is optimized taking into account another interpretation of synchronizability, i.e., synchronization cost, the optimal network has the same synchronization properties. Indeed, in networks with optimized synchronizability, different interpretations of synchronizability coincide. The optimized networks are Ramanujan graphs

  10. Rewiring Chemical Networks Based on Dynamic Dithioacetal and Disulfide Bonds.

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    Orrillo, A Gastón; La-Venia, Agustina; Escalante, Andrea M; Furlan, Ricardo L E

    2018-01-18

    The control of the connectivity between nodes of synthetic networks is still largely unexplored. To address this point we take advantage of a simple dynamic chemical system with two exchange levels that are mutually connected and can be activated simultaneously or sequentially. Dithioacetals and disulfides can be exchanged simultaneously under UV light in the presence of a sensitizer. Crossover reactions between both exchange processes produce a fully connected chemical network. On the other hand, the use of acid, base or UV light connects different nodes allowing network rewiring. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Evolutionary rewiring of bacterial regulatory networks

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    Tiffany B. Taylor

    2015-07-01

    Full Text Available Bacteria have evolved complex regulatory networks that enable integration of multiple intracellular and extracellular signals to coordinate responses to environmental changes. However, our knowledge of how regulatory systems function and evolve is still relatively limited. There is often extensive homology between components of different networks, due to past cycles of gene duplication, divergence, and horizontal gene transfer, raising the possibility of cross-talk or redundancy. Consequently, evolutionary resilience is built into gene networks – homology between regulators can potentially allow rapid rescue of lost regulatory function across distant regions of the genome. In our recent study [Taylor, et al. Science (2015, 347(6225] we find that mutations that facilitate cross-talk between pathways can contribute to gene network evolution, but that such mutations come with severe pleiotropic costs. Arising from this work are a number of questions surrounding how this phenomenon occurs.

  12. Network evolution: rewiring and signatures of conservation in signaling.

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    Mark G F Sun

    Full Text Available The analysis of network evolution has been hampered by limited availability of protein interaction data for different organisms. In this study, we investigate evolutionary mechanisms in Src Homology 3 (SH3 domain and kinase interaction networks using high-resolution specificity profiles. We constructed and examined networks for 23 fungal species ranging from Saccharomyces cerevisiae to Schizosaccharomyces pombe. We quantify rates of different rewiring mechanisms and show that interaction change through binding site evolution is faster than through gene gain or loss. We found that SH3 interactions evolve swiftly, at rates similar to those found in phosphoregulation evolution. Importantly, we show that interaction changes are sufficiently rapid to exhibit saturation phenomena at the observed timescales. Finally, focusing on the SH3 interaction network, we observe extensive clustering of binding sites on target proteins by SH3 domains and a strong correlation between the number of domains that bind a target protein (target in-degree and interaction conservation. The relationship between in-degree and interaction conservation is driven by two different effects, namely the number of clusters that correspond to interaction interfaces and the number of domains that bind to each cluster leads to sequence specific conservation, which in turn results in interaction conservation. In summary, we uncover several network evolution mechanisms likely to generalize across peptide recognition modules.

  13. Reconstructing context-specific gene regulatory network and identifying modules and network rewiring through data integration.

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    Ma, Tianle; Zhang, Aidong

    2017-07-15

    Reconstructing context-specific transcriptional regulatory network is crucial for deciphering principles of regulatory mechanisms underlying various conditions. Recently studies that reconstructed transcriptional networks have focused on individual organisms or cell types and relied on data repositories of context-free regulatory relationships. Here we present a comprehensive framework to systematically derive putative regulator-target pairs in any given context by integrating context-specific transcriptional profiling and public data repositories of gene regulatory networks. Moreover, our framework can identify core regulatory modules and signature genes underlying global regulatory circuitry, and detect network rewiring and core rewired modules in different contexts by considering gene modules and edge (gene interaction) modules collaboratively. We applied our methods to analyzing Autism RNA-seq experiment data and produced biologically meaningful results. In particular, all 11 hub genes in a predicted rewired autistic regulatory subnetwork have been linked to autism based on literature review. The predicted rewired autistic regulatory network may shed some new insight into disease mechanism. Published by Elsevier Inc.

  14. Nonlinear preferential rewiring in fixed-size networks as a diffusion process.

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    Johnson, Samuel; Torres, Joaquín J; Marro, Joaquín

    2009-05-01

    We present an evolving network model in which the total numbers of nodes and edges are conserved, but in which edges are continuously rewired according to nonlinear preferential detachment and reattachment. Assuming power-law kernels with exponents alpha and beta , the stationary states which the degree distributions evolve toward exhibit a second-order phase transition-from relatively homogeneous to highly heterogeneous (with the emergence of starlike structures) at alpha=beta . Temporal evolution of the distribution in this critical regime is shown to follow a nonlinear diffusion equation, arriving at either pure or mixed power laws of exponents -alpha and 1-alpha .

  15. Regulatory network rewiring for secondary metabolism in Arabidopsis thaliana under various conditions

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    2014-01-01

    Background Plant secondary metabolites are critical to various biological processes. However, the regulations of these metabolites are complex because of regulatory rewiring or crosstalk. To unveil how regulatory behaviors on secondary metabolism reshape biological processes, we constructed and analyzed a dynamic regulatory network of secondary metabolic pathways in Arabidopsis. Results The dynamic regulatory network was constructed through integrating co-expressed gene pairs and regulatory interactions. Regulatory interactions were either predicted by conserved transcription factor binding sites (TFBSs) or proved by experiments. We found that integrating two data (co-expression and predicted regulatory interactions) enhanced the number of highly confident regulatory interactions by over 10% compared with using single data. The dynamic changes of regulatory network systematically manifested regulatory rewiring to explain the mechanism of regulation, such as in terpenoids metabolism, the regulatory crosstalk of RAV1 (AT1G13260) and ATHB1 (AT3G01470) on HMG1 (hydroxymethylglutaryl-CoA reductase, AT1G76490); and regulation of RAV1 on epoxysqualene biosynthesis and sterol biosynthesis. Besides, we investigated regulatory rewiring with expression, network topology and upstream signaling pathways. Regulatory rewiring was revealed by the variability of genes’ expression: pathway genes and transcription factors (TFs) were significantly differentially expressed under different conditions (such as terpenoids biosynthetic genes in tissue experiments and E2F/DP family members in genotype experiments). Both network topology and signaling pathways supported regulatory rewiring. For example, we discovered correlation among the numbers of pathway genes, TFs and network topology: one-gene pathways (such as δ-carotene biosynthesis) were regulated by a fewer TFs, and were not critical to metabolic network because of their low degrees in topology. Upstream signaling pathways of 50

  16. Interaction rewiring and the rapid turnover of plant-pollinator networks.

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    CaraDonna, Paul J; Petry, William K; Brennan, Ross M; Cunningham, James L; Bronstein, Judith L; Waser, Nickolas M; Sanders, Nathan J

    2017-03-01

    Whether species interactions are static or change over time has wide-reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby implicitly assuming that interactions are fixed. This approach has advanced our understanding of communities, but it obscures the timescale at which interactions form (or dissolve) and the drivers and consequences of such dynamics. We address this knowledge gap by quantifying the within-season turnover of plant-pollinator interactions from weekly censuses across 3 years in a subalpine ecosystem. Week-to-week turnover of interactions (1) was high, (2) followed a consistent seasonal progression in all years of study and (3) was dominated by interaction rewiring (the reassembly of interactions among species). Simulation models revealed that species' phenologies and relative abundances constrained both total interaction turnover and rewiring. Our findings reveal the diversity of species interactions that may be missed when the temporal dynamics of networks are ignored. © 2017 John Wiley & Sons Ltd/CNRS.

  17. Dynamic rewiring of the Drosophila retinal determination network switches its function from selector to differentiation.

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    Mardelle Atkins

    2013-08-01

    Full Text Available Organ development is directed by selector gene networks. Eye development in the fruit fly Drosophila melanogaster is driven by the highly conserved selector gene network referred to as the "retinal determination gene network," composed of approximately 20 factors, whose core comprises twin of eyeless (toy, eyeless (ey, sine oculis (so, dachshund (dac, and eyes absent (eya. These genes encode transcriptional regulators that are each necessary for normal eye development, and sufficient to direct ectopic eye development when misexpressed. While it is well documented that the downstream genes so, eya, and dac are necessary not only during early growth and determination stages but also during the differentiation phase of retinal development, it remains unknown how the retinal determination gene network terminates its functions in determination and begins to promote differentiation. Here, we identify a switch in the regulation of ey by the downstream retinal determination genes, which is essential for the transition from determination to differentiation. We found that central to the transition is a switch from positive regulation of ey transcription to negative regulation and that both types of regulation require so. Our results suggest a model in which the retinal determination gene network is rewired to end the growth and determination stage of eye development and trigger terminal differentiation. We conclude that changes in the regulatory relationships among members of the retinal determination gene network are a driving force for key transitions in retinal development.

  18. Rewiring the network. What helps an innovation to diffuse?

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    Sznajd-Weron, Katarzyna; Szwabiński, Janusz; Weron, Rafał; Weron, Tomasz

    2014-03-01

    A fundamental question related to innovation diffusion is how the structure of the social network influences the process. Empirical evidence regarding real-world networks of influence is very limited. On the other hand, agent-based modeling literature reports different, and at times seemingly contradictory, results. In this paper we study innovation diffusion processes for a range of Watts-Strogatz networks in an attempt to shed more light on this problem. Using the so-called Sznajd model as the backbone of opinion dynamics, we find that the published results are in fact consistent and allow us to predict the role of network topology in various situations. In particular, the diffusion of innovation is easier on more regular graphs, i.e. with a higher clustering coefficient. Moreover, in the case of uncertainty—which is particularly high for innovations connected to public health programs or ecological campaigns—a more clustered network will help the diffusion. On the other hand, when social influence is less important (i.e. in the case of perfect information), a shorter path will help the innovation to spread in the society and—as a result—the diffusion will be easiest on a random graph.

  19. Topological, functional, and dynamic properties of the protein interaction networks rewired by benzo(a)pyrene

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    Ba, Qian [Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai (China); Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing (China); Li, Junyang; Huang, Chao [Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai (China); Li, Jingquan; Chu, Ruiai [Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai (China); Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing (China); Wu, Yongning, E-mail: wuyongning@cfsa.net.cn [Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing (China); Wang, Hui, E-mail: huiwang@sibs.ac.cn [Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai (China); Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing (China); School of Life Science and Technology, ShanghaiTech University, Shanghai (China)

    2015-03-01

    Benzo(a)pyrene is a common environmental and foodborne pollutant that has been identified as a human carcinogen. Although the carcinogenicity of benzo(a)pyrene has been extensively reported, its precise molecular mechanisms and the influence on system-level protein networks are not well understood. To investigate the system-level influence of benzo(a)pyrene on protein interactions and regulatory networks, a benzo(a)pyrene-rewired protein interaction network was constructed based on 769 key proteins derived from more than 500 literature reports. The protein interaction network rewired by benzo(a)pyrene was a scale-free, highly-connected biological system. Ten modules were identified, and 25 signaling pathways were enriched, most of which belong to the human diseases category, especially cancer and infectious disease. In addition, two lung-specific and two liver-specific pathways were identified. Three pathways were specific in short and medium-term networks (< 48 h), and five pathways were enriched only in the medium-term network (6 h–48 h). Finally, the expression of linker genes in the network was validated by Western blotting. These findings establish the overall, tissue- and time-specific benzo(a)pyrene-rewired protein interaction networks and provide insights into the biological effects and molecular mechanisms of action of benzo(a)pyrene. - Highlights: • Benzo(a)pyrene induced scale-free, highly-connected protein interaction networks. • 25 signaling pathways were enriched through modular analysis. • Tissue- and time-specific pathways were identified.

  20. Development of structural correlations and synchronization from adaptive rewiring in networks of Kuramoto oscillators

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    Papadopoulos, Lia; Kim, Jason Z.; Kurths, Jürgen; Bassett, Danielle S.

    2017-07-01

    Synchronization of non-identical oscillators coupled through complex networks is an important example of collective behavior, and it is interesting to ask how the structural organization of network interactions influences this process. Several studies have explored and uncovered optimal topologies for synchronization by making purposeful alterations to a network. On the other hand, the connectivity patterns of many natural systems are often not static, but are rather modulated over time according to their dynamics. However, this co-evolution and the extent to which the dynamics of the individual units can shape the organization of the network itself are less well understood. Here, we study initially randomly connected but locally adaptive networks of Kuramoto oscillators. In particular, the system employs a co-evolutionary rewiring strategy that depends only on the instantaneous, pairwise phase differences of neighboring oscillators, and that conserves the total number of edges, allowing the effects of local reorganization to be isolated. We find that a simple rule—which preserves connections between more out-of-phase oscillators while rewiring connections between more in-phase oscillators—can cause initially disordered networks to organize into more structured topologies that support enhanced synchronization dynamics. We examine how this process unfolds over time, finding a dependence on the intrinsic frequencies of the oscillators, the global coupling, and the network density, in terms of how the adaptive mechanism reorganizes the network and influences the dynamics. Importantly, for large enough coupling and after sufficient adaptation, the resulting networks exhibit interesting characteristics, including degree-frequency and frequency-neighbor frequency correlations. These properties have previously been associated with optimal synchronization or explosive transitions in which the networks were constructed using global information. On the contrary, by

  1. Depolarizing γ-aminobutyric acid contributes to glutamatergic network rewiring in epilepsy.

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    Kourdougli, Nazim; Pellegrino, Christophe; Renko, Juho-Matti; Khirug, Stanislav; Chazal, Geneviève; Kukko-Lukjanov, Tiina-Kaisa; Lauri, Sari E; Gaiarsa, Jean-Luc; Zhou, Liang; Peret, Angélique; Castrén, Eero; Tuominen, Raimo K; Crépel, Valérie; Rivera, Claudio

    2017-02-01

    Rewiring of excitatory glutamatergic neuronal circuits is a major abnormality in epilepsy. Besides the rewiring of excitatory circuits, an abnormal depolarizing γ-aminobutyric acidergic (GABAergic) drive has been hypothesized to participate in the epileptogenic processes. However, a remaining clinically relevant question is whether early post-status epilepticus (SE) evoked chloride dysregulation is important for the remodeling of aberrant glutamatergic neuronal circuits. Osmotic minipumps were used to infuse intracerebrally a specific inhibitor of depolarizing GABAergic transmission as well as a functionally blocking antibody toward the pan-neurotrophin receptor p75 (p75NTR ). The compounds were infused between 2 and 5 days after pilocarpine-induced SE. Immunohistochemistry for NKCC1, KCC2, and ectopic recurrent mossy fiber (rMF) sprouting as well as telemetric electroencephalographic and electrophysiological recordings were performed at day 5 and 2 months post-SE. Blockade of NKCC1 after SE with the specific inhibitor bumetanide restored NKCC1 and KCC2 expression, normalized chloride homeostasis, and significantly reduced the glutamatergic rMF sprouting within the dentate gyrus. This mechanism partially involves p75NTR signaling, as bumetanide application reduced SE-induced p75NTR expression and functional blockade of p75NTR decreased rMF sprouting. The early transient (3 days) post-SE infusion of bumetanide reduced rMF sprouting and recurrent seizures in the chronic epileptic phase. Our findings show that early post-SE abnormal depolarizing GABA and p75NTR signaling fosters a long-lasting rearrangement of glutamatergic network that contributes to the epileptogenic process. This finding defines promising and novel targets to constrain reactive glutamatergic network rewiring in adult epilepsy. Ann Neurol 2017;81:251-265. © 2017 American Neurological Association.

  2. Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling

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    Creixell, Pau; Schoof, Erwin M; Simpson, Craig D.

    2015-01-01

    Cancer cells acquire pathological phenotypes through accumulation of mutations that perturb signaling networks. However, global analysis of these events is currently limited. Here, we identify six types of network-attacking mutations (NAMs), including changes in kinase and SH2 modulation, network...... rewiring, and the genesis and extinction of phosphorylation sites. We developed a computational platform (ReKINect) to identify NAMs and systematically interpreted the exomes and quantitative (phospho-)proteomes of five ovarian cancer cell lines and the global cancer genome repository. We identified......-inactivating hotspots in cancer. Our method pinpoints functional NAMs, scales with the complexity of cancer genomes and cell signaling, and may enhance our capability to therapeutically target tumor-specific networks....

  3. Ablation as targeted perturbation to rewire communication network of persistent atrial fibrillation.

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    Tao, Susumu; Way, Samuel F; Garland, Joshua; Chrispin, Jonathan; Ciuffo, Luisa A; Balouch, Muhammad A; Nazarian, Saman; Spragg, David D; Marine, Joseph E; Berger, Ronald D; Calkins, Hugh; Ashikaga, Hiroshi

    2017-01-01

    Persistent atrial fibrillation (AF) can be viewed as disintegrated patterns of information transmission by action potential across the communication network consisting of nodes linked by functional connectivity. To test the hypothesis that ablation of persistent AF is associated with improvement in both local and global connectivity within the communication networks, we analyzed multi-electrode basket catheter electrograms of 22 consecutive patients (63.5 ± 9.7 years, 78% male) during persistent AF before and after the focal impulse and rotor modulation-guided ablation. Eight patients (36%) developed recurrence within 6 months after ablation. We defined communication networks of AF by nodes (cardiac tissue adjacent to each electrode) and edges (mutual information between pairs of nodes). To evaluate patient-specific parameters of communication, thresholds of mutual information were applied to preserve 10% to 30% of the strongest edges. There was no significant difference in network parameters between both atria at baseline. Ablation effectively rewired the communication network of persistent AF to improve the overall connectivity. In addition, successful ablation improved local connectivity by increasing the average clustering coefficient, and also improved global connectivity by decreasing the characteristic path length. As a result, successful ablation improved the efficiency and robustness of the communication network by increasing the small-world index. These changes were not observed in patients with AF recurrence. Furthermore, a significant increase in the small-world index after ablation was associated with synchronization of the rhythm by acute AF termination. In conclusion, successful ablation rewires communication networks during persistent AF, making it more robust, efficient, and easier to synchronize. Quantitative analysis of communication networks provides not only a mechanistic insight that AF may be sustained by spatially localized sources and

  4. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans

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    Watson, Emma; Olin-Sandoval, Viridiana; Hoy, Michael J; Li, Chi-Hua; Louisse, Timo; Yao, Victoria; Mori, Akihiro; Holdorf, Amy D; Troyanskaya, Olga G; Ralser, Markus; Walhout, Albertha JM

    2016-01-01

    Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with metabolic plasticity and thus a selective advantage on different diets in the wild. DOI: http://dx.doi.org/10.7554/eLife.17670.001 PMID:27383050

  5. Effects of time delay and random rewiring on the stochastic resonance in excitable small-world neuronal networks.

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    Yu, Haitao; Wang, Jiang; Du, Jiwei; Deng, Bin; Wei, Xile; Liu, Chen

    2013-05-01

    The effects of time delay and rewiring probability on stochastic resonance and spatiotemporal order in small-world neuronal networks are studied in this paper. Numerical results show that, irrespective of the pacemaker introduced to one single neuron or all neurons of the network, the phenomenon of stochastic resonance occurs. The time delay in the coupling process can either enhance or destroy stochastic resonance on small-world neuronal networks. In particular, appropriately tuned delays can induce multiple stochastic resonances, which appear intermittently at integer multiples of the oscillation period of the pacemaker. More importantly, it is found that the small-world topology can significantly affect the stochastic resonance on excitable neuronal networks. For small time delays, increasing the rewiring probability can largely enhance the efficiency of pacemaker-driven stochastic resonance. We argue that the time delay and the rewiring probability both play a key role in determining the ability of the small-world neuronal network to improve the noise-induced outreach of the localized subthreshold pacemaker.

  6. Dreams Rewired

    DEFF Research Database (Denmark)

    Thomsen, Bodil Marie Stavning; Luksch, Manu

    2016-01-01

    Bidraget kommenterer filmen Dreams Rewired og skaber refleksive spor i det vidt forgrenede film-arkiviske materiale om mere end et århundredes tele- og real-time kommunikation, hvor kropslig bevægelse bl.a gøres til data.......Bidraget kommenterer filmen Dreams Rewired og skaber refleksive spor i det vidt forgrenede film-arkiviske materiale om mere end et århundredes tele- og real-time kommunikation, hvor kropslig bevægelse bl.a gøres til data....

  7. A UV-Induced Genetic Network Links the RSC Complex to Nucleotide Excision Repair and Shows Dose-Dependent Rewiring

    Directory of Open Access Journals (Sweden)

    Rohith Srivas

    2013-12-01

    Full Text Available Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. Integration of genetic data with physical interaction networks identified a global map of 89 UV-induced functional interactions among 62 protein complexes, including a number of links between the RSC complex and several NER factors. We show that RSC is recruited to both silenced and transcribed loci following UV damage where it facilitates efficient repair by promoting nucleosome remodeling. Finally, a comparison of the response to high versus low levels of UV shows that the degree of genetic rewiring correlates with dose of UV and reveals a network of dose-specific interactions. This study makes available a large resource of UV-induced interactions, and it illustrates a methodology for identifying dose-dependent interactions based on quantitative shifts in genetic networks.

  8. Impact of Bounded Noise and Rewiring on the Formation and Instability of Spiral Waves in a Small-World Network of Hodgkin-Huxley Neurons.

    Science.gov (United States)

    Yao, Yuangen; Deng, Haiyou; Ma, Chengzhang; Yi, Ming; Ma, Jun

    2017-01-01

    Spiral waves are observed in the chemical, physical and biological systems, and the emergence of spiral waves in cardiac tissue is linked to some diseases such as heart ventricular fibrillation and epilepsy; thus it has importance in theoretical studies and potential medical applications. Noise is inevitable in neuronal systems and can change the electrical activities of neuron in different ways. Many previous theoretical studies about the impacts of noise on spiral waves focus an unbounded Gaussian noise and even colored noise. In this paper, the impacts of bounded noise and rewiring of network on the formation and instability of spiral waves are discussed in small-world (SW) network of Hodgkin-Huxley (HH) neurons through numerical simulations, and possible statistical analysis will be carried out. Firstly, we present SW network of HH neurons subjected to bounded noise. Then, it is numerically demonstrated that bounded noise with proper intensity σ, amplitude A, or frequency f can facilitate the formation of spiral waves when rewiring probability p is below certain thresholds. In other words, bounded noise-induced resonant behavior can occur in the SW network of neurons. In addition, rewiring probability p always impairs spiral waves, while spiral waves are confirmed to be robust for small p, thus shortcut-induced phase transition of spiral wave with the increase of p is induced. Furthermore, statistical factors of synchronization are calculated to discern the phase transition of spatial pattern, and it is confirmed that larger factor of synchronization is approached with increasing of rewiring probability p, and the stability of spiral wave is destroyed.

  9. Pyruvate decarboxylase and alcohol dehydrogenase overexpression in Escherichia coli resulted in high ethanol production and rewired metabolic enzyme networks.

    Science.gov (United States)

    Yang, Mingfeng; Li, Xuefeng; Bu, Chunya; Wang, Hui; Shi, Guanglu; Yang, Xiushan; Hu, Yong; Wang, Xiaoqin

    2014-11-01

    Pyruvate decarboxylase and alcohol dehydrogenase are efficient enzymes for ethanol production in Zymomonas mobilis. These two enzymes were over-expressed in Escherichia coli, a promising candidate for industrial ethanol production, resulting in high ethanol production in the engineered E. coli. To investigate the intracellular changes to the enzyme overexpression for homoethanol production, 2-DE and LC-MS/MS were performed. More than 1,000 protein spots were reproducibly detected in the gel by image analysis. Compared to the wild-type, 99 protein spots showed significant changes in abundance in the recombinant E. coli, in which 46 were down-regulated and 53 were up-regulated. Most proteins related to tricarboxylic acid cycle, glycerol metabolism and other energy metabolism were up-regulated, whereas proteins involved in glycolysis and glyoxylate pathway were down-regulated, indicating the rewired metabolism in the engineered E. coli. As glycolysis is the main pathway for ethanol production, and it was inhibited significantly in engineered E. coli, further efforts should be directed at minimizing the repression of glycolysis to optimize metabolism network for higher yields of ethanol production.

  10. Enhancing CNS repair in neurological disease: challenges arising from neurodegeneration and rewiring of the network.

    Science.gov (United States)

    Xu, Xiaohua; Warrington, Arthur E; Bieber, Allan J; Rodriguez, Moses

    2011-07-01

    Repair of the central nervous system (CNS) constitutes an integral part of treating neurological disease and plays a crucial role in restoring CNS architecture and function. Distinct strategies have been developed to reconstruct the damaged neural tissue, with many tested preclinically in animal models. We review cell replacement-based repair strategies. By taking spinal cord injury, cerebral ischaemia and degenerative CNS disorders as examples for CNS repair, we discuss progress and potential problems in utilizing embryonic stem cells and adult neural/non-neural stem cells to repair cell loss in the CNS. Nevertheless, CNS repair is not simply a matter of cell transplantation. The major challenge is to induce regenerating neural cells to integrate into the neural network and compensate for damaged neural function. The neural cells confront an environment very different from that of the developmental stage in which these cells differentiate to form interwoven networks. During the repair process, one of the challenges is neurodegeneration, which can develop from interrupted innervations to/from the targets, chronic inflammation, ischaemia, aging or idiopathic neural toxicity. Neurodegeneration, which occurs on the basis of a characteristic vascular and neural web, usually presents as a chronically progressive process with unknown aetiology. Currently, there is no effective treatment to stop or slow down neurodegeneration. Pathological changes from patients with Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis indicate a broken homeostasis in the CNS. We discuss how the blood-brain barrier and neural networks are formed to maintain CNS homeostasis and their contribution to neurodegeneration in diseased conditions. Another challenge is that some inhibitors produced by CNS injury do not facilitate the regenerating neural cells to incorporate into a pre-existing network. We review glial responses to CNS injury. Of note, the reactive astrocytes

  11. Rewiring of Signaling Networks Modulating Thermotolerance in the Human Pathogen Cryptococcus neoformans.

    Science.gov (United States)

    Yang, Dong-Hoon; Jung, Kwang-Woo; Bang, Soohyun; Lee, Jang-Won; Song, Min-Hee; Floyd-Averette, Anna; Festa, Richard A; Ianiri, Giuseppe; Idnurm, Alexander; Thiele, Dennis J; Heitman, Joseph; Bahn, Yong-Sun

    2017-01-01

    Thermotolerance is a crucial virulence attribute for human pathogens, including the fungus Cryptococcus neoformans that causes fatal meningitis in humans. Loss of the protein kinase Sch9 increases C. neoformans thermotolerance, but its regulatory mechanism has remained unknown. Here, we studied the Sch9-dependent and Sch9-independent signaling networks modulating C. neoformans thermotolerance by using genome-wide transcriptome analysis and reverse genetic approaches. During temperature upshift, genes encoding for molecular chaperones and heat shock proteins were upregulated, whereas those for translation, transcription, and sterol biosynthesis were highly suppressed. In this process, Sch9 regulated basal expression levels or induced/repressed expression levels of some temperature-responsive genes, including heat shock transcription factor (HSF1) and heat shock proteins (HSP104 and SSA1). Notably, we found that the HSF1 transcript abundance decreased but the Hsf1 protein became transiently phosphorylated during temperature upshift. Nevertheless, Hsf1 is essential for growth and its overexpression promoted C. neoformans thermotolerance. Transcriptome analysis using an HSF1 overexpressing strain revealed a dual role of Hsf1 in the oxidative stress response and thermotolerance. Chromatin immunoprecipitation demonstrated that Hsf1 binds to the step-type like heat shock element (HSE) of its target genes more efficiently than to the perfect- or gap-type HSE. This study provides insight into the thermotolerance of C. neoformans by elucidating the regulatory mechanisms of Sch9 and Hsf1 through the genome-scale identification of temperature-dependent genes. Copyright © 2017 by the Genetics Society of America.

  12. Infection dynamics on spatial small-world network models

    Science.gov (United States)

    Iotti, Bryan; Antonioni, Alberto; Bullock, Seth; Darabos, Christian; Tomassini, Marco; Giacobini, Mario

    2017-11-01

    The study of complex networks, and in particular of social networks, has mostly concentrated on relational networks, abstracting the distance between nodes. Spatial networks are, however, extremely relevant in our daily lives, and a large body of research exists to show that the distances between nodes greatly influence the cost and probability of establishing and maintaining a link. A random geometric graph (RGG) is the main type of synthetic network model used to mimic the statistical properties and behavior of many social networks. We propose a model, called REDS, that extends energy-constrained RGGs to account for the synergic effect of sharing the cost of a link with our neighbors, as is observed in real relational networks. We apply both the standard Watts-Strogatz rewiring procedure and another method that conserves the degree distribution of the network. The second technique was developed to eliminate unwanted forms of spatial correlation between the degree of nodes that are affected by rewiring, limiting the effect on other properties such as clustering and assortativity. We analyze both the statistical properties of these two network types and their epidemiological behavior when used as a substrate for a standard susceptible-infected-susceptible compartmental model. We consider and discuss the differences in properties and behavior between RGGs and REDS as rewiring increases and as infection parameters are changed. We report considerable differences both between the network types and, in the case of REDS, between the two rewiring schemes. We conclude that REDS represent, with the application of these rewiring mechanisms, extremely useful and interesting tools in the study of social and epidemiological phenomena in synthetic complex networks.

  13. Firing Correlation in Spiking Neurons with Watts-Strogatz Rewiring

    Science.gov (United States)

    Yamanishi, Teruya; Nishimura, Haruhiko

    The brain is organized as neuron assemblies with hierarchies of complex network connectivity. In 1998, Watts and Strogatz conjectured that the structures of most complex networks in the real world have the so-called small-world properties of a small mean path between nodes and a high cluster value, regardless of whether they are artificial networks, such as the Internet, or natural networks, such as the brain. Here we explore the nature of a small-world network of neuron assemblies by simulating the network structural dependence of Izhikevich's spiking neuron model. The synchronized rhythmical firing is estimated in terms of rewiring probabilities, and the structural dependence of the firing correlation coefficient is discussed.

  14. Coevolutionary network approach to cultural dynamics controlled by intolerance

    Science.gov (United States)

    Gracia-Lázaro, Carlos; Quijandría, Fernando; Hernández, Laura; Floría, Luis Mario; Moreno, Yamir

    2011-12-01

    Starting from Axelrod's model of cultural dissemination, we introduce a rewiring probability, enabling agents to cut the links with their unfriendly neighbors if their cultural similarity is below a tolerance parameter. For low values of tolerance, rewiring promotes the convergence to a frozen monocultural state. However, intermediate tolerance values prevent rewiring once the network is fragmented, resulting in a multicultural society even for values of initial cultural diversity in which the original Axelrod model reaches globalization.

  15. Co-evolutionnary network approach to cultural dynamics controlled by intolerance

    CERN Document Server

    Gracia-Lázaro, Carlos; Hernández, Laura; Floría, Luis Mario; Moreno, Yamir

    2011-01-01

    Starting from Axelrod's model of cultural dissemination, we introduce a rewiring probability, enabling agents to cut the links with their unfriendly neighbors if their cultural similarity is below a tolerance parameter. For low values of tolerance, rewiring promotes the convergence to a frozen monocultural state. However, intermediate tolerance values prevent rewiring once the network is fragmented, resulting in a multicultural society even for values of initial cultural diversity in which the original Axelrod model reaches globalization.

  16. Efficient randomization of biological networks while preserving functional characterization of individual nodes.

    Science.gov (United States)

    Iorio, Francesco; Bernardo-Faura, Marti; Gobbi, Andrea; Cokelaer, Thomas; Jurman, Giuseppe; Saez-Rodriguez, Julio

    2016-12-20

    Networks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and combinations of both. Additionally, a wide range of tools has been developed to map experimental data onto reference biological networks, in order to extract meaningful modules. Many of these methods assess results' significance against null distributions of randomized networks. However, these standard unconstrained randomizations do not preserve the functional characterization of the nodes in the reference networks (i.e. their degrees and connection signs), hence including potential biases in the assessment. Building on our previous work about rewiring bipartite networks, we propose a method for rewiring any type of unweighted networks. In particular we formally demonstrate that the problem of rewiring a signed and directed network preserving its functional connectivity (F-rewiring) reduces to the problem of rewiring two induced bipartite networks. Additionally, we reformulate the lower bound to the iterations' number of the switching-algorithm to make it suitable for the F-rewiring of networks of any size. Finally, we present BiRewire3, an open-source Bioconductor package enabling the F-rewiring of any type of unweighted network. We illustrate its application to a case study about the identification of modules from gene expression data mapped on protein interaction networks, and a second one focused on building logic models from more complex signed-directed reference signaling networks and phosphoproteomic data. BiRewire3 it is freely available at https://www.bioconductor.org/packages/BiRewire/ , and it should have a broad application as it allows an efficient and analytically derived statistical assessment of results from any network biology tool.

  17. 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.

  18. Coevolving complex networks in the model of social interactions

    Science.gov (United States)

    Raducha, Tomasz; Gubiec, Tomasz

    2017-04-01

    We analyze Axelrod's model of social interactions on coevolving complex networks. We introduce four extensions with different mechanisms of edge rewiring. The models are intended to catch two kinds of interactions-preferential attachment, which can be observed in scientists or actors collaborations, and local rewiring, which can be observed in friendship formation in everyday relations. Numerical simulations show that proposed dynamics can lead to the power-law distribution of nodes' degree and high value of the clustering coefficient, while still retaining the small-world effect in three models. All models are characterized by two phase transitions of a different nature. In case of local rewiring we obtain order-disorder discontinuous phase transition even in the thermodynamic limit, while in case of long-distance switching discontinuity disappears in the thermodynamic limit, leaving one continuous phase transition. In addition, we discover a new and universal characteristic of the second transition point-an abrupt increase of the clustering coefficient, due to formation of many small complete subgraphs inside the network.

  19. Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling Networks Away from a Pro-growth State.

    Science.gov (United States)

    Sacco, Francesca; Silvestri, Alessandra; Posca, Daniela; Pirrò, Stefano; Gherardini, Pier Federico; Castagnoli, Luisa; Mann, Matthias; Cesareni, Gianni

    2016-03-23

    Metformin is the most frequently prescribed drug for type 2 diabetes. In addition to its hypoglycemic effects, metformin also lowers cancer incidence. This anti-cancer activity is incompletely understood. Here, we profiled the metformin-dependent changes in the proteome and phosphoproteome of breast cancer cells using high-resolution mass spectrometry. In total, we quantified changes of 7,875 proteins and 15,813 phosphosites after metformin changes. To interpret these datasets, we developed a generally applicable strategy that overlays metformin-dependent changes in the proteome and phosphoproteome onto a literature-derived network. This approach suggested that metformin treatment makes cancer cells more sensitive to apoptotic stimuli and less sensitive to pro-growth stimuli. These hypotheses were tested in vivo; as a proof-of-principle, we demonstrated that metformin inhibits the p70S6K-rpS6 axis in a PP2A-phosphatase dependent manner. In conclusion, analysis of deep proteomics reveals both detailed and global mechanisms that contribute to the anti-cancer activity of metformin. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Modified Penna bit-string network evolution model for scale-free networks with assortative mixing

    Science.gov (United States)

    Kim, Yup; Choi, Woosik; Yook, Soon-Hyung

    2012-02-01

    Motivated by biological aging dynamics, we introduce a network evolution model for social interaction networks. In order to study the effect of social interactions originating from biological and sociological reasons on the topological properties of networks, we introduce the activitydependent rewiring process. From the numerical simulations, we show that the degree distribution of the obtained networks follows a power-law distribution with an exponentially decaying tail, P( k) ˜ ( k + c)- γ exp(- k/k 0). The obtained value of γ is in the range 2 networks. Moreover, we also show that the degree-degree correlation of the network is positive, which is a characteristic of social interaction networks. The possible applications of our model to real systems are also discussed.

  1. Network Inoculation: Heteroclinics and phase transitions in an epidemic model

    CERN Document Server

    Yang, Hui; Gross, Thilo

    2016-01-01

    In epidemiological modelling, dynamics on networks, and in particular adaptive and heterogeneous networks have recently received much interest. Here we present a detailed analysis of a previously proposed model that combines heterogeneity in the individuals with adaptive rewiring of the network structure in response to a disease. We show that in this model qualitative changes in the dynamics occur in two phase transitions. In a macroscopic description one of these corresponds to a local bifurcation whereas the other one corresponds to a non-local heteroclinic bifurcation. This model thus provides a rare example of a system where a phase transition is caused by a non-local bifurcation, while both micro- and macro-level dynamics are accessible to mathematical analysis. The bifurcation points mark the onset of a behaviour that we call network inoculation. In the respective parameter region exposure of the system to a pathogen will lead to an outbreak that collapses, but leaves the network in a configuration wher...

  2. Majority-vote model with a bimodal distribution of noises in small-world networks

    Science.gov (United States)

    Vilela, André L. M.; de Souza, Adauto J. F.

    2017-12-01

    We consider a generalized version of the majority-vote model in small-world networks. In our model, each site of the network has noise q = 0 and q ≠ 0 with probability f and 1 - f, respectively. The connections of the two-dimensional square lattice are rewired with probability p. We performed Monte Carlo simulations to characterize the order-disorder phase transition of the system. Through finite-size scaling analysis, we calculated the critical noise value qc and the standard critical exponents β / ν, γ / ν, 1 / ν. Our results suggest that these exponents are different from those of the isotropic majority-vote model. We concluded that the zero noise fraction f when combined with the rewiring probability p drive the system to a different universality class from that of the isotropic majority-vote model.

  3. Rescue of endemic states in interconnected networks with adaptive coupling

    CERN Document Server

    Vazquez, F; Miguel, M San

    2015-01-01

    We study the Susceptible-Infected-Susceptible model of epidemic spreading on two layers of networks interconnected by adaptive links, which are rewired at random to avoid contacts between infected and susceptible nodes at the interlayer. We find that the rewiring reduces the effective connectivity for the transmission of the disease between layers, and may even totally decouple the networks. Weak endemic states, in which the epidemics spreads only if the two layers are interconnected, show a transition from the endemic to the healthy phase when the rewiring overcomes a threshold value that depends on the infection rate, the strength of the coupling and the mean connectivity of the networks. In the strong endemic scenario, in which the epidemics is able to spread on each separate network, the prevalence in each layer decreases when increasing the rewiring, arriving to single network values only in the limit of infinitely fast rewiring. We also find that finite-size effects are amplified by the rewiring, as the...

  4. Modelling opinion formation driven communities in social networks

    CERN Document Server

    Iñiguez, Gerardo; Kertész, János; Kaski, Kimmo K

    2010-01-01

    In a previous paper we proposed a model to study the dynamics of opinion formation in human societies by a co-evolution process involving two distinct time scales of fast transaction and slower network evolution dynamics. In the transaction dynamics we take into account short range interactions as discussions between individuals and long range interactions to describe the attitude to the overall mood of society. The latter is handled by a uniformly distributed parameter $\\alpha$, assigned randomly to each individual, as quenched personal bias. The network evolution dynamics is realized by rewiring the societal network due to state variable changes as a result of transaction dynamics. The main consequence of this complex dynamics is that communities emerge in the social network for a range of values in the ratio between time scales. In this paper we focus our attention on the attitude parameter $\\alpha$ and its influence on the conformation of opinion and the size of the resulting communities. We present numer...

  5. Basic concepts and principles of stoichiometric modeling of metabolic networks

    NARCIS (Netherlands)

    T.R. Maarleveld (Timo); R.A. Khandelwal; B.E. Olivier; B. Teusink (Bas); F.J. Bruggeman (Frank)

    2013-01-01

    htmlabstractMetabolic networks supply the energy and building blocks for cell growth and maintenance. Cells continuously rewire their metabolic networks in response to changes in environmental conditions to sustain fitness. Studies of the systemic properties of metabolic networks give insight into

  6. Collaborative networks: Reference modeling

    NARCIS (Netherlands)

    Camarinha-Matos, L.M.; Afsarmanesh, H.

    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

  7. Rewiring monocyte glucose metabolism via C-type lectin signaling protects against disseminated candidiasis.

    Science.gov (United States)

    Domínguez-Andrés, Jorge; Arts, Rob J W; Ter Horst, Rob; Gresnigt, Mark S; Smeekens, Sanne P; Ratter, Jacqueline M; Lachmandas, Ekta; Boutens, Lily; van de Veerdonk, Frank L; Joosten, Leo A B; Notebaart, Richard A; Ardavín, Carlos; Netea, Mihai G

    2017-09-01

    Monocytes are innate immune cells that play a pivotal role in antifungal immunity, but little is known regarding the cellular metabolic events that regulate their function during infection. Using complementary transcriptomic and immunological studies in human primary monocytes, we show that activation of monocytes by Candida albicans yeast and hyphae was accompanied by metabolic rewiring induced through C-type lectin-signaling pathways. We describe that the innate immune responses against Candida yeast are energy-demanding processes that lead to the mobilization of intracellular metabolite pools and require induction of glucose metabolism, oxidative phosphorylation and glutaminolysis, while responses to hyphae primarily rely on glycolysis. Experimental models of systemic candidiasis models validated a central role for glucose metabolism in anti-Candida immunity, as the impairment of glycolysis led to increased susceptibility in mice. Collectively, these data highlight the importance of understanding the complex network of metabolic responses triggered during infections, and unveil new potential targets for therapeutic approaches against fungal diseases.

  8. A distance constrained synaptic plasticity model of C. elegans neuronal network

    Science.gov (United States)

    Badhwar, Rahul; Bagler, Ganesh

    2017-03-01

    Brain research has been driven by enquiry for principles of brain structure organization and its control mechanisms. The neuronal wiring map of C. elegans, the only complete connectome available till date, presents an incredible opportunity to learn basic governing principles that drive structure and function of its neuronal architecture. Despite its apparently simple nervous system, C. elegans is known to possess complex functions. The nervous system forms an important underlying framework which specifies phenotypic features associated to sensation, movement, conditioning and memory. In this study, with the help of graph theoretical models, we investigated the C. elegans neuronal network to identify network features that are critical for its control. The 'driver neurons' are associated with important biological functions such as reproduction, signalling processes and anatomical structural development. We created 1D and 2D network models of C. elegans neuronal system to probe the role of features that confer controllability and small world nature. The simple 1D ring model is critically poised for the number of feed forward motifs, neuronal clustering and characteristic path-length in response to synaptic rewiring, indicating optimal rewiring. Using empirically observed distance constraint in the neuronal network as a guiding principle, we created a distance constrained synaptic plasticity model that simultaneously explains small world nature, saturation of feed forward motifs as well as observed number of driver neurons. The distance constrained model suggests optimum long distance synaptic connections as a key feature specifying control of the network.

  9. Increasing signal specificity of the TOL network of Pseudomonas putida mt-2 by rewiring the connectivity of the master regulator XylR.

    Directory of Open Access Journals (Sweden)

    Aitor de Las Heras

    Full Text Available Prokaryotic transcription factors (TFs that bind small xenobiotic molecules (e.g., TFs that drive genes that respond to environmental pollutants often display a promiscuous effector profile for analogs of the bona fide chemical signals. XylR, the master TF for expression of the m-xylene biodegradation operons encoded in the TOL plasmid pWW0 of Pseudomonas putida, responds not only to the aromatic compound but also, albeit to a lesser extent, to many other aromatic compounds, such as 3-methylbenzylalcohol (3MBA. We have examined whether such a relaxed regulatory scenario can be reshaped into a high-capacity/high-specificity regime by changing the connectivity of this effector-sensing TF within the rest of the circuit rather than modifying XylR structure itself. To this end, the natural negative feedback loop that operates on xylR transcription was modified with a translational attenuator that brings down the response to 3MBA while maintaining the transcriptional output induced by m-xylene (as measured with a luxCDABE reporter system. XylR expression was then subject to a positive feedback loop in which the TF was transcribed from its own target promoters, each known to hold different input/output transfer functions. In the first case (xylR under the strong promoter of the upper TOL operon, Pu, the reporter system displayed an increased transcriptional capacity in the resulting network for both the optimal and the suboptimal XylR effectors. In contrast, when xylR was expressed under the weaker Ps promoter, the resulting circuit unmistakably discriminated m-xylene from 3MBA. The non-natural connectivity engineered in the network resulted both in a higher promoter activity and also in a much-increased signal-to-background ratio. These results indicate that the working regimes of given genetic circuits can be dramatically altered through simple changes in the way upstream transcription factors are self-regulated by positive or negative feedback loops.

  10. The data-driven null models for information dissemination tree in social networks

    Science.gov (United States)

    Zhang, Zhiwei; Wang, Zhenyu

    2017-10-01

    For the purpose of detecting relatedness and co-occurrence between users, as well as the distribution features of nodes in spreading path of a social network, this paper explores topological characteristics of information dissemination trees (IDT) that can be employed indirectly to probe the information dissemination laws within social networks. Hence, three different null models of IDT are presented in this article, including the statistical-constrained 0-order IDT null model, the random-rewire-broken-edge 0-order IDT null model and the random-rewire-broken-edge 2-order IDT null model. These null models firstly generate the corresponding randomized copy of an actual IDT; then the extended significance profile, which is developed by adding the cascade ratio of information dissemination path, is exploited not only to evaluate degree correlation of two nodes associated with an edge, but also to assess the cascade ratio of different length of information dissemination paths. The experimental correspondences of the empirical analysis for several SinaWeibo IDTs and Twitter IDTs indicate that the IDT null models presented in this paper perform well in terms of degree correlation of nodes and dissemination path cascade ratio, which can be better to reveal the features of information dissemination and to fit the situation of real social networks.

  11. Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris.

    Directory of Open Access Journals (Sweden)

    Jennifer W Israel

    2016-03-01

    Full Text Available The ecologically significant shift in developmental strategy from planktotrophic (feeding to lecithotrophic (nonfeeding development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species

  12. Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris.

    Science.gov (United States)

    Israel, Jennifer W; Martik, Megan L; Byrne, Maria; Raff, Elizabeth C; Raff, Rudolf A; McClay, David R; Wray, Gregory A

    2016-03-01

    The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results

  13. Topological plasticity increases robustness of mutualistic networks.

    Science.gov (United States)

    Ramos-Jiliberto, Rodrigo; Valdovinos, Fernanda S; Moisset de Espanés, Pablo; Flores, José D

    2012-07-01

    1. Earlier studies used static models to evaluate the responses of mutualistic networks to external perturbations. Two classes of dynamics can be distinguished in ecological networks; population dynamics, represented mainly by changes in species abundances, and topological dynamics, represented by changes in the architecture of the web. 2. In this study, we model the temporal evolution of three empirical plant-pollination networks incorporating both population and topological dynamics. We test the hypothesis that topological plasticity, realized through the ability of animals to rewire their connections after depletion of host abundances, enhances tolerance of mutualistic networks to species loss. We also compared the performance of various rewiring rules in affecting robustness. 3. The results show that topological plasticity markedly increased the robustness of mutualistic networks. Our analyses also revealed that network robustness reached maximum levels when animals with less host plant availability were more likely to rewire. Also, preferential attachment to richer host plants, that is, to plants exhibiting higher abundance and few exploiters, enhances robustness more than other rewiring alternatives. 4. Our results highlight the potential role of topological plasticity in the robustness of mutualistic networks to species extinctions and suggest some plausible mechanisms by which the decisions of foragers may shape the collective dynamics of plant-pollinator systems. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

  14. Rewiring cell signalling through chimaeric regulatory protein engineering.

    Science.gov (United States)

    Wang, Baojun; Barahona, Mauricio; Buck, Martin; Schumacher, Jörg

    2013-10-01

    Bacterial cells continuously sense and respond to their environment using their inherent signalling and gene regulatory networks. Cells are equipped with parallel signalling pathways, which can specifically cope with individual input signals, while interconnectivities between pathways lead to an enhanced complexity of regulatory responses that enable sophisticated adaptation. In principle, any cell signalling pathway may be rewired to respond to non-cognate signals by exchanging and recombining their underlying cognate signalling components. In the present article, we review the engineering strategies and use of chimaeric regulatory proteins in cell signalling pathways, especially the TCS (two-component signalling) system in bacteria, to achieve novel customized signalling or regulatory functions. We envisage that engineered chimaeric regulatory proteins can play an important role to aid both forward and reverse engineering of biological systems for many desired applications.

  15. Modeling the citation network by network cosmology.

    Science.gov (United States)

    Xie, Zheng; Ouyang, Zhenzheng; Zhang, Pengyuan; Yi, Dongyun; Kong, Dexing

    2015-01-01

    Citation between papers can be treated as a causal relationship. In addition, some citation networks have a number of similarities to the causal networks in network cosmology, e.g., the similar in-and out-degree distributions. Hence, it is possible to model the citation network using network cosmology. The casual network models built on homogenous spacetimes have some restrictions when describing some phenomena in citation networks, e.g., the hot papers receive more citations than other simultaneously published papers. We propose an inhomogenous causal network model to model the citation network, the connection mechanism of which well expresses some features of citation. The node growth trend and degree distributions of the generated networks also fit those of some citation networks well.

  16. Modeling the citation network by network cosmology.

    Directory of Open Access Journals (Sweden)

    Zheng Xie

    Full Text Available Citation between papers can be treated as a causal relationship. In addition, some citation networks have a number of similarities to the causal networks in network cosmology, e.g., the similar in-and out-degree distributions. Hence, it is possible to model the citation network using network cosmology. The casual network models built on homogenous spacetimes have some restrictions when describing some phenomena in citation networks, e.g., the hot papers receive more citations than other simultaneously published papers. We propose an inhomogenous causal network model to model the citation network, the connection mechanism of which well expresses some features of citation. The node growth trend and degree distributions of the generated networks also fit those of some citation networks well.

  17. Modelling opinion formation driven communities in social networks

    Science.gov (United States)

    Iñiguez, Gerardo; Barrio, Rafael A.; Kertész, János; Kaski, Kimmo K.

    2011-09-01

    In a previous paper we proposed a model to study the dynamics of opinion formation in human societies by a co-evolution process involving two distinct time scales of fast transaction and slower network evolution dynamics. In the transaction dynamics we take into account short range interactions as discussions between individuals and long range interactions to describe the attitude to the overall mood of society. The latter is handled by a uniformly distributed parameter α, assigned randomly to each individual, as quenched personal bias. The network evolution dynamics is realised by rewiring the societal network due to state variable changes as a result of transaction dynamics. The main consequence of this complex dynamics is that communities emerge in the social network for a range of values in the ratio between time scales. In this paper we focus our attention on the attitude parameter α and its influence on the conformation of opinion and the size of the resulting communities. We present numerical studies and extract interesting features of the model that can be interpreted in terms of social behaviour.

  18. 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...

  19. 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. .

  20. Modeling network technology deployment rates with different network models

    OpenAIRE

    Chung, Yoo

    2011-01-01

    To understand the factors that encourage the deployment of a new networking technology, we must be able to model how such technology gets deployed. We investigate how network structure influences deployment with a simple deployment model and different network models through computer simulations. The results indicate that a realistic model of networking technology deployment should take network structure into account.

  1. Cellular plasticity enables adaptation to unforeseen cell-cycle rewiring challenges.

    Directory of Open Access Journals (Sweden)

    Yair Katzir

    Full Text Available The fundamental dynamics of the cell cycle, underlying cell growth and reproduction, were previously found to be robust under a wide range of environmental and internal perturbations. This property was commonly attributed to its network structure, which enables the coordinated interactions among hundreds of proteins. Despite significant advances in deciphering the components and autonomous interactions of this network, understanding the interfaces of the cell cycle with other major cellular processes is still lacking. To gain insight into these interfaces, we used the process of genome-rewiring in yeast by placing an essential metabolic gene HIS3 from the histidine biosynthesis pathway, under the exclusive regulation of different cell-cycle promoters. In a medium lacking histidine and under partial inhibition of the HIS3p, the rewired cells encountered an unforeseen multitasking challenge; the cell-cycle regulatory genes were required to regulate the essential histidine-pathway gene in concert with the other metabolic demands, while simultaneously driving the cell cycle through its proper temporal phases. We show here that chemostat cell populations with rewired cell-cycle promoters adapted within a short time to accommodate the inhibition of HIS3p and stabilized a new phenotypic state. Furthermore, a significant fraction of the population was able to adapt and grow into mature colonies on plates under such inhibiting conditions. The adapted state was shown to be stably inherited across generations. These adaptation dynamics were accompanied by a non-specific and irreproducible genome-wide transcriptional response. Adaptation of the cell-cycle attests to its multitasking capabilities and flexible interface with cellular metabolic processes and requirements. Similar adaptation features were found in our previous work when rewiring HIS3 to the GAL system and switching cells from galactose to glucose. Thus, at the basis of cellular plasticity is

  2. 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...

  3. Rewiring monocyte glucose metabolism via C-type lectin signaling protects against disseminated candidiasis.

    Directory of Open Access Journals (Sweden)

    Jorge Domínguez-Andrés

    2017-09-01

    Full Text Available Monocytes are innate immune cells that play a pivotal role in antifungal immunity, but little is known regarding the cellular metabolic events that regulate their function during infection. Using complementary transcriptomic and immunological studies in human primary monocytes, we show that activation of monocytes by Candida albicans yeast and hyphae was accompanied by metabolic rewiring induced through C-type lectin-signaling pathways. We describe that the innate immune responses against Candida yeast are energy-demanding processes that lead to the mobilization of intracellular metabolite pools and require induction of glucose metabolism, oxidative phosphorylation and glutaminolysis, while responses to hyphae primarily rely on glycolysis. Experimental models of systemic candidiasis models validated a central role for glucose metabolism in anti-Candida immunity, as the impairment of glycolysis led to increased susceptibility in mice. Collectively, these data highlight the importance of understanding the complex network of metabolic responses triggered during infections, and unveil new potential targets for therapeutic approaches against fungal diseases.

  4. Models of educational institutions' networking

    OpenAIRE

    Shilova Olga Nikolaevna

    2015-01-01

    The importance of educational institutions' networking in modern sociocultural conditions and a definition of networking in education are presented in the article. The results of research levels, methods and models of educational institutions' networking are presented and substantially disclosed.

  5. Tools and Models for Integrating Multiple Cellular Networks

    Energy Technology Data Exchange (ETDEWEB)

    Gerstein, Mark [Yale Univ., New Haven, CT (United States). Gerstein Lab.

    2015-11-06

    In this grant, we have systematically investigated the integrated networks, which are responsible for the coordination of activity between metabolic pathways in prokaryotes. We have developed several computational tools to analyze the topology of the integrated networks consisting of metabolic, regulatory, and physical interaction networks. The tools are all open-source, and they are available to download from Github, and can be incorporated in the Knowledgebase. Here, we summarize our work as follow. Understanding the topology of the integrated networks is the first step toward understanding its dynamics and evolution. For Aim 1 of this grant, we have developed a novel algorithm to determine and measure the hierarchical structure of transcriptional regulatory networks [1]. The hierarchy captures the direction of information flow in the network. The algorithm is generally applicable to regulatory networks in prokaryotes, yeast and higher organisms. Integrated datasets are extremely beneficial in understanding the biology of a system in a compact manner due to the conflation of multiple layers of information. Therefore for Aim 2 of this grant, we have developed several tools and carried out analysis for integrating system-wide genomic information. To make use of the structural data, we have developed DynaSIN for protein-protein interactions networks with various dynamical interfaces [2]. We then examined the association between network topology with phenotypic effects such as gene essentiality. In particular, we have organized E. coli and S. cerevisiae transcriptional regulatory networks into hierarchies. We then correlated gene phenotypic effects by tinkering with different layers to elucidate which layers were more tolerant to perturbations [3]. In the context of evolution, we also developed a workflow to guide the comparison between different types of biological networks across various species using the concept of rewiring [4], and Furthermore, we have developed

  6. Techniques for Modelling Network Security

    OpenAIRE

    Lech Gulbinovič

    2012-01-01

    The article compares modelling techniques for network security, including the theory of probability, Markov processes, Petri networks and application of stochastic activity networks. The paper introduces the advantages and disadvantages of the above proposed methods and accepts the method of modelling the network of stochastic activity as one of the most relevant. The stochastic activity network allows modelling the behaviour of the dynamic system where the theory of probability is inappropri...

  7. Modeling Network Interdiction Tasks

    Science.gov (United States)

    2015-09-17

    allow professionals and families to stay in touch through voice or video calls. Power grids provide electricity to homes , offices, and recreational...instances using IBMr ILOGr CPLEXr Optimization Studio V12.6. For each instance, two solutions are deter- mined. First, the MNDP-a model is solved with no...three values: 0.25, 0.50, or 0.75. The DMP-a model is solved for the various random network instances using IBMr ILOGr CPLEXr Optimization Studio V12.6

  8. 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.

  9. Do Network Models Just Model Networks? On The Applicability of Network-Oriented Modeling

    NARCIS (Netherlands)

    Treur, J.; Shmueli, Erez

    2017-01-01

    In this paper for a Network-Oriented Modelling perspective based on temporal-causal networks it is analysed how generic and applicable it is as a general modelling approach and as a computational paradigm. This results in an answer to the question in the title different from: network models just

  10. Regulatory Rewiring in a Cross Causes Extensive Genetic Heterogeneity.

    Science.gov (United States)

    Matsui, Takeshi; Linder, Robert; Phan, Joann; Seidl, Fabian; Ehrenreich, Ian M

    2015-10-01

    Genetic heterogeneity occurs when individuals express similar phenotypes as a result of different underlying mechanisms. Although such heterogeneity is known to be a potential source of unexplained heritability in genetic mapping studies, its prevalence and molecular basis are not fully understood. Here we show that substantial genetic heterogeneity underlies a model phenotype--the ability to grow invasively--in a cross of two Saccharomyces cerevisiae strains. The heterogeneous basis of this trait across genotypes and environments makes it difficult to detect causal loci with standard genetic mapping techniques. However, using selective genotyping in the original cross, as well as in targeted backcrosses, we detected four loci that contribute to differences in the ability to grow invasively. Identification of causal genes at these loci suggests that they act by changing the underlying regulatory architecture of invasion. We verified this point by deleting many of the known transcriptional activators of invasion, as well as the gene encoding the cell surface protein Flo11 from five relevant segregants and showing that these individuals differ in the genes they require for invasion. Our work illustrates the extensive genetic heterogeneity that can underlie a trait and suggests that regulatory rewiring is a basic mechanism that gives rise to this heterogeneity. Copyright © 2015 by the Genetics Society of America.

  11. Different pathogenic stimuli induce specific metabolic rewiring in human monocytes

    NARCIS (Netherlands)

    Lachmandas, Ekta; Boutens, Lily; Ratter, Jacqueline; Hijmans, Anneke; Hooiveld, Guido; Crevel, van Reinout; Netea, Mihai; Stienstra, Rinke

    2016-01-01

    Recent studies have demonstrated that upon encountering a pathogenic stimulus, robust metabolic rewiring of immune cells occurs. A switch away from oxidative phosphorylation to glycolysis, even in the presence of sufficient amounts of oxygen (akin the Warburg effect), is typically observed in

  12. Modeling semiflexible polymer networks

    OpenAIRE

    Broedersz, Chase P.; MacKintosh, Fred C.

    2014-01-01

    Here, we provide an overview of theoretical approaches to semiflexible polymers and their networks. Such semiflexible polymers have large bending rigidities that can compete with the entropic tendency of a chain to crumple up into a random coil. Many studies on semiflexible polymers and their assemblies have been motivated by their importance in biology. Indeed, crosslinked networks of semiflexible polymers form a major structural component of tissue and living cells. Reconstituted networks o...

  13. 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.

  14. Developing Personal Network Business Models

    DEFF Research Database (Denmark)

    Saugstrup, Dan; Henten, Anders

    2006-01-01

    on the 'state of the art' in the field of business modeling. Furthermore, the paper suggests three generic business models for PNs: a service oriented model, a self-organized model, and a combination model. Finally, examples of relevant services and applications in relation to three different cases......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...... are presented and analyzed in light of business modeling of PN....

  15. A model of coauthorship networks

    Science.gov (United States)

    Zhou, Guochang; Li, Jianping; Xie, Zonglin

    2017-10-01

    A natural way of representing the coauthorship of authors is to use a generalization of graphs known as hypergraphs. A random geometric hypergraph model is proposed here to model coauthorship networks, which is generated by placing nodes on a region of Euclidean space randomly and uniformly, and connecting some nodes if the nodes satisfy particular geometric conditions. Two kinds of geometric conditions are designed to model the collaboration patterns of academic authorities and basic researches respectively. The conditions give geometric expressions of two causes of coauthorship: the authority and similarity of authors. By simulation and calculus, we show that the forepart of the degree distribution of the network generated by the model is mixture Poissonian, and the tail is power-law, which are similar to these of some coauthorship networks. Further, we show more similarities between the generated network and real coauthorship networks: the distribution of cardinalities of hyperedges, high clustering coefficient, assortativity, and small-world property

  16. A Model of Network Porosity

    Science.gov (United States)

    2016-11-09

    standpoint remains more of an art than a science . Even when well executed, the ongoing evolution of the network may violate initial, security-critical design...from a security standpoint remains more of an art than a science . Even when well executed, the ongoing evolution of the network may violate initial...is outside the scope of this paper. As such, we focus on event probabilities. The output of the network porosity model is a stream of timestamped

  17. Node-based learning of differential networks from multi-platform gene expression data.

    Science.gov (United States)

    Ou-Yang, Le; Zhang, Xiao-Fei; Wu, Min; Li, Xiao-Li

    2017-10-01

    Recovering gene regulatory networks and exploring the network rewiring between two different disease states are important for revealing the mechanisms behind disease progression. The advent of high-throughput experimental techniques has enabled the possibility of inferring gene regulatory networks and differential networks using computational methods. However, most of existing differential network analysis methods are designed for single-platform data analysis and assume that differences between networks are driven by individual edges. Therefore, they cannot take into account the common information shared across different data platforms and may fail in identifying driver genes that lead to the change of network. In this study, we develop a node-based multi-view differential network analysis model to simultaneously estimate multiple gene regulatory networks and their differences from multi-platform gene expression data. Our model can leverage the strength across multiple data platforms to improve the accuracy of network inference and differential network estimation. Simulation studies demonstrate that our model can obtain more accurate estimations of gene regulatory networks and differential networks than other existing state-of-the-art models. We apply our model on TCGA ovarian cancer samples to identify network rewiring associated with drug resistance. We observe from our experiments that the hub nodes of our identified differential networks include known drug resistance-related genes and potential targets that are useful to improve the treatment of drug resistant tumors. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. 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.

  19. Statistical Inference for Detecting Structures and Anomalies in Networks

    Science.gov (United States)

    2015-08-27

    5 DISTRIBUTION A: Distribution approved for public release asymptotically optimal accuracy, and the second is a fast spectral clustering algorithm...from a null model where the network is rewired randomly. However, maximizing the modularity can lead to many competing partitions , which have almost the...same modularity but which have little in common with each other; it can also overfit, producing illusory “communities” in random graphs where none

  20. Campus network security model study

    Science.gov (United States)

    Zhang, Yong-ku; Song, Li-ren

    2011-12-01

    Campus network security is growing importance, Design a very effective defense hacker attacks, viruses, data theft, and internal defense system, is the focus of the study in this paper. This paper compared the firewall; IDS based on the integrated, then design of a campus network security model, and detail the specific implementation principle.

  1. Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements.

    Directory of Open Access Journals (Sweden)

    Amaury Herpin

    2010-02-01

    Full Text Available Control and coordination of eukaryotic gene expression rely on transcriptional and posttranscriptional regulatory networks. Evolutionary innovations and adaptations often require rapid changes of such networks. It has long been hypothesized that transposable elements (TE might contribute to the rewiring of regulatory interactions. More recently it emerged that TEs might bring in ready-to-use transcription factor binding sites to create alterations to the promoters by which they were captured. A process where the gene regulatory architecture is of remarkable plasticity is sex determination. While the more downstream components of the sex determination cascades are evolutionary conserved, the master regulators can switch between groups of organisms even on the interspecies level or between populations. In the medaka fish (Oryzias latipes a duplicated copy of dmrt1, designated dmrt1bY or DMY, on the Y chromosome was shown to be the master regulator of male development, similar to Sry in mammals. We found that the dmrt1bY gene has acquired a new feedback downregulation of its expression. Additionally, the autosomal dmrt1a gene is also able to regulate transcription of its duplicated paralog by binding to a unique target Dmrt1 site nested within the dmrt1bY proximal promoter region. We could trace back this novel regulatory element to a highly conserved sequence within a new type of TE that inserted into the upstream region of dmrt1bY shortly after the duplication event. Our data provide functional evidence for a role of TEs in transcriptional network rewiring for sub- and/or neo-functionalization of duplicated genes. In the particular case of dmrt1bY, this contributed to create new hierarchies of sex-determining genes.

  2. Krebs cycle rewired for macrophage and dendritic cell effector functions.

    Science.gov (United States)

    Ryan, Dylan Gerard; O'Neill, Luke A J

    2017-10-01

    The Krebs cycle is an amphibolic pathway operating in the mitochondrial matrix of all eukaryotic organisms. In response to proinflammatory stimuli, macrophages and dendritic cells undergo profound metabolic remodelling to support the biosynthetic and bioenergetic requirements of the cell. Recently, it has been discovered that this metabolic shift also involves the rewiring of the Krebs cycle to regulate cellular metabolic flux and the accumulation of Krebs cycle intermediates, notably, citrate, succinate and fumarate. Interestingly, a new role for Krebs cycle intermediates as signalling molecules and immunomodulators that dictate the inflammatory response has begun to emerge. This review will discuss the latest developments in Krebs cycle rewiring and immune cell effector functions, with a particular focus on the regulation of cytokine production. © 2017 Federation of European Biochemical Societies.

  3. 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.

  4. Modeling semiflexible polymer networks

    NARCIS (Netherlands)

    Broedersz, C.P.; MacKintosh, F.C.

    2014-01-01

    This is an overview of theoretical approaches to semiflexible polymers and their networks. Such semiflexible polymers have large bending rigidities that can compete with the entropic tendency of a chain to crumple up into a random coil. Many studies on semiflexible polymers and their assemblies have

  5. Mobility Model for Tactical Networks

    Science.gov (United States)

    Rollo, Milan; Komenda, Antonín

    In this paper a synthetic mobility model which represents behavior and movement pattern of heterogeneous units in disaster relief and battlefield scenarios is proposed. These operations usually take place in environment without preexisting communication infrastructure and units thus have to be connected by wireless communication network. Units cooperate to fulfill common tasks and communication network has to serve high amount of communication requests, especially data, voice and video stream transmissions. To verify features of topology control, routing and interaction protocols software simulations are usually used, because of their scalability, repeatability and speed. Behavior of all these protocols relies on the mobility model of the network nodes, which has to resemble real-life movement pattern. Proposed mobility model is goal-driven and provides support for various types of units, group mobility and realistic environment model with obstacles. Basic characteristics of the mobility model like node spatial distribution and average node degree were analyzed.

  6. Modelling freeway networks by hybrid stochastic models

    OpenAIRE

    Boel, R.; Mihaylova, L.

    2004-01-01

    Traffic flow on freeways is a nonlinear, many-particle phenomenon, with complex interactions between the vehicles. This paper presents a stochastic hybrid model of freeway traffic at a time scale and at a level of detail suitable for on-line flow estimation, for routing and ramp metering control. The model describes the evolution of continuous and discrete state variables. The freeway is considered as a network of components, each component representing a different section of the network. The...

  7. Rewiring neural interactions by micro-stimulation

    Directory of Open Access Journals (Sweden)

    James M Rebesco

    2010-08-01

    Full Text Available Plasticity is a crucial component of normal brain function and a critical mechanism for recovery from injury. In vitro, associative pairing of presynaptic spiking and stimulus-induced postsynaptic depolarization causes changes in the synaptic efficacy of the presynaptic neuron, when activated by extrinsic stimulation. In vivo, such paradigms can alter the responses of whole groups of neurons to stimulation. Here, we used in vivo spike-triggered stimulation to drive plastic changes in rat forelimb sensorimotor cortex, which we monitored using a statistical measure of functional connectivity inferred from the spiking statistics of the neurons during normal, spontaneous behavior. These induced plastic changes in inferred functional connectivity depended on the latency between trigger spike and stimulation, and appear to reflect a robust reorganization of the network. Such targeted connectivity changes might provide a tool for rerouting the flow of information through a network, with implications for both rehabilitation and brain-machine interface applications.

  8. Network model of security system

    Directory of Open Access Journals (Sweden)

    Adamczyk Piotr

    2016-01-01

    Full Text Available The article presents the concept of building a network security model and its application in the process of risk analysis. It indicates the possibility of a new definition of the role of the network models in the safety analysis. Special attention was paid to the development of the use of an algorithm describing the process of identifying the assets, vulnerability and threats in a given context. The aim of the article is to present how this algorithm reduced the complexity of the problem by eliminating from the base model these components that have no links with others component and as a result and it was possible to build a real network model corresponding to reality.

  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. Data modeling of network dynamics

    Science.gov (United States)

    Jaenisch, Holger M.; Handley, James W.; Faucheux, Jeffery P.; Harris, Brad

    2004-01-01

    This paper highlights Data Modeling theory and its use for text data mining as a graphical network search engine. Data Modeling is then used to create a real-time filter capable of monitoring network traffic down to the port level for unusual dynamics and changes in business as usual. This is accomplished in an unsupervised fashion without a priori knowledge of abnormal characteristics. Two novel methods for converting streaming binary data into a form amenable to graphics based search and change detection are introduced. These techniques are then successfully applied to 1999 KDD Cup network attack data log-on sessions to demonstrate that Data Modeling can detect attacks without prior training on any form of attack behavior. Finally, two new methods for data encryption using these ideas are proposed.

  11. Neuropsychological Definition of Learning: Strategies for Rewiring Neural Networks

    Science.gov (United States)

    Barwegen, Laura

    2008-01-01

    For many years, most scientists believed that the physical structure of our brains, and by definition the people we had become, was set after the initial developmental period of early childhood and adolescence. New research in the area of neurology and neuropsychology is revealing that our brain is a much more open system than ever thought…

  12. Thermal Network Modelling Handbook

    Science.gov (United States)

    1972-01-01

    Thermal mathematical modelling is discussed in detail. A three-fold purpose was established: (1) to acquaint the new user with the terminology and concepts used in thermal mathematical modelling, (2) to present the more experienced and occasional user with quick formulas and methods for solving everyday problems, coupled with study cases which lend insight into the relationships that exist among the various solution techniques and parameters, and (3) to begin to catalog in an orderly fashion the common formulas which may be applied to automated conversational language techniques.

  13. Network Models of Mechanical Assemblies

    Science.gov (United States)

    Whitney, Daniel E.

    Recent network research has sought to characterize complex systems with a number of statistical metrics, such as power law exponent (if any), clustering coefficient, community behavior, and degree correlation. Use of such metrics represents a choice of level of abstraction, a balance of generality and detailed accuracy. It has been noted that "social networks" consistently display clustering coefficients that are higher than those of random or generalized random networks, that they have small world properties such as short path lengths, and that they have positive degree correlations (assortative mixing). "Technological" or "non-social" networks display many of these characteristics except that they generally have negative degree correlations (disassortative mixing). [Newman 2003i] In this paper we examine network models of mechanical assemblies. Such systems are well understood functionally. We show that there is a cap on their average nodal degree and that they have negative degree correlations (disassortative mixing). We identify specific constraints arising from first principles, their structural patterns, and engineering practice that suggest why they have these properties. In addition, we note that their main "motif" is closed loops (as it is for electric and electronic circuits), a pattern that conventional network analysis does not detect but which is used by software intended to aid in the design of such systems.

  14. Service entity network virtualization architecture and model

    Science.gov (United States)

    Jin, Xue-Guang; Shou, Guo-Chu; Hu, Yi-Hong; Guo, Zhi-Gang

    2017-07-01

    Communication network can be treated as a complex network carrying a variety of services and service can be treated as a network composed of functional entities. There are growing interests in multiplex service entities where individual entity and link can be used for different services simultaneously. Entities and their relationships constitute a service entity network. In this paper, we introduced a service entity network virtualization architecture including service entity network hierarchical model, service entity network model, service implementation and deployment of service entity networks. Service entity network oriented multiplex planning model were also studied and many of these multiplex models were characterized by a significant multiplex of the links or entities in different service entity network. Service entity networks were mapped onto shared physical resources by dynamic resource allocation controller. The efficiency of the proposed architecture was illustrated in a simulation environment that allows for comparative performance evaluation. The results show that, compared to traditional networking architecture, this architecture has a better performance.

  15. Polymer networks: Modeling and applications

    Science.gov (United States)

    Masoud, Hassan

    Polymer networks are an important class of materials that are ubiquitously found in natural, biological, and man-made systems. The complex mesoscale structure of these soft materials has made it difficult for researchers to fully explore their properties. In this dissertation, we introduce a coarse-grained computational model for permanently cross-linked polymer networks than can properly capture common properties of these materials. We use this model to study several practical problems involving dry and solvated networks. Specifically, we analyze the permeability and diffusivity of polymer networks under mechanical deformations, we examine the release of encapsulated solutes from microgel capsules during volume transitions, and we explore the complex tribological behavior of elastomers. Our simulations reveal that the network transport properties are defined by the network porosity and by the degree of network anisotropy due to mechanical deformations. In particular, the permeability of mechanically deformed networks can be predicted based on the alignment of network filaments that is characterized by a second order orientation tensor. Moreover, our numerical calculations demonstrate that responsive microcapsules can be effectively utilized for steady and pulsatile release of encapsulated solutes. We show that swollen gel capsules allow steady, diffusive release of nanoparticles and polymer chains, whereas gel deswelling causes burst-like discharge of solutes driven by an outward flow of the solvent initially enclosed within a shrinking capsule. We further demonstrate that this hydrodynamic release can be regulated by introducing rigid microscopic rods in the capsule interior. We also probe the effects of velocity, temperature, and normal load on the sliding of elastomers on smooth and corrugated substrates. Our friction simulations predict a bell-shaped curve for the dependence of the friction coefficient on the sliding velocity. Our simulations also illustrate

  16. 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......, 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....... Working through these cases, students will learn to manage and evaluate realistic intelligence accounts....

  17. CNEM: Cluster Based Network Evolution Model

    Directory of Open Access Journals (Sweden)

    Sarwat Nizamani

    2015-01-01

    Full Text Available This paper presents a network evolution model, which is based on the clustering approach. The proposed approach depicts the network evolution, which demonstrates the network formation from individual nodes to fully evolved network. An agglomerative hierarchical clustering method is applied for the evolution of network. In the paper, we present three case studies which show the evolution of the networks from the scratch. These case studies include: terrorist network of 9/11 incidents, terrorist network of WMD (Weapons Mass Destruction plot against France and a network of tweets discussing a topic. The network of 9/11 is also used for evaluation, using other social network analysis methods which show that the clusters created using the proposed model of network evolution are of good quality, thus the proposed method can be used by law enforcement agencies in order to further investigate the criminal networks

  18. Detection of statistically significant network changes in complex biological networks.

    Science.gov (United States)

    Mall, Raghvendra; Cerulo, Luigi; Bensmail, Halima; Iavarone, Antonio; Ceccarelli, Michele

    2017-03-04

    Biological networks contribute effectively to unveil the complex structure of molecular interactions and to discover driver genes especially in cancer context. It can happen that due to gene mutations, as for example when cancer progresses, the gene expression network undergoes some amount of localized re-wiring. The ability to detect statistical relevant changes in the interaction patterns induced by the progression of the disease can lead to the discovery of novel relevant signatures. Several procedures have been recently proposed to detect sub-network differences in pairwise labeled weighted networks. In this paper, we propose an improvement over the state-of-the-art based on the Generalized Hamming Distance adopted for evaluating the topological difference between two networks and estimating its statistical significance. The proposed procedure exploits a more effective model selection criteria to generate p-values for statistical significance and is more efficient in terms of computational time and prediction accuracy than literature methods. Moreover, the structure of the proposed algorithm allows for a faster parallelized implementation. In the case of dense random geometric networks the proposed approach is 10-15x faster and achieves 5-10% higher AUC, Precision/Recall, and Kappa value than the state-of-the-art. We also report the application of the method to dissect the difference between the regulatory networks of IDH-mutant versus IDH-wild-type glioma cancer. In such a case our method is able to identify some recently reported master regulators as well as novel important candidates. We show that our network differencing procedure can effectively and efficiently detect statistical significant network re-wirings in different conditions. When applied to detect the main differences between the networks of IDH-mutant and IDH-wild-type glioma tumors, it correctly selects sub-networks centered on important key regulators of these two different subtypes. In

  19. Biological transportation networks: Modeling and simulation

    KAUST Repository

    Albi, Giacomo

    2015-09-15

    We present a model for biological network formation originally introduced by Cai and Hu [Adaptation and optimization of biological transport networks, Phys. Rev. Lett. 111 (2013) 138701]. The modeling of fluid transportation (e.g., leaf venation and angiogenesis) and ion transportation networks (e.g., neural networks) is explained in detail and basic analytical features like the gradient flow structure of the fluid transportation network model and the impact of the model parameters on the geometry and topology of network formation are analyzed. We also present a numerical finite-element based discretization scheme and discuss sample cases of network formation simulations.

  20. Role of social environment and social clustering in spread of opinions in coevolving networks.

    Science.gov (United States)

    Malik, Nishant; Mucha, Peter J

    2013-12-01

    Taking a pragmatic approach to the processes involved in the phenomena of collective opinion formation, we investigate two specific modifications to the coevolving network voter model of opinion formation studied by Holme and Newman [Phys. Rev. E 74, 056108 (2006)]. First, we replace the rewiring probability parameter by a distribution of probability of accepting or rejecting opinions between individuals, accounting for heterogeneity and asymmetric influences in relationships between individuals. Second, we modify the rewiring step by a path-length-based preference for rewiring that reinforces local clustering. We have investigated the influences of these modifications on the outcomes of simulations of this model. We found that varying the shape of the distribution of probability of accepting or rejecting opinions can lead to the emergence of two qualitatively distinct final states, one having several isolated connected components each in internal consensus, allowing for the existence of diverse opinions, and the other having a single dominant connected component with each node within that dominant component having the same opinion. Furthermore, more importantly, we found that the initial clustering in the network can also induce similar transitions. Our investigation also indicates that these transitions are governed by a weak and complex dependence on system size. We found that the networks in the final states of the model have rich structural properties including the small world property for some parameter regimes.

  1. Synaptic rewiring of stress-sensitive neurons by early-life experience: a mechanism for resilience?

    Science.gov (United States)

    Singh-Taylor, Akanksha; Korosi, Aniko; Molet, Jenny; Gunn, Benjamin G; Baram, Tallie Z

    2015-01-01

    Genes and environment interact to influence cognitive and emotional functions throughout life. Early-life experiences in particular contribute to vulnerability or resilience to a number of emotional and cognitive illnesses in humans. In rodents, early-life experiences directly lead to resilience or vulnerability to stress later in life, and influence the development of cognitive and emotional deficits. The mechanisms for the enduring effects of early-life experiences on cognitive and emotional outcomes are not completely understood. Here, we present emerging information supporting experience-dependent modulation of the number and efficacy of synaptic inputs onto stress-sensitive neurons. This synaptic 'rewiring', in turn, may influence the expression of crucial neuronal genes. The persistent changes in gene expression in resilient versus vulnerable rodent models are likely maintained via epigenetic mechanisms. Thus, early-life experience may generate resilience by altering synaptic input to neurons, which informs them to modulate their epigenetic machinery.

  2. DNA adenine hypomethylation leads to metabolic rewiring in Deinococcus radiodurans.

    Science.gov (United States)

    Shaiwale, Nayana S; Basu, Bhakti; Deobagkar, Deepti D; Deobagkar, Dileep N; Apte, Shree K

    2015-08-03

    The protein encoded by DR_0643 gene from Deinococcus radiodurans was shown to be an active N-6 adenine-specific DNA methyltransferase (Dam). Deletion of corresponding protein reduced adenine methylation in the genome by 60% and resulted in slow-growth phenotype. Proteomic changes induced by DNA adenine hypomethylation were mapped by two-dimensional protein electrophoresis coupled with mass spectrometry. As compared to wild type D. radiodurans cells, at least 54 proteins were differentially expressed in Δdam mutant. Among these, 39 metabolic enzymes were differentially expressed in Δdam mutant. The most prominent change was DNA adenine hypomethylation induced de-repression of pyruvate dehydrogenase complex, E1 component (aceE) gene resulting in 10 fold increase in the abundance of corresponding protein. The observed differential expression profile of metabolic enzymes included increased abundance of enzymes involved in fatty acid and amino acid degradation to replenish acetyl Co-A and TCA cycle intermediates and diversion of phosphoenolpyruvate and pyruvate into amino acid biosynthesis, a metabolic rewiring attempt by Δdam mutant to restore energy generation via glycolysis-TCA cycle axis. This is the first report of DNA adenine hypomethylation mediated rewiring of metabolic pathways in prokaryotes. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Rewiring protein synthesis: From natural to synthetic amino acids.

    Science.gov (United States)

    Fan, Yongqiang; Evans, Christopher R; Ling, Jiqiang

    2017-11-01

    The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Rewiring Lactococcus lactis for Ethanol Production

    DEFF Research Database (Denmark)

    Solem, Christian; Dehli, Tore Ibsen; Jensen, Peter Ruhdal

    2013-01-01

    to redirect the metabolism of LAB model organism Lactococcus lactis toward ethanol production. Codon-optimized Zymomonas mobilis pyruvate decarboxylase (PDC) was introduced and expressed from synthetic promoters in different strain backgrounds. In the wild-type L. lactis strain MG1363 growing on glucose, only...... small amounts of ethanol were obtained after introducing PDC, probably due to a low native alcohol dehydrogenase activity. When the same strains were grown on maltose, ethanol was the major product and lesser amounts of lactate, formate, and acetate were formed. Inactivating the lactate dehydrogenase...... genes ldhX, ldhB, and ldh and introducing codon-optimized Z. mobilis alcohol dehydrogenase (ADHB) in addition to PDC resulted in high-yield ethanol formation when strains were grown on glucose, with only minor amounts of by-products formed. Finally, a strain with ethanol as the sole observed...

  5. 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.

  6. 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.

  7. 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.

  8. Generalization performance of regularized neural network models

    DEFF Research Database (Denmark)

    Larsen, Jan; Hansen, Lars Kai

    1994-01-01

    Architecture optimization is a fundamental problem of neural network modeling. The optimal architecture is defined as the one which minimizes the generalization error. This paper addresses estimation of the generalization performance of regularized, complete neural network models. Regularization...

  9. 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.

  10. 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...

  11. 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.

  12. Single-neuron NMDA receptor phenotype influences neuronal rewiring and reintegration following traumatic injury.

    Science.gov (United States)

    Patel, Tapan P; Ventre, Scott C; Geddes-Klein, Donna; Singh, Pallab K; Meaney, David F

    2014-03-19

    Alterations in the activity of neural circuits are a common consequence of traumatic brain injury (TBI), but the relationship between single-neuron properties and the aggregate network behavior is not well understood. We recently reported that the GluN2B-containing NMDA receptors (NMDARs) are key in mediating mechanical forces during TBI, and that TBI produces a complex change in the functional connectivity of neuronal networks. Here, we evaluated whether cell-to-cell heterogeneity in the connectivity and aggregate contribution of GluN2B receptors to [Ca(2+)]i before injury influenced the functional rewiring, spontaneous activity, and network plasticity following injury using primary rat cortical dissociated neurons. We found that the functional connectivity of a neuron to its neighbors, combined with the relative influx of calcium through distinct NMDAR subtypes, together contributed to the individual neuronal response to trauma. Specifically, individual neurons whose [Ca(2+)]i oscillations were largely due to GluN2B NMDAR activation lost many of their functional targets 1 h following injury. In comparison, neurons with large GluN2A contribution or neurons with high functional connectivity both independently protected against injury-induced loss in connectivity. Mechanistically, we found that traumatic injury resulted in increased uncorrelated network activity, an effect linked to reduction of the voltage-sensitive Mg(2+) block of GluN2B-containing NMDARs. This uncorrelated activation of GluN2B subtypes after injury significantly limited the potential for network remodeling in response to a plasticity stimulus. Together, our data suggest that two single-cell characteristics, the aggregate contribution of NMDAR subtypes and the number of functional connections, influence network structure following traumatic injury.

  13. 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.

  14. Rewiring food systems to enhance human health and biosphere stewardship

    Science.gov (United States)

    Gordon, Line J.; Bignet, Victoria; Crona, Beatrice; Henriksson, Patrik J. G.; Van Holt, Tracy; Jonell, Malin; Lindahl, Therese; Troell, Max; Barthel, Stephan; Deutsch, Lisa; Folke, Carl; Jamila Haider, L.; Rockström, Johan; Queiroz, Cibele

    2017-10-01

    Food lies at the heart of both health and sustainability challenges. We use a social-ecological framework to illustrate how major changes to the volume, nutrition and safety of food systems between 1961 and today impact health and sustainability. These changes have almost halved undernutrition while doubling the proportion who are overweight. They have also resulted in reduced resilience of the biosphere, pushing four out of six analysed planetary boundaries across the safe operating space of the biosphere. Our analysis further illustrates that consumers and producers have become more distant from one another, with substantial power consolidated within a small group of key actors. Solutions include a shift from a volume-focused production system to focus on quality, nutrition, resource use efficiency, and reduced antimicrobial use. To achieve this, we need to rewire food systems in ways that enhance transparency between producers and consumers, mobilize key actors to become biosphere stewards, and re-connect people to the biosphere.

  15. Neural circuit rewiring: insights from DD synapse remodeling.

    Science.gov (United States)

    Kurup, Naina; Jin, Yishi

    2016-01-01

    Nervous systems exhibit many forms of neuronal plasticity during growth, learning and memory consolidation, as well as in response to injury. Such plasticity can occur across entire nervous systems as with the case of insect metamorphosis, in individual classes of neurons, or even at the level of a single neuron. A striking example of neuronal plasticity in C. elegans is the synaptic rewiring of the GABAergic Dorsal D-type motor neurons during larval development, termed DD remodeling. DD remodeling entails multi-step coordination to concurrently eliminate pre-existing synapses and form new synapses on different neurites, without changing the overall morphology of the neuron. This mini-review focuses on recent advances in understanding the cellular and molecular mechanisms driving DD remodeling.

  16. 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.

  17. Network bandwidth utilization forecast model on high bandwidth networks

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Wuchert (William) [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sim, Alex [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2015-03-30

    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 83.2%. It also shows resilience against abrupt network usage change. The accuracy of the forecast model is within the standard deviation of the monitored measurements.

  18. 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

  19. An adaptive complex network model for brain functional networks.

    Directory of Open Access Journals (Sweden)

    Ignacio J Gomez Portillo

    Full Text Available Brain functional networks are graph representations of activity in the brain, where the vertices represent anatomical regions and the edges their functional connectivity. These networks present a robust small world topological structure, characterized by highly integrated modules connected sparsely by long range links. Recent studies showed that other topological properties such as the degree distribution and the presence (or absence of a hierarchical structure are not robust, and show different intriguing behaviors. In order to understand the basic ingredients necessary for the emergence of these complex network structures we present an adaptive complex network model for human brain functional networks. The microscopic units of the model are dynamical nodes that represent active regions of the brain, whose interaction gives rise to complex network structures. The links between the nodes are chosen following an adaptive algorithm that establishes connections between dynamical elements with similar internal states. We show that the model is able to describe topological characteristics of human brain networks obtained from functional magnetic resonance imaging studies. In particular, when the dynamical rules of the model allow for integrated processing over the entire network scale-free non-hierarchical networks with well defined communities emerge. On the other hand, when the dynamical rules restrict the information to a local neighborhood, communities cluster together into larger ones, giving rise to a hierarchical structure, with a truncated power law degree distribution.

  20. Modeling gene regulatory networks: A network simplification algorithm

    Science.gov (United States)

    Ferreira, Luiz Henrique O.; de Castro, Maria Clicia S.; da Silva, Fabricio A. B.

    2016-12-01

    Boolean networks have been used for some time to model Gene Regulatory Networks (GRNs), which describe cell functions. Those models can help biologists to make predictions, prognosis and even specialized treatment when some disturb on the GRN lead to a sick condition. However, the amount of information related to a GRN can be huge, making the task of inferring its boolean network representation quite a challenge. The method shown here takes into account information about the interactome to build a network, where each node represents a protein, and uses the entropy of each node as a key to reduce the size of the network, allowing the further inferring process to focus only on the main protein hubs, the ones with most potential to interfere in overall network behavior.

  1. The model of social crypto-network

    Directory of Open Access Journals (Sweden)

    Марк Миколайович Орел

    2015-06-01

    Full Text Available The article presents the theoretical model of social network with the enhanced mechanism of privacy policy. It covers the problems arising in the process of implementing the mentioned type of network. There are presented the methods of solving problems arising in the process of building the social network with privacy policy. It was built a theoretical model of social networks with enhanced information protection methods based on information and communication blocks

  2. Entropy Characterization of Random Network Models

    Directory of Open Access Journals (Sweden)

    Pedro J. Zufiria

    2017-06-01

    Full Text Available This paper elaborates on the Random Network Model (RNM as a mathematical framework for modelling and analyzing the generation of complex networks. Such framework allows the analysis of the relationship between several network characterizing features (link density, clustering coefficient, degree distribution, connectivity, etc. and entropy-based complexity measures, providing new insight on the generation and characterization of random networks. Some theoretical and computational results illustrate the utility of the proposed framework.

  3. The model of social crypto-network

    OpenAIRE

    Марк Миколайович Орел

    2015-01-01

    The article presents the theoretical model of social network with the enhanced mechanism of privacy policy. It covers the problems arising in the process of implementing the mentioned type of network. There are presented the methods of solving problems arising in the process of building the social network with privacy policy. It was built a theoretical model of social networks with enhanced information protection methods based on information and communication blocks

  4. Modeling Diagnostic Assessments with Bayesian Networks

    Science.gov (United States)

    Almond, Russell G.; DiBello, Louis V.; Moulder, Brad; Zapata-Rivera, Juan-Diego

    2007-01-01

    This paper defines Bayesian network models and examines their applications to IRT-based cognitive diagnostic modeling. These models are especially suited to building inference engines designed to be synchronous with the finer grained student models that arise in skills diagnostic assessment. Aspects of the theory and use of Bayesian network models…

  5. Bayesian Network Webserver: a comprehensive tool for biological network modeling.

    Science.gov (United States)

    Ziebarth, Jesse D; Bhattacharya, Anindya; Cui, Yan

    2013-11-01

    The Bayesian Network Webserver (BNW) is a platform for comprehensive network modeling of systems genetics and other biological datasets. It allows users to quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data and use the model to understand relationships between network variables. Many datasets, including those used to create genetic network models, contain both discrete (e.g. genotype) and continuous (e.g. gene expression traits) variables, and BNW allows for modeling hybrid datasets. Users of BNW can incorporate prior knowledge during structure learning through an easy-to-use structural constraint interface. After structure learning, users are immediately presented with an interactive network model, which can be used to make testable hypotheses about network relationships. BNW, including a downloadable structure learning package, is available at http://compbio.uthsc.edu/BNW. (The BNW interface for adding structural constraints uses HTML5 features that are not supported by current version of Internet Explorer. We suggest using other browsers (e.g. Google Chrome or Mozilla Firefox) when accessing BNW). ycui2@uthsc.edu. Supplementary data are available at Bioinformatics online.

  6. Computational design of genomic transcriptional networks with adaptation to varying environments

    Science.gov (United States)

    Carrera, Javier; Elena, Santiago F.; Jaramillo, Alfonso

    2012-01-01

    Transcriptional profiling has been widely used as a tool for unveiling the coregulations of genes in response to genetic and environmental perturbations. These coregulations have been used, in a few instances, to infer global transcriptional regulatory models. Here, using the large amount of transcriptomic information available for the bacterium Escherichia coli, we seek to understand the design principles determining the regulation of its transcriptome. Combining transcriptomic and signaling data, we develop an evolutionary computational procedure that allows obtaining alternative genomic transcriptional regulatory network (GTRN) that still maintains its adaptability to dynamic environments. We apply our methodology to an E. coli GTRN and show that it could be rewired to simpler transcriptional regulatory structures. These rewired GTRNs still maintain the global physiological response to fluctuating environments. Rewired GTRNs contain 73% fewer regulated operons. Genes with similar functions and coordinated patterns of expression across environments are clustered into longer regulated operons. These synthetic GTRNs are more sensitive and show a more robust response to challenging environments. This result illustrates that the natural configuration of E. coli GTRN does not necessarily result from selection for robustness to environmental perturbations, but that evolutionary contingencies may have been important as well. We also discuss the limitations of our methodology in the context of the demand theory. Our procedure will be useful as a novel way to analyze global transcription regulation networks and in synthetic biology for the de novo design of genomes. PMID:22927389

  7. Object Oriented Modeling Of Social Networks

    NARCIS (Netherlands)

    Zeggelink, Evelien P.H.; Oosten, Reinier van; Stokman, Frans N.

    1996-01-01

    The aim of this paper is to explain principles of object oriented modeling in the scope of modeling dynamic social networks. As such, the approach of object oriented modeling is advocated within the field of organizational research that focuses on networks. We provide a brief introduction into the

  8. Bayesian estimation of the network autocorrelation model

    NARCIS (Netherlands)

    Dittrich, D.; Leenders, R.T.A.J.; Mulder, J.

    2017-01-01

    The network autocorrelation model has been extensively used by researchers interested modeling social influence effects in social networks. The most common inferential method in the model is classical maximum likelihood estimation. This approach, however, has known problems such as negative bias of

  9. 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...

  10. 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.

  11. Settings in Social Networks : a Measurement Model

    NARCIS (Netherlands)

    Schweinberger, Michael; Snijders, Tom A.B.

    2003-01-01

    A class of statistical models is proposed that aims to recover latent settings structures in social networks. Settings may be regarded as clusters of vertices. The measurement model is based on two assumptions. (1) The observed network is generated by hierarchically nested latent transitive

  12. Settings in social networks : A measurement model

    NARCIS (Netherlands)

    Schweinberger, M; Snijders, TAB

    2003-01-01

    A class of statistical models is proposed that aims to recover latent settings structures in social networks. Settings may be regarded as clusters of vertices. The measurement model is based on two assumptions. (1) The observed network is generated by hierarchically nested latent transitive

  13. Spinal Cord Injury Model System Information Network

    Science.gov (United States)

    ... the UAB-SCIMS Contact the UAB-SCIMS UAB Spinal Cord Injury Model System Newly Injured Health Daily Living Consumer ... Information Network The University of Alabama at Birmingham Spinal Cord Injury Model System (UAB-SCIMS) maintains this Information Network ...

  14. Radio Channel Modeling in Body Area Networks

    NARCIS (Netherlands)

    An, L.; Bentum, Marinus Jan; Meijerink, Arjan; Scanlon, W.G.

    2009-01-01

    A body area network (BAN) is a network of bodyworn or implanted electronic devices, including wireless sensors which can monitor body parameters or to de- tect movements. One of the big challenges in BANs is the propagation channel modeling. Channel models can be used to understand wave propagation

  15. Radio channel modeling in body area networks

    NARCIS (Netherlands)

    An, L.; Bentum, Marinus Jan; Meijerink, Arjan; Scanlon, W.G.

    2010-01-01

    A body area network (BAN) is a network of bodyworn or implanted electronic devices, including wireless sensors which can monitor body parameters or to detect movements. One of the big challenges in BANs is the propagation channel modeling. Channel models can be used to understand wave propagation in

  16. Network interconnections: an architectural reference model

    NARCIS (Netherlands)

    Butscher, B.; Lenzini, L.; Morling, R.; Vissers, C.A.; Popescu-Zeletin, R.; van Sinderen, Marten J.; Heger, D.; Krueger, G.; Spaniol, O.; Zorn, W.

    1985-01-01

    One of the major problems in understanding the different approaches in interconnecting networks of different technologies is the lack of reference to a general model. The paper develops the rationales for a reference model of network interconnection and focuses on the architectural implications for

  17. 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.

  18. Learning Bayesian Network Model Structure from Data

    National Research Council Canada - National Science Library

    Margaritis, Dimitris

    2003-01-01

    In this thesis I address the important problem of the determination of the structure of directed statistical models, with the widely used class of Bayesian network models as a concrete vehicle of my ideas...

  19. NC truck network model development research.

    Science.gov (United States)

    2008-09-01

    This research develops a validated prototype truck traffic network model for North Carolina. The model : includes all counties and metropolitan areas of North Carolina and major economic areas throughout the : U.S. Geographic boundaries, population a...

  20. 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.

  1. Modelling the structure of complex networks

    DEFF Research Database (Denmark)

    Herlau, Tue

    networks has been independently studied as mathematical objects in their own right. As such, there has been both an increased demand for statistical methods for complex networks as well as a quickly growing mathematical literature on the subject. In this dissertation we explore aspects of modelling complex......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....... The 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...

  2. A Network Formation Model Based on Subgraphs

    CERN Document Server

    Chandrasekhar, Arun

    2016-01-01

    We develop a new class of random-graph models for the statistical estimation of network formation that allow for substantial correlation in links. Various subgraphs (e.g., links, triangles, cliques, stars) are generated and their union results in a network. We provide estimation techniques for recovering the rates at which the underlying subgraphs were formed. We illustrate the models via a series of applications including testing for incentives to form cross-caste relationships in rural India, testing to see whether network structure is used to enforce risk-sharing, testing as to whether networks change in response to a community's exposure to microcredit, and show that these models significantly outperform stochastic block models in matching observed network characteristics. We also establish asymptotic properties of the models and various estimators, which requires proving a new Central Limit Theorem for correlated random variables.

  3. Gossip spread in social network Models

    Science.gov (United States)

    Johansson, Tobias

    2017-04-01

    Gossip almost inevitably arises in real social networks. In this article we investigate the relationship between the number of friends of a person and limits on how far gossip about that person can spread in the network. How far gossip travels in a network depends on two sets of factors: (a) factors determining gossip transmission from one person to the next and (b) factors determining network topology. For a simple model where gossip is spread among people who know the victim it is known that a standard scale-free network model produces a non-monotonic relationship between number of friends and expected relative spread of gossip, a pattern that is also observed in real networks (Lind et al., 2007). Here, we study gossip spread in two social network models (Toivonen et al., 2006; Vázquez, 2003) by exploring the parameter space of both models and fitting them to a real Facebook data set. Both models can produce the non-monotonic relationship of real networks more accurately than a standard scale-free model while also exhibiting more realistic variability in gossip spread. Of the two models, the one given in Vázquez (2003) best captures both the expected values and variability of gossip spread.

  4. Synergistic effects in threshold models on networks

    Science.gov (United States)

    Juul, Jonas S.; Porter, Mason A.

    2018-01-01

    Network structure can have a significant impact on the propagation of diseases, memes, and information on social networks. Different types of spreading processes (and other dynamical processes) are affected by network architecture in different ways, and it is important to develop tractable models of spreading processes on networks to explore such issues. In this paper, we incorporate the idea of synergy into a two-state ("active" or "passive") threshold model of social influence on networks. Our model's update rule is deterministic, and the influence of each meme-carrying (i.e., active) neighbor can—depending on a parameter—either be enhanced or inhibited by an amount that depends on the number of active neighbors of a node. Such a synergistic system models social behavior in which the willingness to adopt either accelerates or saturates in a way that depends on the number of neighbors who have adopted that behavior. We illustrate that our model's synergy parameter has a crucial effect on system dynamics, as it determines whether degree-k nodes are possible or impossible to activate. We simulate synergistic meme spreading on both random-graph models and networks constructed from empirical data. Using a heterogeneous mean-field approximation, which we derive under the assumption that a network is locally tree-like, we are able to determine which synergy-parameter values allow degree-k nodes to be activated for many networks and for a broad family of synergistic models.

  5. Optimized null model for protein structure networks.

    Science.gov (United States)

    Milenković, Tijana; Filippis, Ioannis; Lappe, Michael; Przulj, Natasa

    2009-06-26

    Much attention has recently been given to the statistical significance of topological features observed in biological networks. Here, we consider residue interaction graphs (RIGs) as network representations of protein structures with residues as nodes and inter-residue interactions as edges. Degree-preserving randomized models have been widely used for this purpose in biomolecular networks. However, such a single summary statistic of a network may not be detailed enough to capture the complex topological characteristics of protein structures and their network counterparts. Here, we investigate a variety of topological properties of RIGs to find a well fitting network null model for them. The RIGs are derived from a structurally diverse protein data set at various distance cut-offs and for different groups of interacting atoms. We compare the network structure of RIGs to several random graph models. We show that 3-dimensional geometric random graphs, that model spatial relationships between objects, provide the best fit to RIGs. We investigate the relationship between the strength of the fit and various protein structural features. We show that the fit depends on protein size, structural class, and thermostability, but not on quaternary structure. We apply our model to the identification of significantly over-represented structural building blocks, i.e., network motifs, in protein structure networks. As expected, choosing geometric graphs as a null model results in the most specific identification of motifs. Our geometric random graph model may facilitate further graph-based studies of protein conformation space and have important implications for protein structure comparison and prediction. The choice of a well-fitting null model is crucial for finding structural motifs that play an important role in protein folding, stability and function. To our knowledge, this is the first study that addresses the challenge of finding an optimized null model for RIGs, by

  6. Optimized null model for protein structure networks.

    Directory of Open Access Journals (Sweden)

    Tijana Milenković

    Full Text Available Much attention has recently been given to the statistical significance of topological features observed in biological networks. Here, we consider residue interaction graphs (RIGs as network representations of protein structures with residues as nodes and inter-residue interactions as edges. Degree-preserving randomized models have been widely used for this purpose in biomolecular networks. However, such a single summary statistic of a network may not be detailed enough to capture the complex topological characteristics of protein structures and their network counterparts. Here, we investigate a variety of topological properties of RIGs to find a well fitting network null model for them. The RIGs are derived from a structurally diverse protein data set at various distance cut-offs and for different groups of interacting atoms. We compare the network structure of RIGs to several random graph models. We show that 3-dimensional geometric random graphs, that model spatial relationships between objects, provide the best fit to RIGs. We investigate the relationship between the strength of the fit and various protein structural features. We show that the fit depends on protein size, structural class, and thermostability, but not on quaternary structure. We apply our model to the identification of significantly over-represented structural building blocks, i.e., network motifs, in protein structure networks. As expected, choosing geometric graphs as a null model results in the most specific identification of motifs. Our geometric random graph model may facilitate further graph-based studies of protein conformation space and have important implications for protein structure comparison and prediction. The choice of a well-fitting null model is crucial for finding structural motifs that play an important role in protein folding, stability and function. To our knowledge, this is the first study that addresses the challenge of finding an optimized null model

  7. Towards Reproducible Descriptions of Neuronal Network Models

    Science.gov (United States)

    Nordlie, Eilen; Gewaltig, Marc-Oliver; Plesser, Hans Ekkehard

    2009-01-01

    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. PMID:19662159

  8. 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.

  9. 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....... The model investigates the traffic generation mechanisms, and grouping traffic into flows and applications....

  10. Modeling, Optimization & Control of Hydraulic Networks

    DEFF Research Database (Denmark)

    Tahavori, Maryamsadat

    2014-01-01

    in water network is pressure management. By reducing the pressure in the water network, the leakage can be reduced significantly. Also it reduces the amount of energy consumption in water networks. The primary purpose of this work is to develop control algorithms for pressure control in water supply....... 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...

  11. A network model of the interbank market

    Science.gov (United States)

    Li, Shouwei; He, Jianmin; Zhuang, Yaming

    2010-12-01

    This work introduces a network model of an interbank market based on interbank credit lending relationships. It generates some network features identified through empirical analysis. The critical issue to construct an interbank network is to decide the edges among banks, which is realized in this paper based on the interbank’s degree of trust. Through simulation analysis of the interbank network model, some typical structural features are identified in our interbank network, which are also proved to exist in real interbank networks. They are namely, a low clustering coefficient and a relatively short average path length, community structures, and a two-power-law distribution of out-degree and in-degree.

  12. Model for Microcirculation Transportation Network Design

    Directory of Open Access Journals (Sweden)

    Qun Chen

    2012-01-01

    Full Text Available The idea of microcirculation transportation was proposed to shunt heavy traffic on arterial roads through branch roads. The optimization model for designing micro-circulation transportation network was developed to pick out branch roads as traffic-shunting channels and determine their required capacity, trying to minimize the total reconstruction expense and land occupancy subject to saturation and reconstruction space constraints, while accounting for the route choice behaviour of network users. Since micro-circulation transportation network design problem includes both discrete and continuous variables, a discretization method was developed to convert two groups of variables (discrete variables and continuous variables into one group of new discrete variables, transforming the mixed network design problem into a new kind of discrete network design problem with multiple values. The genetic algorithm was proposed to solve the new discrete network design problem. Finally a numerical example demonstrated the efficiency of the model and algorithm.

  13. Re-wiring of energy metabolism promotes viability during hyperreplication stress in E. coli.

    Directory of Open Access Journals (Sweden)

    Godefroid Charbon

    2017-01-01

    Full Text Available Chromosome replication in Escherichia coli is initiated by DnaA. DnaA binds ATP which is essential for formation of a DnaA-oriC nucleoprotein complex that promotes strand opening, helicase loading and replisome assembly. Following initiation, DnaAATP is converted to DnaAADP primarily by the Regulatory Inactivation of DnaA process (RIDA. In RIDA deficient cells, DnaAATP accumulates leading to uncontrolled initiation of replication and cell death by accumulation of DNA strand breaks. Mutations that suppress RIDA deficiency either dampen overinitiation or permit growth despite overinitiation. We characterize mutations of the last group that have in common that distinct metabolic routes are rewired resulting in the redirection of electron flow towards the cytochrome bd-1. We propose a model where cytochrome bd-1 lowers the formation of reactive oxygen species and hence oxidative damage to the DNA in general. This increases the processivity of replication forks generated by overinitiation to a level that sustains viability.

  14. Modelling of virtual production networks

    Directory of Open Access Journals (Sweden)

    2011-03-01

    Full Text Available Nowadays many companies, especially small and medium-sized enterprises (SMEs, specialize in a limited field of production. It requires forming virtual production networks of cooperating enterprises to manufacture better, faster and cheaper. Apart from that, some production orders cannot be realized, because there is not a company of sufficient production potential. In this case the virtual production networks of cooperating companies can realize these production orders. These networks have larger production capacity and many different resources. Therefore it can realize many more production orders together than each of them separately. Such organization allows for executing high quality product. The maintenance costs of production capacity and used resources are not so high. In this paper a methodology of rapid prototyping of virtual production networks is proposed. It allows to execute production orders on time considered existing logistic constraints.

  15. Modeling Epidemics Spreading on Social Contact Networks.

    Science.gov (United States)

    Zhang, Zhaoyang; Wang, Honggang; Wang, Chonggang; Fang, Hua

    2015-09-01

    Social contact networks and the way people interact with each other are the key factors that impact on epidemics spreading. However, it is challenging to model the behavior of epidemics based on social contact networks due to their high dynamics. Traditional models such as susceptible-infected-recovered (SIR) model ignore the crowding or protection effect and thus has some unrealistic assumption. In this paper, we consider the crowding or protection effect and develop a novel model called improved SIR model. Then, we use both deterministic and stochastic models to characterize the dynamics of epidemics on social contact networks. The results from both simulations and real data set conclude that the epidemics are more likely to outbreak on social contact networks with higher average degree. We also present some potential immunization strategies, such as random set immunization, dominating set immunization, and high degree set immunization to further prove the conclusion.

  16. Random graph models for dynamic networks

    Science.gov (United States)

    Zhang, Xiao; Moore, Cristopher; Newman, Mark E. J.

    2017-10-01

    Recent theoretical work on the modeling of network structure has focused primarily on networks that are static and unchanging, but many real-world networks change their structure over time. There exist natural generalizations to the dynamic case of many static network models, including the classic random graph, the configuration model, and the stochastic block model, where one assumes that the appearance and disappearance of edges are governed by continuous-time Markov processes with rate parameters that can depend on properties of the nodes. Here we give an introduction to this class of models, showing for instance how one can compute their equilibrium properties. We also demonstrate their use in data analysis and statistical inference, giving efficient algorithms for fitting them to observed network data using the method of maximum likelihood. This allows us, for example, 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 these methods with a selection of applications, both to computer-generated test networks and real-world examples.

  17. Modeling the interdependent network based on two-mode networks

    Science.gov (United States)

    An, Feng; Gao, Xiangyun; Guan, Jianhe; Huang, Shupei; Liu, Qian

    2017-10-01

    Among heterogeneous networks, there exist obviously and closely interdependent linkages. Unlike existing research primarily focus on the theoretical research of physical interdependent network model. We propose a two-layer interdependent network model based on two-mode networks to explore the interdependent features in the reality. Specifically, we construct a two-layer interdependent loan network and develop several dependent features indices. The model is verified to enable us to capture the loan dependent features of listed companies based on loan behaviors and shared shareholders. Taking Chinese debit and credit market as case study, the main conclusions are: (1) only few listed companies shoulder the main capital transmission (20% listed companies occupy almost 70% dependent degree). (2) The control of these key listed companies will be more effective of avoiding the spreading of financial risks. (3) Identifying the companies with high betweenness centrality and controlling them could be helpful to monitor the financial risk spreading. (4) The capital transmission channel among Chinese financial listed companies and Chinese non-financial listed companies are relatively strong. However, under greater pressure of demand of capital transmission (70% edges failed), the transmission channel, which constructed by debit and credit behavior, will eventually collapse.

  18. 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.

  19. Tensor network models of multiboundary wormholes

    Science.gov (United States)

    Peach, Alex; Ross, Simon F.

    2017-05-01

    We study the entanglement structure of states dual to multiboundary wormhole geometries using tensor network models. Perfect and random tensor networks tiling the hyperbolic plane have been shown to provide good models of the entanglement structure in holography. We extend this by quotienting the plane by discrete isometries to obtain models of the multiboundary states. We show that there are networks where the entanglement structure is purely bipartite, extending results obtained in the large temperature limit. We analyse the entanglement structure in a range of examples.

  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. Designing Network-based Business Model Ontology

    DEFF Research Database (Denmark)

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

    2015-01-01

    Survival on dynamic environment is not achieved without a map. Scanning and monitoring of the market show business models as a fruitful tool. But scholars believe that old-fashioned business models are dead; as they are not included the effect of internet and network in themselves. This paper...... 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....

  2. Queueing Models for Mobile Ad Hoc Networks

    NARCIS (Netherlands)

    de Haan, Roland

    2009-01-01

    This thesis presents models for the performance analysis of a recent communication paradigm: \\emph{mobile ad hoc networking}. The objective of mobile ad hoc networking is to provide wireless connectivity between stations in a highly dynamic environment. These dynamics are driven by the mobility of

  3. Modelling traffic congestion using queuing networks

    Indian Academy of Sciences (India)

    Traffic Flow-Density diagrams are obtained using simple Jackson queuing network analysis. Such simple analytical models can be used to capture the effect of non- homogenous traffic. Keywords. Flow-density curves; uninterrupted traffic; Jackson networks. 1. Introduction. Traffic management has become very essential in ...

  4. Mathematical model of highways network optimization

    Science.gov (United States)

    Sakhapov, R. L.; Nikolaeva, R. V.; Gatiyatullin, M. H.; Makhmutov, M. M.

    2017-12-01

    The article deals with the issue of highways network design. Studies show that the main requirement from road transport for the road network is to ensure the realization of all the transport links served by it, with the least possible cost. The goal of optimizing the network of highways is to increase the efficiency of transport. It is necessary to take into account a large number of factors that make it difficult to quantify and qualify their impact on the road network. In this paper, we propose building an optimal variant for locating the road network on the basis of a mathematical model. The article defines the criteria for optimality and objective functions that reflect the requirements for the road network. The most fully satisfying condition for optimality is the minimization of road and transport costs. We adopted this indicator as a criterion of optimality in the economic-mathematical model of a network of highways. Studies have shown that each offset point in the optimal binding road network is associated with all other corresponding points in the directions providing the least financial costs necessary to move passengers and cargo from this point to the other corresponding points. The article presents general principles for constructing an optimal network of roads.

  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. 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 ...

  7. Complex networks repair strategies: Dynamic models

    Science.gov (United States)

    Fu, Chaoqi; Wang, Ying; Gao, Yangjun; Wang, Xiaoyang

    2017-09-01

    Network repair strategies are tactical methods that restore the efficiency of damaged networks; however, unreasonable repair strategies not only waste resources, they are also ineffective for network recovery. Most extant research on network repair focuses on static networks, but results and findings on static networks cannot be applied to evolutionary dynamic networks because, in dynamic models, complex network repair has completely different characteristics. For instance, repaired nodes face more severe challenges, and require strategic repair methods in order to have a significant effect. In this study, we propose the Shell Repair Strategy (SRS) to minimize the risk of secondary node failures due to the cascading effect. Our proposed method includes the identification of a set of vital nodes that have a significant impact on network repair and defense. Our identification of these vital nodes reduces the number of switching nodes that face the risk of secondary failures during the dynamic repair process. This is positively correlated with the size of the average degree 〈 k 〉 and enhances network invulnerability.

  8. 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.

  9. Gene Regulation Networks for Modeling Drosophila Development

    Science.gov (United States)

    Mjolsness, E.

    1999-01-01

    This chapter will very briefly introduce and review some computational experiments in using trainable gene regulation network models to simulate and understand selected episodes in the development of the fruit fly, Drosophila Melanogaster.

  10. 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.

  11. Mitigating risk during strategic supply network modeling

    OpenAIRE

    Müssigmann, Nikolaus

    2006-01-01

    Mitigating risk during strategic supply network modeling. - In: Managing risks in supply chains / ed. by Wolfgang Kersten ... - Berlin : Schmidt, 2006. - S. 213-226. - (Operations and technology management ; 1)

  12. A high throughput amenable Arabidopsis-P. aeruginosa system reveals a rewired regulatory module and the utility to identify potent anti-infectives.

    Directory of Open Access Journals (Sweden)

    Suresh Gopalan

    2011-01-01

    Full Text Available We previously demonstrated that in a metasystem consisting of Arabidopsis seedlings growing in liquid medium (in 96 well plates even microbes considered to be innocuous such as laboratory strains of E. coli and B. subtilis can cause potent damage to the host. We further posited that such environment-induced adaptations are brought about by 'system status changes' (rewiring of pre-existing cellular signaling networks and components of the host and the microbe, and that prolongation of such a situation could lead to the emergence of pathogenic states in real-life. Here, using this infection model, we show that the master regulator GacA of the human opportunistic pathogen P. aeruginosa (strain PA14 is dispensable for pathogenesis, as evidenced by three independent read-outs. The gene expression profile of the host after infection with wild type PA14 or the gacA mutant are also identical. GacA normally acts upstream of the quorum sensing regulatory circuit (that includes the regulator LasR that controls a subset of virulence factors. Double mutants in gacA and lasR behave similar to the lasR mutant, as seen by abrogation of a characteristic cell type specific host cell damage caused by PA14 or the gacA mutant. This indicates that a previously unrecognized regulatory mechanism is operative under these conditions upstream of LasR. In addition, the detrimental effect of PA14 on Arabidopsis seedlings is resistant to high concentrations of the aminoglycoside antibiotic gentamicin. These data suggest that the Arabidopsis seedling infection system could be used to identify anti-infectives with potentially novel modes of action.

  13. A high throughput amenable Arabidopsis-P. aeruginosa system reveals a rewired regulatory module and the utility to identify potent anti-infectives.

    Science.gov (United States)

    Gopalan, Suresh; Ausubel, Frederick M

    2011-01-21

    We previously demonstrated that in a metasystem consisting of Arabidopsis seedlings growing in liquid medium (in 96 well plates) even microbes considered to be innocuous such as laboratory strains of E. coli and B. subtilis can cause potent damage to the host. We further posited that such environment-induced adaptations are brought about by 'system status changes' (rewiring of pre-existing cellular signaling networks and components) of the host and the microbe, and that prolongation of such a situation could lead to the emergence of pathogenic states in real-life. Here, using this infection model, we show that the master regulator GacA of the human opportunistic pathogen P. aeruginosa (strain PA14) is dispensable for pathogenesis, as evidenced by three independent read-outs. The gene expression profile of the host after infection with wild type PA14 or the gacA mutant are also identical. GacA normally acts upstream of the quorum sensing regulatory circuit (that includes the regulator LasR) that controls a subset of virulence factors. Double mutants in gacA and lasR behave similar to the lasR mutant, as seen by abrogation of a characteristic cell type specific host cell damage caused by PA14 or the gacA mutant. This indicates that a previously unrecognized regulatory mechanism is operative under these conditions upstream of LasR. In addition, the detrimental effect of PA14 on Arabidopsis seedlings is resistant to high concentrations of the aminoglycoside antibiotic gentamicin. These data suggest that the Arabidopsis seedling infection system could be used to identify anti-infectives with potentially novel modes of action.

  14. Road maintenance planning using network flow modelling

    OpenAIRE

    Yang, Chao; Remenyte-Prescott, Rasa; Andrews, John

    2015-01-01

    This paper presents a road maintenance planning model that can be used to balance out maintenance cost and road user cost, since performing road maintenance at night can be convenient for road users but costly for highway agency. Based on the platform of the network traffic flow modelling, the traffic through the worksite and its adjacent road links is evaluated. Thus, maintenance arrangements at a worksite can be optimized considering the overall network performance. In addition, genetic alg...

  15. Posterior Predictive Model Checking in Bayesian Networks

    Science.gov (United States)

    Crawford, Aaron

    2014-01-01

    This simulation study compared the utility of various discrepancy measures within a posterior predictive model checking (PPMC) framework for detecting different types of data-model misfit in multidimensional Bayesian network (BN) models. The investigated conditions were motivated by an applied research program utilizing an operational complex…

  16. 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.

  17. Modeling gene regulatory network motifs using Statecharts.

    Science.gov (United States)

    Fioravanti, Fabio; Helmer-Citterich, Manuela; Nardelli, Enrico

    2012-03-28

    Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. Recently, a great effort has been devoted to give gene regulatory networks a formal semantics based on existing computational frameworks.For this purpose, we consider Statecharts, which are a modular, hierarchical and executable formal model widely used to represent software systems. We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs. We present an improved method for modeling gene regulatory network motifs using Statecharts and we describe the successful modeling of several motifs, including those which could not be modeled or whose models could not be distinguished using the method of a previous proposal.We model motifs in an easy and intuitive way by taking advantage of the visual features of Statecharts. Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation. We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. The basic motifs used to build more complex networks (that is, simple regulation, reciprocal regulation, feedback loop, feedforward loop, and autoregulation) can be faithfully described and their temporal dynamics can be analyzed.

  18. Neural network approaches for noisy language modeling.

    Science.gov (United States)

    Li, Jun; Ouazzane, Karim; Kazemian, Hassan B; Afzal, Muhammad Sajid

    2013-11-01

    Text entry from people is not only grammatical and distinct, but also noisy. For example, a user's typing stream contains all the information about the user's interaction with computer using a QWERTY keyboard, which may include the user's typing mistakes as well as specific vocabulary, typing habit, and typing performance. In particular, these features are obvious in disabled users' typing streams. This paper proposes a new concept called noisy language modeling by further developing information theory and applies neural networks to one of its specific application-typing stream. This paper experimentally uses a neural network approach to analyze the disabled users' typing streams both in general and specific ways to identify their typing behaviors and subsequently, to make typing predictions and typing corrections. In this paper, a focused time-delay neural network (FTDNN) language model, a time gap model, a prediction model based on time gap, and a probabilistic neural network model (PNN) are developed. A 38% first hitting rate (HR) and a 53% first three HR in symbol prediction are obtained based on the analysis of a user's typing history through the FTDNN language modeling, while the modeling results using the time gap prediction model and the PNN model demonstrate that the correction rates lie predominantly in between 65% and 90% with the current testing samples, and 70% of all test scores above basic correction rates, respectively. The modeling process demonstrates that a neural network is a suitable and robust language modeling tool to analyze the noisy language stream. The research also paves the way for practical application development in areas such as informational analysis, text prediction, and error correction by providing a theoretical basis of neural network approaches for noisy language modeling.

  19. A quantum-implementable neural network model

    Science.gov (United States)

    Chen, Jialin; Wang, Lingli; Charbon, Edoardo

    2017-10-01

    A quantum-implementable neural network, namely quantum probability neural network (QPNN) model, is proposed in this paper. QPNN can use quantum parallelism to trace all possible network states to improve the result. Due to its unique quantum nature, this model is robust to several quantum noises under certain conditions, which can be efficiently implemented by the qubus quantum computer. Another advantage is that QPNN can be used as memory to retrieve the most relevant data and even to generate new data. The MATLAB experimental results of Iris data classification and MNIST handwriting recognition show that much less neuron resources are required in QPNN to obtain a good result than the classical feedforward neural network. The proposed QPNN model indicates that quantum effects are useful for real-life classification tasks.

  20. Telestroke network business model strategies.

    Science.gov (United States)

    Fanale, Christopher V; Demaerschalk, Bart M

    2012-10-01

    Our objective is to summarize the evidence that supports the reliability of telemedicine for diagnosis and efficacy in acute stroke treatment, identify strategies for funding the development of a telestroke network, and to present issues with respect to economic sustainability, cost effectiveness, and the status of reimbursement for telestroke. Copyright © 2012 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  1. Complex networks under dynamic repair model

    Science.gov (United States)

    Chaoqi, Fu; Ying, Wang; Kun, Zhao; Yangjun, Gao

    2018-01-01

    Invulnerability is not the only factor of importance when considering complex networks' security. It is also critical to have an effective and reasonable repair strategy. Existing research on network repair is confined to the static model. The dynamic model makes better use of the redundant capacity of repaired nodes and repairs the damaged network more efficiently than the static model; however, the dynamic repair model is complex and polytropic. In this paper, we construct a dynamic repair model and systematically describe the energy-transfer relationships between nodes in the repair process of the failure network. Nodes are divided into three types, corresponding to three structures. We find that the strong coupling structure is responsible for secondary failure of the repaired nodes and propose an algorithm that can select the most suitable targets (nodes or links) to repair the failure network with minimal cost. Two types of repair strategies are identified, with different effects under the two energy-transfer rules. The research results enable a more flexible approach to network repair.

  2. Markov State Models of gene regulatory networks.

    Science.gov (United States)

    Chu, Brian K; Tse, Margaret J; Sato, Royce R; Read, Elizabeth L

    2017-02-06

    Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have the potential to guide cell-reprogramming strategies. Networks are often modeled by the stochastic Chemical Master Equation, but methods for systematic identification of key properties of the global dynamics are currently lacking. The method identifies the number, phenotypes, and lifetimes of long-lived states for a set of common gene regulatory network models. Application of transition path theory to the constructed Markov State Model decomposes global dynamics into a set of dominant transition paths and associated relative probabilities for stochastic state-switching. In this proof-of-concept study, we found that the Markov State Model provides a general framework for analyzing and visualizing stochastic multistability and state-transitions in gene networks. Our results suggest that this framework-adopted from the field of atomistic Molecular Dynamics-can be a useful tool for quantitative Systems Biology at the network scale.

  3. TCA cycle rewiring fosters metabolic adaptation to oxygen restriction in skeletal muscle from rodents and humans.

    Science.gov (United States)

    Capitanio, Daniele; Fania, Chiara; Torretta, Enrica; Viganò, Agnese; Moriggi, Manuela; Bravatà, Valentina; Caretti, Anna; Levett, Denny Z H; Grocott, Michael P W; Samaja, Michele; Cerretelli, Paolo; Gelfi, Cecilia

    2017-08-29

    In mammals, hypoxic stress management is under the control of the Hypoxia Inducible Factors, whose activity depends on the stabilization of their labile α subunit. In particular, the skeletal muscle appears to be able to react to changes in substrates and O2 delivery by tuning its metabolism. The present study provides a comprehensive overview of skeletal muscle metabolic adaptation to hypoxia in mice and in human subjects exposed for 7/9 and 19 days to high altitude levels. The investigation was carried out combining proteomics, qRT-PCR mRNA transcripts analysis, and enzyme activities assessment in rodents, and protein detection by antigen antibody reactions in humans and rodents. Results indicate that the skeletal muscle react to a decreased O2 delivery by rewiring the TCA cycle. The first TCA rewiring occurs in mice in 2-day hypoxia and is mediated by cytosolic malate whereas in 10-day hypoxia the rewiring is mediated by Idh1 and Fasn, supported by glutamine and HIF-2α increments. The combination of these specific anaplerotic steps can support energy demand despite HIFs degradation. These results were confirmed in human subjects, demonstrating that the TCA double rewiring represents an essential factor for the maintenance of muscle homeostasis during adaptation to hypoxia.

  4. 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

  5. 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

  6. Flood routing modelling with Artificial Neural Networks

    Directory of Open Access Journals (Sweden)

    R. Peters

    2006-01-01

    Full Text Available For the modelling of the flood routing in the lower reaches of the Freiberger Mulde river and its tributaries the one-dimensional hydrodynamic modelling system HEC-RAS has been applied. Furthermore, this model was used to generate a database to train multilayer feedforward networks. To guarantee numerical stability for the hydrodynamic modelling of some 60 km of streamcourse an adequate resolution in space requires very small calculation time steps, which are some two orders of magnitude smaller than the input data resolution. This leads to quite high computation requirements seriously restricting the application – especially when dealing with real time operations such as online flood forecasting. In order to solve this problem we tested the application of Artificial Neural Networks (ANN. First studies show the ability of adequately trained multilayer feedforward networks (MLFN to reproduce the model performance.

  7. 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.

  8. A Transfer Learning Approach for Network Modeling

    Science.gov (United States)

    Huang, Shuai; Li, Jing; Chen, Kewei; Wu, Teresa; Ye, Jieping; Wu, Xia; Yao, Li

    2012-01-01

    Networks models have been widely used in many domains to characterize the interacting relationship between physical entities. A typical problem faced is to identify the networks of multiple related tasks that share some similarities. In this case, a transfer learning approach that can leverage the knowledge gained during the modeling of one task to help better model another task is highly desirable. In this paper, we propose a transfer learning approach, which adopts a Bayesian hierarchical model framework to characterize task relatedness and additionally uses the L1-regularization to ensure robust learning of the networks with limited sample sizes. A method based on the Expectation-Maximization (EM) algorithm is further developed to learn the networks from data. Simulation studies are performed, which demonstrate the superiority of the proposed transfer learning approach over single task learning that learns the network of each task in isolation. The proposed approach is also applied to identification of brain connectivity networks of Alzheimer’s disease (AD) from functional magnetic resonance image (fMRI) data. The findings are consistent with the AD literature. PMID:24526804

  9. Macroscopic description of complex adaptive networks co-evolving with dynamic node states

    CERN Document Server

    Wiedermann, Marc; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

    2015-01-01

    In many real-world complex systems, the time-evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here, we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the co-evolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we show that in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability play a crucial role for the sustainability of the system's equilibrium state. We derive a macroscopic description of the system which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network and is applicable to many fields of study, such as epidemic spreading or social modeling.

  10. Collective dynamics of `small-world' networks

    Science.gov (United States)

    Watts, Duncan J.; Strogatz, Steven H.

    1998-06-01

    Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays,, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks `rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call them `small-world' networks, by analogy with the small-world phenomenon, (popularly known as six degrees of separation). The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational power, and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices.

  11. 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.

  12. A Network Model of Credit Risk Contagion

    Directory of Open Access Journals (Sweden)

    Ting-Qiang Chen

    2012-01-01

    Full Text Available 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 the network structure on credit risk contagion. Then some derived and proofed propositions were verified through numerical simulations.

  13. Deep space network software cost estimation model

    Science.gov (United States)

    Tausworthe, R. C.

    1981-01-01

    A parametric software cost estimation model prepared for Jet PRopulsion Laboratory (JPL) Deep Space Network (DSN) Data System implementation tasks is described. The resource estimation mdel modifies and combines a number of existing models. The model calibrates the task magnitude and difficulty, development environment, and software technology effects through prompted responses to a set of approximately 50 questions. Parameters in the model are adjusted to fit JPL software life-cycle statistics.

  14. Continuum Modeling of Biological Network Formation

    KAUST Repository

    Albi, Giacomo

    2017-04-10

    We present an overview of recent analytical and numerical results for the elliptic–parabolic system of partial differential equations proposed by Hu and Cai, which models the formation of biological transportation networks. The model describes the pressure field using a Darcy type equation and the dynamics of the conductance network under pressure force effects. Randomness in the material structure is represented by a linear diffusion term and conductance relaxation by an algebraic decay term. We first introduce micro- and mesoscopic models and show how they are connected to the macroscopic PDE system. Then, we provide an overview of analytical results for the PDE model, focusing mainly on the existence of weak and mild solutions and analysis of the steady states. The analytical part is complemented by extensive numerical simulations. We propose a discretization based on finite elements and study the qualitative properties of network structures for various parameter values.

  15. 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

  16. Neural networks as models of psychopathology.

    Science.gov (United States)

    Aakerlund, L; Hemmingsen, R

    1998-04-01

    Neural network modeling is situated between neurobiology, cognitive science, and neuropsychology. The structural and functional resemblance with biological computation has made artificial neural networks (ANN) useful for exploring the relationship between neurobiology and computational performance, i.e., cognition and behavior. This review provides an introduction to the theory of ANN and how they have linked theories from neurobiology and psychopathology in schizophrenia, affective disorders, and dementia.

  17. 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.

  18. Green Network Planning Model for Optical Backbones

    DEFF Research Database (Denmark)

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

    2010-01-01

    on the environment in general. In network planning there are existing planning models focused on QoS provisioning, investment minimization or combinations of both and other parameters. But there is a lack of a model for designing green optical backbones. This paper presents novel ideas to be able to define...

  19. 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...

  20. 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...

  1. Phenomenological network models: Lessons for epilepsy surgery.

    Science.gov (United States)

    Hebbink, Jurgen; Meijer, Hil; Huiskamp, Geertjan; van Gils, Stephan; Leijten, Frans

    2017-10-01

    The current opinion in epilepsy surgery is that successful surgery is about removing pathological cortex in the anatomic sense. This contrasts with recent developments in epilepsy research, where epilepsy is seen as a network disease. Computational models offer a framework to investigate the influence of networks, as well as local tissue properties, and to explore alternative resection strategies. Here we study, using such a model, the influence of connections on seizures and how this might change our traditional views of epilepsy surgery. We use a simple network model consisting of four interconnected neuronal populations. One of these populations can be made hyperexcitable, modeling a pathological region of cortex. Using model simulations, the effect of surgery on the seizure rate is studied. We find that removal of the hyperexcitable population is, in most cases, not the best approach to reduce the seizure rate. Removal of normal populations located at a crucial spot in the network, the "driver," is typically more effective in reducing seizure rate. This work strengthens the idea that network structure and connections may be more important than localizing the pathological node. This can explain why lesionectomy may not always be sufficient. © 2017 The Authors. Epilepsia published by Wiley Periodicals, Inc. on behalf of International League Against Epilepsy.

  2. Models of network reliability analysis, combinatorics, and Monte Carlo

    CERN Document Server

    Gertsbakh, Ilya B

    2009-01-01

    Unique in its approach, Models of Network Reliability: Analysis, Combinatorics, and Monte Carlo provides a brief introduction to Monte Carlo methods along with a concise exposition of reliability theory ideas. From there, the text investigates a collection of principal network reliability models, such as terminal connectivity for networks with unreliable edges and/or nodes, network lifetime distribution in the process of its destruction, network stationary behavior for renewable components, importance measures of network elements, reliability gradient, and network optimal reliability synthesis

  3. Delay and Disruption Tolerant Networking MACHETE Model

    Science.gov (United States)

    Segui, John S.; Jennings, Esther H.; Gao, Jay L.

    2011-01-01

    To verify satisfaction of communication requirements imposed by unique missions, as early as 2000, the Communications Networking Group at the Jet Propulsion Laboratory (JPL) saw the need for an environment to support interplanetary communication protocol design, validation, and characterization. JPL's Multi-mission Advanced Communications Hybrid Environment for Test and Evaluation (MACHETE), described in Simulator of Space Communication Networks (NPO-41373) NASA Tech Briefs, Vol. 29, No. 8 (August 2005), p. 44, combines various commercial, non-commercial, and in-house custom tools for simulation and performance analysis of space networks. The MACHETE environment supports orbital analysis, link budget analysis, communications network simulations, and hardware-in-the-loop testing. As NASA is expanding its Space Communications and Navigation (SCaN) capabilities to support planned and future missions, building infrastructure to maintain services and developing enabling technologies, an important and broader role is seen for MACHETE in design-phase evaluation of future SCaN architectures. To support evaluation of the developing Delay Tolerant Networking (DTN) field and its applicability for space networks, JPL developed MACHETE models for DTN Bundle Protocol (BP) and Licklider/Long-haul Transmission Protocol (LTP). DTN is an Internet Research Task Force (IRTF) architecture providing communication in and/or through highly stressed networking environments such as space exploration and battlefield networks. Stressed networking environments include those with intermittent (predictable and unknown) connectivity, large and/or variable delays, and high bit error rates. To provide its services over existing domain specific protocols, the DTN protocols reside at the application layer of the TCP/IP stack, forming a store-and-forward overlay network. The key capabilities of the Bundle Protocol include custody-based reliability, the ability to cope with intermittent connectivity

  4. A comprehensive Network Security Risk Model for process control networks.

    Science.gov (United States)

    Henry, Matthew H; Haimes, Yacov Y

    2009-02-01

    The risk of cyber attacks on process control networks (PCN) is receiving significant attention due to the potentially catastrophic extent to which PCN failures can damage the infrastructures and commodity flows that they support. Risk management addresses the coupled problems of (1) reducing the likelihood that cyber attacks would succeed in disrupting PCN operation and (2) reducing the severity of consequences in the event of PCN failure or manipulation. The Network Security Risk Model (NSRM) developed in this article provides a means of evaluating the efficacy of candidate risk management policies by modeling the baseline risk and assessing expectations of risk after the implementation of candidate measures. Where existing risk models fall short of providing adequate insight into the efficacy of candidate risk management policies due to shortcomings in their structure or formulation, the NSRM provides model structure and an associated modeling methodology that captures the relevant dynamics of cyber attacks on PCN for risk analysis. This article develops the NSRM in detail in the context of an illustrative example.

  5. Personalized Learning Network Teaching Model

    Science.gov (United States)

    Feng, Zhou

    Adaptive learning system on the salient features, expounded personalized learning is adaptive learning system adaptive to learners key to learning. From the perspective of design theory, put forward an adaptive learning system to learn design thinking individual model, and using data mining techniques, the initial establishment of personalized adaptive systems model of learning.

  6. Image Informatics Strategies for Deciphering Neuronal Network Connectivity.

    Science.gov (United States)

    Detrez, Jan R; Verstraelen, Peter; Gebuis, Titia; Verschuuren, Marlies; Kuijlaars, Jacobine; Langlois, Xavier; Nuydens, Rony; Timmermans, Jean-Pierre; De Vos, Winnok H

    2016-01-01

    Brain function relies on an intricate network of highly dynamic neuronal connections that rewires dramatically under the impulse of various external cues and pathological conditions. Amongst the neuronal structures that show morphological plasticity are neurites, synapses, dendritic spines and even nuclei. This structural remodelling is directly connected with functional changes such as intercellular communication and the associated calcium bursting behaviour. In vitro cultured neuronal networks are valuable models for studying these morpho-functional changes. Owing to the automation and standardization of both image acquisition and image analysis, it has become possible to extract statistically relevant readouts from such networks. Here, we focus on the current state-of-the-art in image informatics that enables quantitative microscopic interrogation of neuronal networks. We describe the major correlates of neuronal connectivity and present workflows for analysing them. Finally, we provide an outlook on the challenges that remain to be addressed, and discuss how imaging algorithms can be extended beyond in vitro imaging studies.

  7. Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals.

    Science.gov (United States)

    Piasecki, Brian P; Burghoorn, Jan; Swoboda, Peter

    2010-07-20

    Cilia were present in the last eukaryotic common ancestor (LECA) and were retained by most organisms spanning all extant eukaryotic lineages, including organisms in the Unikonta (Amoebozoa, fungi, choanoflagellates, and animals), Archaeplastida, Excavata, Chromalveolata, and Rhizaria. In certain animals, including humans, ciliary gene regulation is mediated by Regulatory Factor X (RFX) transcription factors (TFs). RFX TFs bind X-box promoter motifs and thereby positively regulate >50 ciliary genes. Though RFX-mediated ciliary gene regulation has been studied in several bilaterian animals, little is known about the evolutionary conservation of ciliary gene regulation. Here, we explore the evolutionary relationships between RFX TFs and cilia. By sampling the genome sequences of >120 eukaryotic organisms, we show that RFX TFs are exclusively found in unikont organisms (whether ciliated or not), but are completely absent from the genome sequences of all nonunikont organisms (again, whether ciliated or not). Sampling the promoter sequences of 12 highly conserved ciliary genes from 23 diverse unikont and nonunikont organisms further revealed that phylogenetic footprints of X-box promoter motif sequences are found exclusively in ciliary genes of certain animals. Thus, there is no correlation between cilia/ciliary genes and the presence or absence of RFX TFs and X-box promoter motifs in nonanimal unikont and in nonunikont organisms. These data suggest that RFX TFs originated early in the unikont lineage, distinctly after cilia evolved. The evolutionary model that best explains these observations indicates that the transcriptional rewiring of many ciliary genes by RFX TFs occurred early in the animal lineage.

  8. 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.

  9. Higher-order structure and epidemic dynamics in clustered networks.

    Science.gov (United States)

    Ritchie, Martin; Berthouze, Luc; House, Thomas; Kiss, Istvan Z

    2014-05-07

    Clustering is typically measured by the ratio of triangles to all triples regardless of whether open or closed. Generating clustered networks, and how clustering affects dynamics on networks, is reasonably well understood for certain classes of networks (Volz et al., 2011; Karrer and Newman, 2010), e.g. networks composed of lines and non-overlapping triangles. In this paper we show that it is possible to generate networks which, despite having the same degree distribution and equal clustering, exhibit different higher-order structure, specifically, overlapping triangles and other order-four (a closed network motif composed of four nodes) structures. To distinguish and quantify these additional structural features, we develop a new network metric capable of measuring order-four structure which, when used alongside traditional network metrics, allows us to more accurately describe a network׳s topology. Three network generation algorithms are considered: a modified configuration model and two rewiring algorithms. By generating homogeneous networks with equal clustering we study and quantify their structural differences, and using SIS (Susceptible-Infected-Susceptible) and SIR (Susceptible-Infected-Recovered) dynamics we investigate computationally how differences in higher-order structure impact on epidemic threshold, final epidemic or prevalence levels and time evolution of epidemics. Our results suggest that characterising and measuring higher-order network structure is needed to advance our understanding of the impact of network topology on dynamics unfolding on the networks. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  10. Model Microvascular Networks Can Have Many Equilibria.

    Science.gov (United States)

    Karst, Nathaniel J; Geddes, John B; Carr, Russell T

    2017-03-01

    We show that large microvascular networks with realistic topologies, geometries, boundary conditions, and constitutive laws can exhibit many steady-state flow configurations. This is in direct contrast to most previous studies which have assumed, implicitly or explicitly, that a given network can only possess one equilibrium state. While our techniques are general and can be applied to any network, we focus on two distinct network types that model human tissues: perturbed honeycomb networks and random networks generated from Voronoi diagrams. We demonstrate that the disparity between observed and predicted flow directions reported in previous studies might be attributable to the presence of multiple equilibria. We show that the pathway effect, in which hematocrit is steadily increased along a series of diverging junctions, has important implications for equilibrium discovery, and that our estimates of the number of equilibria supported by these networks are conservative. If a more complete description of the plasma skimming effect that captures red blood cell allocation at junctions with high feed hematocrit were to be obtained empirically, then the number of equilibria found by our approach would at worst remain the same and would in all likelihood increase significantly.

  11. PREDIKSI FOREX MENGGUNAKAN MODEL NEURAL NETWORK

    Directory of Open Access Journals (Sweden)

    R. Hadapiningradja Kusumodestoni

    2015-11-01

    Full Text Available ABSTRAK Prediksi adalah salah satu teknik yang paling penting dalam menjalankan bisnis forex. Keputusan dalam memprediksi adalah sangatlah penting, karena dengan prediksi dapat membantu mengetahui nilai forex di waktu tertentu kedepan sehingga dapat mengurangi resiko kerugian. Tujuan dari penelitian ini dimaksudkan memprediksi bisnis fores menggunakan model neural network dengan data time series per 1 menit untuk mengetahui nilai akurasi prediksi sehingga dapat mengurangi resiko dalam menjalankan bisnis forex. Metode penelitian pada penelitian ini meliputi metode pengumpulan data kemudian dilanjutkan ke metode training, learning, testing menggunakan neural network. Setelah di evaluasi hasil penelitian ini menunjukan bahwa penerapan algoritma Neural Network mampu untuk memprediksi forex dengan tingkat akurasi prediksi 0.431 +/- 0.096 sehingga dengan prediksi ini dapat membantu mengurangi resiko dalam menjalankan bisnis forex. Kata kunci: prediksi, forex, neural network.

  12. Artificial neural network cardiopulmonary modeling and diagnosis

    Science.gov (United States)

    Kangas, Lars J.; Keller, Paul E.

    1997-01-01

    The present invention is a method of diagnosing a cardiopulmonary condition in an individual by comparing data from a progressive multi-stage test for the individual to a non-linear multi-variate model, preferably a recurrent artificial neural network having sensor fusion. The present invention relies on a cardiovascular model developed from physiological measurements of an individual. Any differences between the modeled parameters and the parameters of an individual at a given time are used for diagnosis.

  13. Spiking modular neural networks: A neural network modeling approach for hydrological processes

    National Research Council Canada - National Science Library

    Kamban Parasuraman; Amin Elshorbagy; Sean K. Carey

    2006-01-01

    .... In this study, a novel neural network model called the spiking modular neural networks (SMNNs) is proposed. An SMNN consists of an input layer, a spiking layer, and an associator neural network layer...

  14. PROJECT ACTIVITY ANALYSIS WITHOUT THE NETWORK MODEL

    Directory of Open Access Journals (Sweden)

    S. Munapo

    2012-01-01

    Full Text Available

    ENGLISH ABSTRACT: This paper presents a new procedure for analysing and managing activity sequences in projects. The new procedure determines critical activities, critical path, start times, free floats, crash limits, and other useful information without the use of the network model. Even though network models have been successfully used in project management so far, there are weaknesses associated with the use. A network is not easy to generate, and dummies that are usually associated with it make the network diagram complex – and dummy activities have no meaning in the original project management problem. The network model for projects can be avoided while still obtaining all the useful information that is required for project management. What are required are the activities, their accurate durations, and their predecessors.

    AFRIKAANSE OPSOMMING: Die navorsing beskryf ’n nuwerwetse metode vir die ontleding en bestuur van die sekwensiële aktiwiteite van projekte. Die voorgestelde metode bepaal kritiese aktiwiteite, die kritieke pad, aanvangstye, speling, verhasing, en ander groothede sonder die gebruik van ’n netwerkmodel. Die metode funksioneer bevredigend in die praktyk, en omseil die administratiewe rompslomp van die tradisionele netwerkmodelle.

  15. Algebraic Statistics for Network Models

    Science.gov (United States)

    2014-02-19

    use algebra, combinatorics and Markov bases to give a constructing way of answering this question for ERGMs of interest. Question 2: How do we model...for every function. 06/06/13 Petrović. Manuscripts 8, 10. Invited lecture at the Scientific Session on Commutative Algebra and Combinatorics at the

  16. Network Modeling and Simulation (NEMSE)

    Science.gov (United States)

    2013-07-01

    Prioritized Packet Fragmentation", IEEE Trans. Multimedia , Oct. 2012. [13 SYSENG] . Defense Acquisition Guidebook, Chapter 4 System Engineering, and...2012 IEEE High Performance Extreme Computing Conference (HPEC) poster session [1 Ross]. Motivation  Air Force Research Lab needs o Capability...is virtual. These eight virtualizations were: System-in-the-Loop (SITL) using OPNET Modeler, COPE, Field Programmable Gate Array ( FPGA Physical

  17. Security Modeling on the Supply Chain Networks

    Directory of Open Access Journals (Sweden)

    Marn-Ling Shing

    2007-10-01

    Full Text Available In order to keep the price down, a purchaser sends out the request for quotation to a group of suppliers in a supply chain network. The purchaser will then choose a supplier with the best combination of price and quality. A potential supplier will try to collect the related information about other suppliers so he/she can offer the best bid to the purchaser. Therefore, confidentiality becomes an important consideration for the design of a supply chain network. Chen et al. have proposed the application of the Bell-LaPadula model in the design of a secured supply chain network. In the Bell-LaPadula model, a subject can be in one of different security clearances and an object can be in one of various security classifications. All the possible combinations of (Security Clearance, Classification pair in the Bell-LaPadula model can be thought as different states in the Markov Chain model. This paper extends the work done by Chen et al., provides more details on the Markov Chain model and illustrates how to use it to monitor the security state transition in the supply chain network.

  18. 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.

  19. Malware Propagation and Prevention Model for Time-Varying Community Networks within Software Defined Networks

    OpenAIRE

    Lan Liu; Ryan K. L. Ko; Guangming Ren; Xiaoping Xu

    2017-01-01

    As the adoption of Software Defined Networks (SDNs) grows, the security of SDN still has several unaddressed limitations. A key network security research area is in the study of malware propagation across the SDN-enabled networks. To analyze the spreading processes of network malware (e.g., viruses) in SDN, we propose a dynamic model with a time-varying community network, inspired by research models on the spread of epidemics in complex networks across communities. We assume subnets of the ne...

  20. 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.

  1. 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.

  2. 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.

  3. UAV Trajectory Modeling Using Neural Networks

    Science.gov (United States)

    Xue, Min

    2017-01-01

    Massive small unmanned aerial vehicles are envisioned to operate in the near future. While there are lots of research problems need to be addressed before dense operations can happen, trajectory modeling remains as one of the keys to understand and develop policies, regulations, and requirements for safe and efficient unmanned aerial vehicle operations. The fidelity requirement of a small unmanned vehicle trajectory model is high because these vehicles are sensitive to winds due to their small size and low operational altitude. Both vehicle control systems and dynamic models are needed for trajectory modeling, which makes the modeling a great challenge, especially considering the fact that manufactures are not willing to share their control systems. This work proposed to use a neural network approach for modelling small unmanned vehicle's trajectory without knowing its control system and bypassing exhaustive efforts for aerodynamic parameter identification. As a proof of concept, instead of collecting data from flight tests, this work used the trajectory data generated by a mathematical vehicle model for training and testing the neural network. The results showed great promise because the trained neural network can predict 4D trajectories accurately, and prediction errors were less than 2:0 meters in both temporal and spatial dimensions.

  4. Propagation models for computing biochemical reaction networks

    OpenAIRE

    Henzinger, Thomas A; Mateescu, Maria

    2011-01-01

    We introduce propagation models, a formalism designed to support general and efficient data structures for the transient analysis of biochemical reaction networks. We give two use cases for propagation abstract data types: the uniformization method and numerical integration. We also sketch an implementation of a propagation abstract data type, which uses abstraction to approximate states.

  5. Modelling crime linkage with Bayesian networks

    NARCIS (Netherlands)

    de Zoete, J.; Sjerps, M.; Lagnado, D.; Fenton, N.

    2015-01-01

    When two or more crimes show specific similarities, such as a very distinct modus operandi, the probability that they were committed by the same offender becomes of interest. This probability depends on the degree of similarity and distinctiveness. We show how Bayesian networks can be used to model

  6. Lagrangian modeling of switching electrical networks

    NARCIS (Netherlands)

    Scherpen, Jacquelien M.A.; Jeltsema, Dimitri; Klaassens, J. Ben

    2003-01-01

    In this paper, a general and systematic method is presented to model topologically complete electrical networks, with or without multiple or single switches, within the Euler–Lagrange framework. Apart from the physical insight that can be obtained in this way, the framework has proven to be useful

  7. Computational Modeling of Complex Protein Activity Networks

    NARCIS (Netherlands)

    Schivo, Stefano; Leijten, Jeroen; Karperien, Marcel; Post, Janine N.; Prignet, Claude

    2017-01-01

    Because of the numerous entities interacting, the complexity of the networks that regulate cell fate makes it impossible to analyze and understand them using the human brain alone. Computational modeling is a powerful method to unravel complex systems. We recently described the development of a

  8. Modeling Network Transition Constraints with Hypergraphs

    DEFF Research Database (Denmark)

    Harrod, Steven

    2011-01-01

    values. A directed hypergraph formulation is derived to address railway network sequencing constraints, and an experimental problem sample solved to estimate the magnitude of objective inflation when interaction effects are ignored. The model is used to demonstrate the value of advance scheduling...

  9. A neural network model for texture discrimination.

    Science.gov (United States)

    Xing, J; Gerstein, G L

    1993-01-01

    A model of texture discrimination in visual cortex was built using a feedforward network with lateral interactions among relatively realistic spiking neural elements. The elements have various membrane currents, equilibrium potentials and time constants, with action potentials and synapses. The model is derived from the modified programs of MacGregor (1987). Gabor-like filters are applied to overlapping regions in the original image; the neural network with lateral excitatory and inhibitory interactions then compares and adjusts the Gabor amplitudes in order to produce the actual texture discrimination. Finally, a combination layer selects and groups various representations in the output of the network to form the final transformed image material. We show that both texture segmentation and detection of texture boundaries can be represented in the firing activity of such a network for a wide variety of synthetic to natural images. Performance details depend most strongly on the global balance of strengths of the excitatory and inhibitory lateral interconnections. The spatial distribution of lateral connective strengths has relatively little effect. Detailed temporal firing activities of single elements in the lateral connected network were examined under various stimulus conditions. Results show (as in area 17 of cortex) that a single element's response to image features local to its receptive field can be altered by changes in the global context.

  10. Propagating semantic information in biochemical network models

    Directory of Open Access Journals (Sweden)

    Schulz Marvin

    2012-01-01

    Full Text Available Abstract Background To enable automatic searches, alignments, and model combination, the elements of systems biology models need to be compared and matched across models. Elements can be identified by machine-readable biological annotations, but assigning such annotations and matching non-annotated elements is tedious work and calls for automation. Results A new method called "semantic propagation" allows the comparison of model elements based not only on their own annotations, but also on annotations of surrounding elements in the network. One may either propagate feature vectors, describing the annotations of individual elements, or quantitative similarities between elements from different models. Based on semantic propagation, we align partially annotated models and find annotations for non-annotated model elements. Conclusions Semantic propagation and model alignment are included in the open-source library semanticSBML, available on sourceforge. Online services for model alignment and for annotation prediction can be used at http://www.semanticsbml.org.

  11. 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...... of Web-based eLearning platforms. The scenario we are tackling assumes learners who use several systems over time, which are able to create partial Bayesian Networks for user models based on the local system context. In particular, we focus on how to merge these partial user models. Our merge mechanism...... efficiently combines distributed learner models without the need to exchange internal structure of local Bayesian networks, nor local evidence between the involved platforms....

  12. Network traffic model using GIPP and GIBP

    Science.gov (United States)

    Lee, Yong Duk; Van de Liefvoort, Appie; Wallace, Victor L.

    1998-10-01

    In telecommunication networks, the correlated nature of teletraffic patterns can have significant impact on queuing measures such as queue length, blocking and delay. There is, however, not yet a good general analytical description which can easily incorporate the correlation effect of the traffic, while at the same time maintaining the ease of modeling. The authors have shown elsewhere, that the covariance structures of the generalized Interrupted Poisson Process (GIPP) and the generalized Interrupted Bernoulli Process (GIBP) have an invariance property which makes them reasonably general, yet algebraically manageable, models for representing correlated network traffic. The GIPP and GIBP have a surprisingly rich sets of parameters, yet these invariance properties enable us to easily incorporate the covariance function as well as the interarrival time distribution into the model to better matchobservations. In this paper, we show an application of GIPP and GIBP for matching an analytical model to observed or experimental data.

  13. Model Predictive Control of Sewer Networks

    DEFF Research Database (Denmark)

    Pedersen, Einar B.; Herbertsson, Hannes R.; Niemann, Henrik

    2016-01-01

    The developments in solutions for management of urban drainage are of vital importance, as the amount of sewer water from urban areas continues to increase due to the increase of the world’s population and the change in the climate conditions. How a sewer network is structured, monitored and cont...... benchmark model. Due to the inherent constraints the applied approach is based on Model Predictive Control....

  14. 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....

  15. Modelling dendritic ecological networks in space: anintegrated network perspective

    Science.gov (United States)

    Peterson, Erin E.; Ver Hoef, Jay M.; Isaak, Dan J.; Falke, Jeffrey A.; Fortin, Marie-Josée; Jordon, Chris E.; McNyset, Kristina; Monestiez, Pascal; Ruesch, Aaron S.; Sengupta, Aritra; Som, Nicholas; Steel, E. Ashley; Theobald, David M.; Torgersen, Christian E.; Wenger, Seth J.

    2013-01-01

    Dendritic ecological networks (DENs) are a unique form of ecological networks that exhibit a dendritic network topology (e.g. stream and cave networks or plant architecture). DENs have a dual spatial representation; as points within the network and as points in geographical space. Consequently, some analytical methods used to quantify relationships in other types of ecological networks, or in 2-D space, may be inadequate for studying the influence of structure and connectivity on ecological processes within DENs. We propose a conceptual taxonomy of network analysis methods that account for DEN characteristics to varying degrees and provide a synthesis of the different approaches within

  16. 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....... 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...

  17. On traffic modelling in GPRS networks

    DEFF Research Database (Denmark)

    Madsen, Tatiana Kozlova; Schwefel, Hans-Peter; Prasad, Ramjee

    2005-01-01

    Optimal design and dimensioning of wireless data networks, such as GPRS, requires the knowledge of traffic characteristics of different data services. This paper presents an in-detail analysis of an IP-level traffic measurements taken in an operational GPRS network. The data measurements reported...... here are done at the Gi interface. The aim of this paper is to reveal some key statistics of GPRS data applications and to validate if the existing traffic models can adequately describe traffic volume and inter-arrival time distribution for different services. Additionally, we present a method of user...

  18. Neural Network Model of memory retrieval

    Directory of Open Access Journals (Sweden)

    Stefano eRecanatesi

    2015-12-01

    Full Text Available Human memory can store large amount of information. Nevertheless, recalling is often achallenging task. In a classical free recall paradigm, where participants are asked to repeat abriefly presented list of words, people make mistakes for lists as short as 5 words. We present amodel for memory retrieval based on a Hopfield neural network where transition between itemsare determined by similarities in their long-term memory representations. Meanfield analysis ofthe model reveals stable states of the network corresponding (1 to single memory representationsand (2 intersection between memory representations. We show that oscillating feedback inhibitionin the presence of noise induces transitions between these states triggering the retrieval ofdifferent memories. The network dynamics qualitatively predicts the distribution of time intervalsrequired to recall new memory items observed in experiments. It shows that items having largernumber of neurons in their representation are statistically easier to recall and reveals possiblebottlenecks in our ability of retrieving memories. Overall, we propose a neural network model ofinformation retrieval broadly compatible with experimental observations and is consistent with ourrecent graphical model (Romani et al., 2013.

  19. A improved Network Security Situation Awareness Model

    Directory of Open Access Journals (Sweden)

    Li Fangwei

    2015-08-01

    Full Text Available In order to reflect the situation of network security assessment performance fully and accurately, a new network security situation awareness model based on information fusion was proposed. Network security situation is the result of fusion three aspects evaluation. In terms of attack, to improve the accuracy of evaluation, a situation assessment method of DDoS attack based on the information of data packet was proposed. In terms of vulnerability, a improved Common Vulnerability Scoring System (CVSS was raised and maked the assessment more comprehensive. In terms of node weights, the method of calculating the combined weights and optimizing the result by Sequence Quadratic Program (SQP algorithm which reduced the uncertainty of fusion was raised. To verify the validity and necessity of the method, a testing platform was built and used to test through evaluating 2000 DAPRA data sets. Experiments show that the method can improve the accuracy of evaluation results.

  20. Generating confidence intervals on biological networks

    Directory of Open Access Journals (Sweden)

    Stumpf Michael PH

    2007-11-01

    Full Text Available Abstract Background In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interacting nodes. The structure of the network may introduce dependencies among the nodes and it will in general be necessary to account for these dependencies in the statistical analysis. To this end we require some form of Null model of the network: generally rewired replicates of the network are generated which preserve only the degree (number of interactions of each node. We show that this can fail to capture important features of network structure, and may result in unrealistic significance levels, when potentially confounding additional information is available. Methods We present a new network resampling Null model which takes into account the degree sequence as well as available biological annotations. Using gene ontology information as an illustration we show how this information can be accounted for in the resampling approach, and the impact such information has on the assessment of statistical significance of correlations and motif-abundances in the Saccharomyces cerevisiae protein interaction network. An algorithm, GOcardShuffle, is introduced to allow for the efficient construction of an improved Null model for network data. Results We use the protein interaction network of S. cerevisiae; correlations between the evolutionary rates and expression levels of interacting proteins and their statistical significance were assessed for Null models which condition on different aspects of the available data. The novel GOcardShuffle approach results in a Null model for annotated network data which appears better to describe the properties of real biological networks. Conclusion An improved statistical approach for the statistical analysis of biological network data, which conditions on the available biological information, leads to qualitatively different results

  1. 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

  2. Zealotry effects on opinion dynamics in the adaptive voter model

    Science.gov (United States)

    Klamser, Pascal P.; Wiedermann, Marc; Donges, Jonathan F.; Donner, Reik V.

    2017-11-01

    The adaptive voter model has been widely studied as a conceptual model for opinion formation processes on time-evolving social networks. Past studies on the effect of zealots, i.e., nodes aiming to spread their fixed opinion throughout the system, only considered the voter model on a static network. Here we extend the study of zealotry to the case of an adaptive network topology co-evolving with the state of the nodes and investigate opinion spreading induced by zealots depending on their initial density and connectedness. Numerical simulations reveal that below the fragmentation threshold a low density of zealots is sufficient to spread their opinion to the whole network. Beyond the transition point, zealots must exhibit an increased degree as compared to ordinary nodes for an efficient spreading of their opinion. We verify the numerical findings using a mean-field approximation of the model yielding a low-dimensional set of coupled ordinary differential equations. Our results imply that the spreading of the zealots' opinion in the adaptive voter model is strongly dependent on the link rewiring probability and the average degree of normal nodes in comparison with that of the zealots. In order to avoid a complete dominance of the zealots' opinion, there are two possible strategies for the remaining nodes: adjusting the probability of rewiring and/or the number of connections with other nodes, respectively.

  3. 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.

  4. UAV Trajectory Modeling Using Neural Networks

    Science.gov (United States)

    Xue, Min

    2017-01-01

    Large amount of small Unmanned Aerial Vehicles (sUAVs) are projected to operate in the near future. Potential sUAV applications include, but not limited to, search and rescue, inspection and surveillance, aerial photography and video, precision agriculture, and parcel delivery. sUAVs are expected to operate in the uncontrolled Class G airspace, which is at or below 500 feet above ground level (AGL), where many static and dynamic constraints exist, such as ground properties and terrains, restricted areas, various winds, manned helicopters, and conflict avoidance among sUAVs. How to enable safe, efficient, and massive sUAV operations at the low altitude airspace remains a great challenge. NASA's Unmanned aircraft system Traffic Management (UTM) research initiative works on establishing infrastructure and developing policies, requirement, and rules to enable safe and efficient sUAVs' operations. To achieve this goal, it is important to gain insights of future UTM traffic operations through simulations, where the accurate trajectory model plays an extremely important role. On the other hand, like what happens in current aviation development, trajectory modeling should also serve as the foundation for any advanced concepts and tools in UTM. Accurate models of sUAV dynamics and control systems are very important considering the requirement of the meter level precision in UTM operations. The vehicle dynamics are relatively easy to derive and model, however, vehicle control systems remain unknown as they are usually kept by manufactures as a part of intellectual properties. That brings challenges to trajectory modeling for sUAVs. How to model the vehicle's trajectories with unknown control system? This work proposes to use a neural network to model a vehicle's trajectory. The neural network is first trained to learn the vehicle's responses at numerous conditions. Once being fully trained, given current vehicle states, winds, and desired future trajectory, the neural

  5. Kinematic Structural Modelling in Bayesian Networks

    Science.gov (United States)

    Schaaf, Alexander; de la Varga, Miguel; Florian Wellmann, J.

    2017-04-01

    We commonly capture our knowledge about the spatial distribution of distinct geological lithologies in the form of 3-D geological models. Several methods exist to create these models, each with its own strengths and limitations. We present here an approach to combine the functionalities of two modeling approaches - implicit interpolation and kinematic modelling methods - into one framework, while explicitly considering parameter uncertainties and thus model uncertainty. In recent work, we proposed an approach to implement implicit modelling algorithms into Bayesian networks. This was done to address the issues of input data uncertainty and integration of geological information from varying sources in the form of geological likelihood functions. However, one general shortcoming of implicit methods is that they usually do not take any physical constraints into consideration, which can result in unrealistic model outcomes and artifacts. On the other hand, kinematic structural modelling intends to reconstruct the history of a geological system based on physically driven kinematic events. This type of modelling incorporates simplified, physical laws into the model, at the cost of a substantial increment of usable uncertain parameters. In the work presented here, we show an integration of these two different modelling methodologies, taking advantage of the strengths of both of them. First, we treat the two types of models separately, capturing the information contained in the kinematic models and their specific parameters in the form of likelihood functions, in order to use them in the implicit modelling scheme. We then go further and combine the two modelling approaches into one single Bayesian network. This enables the direct flow of information between the parameters of the kinematic modelling step and the implicit modelling step and links the exclusive input data and likelihoods of the two different modelling algorithms into one probabilistic inference framework. In

  6. Systems biology of plant molecular networks: from networks to models

    NARCIS (Netherlands)

    Valentim, F.L.

    2015-01-01

    Developmental processes are controlled by regulatory networks (GRNs), which are tightly coordinated networks of transcription factors (TFs) that activate and repress gene expression within a spatial and temporal context. In Arabidopsis thaliana, the key components and network structures of the GRNs

  7. Advances in dynamic network modeling in complex transportation systems

    CERN Document Server

    Ukkusuri, Satish V

    2013-01-01

    This book focuses on the latest in dynamic network modeling, including route guidance and traffic control in transportation systems and other complex infrastructure networks. Covers dynamic traffic assignment, flow modeling, mobile sensor deployment and more.

  8. A NEURAL OSCILLATOR-NETWORK MODEL OF TEMPORAL PATTERN GENERATION

    NARCIS (Netherlands)

    Schomaker, Lambert

    Most contemporary neural network models deal with essentially static, perceptual problems of classification and transformation. Models such as multi-layer feedforward perceptrons generally do not incorporate time as an essential dimension, whereas biological neural networks are inherently temporal

  9. Model-based redesign of global transcription regulation

    Science.gov (United States)

    Carrera, Javier; Rodrigo, Guillermo; Jaramillo, Alfonso

    2009-01-01

    Synthetic biology aims to the design or redesign of biological systems. In particular, one possible goal could be the rewiring of the transcription regulation network by exchanging the endogenous promoters. To achieve this objective, we have adapted current methods to the inference of a model based on ordinary differential equations that is able to predict the network response after a major change in its topology. Our procedure utilizes microarray data for training. We have experimentally validated our inferred global regulatory model in Escherichia coli by predicting transcriptomic profiles under new perturbations. We have also tested our methodology in silico by providing accurate predictions of the underlying networks from expression data generated with artificial genomes. In addition, we have shown the predictive power of our methodology by obtaining the gene profile in experimental redesigns of the E. coli genome, where rewiring the transcriptional network by means of knockouts of master regulators or by upregulating transcription factors controlled by different promoters. Our approach is compatible with most network inference methods, allowing to explore computationally future genome-wide redesign experiments in synthetic biology. PMID:19188257

  10. Model of Opinion Spreading in Social Networks

    CERN Document Server

    Kanovsky, Igor

    2011-01-01

    We proposed a new model, which capture the main difference between information and opinion spreading. In information spreading additional exposure to certain information has a small effect. Contrary, when an actor is exposed to 2 opinioned actors the probability to adopt the opinion is significant higher than in the case of contact with one such actor (called by J. Kleinberg "the 0-1-2 effect"). In each time step if an actor does not have an opinion, we randomly choose 2 his network neighbors. If one of them has an opinion, the actor adopts opinion with some low probability, if two - with a higher probability. Opinion spreading was simulated on different real world social networks and similar random scale-free networks. The results show that small world structure has a crucial impact on tipping point time. The "0-1-2" effect causes a significant difference between ability of the actors to start opinion spreading. Actor is an influencer according to his topological position in the network.

  11. A Comparison of Geographic Information Systems, Complex Networks, and Other Models for Analyzing Transportation Network Topologies

    Science.gov (United States)

    Alexandrov, Natalia (Technical Monitor); Kuby, Michael; Tierney, Sean; Roberts, Tyler; Upchurch, Christopher

    2005-01-01

    This report reviews six classes of models that are used for studying transportation network topologies. The report is motivated by two main questions. First, what can the "new science" of complex networks (scale-free, small-world networks) contribute to our understanding of transport network structure, compared to more traditional methods? Second, how can geographic information systems (GIS) contribute to studying transport networks? The report defines terms that can be used to classify different kinds of models by their function, composition, mechanism, spatial and temporal dimensions, certainty, linearity, and resolution. Six broad classes of models for analyzing transport network topologies are then explored: GIS; static graph theory; complex networks; mathematical programming; simulation; and agent-based modeling. Each class of models is defined and classified according to the attributes introduced earlier. The paper identifies some typical types of research questions about network structure that have been addressed by each class of model in the literature.

  12. Mathematical model for spreading dynamics of social network worms

    Science.gov (United States)

    Sun, Xin; Liu, Yan-Heng; Li, Bin; Li, Jin; Han, Jia-Wei; Liu, Xue-Jie

    2012-04-01

    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.

  13. Modeling regulatory networks with weight matrices

    DEFF Research Database (Denmark)

    Weaver, D.C.; Workman, Christopher; Stormo, Gary D.

    1999-01-01

    Systematic gene expression analyses provide comprehensive information about the transcriptional responseto different environmental and developmental conditions. With enough gene expression data points,computational biologists may eventually generate predictive computer models of transcription...... regulation.Such models will require computational methodologies consistent with the behavior of known biologicalsystems that remain tractable. We represent regulatory relationships between genes as linear coefficients orweights, with the "net" regulation influence on a gene's expression being...... the mathematical summation of theindependent regulatory inputs. Test regulatory networks generated with this approach display stable andcyclically stable gene expression levels, consistent with known biological systems. We include variables tomodel the effect of environmental conditions on transcription regulation...

  14. Artificial Neural Network Modeling of an Inverse Fluidized Bed ...

    African Journals Online (AJOL)

    The application of neural networks to model a laboratory scale inverse fluidized bed reactor has been studied. A Radial Basis Function neural network has been successfully employed for the modeling of the inverse fluidized bed reactor. In the proposed model, the trained neural network represents the kinetics of biological ...

  15. Modeling social influence through network autocorrelation : constructing the weight matrix

    NARCIS (Netherlands)

    Leenders, Roger Th. A. J.

    Many physical and social phenomena are embedded within networks of interdependencies, the so-called 'context' of these phenomena. In network analysis, this type of process is typically modeled as a network autocorrelation model. Parameter estimates and inferences based on autocorrelation models,

  16. Specification and Estimation of Network Formation and Network Interaction Models with the Exponential Probability Distribution

    OpenAIRE

    Hsieh, Chih-Sheng; Lee, Lung fei

    2017-01-01

    In this paper, we model network formation and network interactions under a unified framework. The key feature of our model is to allow individuals to respond to incentives stemming from interaction benefits on certain activities when they choose friends (network links), while capturing homophily in terms of unobserved characteristic variables in network formation and activities. There are two advantages of this modeling approach: first, one can evaluate whether incentives from certain interac...

  17. Challenges on Probabilistic Modeling for Evolving Networks

    OpenAIRE

    Ding, Jianguo; Bouvry, Pascal

    2013-01-01

    With the emerging of new networks, such as wireless sensor networks, vehicle networks, P2P networks, cloud computing, mobile Internet, or social networks, the network dynamics and complexity expands from system design, hardware, software, protocols, structures, integration, evolution, application, even to business goals. Thus the dynamics and uncertainty are unavoidable characteristics, which come from the regular network evolution and unexpected hardware defects, unavoidable software errors,...

  18. Aeronautical telecommunications network advances, challenges, and modeling

    CERN Document Server

    Musa, Sarhan M

    2015-01-01

    Addresses the Challenges of Modern-Day Air Traffic Air traffic control (ATC) directs aircraft in the sky and on the ground to safety, while the Aeronautical Telecommunications Network (ATN) comprises all systems and phases that assist in aircraft departure and landing. The Aeronautical Telecommunications Network: Advances, Challenges, and Modeling focuses on the development of ATN and examines the role of the various systems that link aircraft with the ground. The book places special emphasis on ATC-introducing the modern ATC system from the perspective of the user and the developer-and provides a thorough understanding of the operating mechanism of the ATC system. It discusses the evolution of ATC, explaining its structure and how it works; includes design examples; and describes all subsystems of the ATC system. In addition, the book covers relevant tools, techniques, protocols, and architectures in ATN, including MIPv6, air traffic control (ATC), security of air traffic management (ATM), very-high-frequenc...

  19. Neural Network Program Package for Prosody Modeling

    Directory of Open Access Journals (Sweden)

    J. Santarius

    2004-04-01

    Full Text Available This contribution describes the programme for one part of theautomatic Text-to-Speech (TTS synthesis. Some experiments (for example[14] documented the considerable improvement of the naturalness ofsynthetic speech, but this approach requires completing the inputfeature values by hand. This completing takes a lot of time for bigfiles. We need to improve the prosody by other approaches which useonly automatically classified features (input parameters. Theartificial neural network (ANN approach is used for the modeling ofprosody parameters. The program package contains all modules necessaryfor the text and speech signal pre-processing, neural network training,sensitivity analysis, result processing and a module for the creationof the input data protocol for Czech speech synthesizer ARTIC [1].

  20. Contributions and challenges for network models in cognitive neuroscience.

    Science.gov (United States)

    Sporns, Olaf

    2014-05-01

    The confluence of new approaches in recording patterns of brain connectivity and quantitative analytic tools from network science has opened new avenues toward understanding the organization and function of brain networks. Descriptive network models of brain structural and functional connectivity have made several important contributions; for example, in the mapping of putative network hubs and network communities. Building on the importance of anatomical and functional interactions, network models have provided insight into the basic structures and mechanisms that enable integrative neural processes. Network models have also been instrumental in understanding the role of structural brain networks in generating spatially and temporally organized brain activity. Despite these contributions, network models are subject to limitations in methodology and interpretation, and they face many challenges as brain connectivity data sets continue to increase in detail and complexity.

  1. Modeling of regional warehouse network generation

    Directory of Open Access Journals (Sweden)

    Popov Pavel Vladimirovich

    2016-08-01

    Full Text Available One of the factors that has a significant impact on the socio-economic development of the Russian Federation’s regions is the logistics infrastructure. It provides integrated transportation and distribution service of material flows. One of the main elements of logistics infrastructure is a storage infrastructure, which includes distribution center, distribution-and-sortout and sortout warehouses. It is the most expedient to place distribution center in the vicinity of the regional center. One of the tasks of the distribution network creation within the regions of the Russian Federation is to determine the location, capacity and number of stores. When determining regional network location of general purpose warehouses methodological approaches to solving the problems of location of production and non-production can be used which depend on various economic factors. The mathematical models for solving relevant problems are the deployment models. However, the existing models focus on the dimensionless power storage. The purpose of the given work is to develop a model to determine the optimal location of general-purpose warehouses on the Russian Federation area. At the first stage of the work, the authors assess the main economic indicators influencing the choice of the location of general purpose warehouses. An algorithm for solving the first stage, based on ABC, discriminant and cluster analysis were proposed by the authors in earlier papers. At the second stage the specific locations of general purpose warehouses and their power is chosen to provide the cost minimization for the construction and subsequent maintenance of warehouses and transportation heterogeneous products. In order to solve this problem the authors developed a mathematical model that takes into account the possibility of delivery in heterogeneous goods from suppliers and manufacturers in the distribution and storage sorting with specified set of capacities. The model allows

  2. Bayesian Recurrent Neural Network for Language Modeling.

    Science.gov (United States)

    Chien, Jen-Tzung; Ku, Yuan-Chu

    2016-02-01

    A language model (LM) is calculated as the probability of a word sequence that provides the solution to word prediction for a variety of information systems. A recurrent neural network (RNN) is powerful to learn the large-span dynamics of a word sequence in the continuous space. However, the training of the RNN-LM is an ill-posed problem because of too many parameters from a large dictionary size and a high-dimensional hidden layer. This paper presents a Bayesian approach to regularize the RNN-LM and apply it for continuous speech recognition. We aim to penalize the too complicated RNN-LM by compensating for the uncertainty of the estimated model parameters, which is represented by a Gaussian prior. The objective function in a Bayesian classification network is formed as the regularized cross-entropy error function. The regularized model is constructed not only by calculating the regularized parameters according to the maximum a posteriori criterion but also by estimating the Gaussian hyperparameter by maximizing the marginal likelihood. A rapid approximation to a Hessian matrix is developed to implement the Bayesian RNN-LM (BRNN-LM) by selecting a small set of salient outer-products. The proposed BRNN-LM achieves a sparser model than the RNN-LM. Experiments on different corpora show the robustness of system performance by applying the rapid BRNN-LM under different conditions.

  3. Statistical mechanics of scale-free gene expression networks

    Science.gov (United States)

    Gross, Eitan

    2012-12-01

    The gene co-expression networks of many organisms including bacteria, mice and man exhibit scale-free distribution. This heterogeneous distribution of connections decreases the vulnerability of the network to random attacks and thus may confer the genetic replication machinery an intrinsic resilience to such attacks, triggered by changing environmental conditions that the organism may be subject to during evolution. This resilience to random attacks comes at an energetic cost, however, reflected by the lower entropy of the scale-free distribution compared to the more homogenous, random network. In this study we found that the cell cycle-regulated gene expression pattern of the yeast Saccharomyces cerevisiae obeys a power-law distribution with an exponent α = 2.1 and an entropy of 1.58. The latter is very close to the maximal value of 1.65 obtained from linear optimization of the entropy function under the constraint of a constant cost function, determined by the average degree connectivity . We further show that the yeast's gene expression network can achieve scale-free distribution in a process that does not involve growth but rather via re-wiring of the connections between nodes of an ordered network. Our results support the idea of an evolutionary selection, which acts at the level of the protein sequence, and is compatible with the notion of greater biological importance of highly connected nodes in the protein interaction network. Our constrained re-wiring model provides a theoretical framework for a putative thermodynamically driven evolutionary selection process.

  4. Optimizing neural network models: motivation and case studies

    OpenAIRE

    Harp, S A; T. Samad

    2012-01-01

    Practical successes have been achieved  with neural network models in a variety of domains, including energy-related industry. The large, complex design space presented by neural networks is only minimally explored in current practice. The satisfactory results that nevertheless have been obtained testify that neural networks are a robust modeling technology; at the same time, however, the lack of a systematic design approach implies that the best neural network models generally  rem...

  5. A Complex Network Approach to Distributional Semantic Models.

    Directory of Open Access Journals (Sweden)

    Akira Utsumi

    Full Text Available A number of studies on network analysis have focused on language networks based on free word association, which reflects human lexical knowledge, and have demonstrated the small-world and scale-free properties in the word association network. Nevertheless, there have been very few attempts at applying network analysis to distributional semantic models, despite the fact that these models have been studied extensively as computational or cognitive models of human lexical knowledge. In this paper, we analyze three network properties, namely, small-world, scale-free, and hierarchical properties, of semantic networks created by distributional semantic models. We demonstrate that the created networks generally exhibit the same properties as word association networks. In particular, we show that the distribution of the number of connections in these networks follows the truncated power law, which is also observed in an association network. This indicates that distributional semantic models can provide a plausible model of lexical knowledge. Additionally, the observed differences in the network properties of various implementations of distributional semantic models are consistently explained or predicted by considering the intrinsic semantic features of a word-context matrix and the functions of matrix weighting and smoothing. Furthermore, to simulate a semantic network with the observed network properties, we propose a new growing network model based on the model of Steyvers and Tenenbaum. The idea underlying the proposed model is that both preferential and random attachments are required to reflect different types of semantic relations in network growth process. We demonstrate that this model provides a better explanation of network behaviors generated by distributional semantic models.

  6. Inferring gene regression networks with model trees

    Directory of Open Access Journals (Sweden)

    Aguilar-Ruiz Jesus S

    2010-10-01

    Full Text Available Abstract Background Novel strategies are required in order to handle the huge amount of data produced by microarray technologies. To infer gene regulatory networks, the first step is to find direct regulatory relationships between genes building the so-called gene co-expression networks. They are typically generated using correlation statistics as pairwise similarity measures. Correlation-based methods are very useful in order to determine whether two genes have a strong global similarity but do not detect local similarities. Results We propose model trees as a method to identify gene interaction networks. While correlation-based methods analyze each pair of genes, in our approach we generate a single regression tree for each gene from the remaining genes. Finally, a graph from all the relationships among output and input genes is built taking into account whether the pair of genes is statistically significant. For this reason we apply a statistical procedure to control the false discovery rate. The performance of our approach, named REGNET, is experimentally tested on two well-known data sets: Saccharomyces Cerevisiae and E.coli data set. First, the biological coherence of the results are tested. Second the E.coli transcriptional network (in the Regulon database is used as control to compare the results to that of a correlation-based method. This experiment shows that REGNET performs more accurately at detecting true gene associations than the Pearson and Spearman zeroth and first-order correlation-based methods. Conclusions REGNET generates gene association networks from gene expression data, and differs from correlation-based methods in that the relationship between one gene and others is calculated simultaneously. Model trees are very useful techniques to estimate the numerical values for the target genes by linear regression functions. They are very often more precise than linear regression models because they can add just different linear

  7. Two stage neural network modelling for robust model predictive control.

    Science.gov (United States)

    Patan, Krzysztof

    2017-11-02

    The paper proposes a novel robust model predictive control scheme realized by means of artificial neural networks. The neural networks are used twofold: to design the so-called fundamental model of a plant and to catch uncertainty associated with the plant model. In order to simplify the optimization process carried out within the framework of predictive control an instantaneous linearization is applied which renders it possible to define the optimization problem in the form of constrained quadratic programming. Stability of the proposed control system is also investigated by showing that a cost function is monotonically decreasing with respect to time. Derived robust model predictive control is tested and validated on the example of a pneumatic servomechanism working at different operating regimes. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  8. An Introduction to Network Psychometrics: Relating Ising Network Models to Item Response Theory Models.

    Science.gov (United States)

    Marsman, M; Borsboom, D; Kruis, J; Epskamp, S; van Bork, R; Waldorp, L J; Maas, H L J van der; Maris, G

    2017-11-07

    In recent years, network models have been proposed as an alternative representation of psychometric constructs such as depression. In such models, the covariance between observables (e.g., symptoms like depressed mood, feelings of worthlessness, and guilt) is explained in terms of a pattern of causal interactions between these observables, which contrasts with classical interpretations in which the observables are conceptualized as the effects of a reflective latent variable. However, few investigations have been directed at the question how these different models relate to each other. To shed light on this issue, the current paper explores the relation between one of the most important network models-the Ising model from physics-and one of the most important latent variable models-the Item Response Theory (IRT) model from psychometrics. The Ising model describes the interaction between states of particles that are connected in a network, whereas the IRT model describes the probability distribution associated with item responses in a psychometric test as a function of a latent variable. Despite the divergent backgrounds of the models, we show a broad equivalence between them and also illustrate several opportunities that arise from this connection.

  9. Social network models predict movement and connectivity in ecological landscapes

    Science.gov (United States)

    Fletcher, Robert J.; Acevedo, M.A.; Reichert, Brian E.; Pias, Kyle E.; Kitchens, Wiley M.

    2011-01-01

    Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

  10. Neural Networks For Electrohydrodynamic Effect Modelling

    Directory of Open Access Journals (Sweden)

    Wiesław Wajs

    2004-01-01

    Full Text Available This paper presents currently achieved results concerning methods of electrohydrodynamiceffect used in geophysics simulated with feedforward networks trained with backpropagation algorithm, radial basis function networks and generalized regression networks.

  11. Significant rewiring of the transcriptome and proteome of an Escherichia coli strain harboring a tailored exogenous global regulator IrrE.

    Directory of Open Access Journals (Sweden)

    Tingjian Chen

    Full Text Available Cell reprogramming for microorganisms via engineered or artificial transcription factors and RNA polymerase mutants has presented a powerful tool for eliciting complex traits that are practically useful particularly for industrial strains, and for understanding at the global level the regulatory network of gene transcription. We previously further showed that an exogenous global regulator IrrE (derived from the extreme radiation-resistant bacterium Deinococcus radiodurans can be tailored to confer Escherichia coli (E. coli with significantly enhanced tolerances to different stresses. In this work, based on comparative transcriptomic and proteomic analyses of the representative strains E1 and E0, harboring the ethanol-tolerant IrrE mutant E1 and the ethanol-intolerant wild type IrrE, respectively, we found that the transcriptome and proteome of E. coli were extensively rewired by the tailored IrrE protein. Overall, 1196 genes (or approximately 27% of E. coli genes were significantly altered at the transcriptomic level, including notably genes in the nitrate-nitrite-nitric oxide (NO pathway, and genes for non-coding RNAs. The proteomic profile revealed significant up- or downregulation of several proteins associated with syntheses of the cell membrane and cell wall. Analyses of the intracellular NO level and cell growth under reduced temperature supported a close correlation between NO and ethanol tolerance, and also suggests a role for membrane fluidity. The significantly different omic profiles of strain E1 indicate that IrrE functions as a global regulator in E. coli, and that IrrE may be evolved for other cellular tolerances. In this sense, it will provide synthetic biology with a practical and evolvable regulatory "part" that operates at a higher level of complexity than local regulators. This work also suggests a possibility of introducing and engineering other exogenous global regulators to rewire the genomes of microorganism cells.

  12. A network-oriented business modeling environment

    Science.gov (United States)

    Bisconti, Cristian; Storelli, Davide; Totaro, Salvatore; Arigliano, Francesco; Savarino, Vincenzo; Vicari, Claudia

    The development of formal models related to the organizational aspects of an enterprise is fundamental when these aspects must be re-engineered and digitalized, especially when the enterprise is involved in the dynamics and value flows of a business network. Business modeling provides an opportunity to synthesize and make business processes, business rules and the structural aspects of an organization explicit, allowing business managers to control their complexity and guide an enterprise through effective decisional and strategic activities. This chapter discusses the main results of the TEKNE project in terms of software components that enable enterprises to configure, store, search and share models of any aspects of their business while leveraging standard and business-oriented technologies and languages to bridge the gap between the world of business people and IT experts and to foster effective business-to-business collaborations.

  13. Compartmentalization analysis using discrete fracture network models

    Energy Technology Data Exchange (ETDEWEB)

    La Pointe, P.R.; Eiben, T.; Dershowitz, W. [Golder Associates, Redmond, VA (United States); Wadleigh, E. [Marathon Oil Co., Midland, TX (United States)

    1997-08-01

    This paper illustrates how Discrete Fracture Network (DFN) technology can serve as a basis for the calculation of reservoir engineering parameters for the development of fractured reservoirs. It describes the development of quantitative techniques for defining the geometry and volume of structurally controlled compartments. These techniques are based on a combination of stochastic geometry, computational geometry, and graph the theory. The parameters addressed are compartment size, matrix block size and tributary drainage volume. The concept of DFN models is explained and methodologies to compute these parameters are demonstrated.

  14. Some queuing network models of computer systems

    Science.gov (United States)

    Herndon, E. S.

    1980-01-01

    Queuing network models of a computer system operating with a single workload type are presented. Program algorithms are adapted for use on the Texas Instruments SR-52 programmable calculator. By slightly altering the algorithm to process the G and H matrices row by row instead of column by column, six devices and an unlimited job/terminal population could be handled on the SR-52. Techniques are also introduced for handling a simple load dependent server and for studying interactive systems with fixed multiprogramming limits.

  15. Networks model of the East Turkistan terrorism

    Science.gov (United States)

    Li, Ben-xian; Zhu, Jun-fang; Wang, Shun-guo

    2015-02-01

    The presence of the East Turkistan terrorist network in China can be traced back to the rebellions on the BAREN region in Xinjiang in April 1990. This article intends to research the East Turkistan networks in China and offer a panoramic view. The events, terrorists and their relationship are described using matrices. Then social network analysis is adopted to reveal the network type and the network structure characteristics. We also find the crucial terrorist leader. Ultimately, some results show that the East Turkistan network has big hub nodes and small shortest path, and that the network follows a pattern of small world network with hierarchical structure.

  16. Fundamentals of complex networks models, structures and dynamics

    CERN Document Server

    Chen, Guanrong; Li, Xiang

    2014-01-01

    Complex networks such as the Internet, WWW, transportationnetworks, power grids, biological neural networks, and scientificcooperation networks of all kinds provide challenges for futuretechnological development. In particular, advanced societies havebecome dependent on large infrastructural networks to an extentbeyond our capability to plan (modeling) and to operate (control).The recent spate of collapses in power grids and ongoing virusattacks on the Internet illustrate the need for knowledge aboutmodeling, analysis of behaviors, optimized planning and performancecontrol in such networks. F

  17. Stochastic simulation of HIV population dynamics through complex network modelling

    NARCIS (Netherlands)

    Sloot, P. M. A.; Ivanov, S. V.; Boukhanovsky, A. V.; van de Vijver, D. A. M. C.; Boucher, C. A. B.

    We propose a new way to model HIV infection spreading through the use of dynamic complex networks. The heterogeneous population of HIV exposure groups is described through a unique network degree probability distribution. The time evolution of the network nodes is modelled by a Markov process and

  18. A Search Model with a Quasi-Network

    DEFF Research Database (Denmark)

    Ejarque, Joao Miguel

    This paper adds a quasi-network to a search model of the labor market. Fitting the model to an average unemployment rate and to other moments in the data implies the presence of the network is not noticeable in the basic properties of the unemployment and job finding rates. However, the network c...

  19. Stochastic simulation of HIV population dynamics through complex network modelling

    NARCIS (Netherlands)

    Sloot, P.M.A.; Ivanov, S.V.; Boukhanovsky, A.V.; van de Vijver, D.A.M.C.; Boucher, C.A.B.

    2008-01-01

    We propose a new way to model HIV infection spreading through the use of dynamic complex networks. The heterogeneous population of HIV exposure groups is described through a unique network degree probability distribution. The time evolution of the network nodes is modelled by a Markov process and

  20. QSAR modelling using combined simple competitive learning networks and RBF neural networks.

    Science.gov (United States)

    Sheikhpour, R; Sarram, M A; Rezaeian, M; Sheikhpour, E

    2018-04-01

    The aim of this study was to propose a QSAR modelling approach based on the combination of simple competitive learning (SCL) networks with radial basis function (RBF) neural networks for predicting the biological activity of chemical compounds. The proposed QSAR method consisted of two phases. In the first phase, an SCL network was applied to determine the centres of an RBF neural network. In the second phase, the RBF neural network was used to predict the biological activity of various phenols and Rho kinase (ROCK) inhibitors. The predictive ability of the proposed QSAR models was evaluated and compared with other QSAR models using external validation. The results of this study showed that the proposed QSAR modelling approach leads to better performances than other models in predicting the biological activity of chemical compounds. This indicated the efficiency of simple competitive learning networks in determining the centres of RBF neural networks.

  1. VEPCO network model reconciliation of LANL and MZA model data

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1992-12-15

    The LANL DC load flow model of the VEPCO transmission network shows 210 more substations than the AC load flow model produced by MZA utility Consultants. MZA was requested to determine the source of the difference. The AC load flow model used for this study utilizes 2 standard network algorithms (Decoupled or Newton). The solution time of each is affected by the number of substations. The more substations included, the longer the model will take to solve. In addition, the ability of the algorithms to converge to a solution is affected by line loadings and characteristics. Convergence is inhibited by numerous lightly loaded and electrically short lines. The MZA model reduces the total substations to 343 by creating equivalent loads and generation. Most of the omitted substations are lightly loaded and rated at 115 kV. The MZA model includes 16 substations not included in the LANL model. These represent new generation including Non-Utility Generator (NUG) sites, additional substations and an intertie (Wake, to CP and L). This report also contains data from the Italian State AC power flow model and the Duke Power Company AC flow model.

  2. Network Medicine Strikes a Blow against Breast Cancer

    DEFF Research Database (Denmark)

    Erler, Janine Terra; Linding, Rune

    2012-01-01

    Drug development for complex diseases is shifting from targeting individual proteins or genes to systems-based attacks targeting dynamic network states. Lee et al. now reveal how the progressive rewiring of a signaling network over time following EGF receptor inhibition leaves triple-negative bre...

  3. A Model of Genetic Variation in Human Social Networks

    CERN Document Server

    Fowler, James H; Christakis, Nicholas A

    2008-01-01

    Social networks influence the evolution of cooperation and they exhibit strikingly systematic patterns across a wide range of human contexts. Both of these facts suggest that variation in the topological attributes of human social networks might have a genetic basis. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric social network attributes is unknown. Here we show that three of these attributes (in-degree, transitivity, and centrality) are heritable. We then develop a "mirror network" method to test extant network models and show that none accounts for observed genetic variation in human social networks. We propose an alternative "attract and introduce" model that generates significant heritability as well as other important network features, and we show that this model with two simple forms of heterogeneity is well suited to the modeling of real social networks in humans. These results suggest that natural selection ...

  4. Feature network models for proximity data : statistical inference, model selection, network representations and links with related models

    NARCIS (Netherlands)

    Frank, Laurence Emmanuelle

    2006-01-01

    Feature Network Models (FNM) are graphical structures that represent proximity data in a discrete space with the use of features. A statistical inference theory is introduced, based on the additivity properties of networks and the linear regression framework. Considering features as predictor

  5. PageRank model of opinion formation on Ulam networks

    Science.gov (United States)

    Chakhmakhchyan, L.; Shepelyansky, D.

    2013-12-01

    We consider a PageRank model of opinion formation on Ulam networks, generated by the intermittency map and the typical Chirikov map. The Ulam networks generated by these maps have certain similarities with such scale-free networks as the World Wide Web (WWW), showing an algebraic decay of the PageRank probability. We find that the opinion formation process on Ulam networks has certain similarities but also distinct features comparing to the WWW. We attribute these distinctions to internal differences in network structure of the Ulam and WWW networks. We also analyze the process of opinion formation in the frame of generalized Sznajd model which protects opinion of small communities.

  6. A scale-free neural network for modelling neurogenesis

    Science.gov (United States)

    Perotti, Juan I.; Tamarit, Francisco A.; Cannas, Sergio A.

    2006-11-01

    In this work we introduce a neural network model for associative memory based on a diluted Hopfield model, which grows through a neurogenesis algorithm that guarantees that the final network is a small-world and scale-free one. We also analyze the storage capacity of the network and prove that its performance is larger than that measured in a randomly dilute network with the same connectivity.

  7. A graph model for opportunistic network coding

    KAUST Repository

    Sorour, Sameh

    2015-08-12

    © 2015 IEEE. Recent advancements in graph-based analysis and solutions of instantly decodable network coding (IDNC) trigger the interest to extend them to more complicated opportunistic network coding (ONC) scenarios, with limited increase in complexity. In this paper, we design a simple IDNC-like graph model for a specific subclass of ONC, by introducing a more generalized definition of its vertices and the notion of vertex aggregation in order to represent the storage of non-instantly-decodable packets in ONC. Based on this representation, we determine the set of pairwise vertex adjacency conditions that can populate this graph with edges so as to guarantee decodability or aggregation for the vertices of each clique in this graph. We then develop the algorithmic procedures that can be applied on the designed graph model to optimize any performance metric for this ONC subclass. A case study on reducing the completion time shows that the proposed framework improves on the performance of IDNC and gets very close to the optimal performance.

  8. Marketing communications model for innovation networks

    Directory of Open Access Journals (Sweden)

    Tiago João Freitas Correia

    2015-10-01

    Full Text Available Innovation is an increasingly relevant concept for the success of any organization, but it also represents a set of internal and external considerations, barriers and challenges to overcome. Along the concept of innovation, new paradigms emerge such as open innovation and co-creation that are simultaneously innovation modifiers and intensifiers in organizations, promoting organizational openness and stakeholder integration within the value creation process. Innovation networks composed by a multiplicity of agents in co-creative work perform as innovation mechanisms to face the increasingly complexity of products, services and markets. Technology, especially the Internet, is an enabler of all process among organizations supported by co-creative platforms for innovation. The definition of marketing communication strategies that promote motivation and involvement of all stakeholders in synergic creation and external promotion is the central aspect of this research. The implementation of the projects is performed by participative workshops with stakeholders from Madan Parque through IDEAS(REVOLUTION methodology and the operational model LinkUp parameterized for the project. The project is divided into the first part, the theoretical framework, and the second part where a model is developed for the marketing communication strategies that appeal to the Madan Parque case study. Keywords: Marketing Communication; Open Innovation, Technology; Innovation Networks; Incubator; Co-Creation.

  9. Determining Application Runtimes Using Queueing Network Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, Michael L. [Univ. of San Francisco, CA (United States)

    2006-12-14

    Determination of application times-to-solution for large-scale clustered computers continues to be a difficult problem in high-end computing, which will only become more challenging as multi-core consumer machines become more prevalent in the market. Both researchers and consumers of these multi-core systems desire reasonable estimates of how long their programs will take to run (time-to-solution, or TTS), and how many resources will be consumed in the execution. Currently there are few methods of determining these values, and those that do exist are either overly simplistic in their assumptions or require great amounts of effort to parameterize and understand. One previously untried method is queuing network modeling (QNM), which is easy to parameterize and solve, and produces results that typically fall within 10 to 30% of the actual TTS for our test cases. Using characteristics of the computer network (bandwidth, latency) and communication patterns (number of messages, message length, time spent in communication), the QNM model of the NAS-PB CG application was applied to MCR and ALC, supercomputers at LLNL, and the Keck Cluster at USF, with average errors of 2.41%, 3.61%, and -10.73%, respectively, compared to the actual TTS observed. While additional work is necessary to improve the predictive capabilities of QNM, current results show that QNM has a great deal of promise for determining application TTS for multi-processor computer systems.

  10. Modeling management of research and education networks

    NARCIS (Netherlands)

    Galagan, D.V.

    2004-01-01

    Computer networks and their services have become an essential part of research and education. Nowadays every modern R&E institution must have a computer network and provide network services to its students and staff. In addition to its internal computer network, every R&E institution must have a

  11. Modeling stochasticity in biochemical reaction networks

    Science.gov (United States)

    Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.

    2016-03-01

    Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.

  12. Modelling of A Trust and Reputation Model in Wireless Networks

    Directory of Open Access Journals (Sweden)

    Saurabh Mishra

    2015-09-01

    Full Text Available Security is the major challenge for Wireless Sensor Networks (WSNs. The sensor nodes are deployed in non controlled environment, facing the danger of information leakage, adversary attacks and other threats. Trust and Reputation models are solutions for this problem and to identify malicious, selfish and compromised nodes. This paper aims to evaluate varying collusion effect with respect to static (SW, dynamic (DW, static with collusion (SWC, dynamic with collusion (DWC and oscillating wireless sensor networks to derive the joint resultant of Eigen Trust Model. An attempt has been made for the same by comparing aforementioned networks that are purely dedicated to protect the WSNs from adversary attacks and maintain the security issues. The comparison has been made with respect to accuracy and path length and founded that, collusion for wireless sensor networks seems intractable with the static and dynamic WSNs when varied with specified number of fraudulent nodes in the scenario. Additionally, it consumes more energy and resources in oscillating and collusive environments.

  13. Multiplicative Attribute Graph Model of Real-World Networks

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Myunghwan [Stanford Univ., CA (United States); Leskovec, Jure [Stanford Univ., CA (United States)

    2010-10-20

    Large scale real-world network data, such as social networks, Internet andWeb graphs, is ubiquitous in a variety of scientific domains. The study of such social and information networks commonly finds patterns and explain their emergence through tractable models. In most networks, especially in social networks, nodes also have a rich set of attributes (e.g., age, gender) associatedwith them. However, most of the existing network models focus only on modeling the network structure while ignoring the features of nodes in the network. Here we present a class of network models that we refer to as the Multiplicative Attribute Graphs (MAG), which naturally captures the interactions between the network structure and node attributes. We consider a model where each node has a vector of categorical features associated with it. The probability of an edge between a pair of nodes then depends on the product of individual attributeattribute similarities. The model yields itself to mathematical analysis as well as fit to real data. We derive thresholds for the connectivity, the emergence of the giant connected component, and show that the model gives rise to graphs with a constant diameter. Moreover, we analyze the degree distribution to show that the model can produce networks with either lognormal or power-law degree distribution depending on certain conditions.

  14. Multilevel method for modeling large-scale networks.

    Energy Technology Data Exchange (ETDEWEB)

    Safro, I. M. (Mathematics and Computer Science)

    2012-02-24

    Understanding the behavior of real complex networks is of great theoretical and practical significance. It includes developing accurate artificial models whose topological properties are similar to the real networks, generating the artificial networks at different scales under special conditions, investigating a network dynamics, reconstructing missing data, predicting network response, detecting anomalies and other tasks. Network generation, reconstruction, and prediction of its future topology are central issues of this field. In this project, we address the questions related to the understanding of the network modeling, investigating its structure and properties, and generating artificial networks. Most of the modern network generation methods are based either on various random graph models (reinforced by a set of properties such as power law distribution of node degrees, graph diameter, and number of triangles) or on the principle of replicating an existing model with elements of randomization such as R-MAT generator and Kronecker product modeling. Hierarchical models operate at different levels of network hierarchy but with the same finest elements of the network. However, in many cases the methods that include randomization and replication elements on the finest relationships between network nodes and modeling that addresses the problem of preserving a set of simplified properties do not fit accurately enough the real networks. Among the unsatisfactory features are numerically inadequate results, non-stability of algorithms on real (artificial) data, that have been tested on artificial (real) data, and incorrect behavior at different scales. One reason is that randomization and replication of existing structures can create conflicts between fine and coarse scales of the real network geometry. Moreover, the randomization and satisfying of some attribute at the same time can abolish those topological attributes that have been undefined or hidden from

  15. CNMO: Towards the Construction of a Communication Network Modelling Ontology

    Science.gov (United States)

    Rahman, Muhammad Azizur; Pakstas, Algirdas; Wang, Frank Zhigang

    Ontologies that explicitly identify objects, properties, and relationships in specific domains are essential for collaboration that involves sharing of data, knowledge or resources. A communications network modelling ontology (CNMO) has been designed to represent a network model as well as aspects related to its development and actual network operation. Network nodes/sites, link, traffic sources, protocols as well as aspects of the modeling/simulation scenario and operational aspects are defined with their formal representation. A CNMO may be beneficial for various network design/simulation/research communities due to the uniform representation of network models. This ontology is designed using terminology and concepts from various network modeling, simulation and topology generation tools.

  16. Topological evolution of virtual social networks by modeling social activities

    Science.gov (United States)

    Sun, Xin; Dong, Junyu; Tang, Ruichun; Xu, Mantao; Qi, Lin; Cai, Yang

    2015-09-01

    With the development of Internet and wireless communication, virtual social networks are becoming increasingly important in the formation of nowadays' social communities. Topological evolution model is foundational and critical for social network related researches. Up to present most of the related research experiments are carried out on artificial networks, however, a study of incorporating the actual social activities into the network topology model is ignored. This paper first formalizes two mathematical abstract concepts of hobbies search and friend recommendation to model the social actions people exhibit. Then a social activities based topology evolution simulation model is developed to satisfy some well-known properties that have been discovered in real-world social networks. Empirical results show that the proposed topology evolution model has embraced several key network topological properties of concern, which can be envisioned as signatures of real social networks.

  17. An Efficient Multitask Scheduling Model for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Hongsheng Yin

    2014-01-01

    Full Text Available The sensor nodes of multitask wireless network are constrained in performance-driven computation. Theoretical studies on the data processing model of wireless sensor nodes suggest satisfying the requirements of high qualities of service (QoS of multiple application networks, thus improving the efficiency of network. In this paper, we present the priority based data processing model for multitask sensor nodes in the architecture of multitask wireless sensor network. The proposed model is deduced with the M/M/1 queuing model based on the queuing theory where the average delay of data packets passing by sensor nodes is estimated. The model is validated with the real data from the Huoerxinhe Coal Mine. By applying the proposed priority based data processing model in the multitask wireless sensor network, the average delay of data packets in a sensor nodes is reduced nearly to 50%. The simulation results show that the proposed model can improve the throughput of network efficiently.

  18. Vehicle Scheduling with Network Flow Models

    Directory of Open Access Journals (Sweden)

    Gustavo P. Silva

    2010-04-01

    Full Text Available

    Este trabalho retrata a primeira fase de uma pesquisa de doutorado voltada para a utilização de modelos de fluxo em redes para programação de veículos (de ônibus, em particular. A utilização de modelos deste tipo ainda e muito pouco explorada na literatura, principalmente pela dificuldade imposta pelo grande numero de variáveis resultante. Neste trabalho são apresentadas formulações para tratamento do problema de programação de veículos associados a um único depósito (ou garagem como problema de fluxo em redes, incluindo duas técnicas para reduzir o numero de arcos na rede criada e, conseqüentemente, o numero de variáveis a tratar. Uma destas técnicas de redução de arcos foi implementada e o problema de fluxo resultante foi direcionado para ser resolvido, nesta fase da pesquisa, por uma versão disponível do algoritmo Simplex para redes. Problemas teste baseados em dados reais da cidade de Reading, UK, foram resolvidos com a utilização da formulação de fluxo em redes adotada, e os resultados comparados com aqueles obtidos pelo método heurístico BOOST, o qual tem sido largamente testado e comercializado pela School of Computer Studies da Universidade de Leeds, UK. Os resultados alcançados demonstram a possibilidade de tratamento de problemas reais com a técnica de redução de arcos.

    ABSTRACT

    This paper presents the successful results of a first phase of a doctoral research addressed to solving vehicle (bus, in particular scheduling problems through network flow formulations. Network flow modeling for this kind of problem is a promising, but not a well explored approach, mainly because of the large number of variables related to number of arcs of real case networks. The paper presents and discusses some network flow formulations for the single depot bus vehicle scheduling problem, along with two techniques of arc reduction. One of these arc reduction techniques has been implemented and the underlying

  19. Bicriteria Models of Vehicles Recycling Network Facility Location

    Science.gov (United States)

    Merkisz-Guranowska, Agnieszka

    2012-06-01

    The paper presents the issues related to modeling of a vehicle recycling network. The functioning of the recycling network is within the realm of interest of a variety of government agendas, companies participating in the network, vehicle manufacturers and vehicle end users. The interests of these groups need to be considered when deciding about the network organization. The paper presents bicriteria models of network entity location that take into account the preferences of the vehicle owners and network participants related to the network construction and reorganization. A mathematical formulation of the optimization tasks has been presented including the objective functions and limitations that the solutions have to comply with. Then, the models were used for the network optimization in Poland.

  20. Models as Tools of Analysis of a Network Organisation

    Directory of Open Access Journals (Sweden)

    Wojciech Pająk

    2013-06-01

    Full Text Available The paper presents models which may be applied as tools of analysis of a network organisation. The starting point of the discussion is defining the following terms: supply chain and network organisation. Further parts of the paper present basic assumptions analysis of a network organisation. Then the study characterises the best known models utilised in analysis of a network organisation. The purpose of the article is to define the notion and the essence of network organizations and to present the models used for their analysis.

  1. Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita.

    Science.gov (United States)

    Wotton, Karl R; Jiménez-Guri, Eva; Crombach, Anton; Janssens, Hilde; Alcaine-Colet, Anna; Lemke, Steffen; Schmidt-Ott, Urs; Jaeger, Johannes

    2015-01-05

    The segmentation gene network in insects can produce equivalent phenotypic outputs despite differences in upstream regulatory inputs between species. We investigate the mechanistic basis of this phenomenon through a systems-level analysis of the gap gene network in the scuttle fly Megaselia abdita (Phoridae). It combines quantification of gene expression at high spatio-temporal resolution with systematic knock-downs by RNA interference (RNAi). Initiation and dynamics of gap gene expression differ markedly between M. abdita and Drosophila melanogaster, while the output of the system converges to equivalent patterns at the end of the blastoderm stage. Although the qualitative structure of the gap gene network is conserved, there are differences in the strength of regulatory interactions between species. We term such network rewiring 'quantitative system drift'. It provides a mechanistic explanation for the developmental hourglass model in the dipteran lineage. Quantitative system drift is likely to be a widespread mechanism for developmental evolution.

  2. Natural Models for Evolution on Networks

    CERN Document Server

    Mertzios, George B; Raptopoulos, Christoforos; Spirakis, Paul G

    2011-01-01

    Evolutionary dynamics have been traditionally studied in the context of homogeneous populations, mainly described my the Moran process. Recently, this approach has been generalized in \\cite{LHN} by arranging individuals on the nodes of a network. Undirected networks seem to have a smoother behavior than directed ones, and thus it is more challenging to find suppressors/amplifiers of selection. In this paper we present the first class of undirected graphs which act as suppressors of selection, by achieving a fixation probability that is at most one half of that of the complete graph, as the number of vertices increases. Moreover, we provide some generic upper and lower bounds for the fixation probability of general undirected graphs. As our main contribution, we introduce the natural alternative of the model proposed in \\cite{LHN}, where all individuals interact simultaneously and the result is a compromise between aggressive and non-aggressive individuals. That is, the behavior of the individuals in our new m...

  3. A last updating evolution model for online social networks

    Science.gov (United States)

    Bu, Zhan; Xia, Zhengyou; Wang, Jiandong; Zhang, Chengcui

    2013-05-01

    As information technology has advanced, people are turning to electronic media more frequently for communication, and social relationships are increasingly found on online channels. However, there is very limited knowledge about the actual evolution of the online social networks. In this paper, we propose and study a novel evolution network model with the new concept of “last updating time”, which exists in many real-life online social networks. The last updating evolution network model can maintain the robustness of scale-free networks and can improve the network reliance against intentional attacks. What is more, we also found that it has the “small-world effect”, which is the inherent property of most social networks. Simulation experiment based on this model show that the results and the real-life data are consistent, which means that our model is valid.

  4. Precise Network Modeling of Systems Genetics Data Using the Bayesian Network Webserver.

    Science.gov (United States)

    Ziebarth, Jesse D; Cui, Yan

    2017-01-01

    The Bayesian Network Webserver (BNW, http://compbio.uthsc.edu/BNW ) is an integrated platform for Bayesian network modeling of biological datasets. It provides a web-based network modeling environment that seamlessly integrates advanced algorithms for probabilistic causal modeling and reasoning with Bayesian networks. BNW is designed for precise modeling of relatively small networks that contain less than 20 nodes. The structure learning algorithms used by BNW guarantee the discovery of the best (most probable) network structure given the data. To facilitate network modeling across multiple biological levels, BNW provides a very flexible interface that allows users to assign network nodes into different tiers and define the relationships between and within the tiers. This function is particularly useful for modeling systems genetics datasets that often consist of multiscalar heterogeneous genotype-to-phenotype data. BNW enables users to, within seconds or minutes, go from having a simply formatted input file containing a dataset to using a network model to make predictions about the interactions between variables and the potential effects of experimental interventions. In this chapter, we will introduce the functions of BNW and show how to model systems genetics datasets with BNW.

  5. Multiple Social Networks, Data Models and Measures for

    DEFF Research Database (Denmark)

    Magnani, Matteo; Rossi, Luca

    2017-01-01

    Multiple Social Network Analysis is a discipline defining models, measures, methodologies, and algorithms to study multiple social networks together as a single social system. It is particularly valuable when the networks are interconnected, e.g., the same actors are present in more than one...

  6. Throughput capacity computation model for hybrid wireless networks

    African Journals Online (AJOL)

    wireless networks. We present in this paper, a computational model for obtaining throughput capacity for hybrid wireless networks. For a hybrid network with n nodes and m base stations, we observe through simulation that the throughput capacity increases linearly with the base station infrastructure connected by the wired ...

  7. Modelling crime linkage with Bayesian networks.

    Science.gov (United States)

    de Zoete, Jacob; Sjerps, Marjan; Lagnado, David; Fenton, Norman

    2015-05-01

    When two or more crimes show specific similarities, such as a very distinct modus operandi, the probability that they were committed by the same offender becomes of interest. This probability depends on the degree of similarity and distinctiveness. We show how Bayesian networks can be used to model different evidential structures that can occur when linking crimes, and how they assist in understanding the complex underlying dependencies. That is, how evidence that is obtained in one case can be used in another and vice versa. The flip side of this is that the intuitive decision to "unlink" a case in which exculpatory evidence is obtained leads to serious overestimation of the strength of the remaining cases. Copyright © 2014 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

  8. Structural equation models from paths to networks

    CERN Document Server

    Westland, J Christopher

    2015-01-01

    This compact reference surveys the full range of available structural equation modeling (SEM) methodologies.  It reviews applications in a broad range of disciplines, particularly in the social sciences where many key concepts are not directly observable.  This is the first book to present SEM’s development in its proper historical context–essential to understanding the application, strengths and weaknesses of each particular method.  This book also surveys the emerging path and network approaches that complement and enhance SEM, and that will grow in importance in the near future.  SEM’s ability to accommodate unobservable theory constructs through latent variables is of significant importance to social scientists.  Latent variable theory and application are comprehensively explained, and methods are presented for extending their power, including guidelines for data preparation, sample size calculation, and the special treatment of Likert scale data.  Tables of software, methodologies and fit st...

  9. A mathematical model for networks with structures in the mesoscale

    OpenAIRE

    Criado, Regino; Flores, Julio; Gacia Del Amo, Alejandro Jose; Gómez, Jesus; Romance, Miguel

    2011-01-01

    Abstract The new concept of multilevel network is introduced in order to embody some topological properties of complex systems with structures in the mesoscale which are not completely captured by the classical models. This new model, which generalizes the hyper-network and hyper-structure models, fits perfectly with several real-life complex systems, including social and public transportation networks. We present an analysis of the structural properties of the mu...

  10. Agent Based Modeling on Organizational Dynamics of Terrorist Network

    OpenAIRE

    Bo Li; Duoyong Sun; Renqi Zhu; Ze Li

    2015-01-01

    Modeling organizational dynamics of terrorist network is a critical issue in computational analysis of terrorism research. The first step for effective counterterrorism and strategic intervention is to investigate how the terrorists operate with the relational network and what affects the performance. In this paper, we investigate the organizational dynamics by employing a computational experimentation methodology. The hierarchical cellular network model and the organizational dynamics model ...

  11. Adaptive Networks Theory, Models and Applications

    CERN Document Server

    Gross, Thilo

    2009-01-01

    With adaptive, complex networks, the evolution of the network topology and the dynamical processes on the network are equally important and often fundamentally entangled. Recent research has shown that such networks can exhibit a plethora of new phenomena which are ultimately required to describe many real-world networks. Some of those phenomena include robust self-organization towards dynamical criticality, formation of complex global topologies based on simple, local rules, and the spontaneous division of "labor" in which an initially homogenous population of network nodes self-organizes into functionally distinct classes. These are just a few. This book is a state-of-the-art survey of those unique networks. In it, leading researchers set out to define the future scope and direction of some of the most advanced developments in the vast field of complex network science and its applications.

  12. A Cascade-Based Emergency Model for Water Distribution Network

    Directory of Open Access Journals (Sweden)

    Qing Shuang

    2015-01-01

    Full Text Available Water distribution network is important in the critical physical infrastructure systems. The paper studies the emergency resource strategies on water distribution network with the approach of complex network and cascading failures. The model of cascade-based emergency for water distribution network is built. The cascade-based model considers the network topology analysis and hydraulic analysis to provide a more realistic result. A load redistribution function with emergency recovery mechanisms is established. From the aspects of uniform distribution, node betweenness, and node pressure, six recovery strategies are given to reflect the network topology and the failure information, respectively. The recovery strategies are evaluated with the complex network indicators to describe the failure scale and failure velocity. The proposed method is applied by an illustrative example. The results showed that the recovery strategy considering the node pressure can enhance the network robustness effectively. Besides, this strategy can reduce the failure nodes and generate the least failure nodes per time.

  13. Integrating public transort networks in the axial model

    NARCIS (Netherlands)

    Gil, J.

    2012-01-01

    This study presents a first step in the development of a model that integrates public transport networks with the space syntax axial model, towards a network model that can describe the multi?modal movement structure of a city and study its patterns and flows. It describes the method for building an

  14. An intercausal cancellation model for Bayesian-network engineering

    NARCIS (Netherlands)

    Woudenberg, Steven P D; Van Der Gaag, Linda C.; Rademaker, Carin M A

    2015-01-01

    When constructing Bayesian networks with domain experts, network engineers often use the noisy-OR model, and causal interaction models more generally, to alleviate the burden of probability elicitation: the use of such a model serves to reduce the number of probabilities to be elicited on the one

  15. Common quandaries and their practical solutions in Bayesian network modeling

    Science.gov (United States)

    Bruce G. Marcot

    2017-01-01

    Use and popularity of Bayesian network (BN) modeling has greatly expanded in recent years, but many common problems remain. Here, I summarize key problems in BN model construction and interpretation,along with suggested practical solutions. Problems in BN model construction include parameterizing probability values, variable definition, complex network structures,...

  16. Malware Propagation and Prevention Model for Time-Varying Community Networks within Software Defined Networks

    Directory of Open Access Journals (Sweden)

    Lan Liu

    2017-01-01

    Full Text Available As the adoption of Software Defined Networks (SDNs grows, the security of SDN still has several unaddressed limitations. A key network security research area is in the study of malware propagation across the SDN-enabled networks. To analyze the spreading processes of network malware (e.g., viruses in SDN, we propose a dynamic model with a time-varying community network, inspired by research models on the spread of epidemics in complex networks across communities. We assume subnets of the network as communities and links that are dense in subnets but sparse between subnets. Using numerical simulation and theoretical analysis, we find that the efficiency of network malware propagation in this model depends on the mobility rate q of the nodes between subnets. We also find that there exists a mobility rate threshold qc. The network malware will spread in the SDN when the mobility rate q>qc. The malware will survive when q>qc and perish when qmodel is effective, and the results may help to decide the SDN control strategy to defend against network malware and provide a theoretical basis to reduce and prevent network security incidents.

  17. Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes.

    Science.gov (United States)

    Coulombe-Huntington, Jasmin; Xia, Yu

    2017-01-01

    Gene gain and loss shape both proteomes and the networks they form. The increasing availability of closely related sequenced genomes and of genome-wide network data should enable a better understanding of the evolutionary forces driving gene gain, gene loss and evolutionary network rewiring. Using orthology mappings across 23 ascomycete fungi genomes, we identified proteins that were lost, gained or universally conserved across the tree, enabling us to compare genes across all stages of their life-cycle. Based on a collection of genome-wide network and gene expression datasets from baker's yeast, as well as a few from fission yeast, we found that gene loss is more strongly associated with network and expression features of closely related species than that of distant species, consistent with the evolutionary modulation of gene loss propensity through network rewiring. We also discovered that lost and gained genes, as compared to universally conserved "core" genes, have more regulators, more complex expression patterns and are much more likely to encode for transcription factors. Finally, we found that the relative rate of network integration of new genes into the different types of networks agrees with experimentally measured rates of network rewiring. This systems-level view of the life-cycle of eukaryotic genes suggests that the gain and loss of genes is tightly coupled to the gain and loss of network interactions, that lineage-specific adaptations drive regulatory complexity and that the relative rates of integration of new genes are consistent with network rewiring rates.

  18. Modeling the reemergence of information diffusion in social network

    Science.gov (United States)

    Yang, Dingda; Liao, Xiangwen; Shen, Huawei; Cheng, Xueqi; Chen, Guolong

    2018-01-01

    Information diffusion in networks is an important research topic in various fields. Existing studies either focus on modeling the process of information diffusion, e.g., independent cascade model and linear threshold model, or investigate information diffusion in networks with certain structural characteristics such as scale-free networks and small world networks. However, there are still several phenomena that have not been captured by existing information diffusion models. One of the prominent phenomena is the reemergence of information diffusion, i.e., a piece of information reemerges after the completion of its initial diffusion process. In this paper, we propose an optimized information diffusion model by introducing a new informed state into traditional susceptible-infected-removed model. We verify the proposed model via simulations in real-world social networks, and the results indicate that the model can reproduce the reemergence of information during the diffusion process.

  19. Spectral Modelling for Spatial Network Analysis

    NARCIS (Netherlands)

    Nourian, P.; Rezvani, S.; Sariyildiz, I.S.; van der Hoeven, F.D.; Attar, Ramtin; Chronis, Angelos; Hanna, Sean; Turrin, Michela

    2016-01-01

    Spatial Networks represent the connectivity structure between units of space as a weighted graph whose links are weighted as to the strength of connections. In case of urban spatial networks, the units of space correspond closely to streets and in architectural spatial networks the units correspond

  20. Rewiring and regulation of cross-compartmentalized metabolism in protists.

    Science.gov (United States)

    Ginger, Michael L; McFadden, Geoffrey I; Michels, Paul A M

    2010-03-12

    Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation.

  1. Infinite Multiple Membership Relational Modeling for Complex Networks

    DEFF Research Database (Denmark)

    Mørup, Morten; Schmidt, Mikkel Nørgaard; Hansen, Lars Kai

    Learning latent structure in complex networks has become an important problem fueled by many types of networked data originating from practically all fields of science. In this paper, we propose a new non-parametric Bayesian multiplemembership latent feature model for networks. Contrary to existing...... multiplemembership models that scale quadratically in the number of vertices the proposedmodel scales linearly in the number of links admittingmultiple-membership analysis in large scale networks. We demonstrate a connection between the single membership relational model and multiple membership models and show...

  2. Performance Modeling for Heterogeneous Wireless Networks with Multiservice Overflow Traffic

    DEFF Research Database (Denmark)

    Huang, Qian; Ko, King-Tim; Iversen, Villy Bæk

    2009-01-01

    Performance modeling is important for the purpose of developing efficient dimensioning tools for large complicated networks. But it is difficult to achieve in heterogeneous wireless networks, where different networks have different statistical characteristics in service and traffic models....... Multiservice loss analysis based on multi-dimensional Markov chain becomes intractable in these networks due to intensive computations required. This paper focuses on performance modeling for heterogeneous wireless networks based on a hierarchical overlay infrastructure. A method based on decomposition...... of the correlated traffic is used to achieve an approximate performance modeling for multiservice in hierarchical heterogeneous wireless networks with overflow traffic. The accuracy of the approximate performance obtained by our proposed modeling is verified by simulations....

  3. Piecewise linear and Boolean models of chemical reaction networks.

    Science.gov (United States)

    Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir

    2014-12-01

    Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions ([Formula: see text]). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent [Formula: see text] is large. However, while the case of small constant [Formula: see text] appears in practice, it is not well understood. We provide a mathematical analysis of this limit and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed-form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator.

  4. Transmission network expansion planning based on hybridization model of neural networks and harmony search algorithm

    Directory of Open Access Journals (Sweden)

    Mohammad Taghi Ameli

    2012-01-01

    Full Text Available Transmission Network Expansion Planning (TNEP is a basic part of power network planning that determines where, when and how many new transmission lines should be added to the network. So, the TNEP is an optimization problem in which the expansion purposes are optimized. Artificial Intelligence (AI tools such as Genetic Algorithm (GA, Simulated Annealing (SA, Tabu Search (TS and Artificial Neural Networks (ANNs are methods used for solving the TNEP problem. Today, by using the hybridization models of AI tools, we can solve the TNEP problem for large-scale systems, which shows the effectiveness of utilizing such models. In this paper, a new approach to the hybridization model of Probabilistic Neural Networks (PNNs and Harmony Search Algorithm (HSA was used to solve the TNEP problem. Finally, by considering the uncertain role of the load based on a scenario technique, this proposed model was tested on the Garver’s 6-bus network.

  5. Heterogeneous information network model for equipment-standard system

    Science.gov (United States)

    Yin, Liang; Shi, Li-Chen; Zhao, Jun-Yan; Du, Song-Yang; Xie, Wen-Bo; Yuan, Fei; Chen, Duan-Bing

    2018-01-01

    Entity information network is used to describe structural relationships between entities. Taking advantage of its extension and heterogeneity, entity information network is more and more widely applied to relationship modeling. Recent years, lots of researches about entity information network modeling have been proposed, while seldom of them concentrate on equipment-standard system with properties of multi-layer, multi-dimension and multi-scale. In order to efficiently deal with some complex issues in equipment-standard system such as standard revising, standard controlling, and production designing, a heterogeneous information network model for equipment-standard system is proposed in this paper. Three types of entities and six types of relationships are considered in the proposed model. Correspondingly, several different similarity-measuring methods are used in the modeling process. The experiments show that the heterogeneous information network model established in this paper can reflect relationships between entities accurately. Meanwhile, the modeling process has a good performance on time consumption.

  6. Ripple-Spreading Network Model Optimization by Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Xiao-Bing Hu

    2013-01-01

    Full Text Available 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 influence of a few local events spreads out through nodes and then largely determines the final network topology. However, the relationships between ripple-spreading related parameters (RSRPs of RSNM and small-world and scale-free topologies are not as obvious or straightforward as in many other network models. This paper attempts to apply genetic algorithm (GA to tune the values of RSRPs, so that the RSNM may generate these two most important network topologies. The study demonstrates that, once RSRPs are properly tuned by GA, the RSNM is capable of generating both network topologies and therefore has a great flexibility to study many real-world complex network systems.

  7. Network models of frugivory and seed dispersal: Challenges and opportunities

    Science.gov (United States)

    Carlo, Tomás A.; Yang, Suann

    2011-11-01

    Network analyses have emerged as a new tool to study frugivory and seed dispersal (FSD) mutualisms because networks can model and simplify the complexity of multiple community-wide species interactions. Moreover, network theory suggests that structural properties, such as the presence of highly generalist species, are linked to the stability of mutualistic communities. However, we still lack empirical validation of network model predictions. Here we outline new research avenues to connect network models to FSD processes, and illustrate the challenges and opportunities of this tool with a field study. We hypothesized that generalist frugivores would be important for forest stability by dispersing seeds into deforested areas and initiating reforestation. We then constructed a network of plant-frugivore interactions using published data and identified the most generalist frugivores. To test the importance of generalists we measured: 1) the frequency with which frugivores moved between pasture and forest, 2) the bird-generated seed rain under perches in the pasture, and 3) the perching frequency of birds above seed traps. The generalist frugivores in the forest network were not important for seed dispersal into pastures, and thus for forest recovery, because the forest network excluded habitat heterogeneities, frugivore behavior, and movements. More research is needed to develop ways to incorporate relevant FSD processes into network models in order for these models to be more useful to community ecology and conservation. The network framework can serve to spark and renew interest in FSD and further our understanding of plant-animal communities.

  8. Hybrid neural network bushing model for vehicle dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Sohn, Jeong Hyun [Pukyong National University, Busan (Korea, Republic of); Lee, Seung Kyu [Hyosung Corporation, Changwon (Korea, Republic of); Yoo, Wan Suk [Pusan National University, Busan (Korea, Republic of)

    2008-12-15

    Although the linear model was widely used for the bushing model in vehicle suspension systems, it could not express the nonlinear characteristics of bushing in terms of the amplitude and the frequency. An artificial neural network model was suggested to consider the hysteretic responses of bushings. This model, however, often diverges due to the uncertainties of the neural network under the unexpected excitation inputs. In this paper, a hybrid neural network bushing model combining linear and neural network is suggested. A linear model was employed to represent linear stiffness and damping effects, and the artificial neural network algorithm was adopted to take into account the hysteretic responses. A rubber test was performed to capture bushing characteristics, where sine excitation with different frequencies and amplitudes is applied. Random test results were used to update the weighting factors of the neural network model. It is proven that the proposed model has more robust characteristics than a simple neural network model under step excitation input. A full car simulation was carried out to verify the proposed bushing models. It was shown that the hybrid model results are almost identical to the linear model under several maneuvers

  9. Optical Network Models and Their Application to Software-Defined Network Management

    Directory of Open Access Journals (Sweden)

    Thomas Szyrkowiec

    2017-01-01

    Full Text Available Software-defined networking is finding its way into optical networks. Here, it promises a simplification and unification of network management for optical networks allowing automation of operational tasks despite the highly diverse and vendor-specific commercial systems and the complexity and analog nature of optical transmission. Common abstractions and interfaces are a fundamental component for software-defined optical networking. Currently, a number of models for optical networks are available. They all claim to provide open and vendor agnostic management of optical equipment. In this work, we survey and compare the most important models and propose an intent interface for creating virtual topologies which is integrated in the existing model ecosystem.

  10. An image segmentation method based on network clustering model

    Science.gov (United States)

    Jiao, Yang; Wu, Jianshe; Jiao, Licheng

    2018-01-01

    Network clustering phenomena are ubiquitous in nature and human society. In this paper, a method involving a network clustering model is proposed for mass segmentation in mammograms. First, the watershed transform is used to divide an image into regions, and features of the image are computed. Then a graph is constructed from the obtained regions and features. The network clustering model is applied to realize clustering of nodes in the graph. Compared with two classic methods, the algorithm based on the network clustering model performs more effectively in experiments.

  11. Small is beautiful: models of small neuronal networks.

    Science.gov (United States)

    Lamb, Damon G; Calabrese, Ronald L

    2012-08-01

    Modeling has contributed a great deal to our understanding of how individual neurons and neuronal networks function. In this review, we focus on models of the small neuronal networks of invertebrates, especially rhythmically active CPG networks. Models have elucidated many aspects of these networks, from identifying key interacting membrane properties to pointing out gaps in our understanding, for example missing neurons. Even the complex CPGs of vertebrates, such as those that underlie respiration, have been reduced to small network models to great effect. Modeling of these networks spans from simplified models, which are amenable to mathematical analyses, to very complicated biophysical models. Some researchers have now adopted a population approach, where they generate and analyze many related models that differ in a few to several judiciously chosen free parameters; often these parameters show variability across animals and thus justify the approach. Models of small neuronal networks will continue to expand and refine our understanding of how neuronal networks in all animals program motor output, process sensory information and learn. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Stochastic Online Learning in Dynamic Networks under Unknown Models

    Science.gov (United States)

    2016-08-02

    Stochastic Online Learning in Dynamic Networks under Unknown Models This research aims to develop fundamental theories and practical algorithms for...12211 Research Triangle Park, NC 27709-2211 Online learning , multi-armed bandit, dynamic networks REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S... Online Learning in Dynamic Networks under Unknown Models Report Title This research aims to develop fundamental theories and practical algorithms for

  13. A Cellular Automata Models of Evolution of Transportation Networks

    Directory of Open Access Journals (Sweden)

    Mariusz Paszkowski

    2002-01-01

    Full Text Available We present a new approach to modelling of transportation networks. Supply of resources and their influence on the evolution of the consuming environment is a princqral problem considered. ne present two concepts, which are based on cellular automata paradigm. In the first model SCAM4N (Simple Cellular Automata Model of Anastomosing Network, the system is represented by a 2D mesh of elementary cells. The rules of interaction between them are introduced for modelling ofthe water flow and other phenomena connected with anastomosing river: Due to limitations of SCAMAN model, we introduce a supplementary model. The MANGraCA (Model of Anastomosing Network with Graph of Cellular Automata model beside the classical mesh of automata, introduces an additional structure: the graph of cellular automata, which represents the network pattern. Finally we discuss the prospective applications ofthe models. The concepts of juture implementation are also presented.

  14. Runoff Modelling in Urban Storm Drainage by Neural Networks

    DEFF Research Database (Denmark)

    Rasmussen, Michael R.; Brorsen, Michael; Schaarup-Jensen, Kjeld

    1995-01-01

    A neural network is used to simulate folw and water levels in a sewer system. The calibration of th neural network is based on a few measured events and the network is validated against measureed events as well as flow simulated with the MOUSE model (Lindberg and Joergensen, 1986). The neural...... network is used to compute flow or water level at selected points in the sewer system, and to forecast the flow from a small residential area. The main advantages of the neural network are the build-in self calibration procedure and high speed performance, but the neural network cannot be used to extract...... knowledge of the runoff process. The neural network was found to simulate 150 times faster than e.g. the MOUSE model....

  15. Interdependent multi-layer networks: modeling and survivability analysis with applications to space-based networks.

    Science.gov (United States)

    Castet, Jean-Francois; Saleh, Joseph H

    2013-01-01

    This article develops a novel approach and algorithmic tools for the modeling and survivability analysis of networks with heterogeneous nodes, and examines their application to space-based networks. Space-based networks (SBNs) allow the sharing of spacecraft on-orbit resources, such as data storage, processing, and downlink. Each spacecraft in the network can have different subsystem composition and functionality, thus resulting in node heterogeneity. Most traditional survivability analyses of networks assume node homogeneity and as a result, are not suited for the analysis of SBNs. This work proposes that heterogeneous networks can be modeled as interdependent multi-layer networks, which enables their survivability analysis. The multi-layer aspect captures the breakdown of the network according to common functionalities across the different nodes, and it allows the emergence of homogeneous sub-networks, while the interdependency aspect constrains the network to capture the physical characteristics of each node. Definitions of primitives of failure propagation are devised. Formal characterization of interdependent multi-layer networks, as well as algorithmic tools for the analysis of failure propagation across the network are developed and illustrated with space applications. The SBN applications considered consist of several networked spacecraft that can tap into each other's Command and Data Handling subsystem, in case of failure of its own, including the Telemetry, Tracking and Command, the Control Processor, and the Data Handling sub-subsystems. Various design insights are derived and discussed, and the capability to perform trade-space analysis with the proposed approach for various network characteristics is indicated. The select results here shown quantify the incremental survivability gains (with respect to a particular class of threats) of the SBN over the traditional monolith spacecraft. Failure of the connectivity between nodes is also examined, and the

  16. Interdependent multi-layer networks: modeling and survivability analysis with applications to space-based networks.

    Directory of Open Access Journals (Sweden)

    Jean-Francois Castet

    Full Text Available This article develops a novel approach and algorithmic tools for the modeling and survivability analysis of networks with heterogeneous nodes, and examines their application to space-based networks. Space-based networks (SBNs allow the sharing of spacecraft on-orbit resources, such as data storage, processing, and downlink. Each spacecraft in the network can have different subsystem composition and functionality, thus resulting in node heterogeneity. Most traditional survivability analyses of networks assume node homogeneity and as a result, are not suited for the analysis of SBNs. This work proposes that heterogeneous networks can be modeled as interdependent multi-layer networks, which enables their survivability analysis. The multi-layer aspect captures the breakdown of the network according to common functionalities across the different nodes, and it allows the emergence of homogeneous sub-networks, while the interdependency aspect constrains the network to capture the physical characteristics of each node. Definitions of primitives of failure propagation are devised. Formal characterization of interdependent multi-layer networks, as well as algorithmic tools for the analysis of failure propagation across the network are developed and illustrated with space applications. The SBN applications considered consist of several networked spacecraft that can tap into each other's Command and Data Handling subsystem, in case of failure of its own, including the Telemetry, Tracking and Command, the Control Processor, and the Data Handling sub-subsystems. Various design insights are derived and discussed, and the capability to perform trade-space analysis with the proposed approach for various network characteristics is indicated. The select results here shown quantify the incremental survivability gains (with respect to a particular class of threats of the SBN over the traditional monolith spacecraft. Failure of the connectivity between nodes is also

  17. Systematic network assessment of the carcinogenic activities of cadmium.

    Science.gov (United States)

    Chen, Peizhan; Duan, Xiaohua; Li, Mian; Huang, Chao; Li, Jingquan; Chu, Ruiai; Ying, Hao; Song, Haiyun; Jia, Xudong; Ba, Qian; Wang, Hui

    2016-11-01

    Cadmium has been defined as type I carcinogen for humans, but the underlying mechanisms of its carcinogenic activity and its influence on protein-protein interactions in cells are not fully elucidated. The aim of the current study was to evaluate, systematically, the carcinogenic activity of cadmium with systems biology approaches. From a literature search of 209 studies that performed with cellular models, 208 proteins influenced by cadmium exposure were identified. All of these were assessed by Western blotting and were recognized as key nodes in network analyses. The protein-protein functional interaction networks were constructed with NetBox software and visualized with Cytoscape software. These cadmium-rewired genes were used to construct a scale-free, highly connected biological protein interaction network with 850 nodes and 8770 edges. Of the network, nine key modules were identified and 60 key signaling pathways, including the estrogen, RAS, PI3K-Akt, NF-κB, HIF-1α, Jak-STAT, and TGF-β signaling pathways, were significantly enriched. With breast cancer, colorectal and prostate cancer cellular models, we validated the key node genes in the network that had been previously reported or inferred form the network by Western blotting methods, including STAT3, JNK, p38, SMAD2/3, P65, AKT1, and HIF-1α. These results suggested the established network was robust and provided a systematic view of the carcinogenic activities of cadmium in human. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Artificial Neural Network Modeling of an Inverse Fluidized Bed ...

    African Journals Online (AJOL)

    MICHAEL

    modeling of the inverse fluidized bed reactor. In the proposed model, the trained neural network represents the kinetics of biological decomposition of pollutants in the reactor. The neural network has been trained with experimental data obtained from an inverse fluidized bed reactor treating the starch industry wastewater.

  19. A control model for district heating networks with storage

    NARCIS (Netherlands)

    Scholten, Tjeert; De Persis, Claudio; Tesi, Pietro

    2014-01-01

    In [1] pressure control of hydraulic networks is investigated. We extend this work to district heating systems with storage capabilities and derive a model taking the topology of the network into account. The goal for the derived model is that it should allow for control of the storage level and

  20. A small-world network model of facial emotion recognition.

    Science.gov (United States)

    Takehara, Takuma; Ochiai, Fumio; Suzuki, Naoto

    2016-01-01

    Various models have been proposed to increase understanding of the cognitive basis of facial emotions. Despite those efforts, interactions between facial emotions have received minimal attention. If collective behaviours relating to each facial emotion in the comprehensive cognitive system could be assumed, specific facial emotion relationship patterns might emerge. In this study, we demonstrate that the frameworks of complex networks can effectively capture those patterns. We generate 81 facial emotion images (6 prototypes and 75 morphs) and then ask participants to rate degrees of similarity in 3240 facial emotion pairs in a paired comparison task. A facial emotion network constructed on the basis of similarity clearly forms a small-world network, which features an extremely short average network distance and close connectivity. Further, even if two facial emotions have opposing valences, they are connected within only two steps. In addition, we show that intermediary morphs are crucial for maintaining full network integration, whereas prototypes are not at all important. These results suggest the existence of collective behaviours in the cognitive systems of facial emotions and also describe why people can efficiently recognize facial emotions in terms of information transmission and propagation. For comparison, we construct three simulated networks--one based on the categorical model, one based on the dimensional model, and one random network. The results reveal that small-world connectivity in facial emotion networks is apparently different from those networks, suggesting that a small-world network is the most suitable model for capturing the cognitive basis of facial emotions.

  1. Systems and methods for modeling and analyzing networks

    Science.gov (United States)

    Hill, Colin C; Church, Bruce W; McDonagh, Paul D; Khalil, Iya G; Neyarapally, Thomas A; Pitluk, Zachary W

    2013-10-29

    The systems and methods described herein utilize a probabilistic modeling framework for reverse engineering an ensemble of causal models, from data and then forward simulating the ensemble of models to analyze and predict the behavior of the network. In certain embodiments, the systems and methods described herein include data-driven techniques for developing causal models for biological networks. Causal network models include computational representations of the causal relationships between independent variables such as a compound of interest and dependent variables such as measured DNA alterations, changes in mRNA, protein, and metabolites to phenotypic readouts of efficacy and toxicity.

  2. Induction of Macrophage Function in Human THP-1 Cells Is Associated with Rewiring of MAPK Signaling and Activation of MAP3K7 (TAK1) Protein Kinase.

    Science.gov (United States)

    Richter, Erik; Ventz, Katharina; Harms, Manuela; Mostertz, Jörg; Hochgräfe, Falko

    2016-01-01

    Macrophages represent the primary human host response to pathogen infection and link the immediate defense to the adaptive immune system. Mature tissue macrophages convert from circulating monocyte precursor cells by terminal differentiation in a process that is not fully understood. Here, we analyzed the protein kinases of the human monocytic cell line THP-1 before and after induction of macrophage differentiation by using kinomics and phosphoproteomics. When comparing the macrophage-like state with the monocytic precursor, 50% of the kinome was altered in expression and even 71% of covered kinase phosphorylation sites were affected. Kinome rearrangements are for example characterized by a shift of overrepresented cyclin-dependent kinases associated with cell cycle control in monocytes to calmodulin-dependent kinases and kinases involved in proinflammatory signaling. Eventually, we show that monocyte-to-macrophage differentiation is associated with major rewiring of mitogen-activated protein kinase signaling networks and demonstrate that protein kinase MAP3K7 (TAK1) acts as the key signaling hub in bacterial killing, chemokine production and differentiation. Our study proves the fundamental role of protein kinases and cellular signaling as major drivers of macrophage differentiation and function. The finding that MAP3K7 is central to macrophage function suggests MAP3K7 and its networking partners as promising targets in host-directed therapy for macrophage-associated disease.

  3. Ocean wave prediction using numerical and neural network models

    Digital Repository Service at National Institute of Oceanography (India)

    Mandal, S.; Prabaharan, N.

    This paper presents an overview of the development of the numerical wave prediction models and recently used neural networks for ocean wave hindcasting and forecasting. The numerical wave models express the physical concepts of the phenomena...

  4. An information spreading model based on online social networks

    Science.gov (United States)

    Wang, Tao; He, Juanjuan; Wang, Xiaoxia

    2018-01-01

    Online social platforms are very popular in recent years. In addition to spreading information, users could review or collect information on online social platforms. According to the information spreading rules of online social network, a new information spreading model, namely IRCSS model, is proposed in this paper. It includes sharing mechanism, reviewing mechanism, collecting mechanism and stifling mechanism. Mean-field equations are derived to describe the dynamics of the IRCSS model. Moreover, the steady states of reviewers, collectors and stiflers and the effects of parameters on the peak values of reviewers, collectors and sharers are analyzed. Finally, numerical simulations are performed on different networks. Results show that collecting mechanism and reviewing mechanism, as well as the connectivity of the network, make information travel wider and faster, and compared to WS network and ER network, the speed of reviewing, sharing and collecting information is fastest on BA network.

  5. A Mathematical Model to Improve the Performance of Logistics Network

    Directory of Open Access Journals (Sweden)

    Muhammad Izman Herdiansyah

    2012-01-01

    Full Text Available The role of logistics nowadays is expanding from just providing transportation and warehousing to offering total integrated logistics. To remain competitive in the global market environment, business enterprises need to improve their logistics operations performance. The improvement will be achieved when we can provide a comprehensive analysis and optimize its network performances. In this paper, a mixed integer linier model for optimizing logistics network performance is developed. It provides a single-product multi-period multi-facilities model, as well as the multi-product concept. The problem is modeled in form of a network flow problem with the main objective to minimize total logistics cost. The problem can be solved using commercial linear programming package like CPLEX or LINDO. Even in small case, the solver in Excel may also be used to solve such model.Keywords: logistics network, integrated model, mathematical programming, network optimization

  6. Completely random measures for modelling block-structured sparse networks

    DEFF Research Database (Denmark)

    Herlau, Tue; Schmidt, Mikkel Nørgaard; Mørup, Morten

    2016-01-01

    Many statistical methods for network data parameterize the edge-probability by attributing latent traits to the vertices such as block structure and assume exchangeability in the sense of the Aldous-Hoover representation theorem. Empirical studies of networks indicate that many real-world networks...... [2014] proposed the use of a different notion of exchangeability due to Kallenberg [2006] and obtained a network model which admits power-law behaviour while retaining desirable statistical properties, however this model does not capture latent vertex traits such as block-structure. In this work we re......-introduce the use of block-structure for network models obeying allenberg’s notion of exchangeability and thereby obtain a model which admits the inference of block-structure and edge inhomogeneity. We derive a simple expression for the likelihood and an efficient sampling method. The obtained model...

  7. A Network Contention Model for the Extreme-scale Simulator

    Energy Technology Data Exchange (ETDEWEB)

    Engelmann, Christian [ORNL; Naughton III, Thomas J [ORNL

    2015-01-01

    The Extreme-scale Simulator (xSim) is a performance investigation toolkit for high-performance computing (HPC) hardware/software co-design. It permits running a HPC application with millions of concurrent execution threads, while observing its performance in a simulated extreme-scale system. This paper details a newly developed network modeling feature for xSim, eliminating the shortcomings of the existing network modeling capabilities. The approach takes a different path for implementing network contention and bandwidth capacity modeling using a less synchronous and accurate enough model design. With the new network modeling feature, xSim is able to simulate on-chip and on-node networks with reasonable accuracy and overheads.

  8. Transcription activator-like effector hybrids for conditional control and rewiring of chromosomal transgene expression.

    Science.gov (United States)

    Li, Yi; Moore, Richard; Guinn, Michael; Bleris, Leonidas

    2012-01-01

    The ability to conditionally rewire pathways in human cells holds great therapeutic potential. Transcription activator-like effectors (TALEs) are a class of naturally occurring specific DNA binding proteins that can be used to introduce targeted genome modifications or control gene expression. Here we present TALE hybrids engineered to respond to endogenous signals and capable of controlling transgenes by applying a predetermined and tunable action at the single-cell level. Specifically, we first demonstrate that combinations of TALEs can be used to modulate the expression of stably integrated genes in kidney cells. We then introduce a general purpose two-hybrid approach that can be customized to regulate the function of any TALE either using effector molecules or a heterodimerization reaction. Finally, we demonstrate the successful interface of TALEs to specific endogenous signals, namely hypoxia signaling and microRNAs, essentially closing the loop between cellular information and chromosomal transgene expression.

  9. Application Interaction Model for Opportunistic Networking

    NARCIS (Netherlands)

    de Souza Schwartz, Ramon; van Dijk, H.W.; Scholten, Johan

    In Opportunistic Networks, autonomous nodes discover, assess and potentially seize opportunities for communication and distributed processing whenever these emerge. In this paper, we consider prerequisites for a successful implementation of such a way of processing in networks that consist mainly of

  10. A Model for Telestrok Network Evaluation

    DEFF Research Database (Denmark)

    Storm, Anna; Günzel, Franziska; Theiss, Stephan

    2011-01-01

    Different telestroke network concepts have been implemented worldwide to enable fast and efficient treatment of stroke patients in underserved rural areas. Networks could demonstrate the improvement in clinical outcome, but have so far excluded a cost-effectiveness analysis. With health economic ...

  11. Concentration dependent model of protein-protein interaction networks

    CERN Document Server

    Zhang, Jingshan

    2007-01-01

    The scale free structure p(k)~k^{-gamma} of protein-protein interaction networks can be produced by a static physical model. We find the earlier study of deterministic threshold models with exponential fitness distributions can be generalized to explain the apparent scale free degree distribution of the physical model, and this explanation provides a generic mechanism of "scale free" networks. We predict the dependence of gamma on experimental protein concentrations. The clustering coefficient distribution of the model is also studied.

  12. Model and simulation of Krause model in dynamic open network

    Science.gov (United States)

    Zhu, Meixia; Xie, Guangqiang

    2017-08-01

    The construction of the concept of evolution is an effective way to reveal the formation of group consensus. This study is based on the modeling paradigm of the HK model (Hegsekmann-Krause). This paper analyzes the evolution of multi - agent opinion in dynamic open networks with member mobility. The results of the simulation show that when the number of agents is constant, the interval distribution of the initial distribution will affect the number of the final view, The greater the distribution of opinions, the more the number of views formed eventually; The trust threshold has a decisive effect on the number of views, and there is a negative correlation between the trust threshold and the number of opinions clusters. The higher the connectivity of the initial activity group, the more easily the subjective opinion in the evolution of opinion to achieve rapid convergence. The more open the network is more conducive to the unity of view, increase and reduce the number of agents will not affect the consistency of the group effect, but not conducive to stability.

  13. Synchrony-optimized networks of Kuramoto oscillators with inertia

    Science.gov (United States)

    Pinto, Rafael S.; Saa, Alberto

    2016-12-01

    We investigate synchronization in networks of Kuramoto oscillators with inertia. More specifically, we introduce a rewiring algorithm consisting basically in a hill climb scheme in which the edges of the network are swapped in order to enhance its synchronization capacity. We show that the synchrony-optimized networks generated by our algorithm have some interesting topological and dynamical properties. In particular, they typically exhibit an anticipation of the synchronization onset and are more robust against certain types of perturbations. We consider synthetic random networks and also a network with a topology based on an approximated model of the (high voltage) power grid of Spain, since networks of Kuramoto oscillators with inertia have been used recently as simplified models for power grids, for which synchronization is obviously a crucial issue. Despite the extreme simplifications adopted in these models, our results, among others recently obtained in the literature, may provide interesting principles to guide the future growth and development of real-world grids, specially in the case of a change of the current paradigm of centralized towards distributed generation power grids.

  14. Collaborative rewiring of the pluripotency network by chromatin and signalling modulating pathways

    OpenAIRE

    Tran, Khoa A.; Jackson, Steven?A.; Olufs, Zachariah P.G.; Zaidan, Nur Zafirah; Leng, Ning; Kendziorski, Christina; Roy, Sushmita; Sridharan, Rupa

    2015-01-01

    Reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) represents a profound change in cell fate. Here, we show that combining ascorbic acid (AA) and 2i (MAP kinase and GSK inhibitors) increases the efficiency of reprogramming from fibroblasts and synergistically enhances conversion of partially reprogrammed intermediates to the iPSC state. AA and 2i induce differential transcriptional responses, each leading to the activation of specific pluripotency loci. A unique cohort o...

  15. Rumor spreading model with noise interference in complex social networks

    Science.gov (United States)

    Zhu, Liang; Wang, Youguo

    2017-03-01

    In this paper, a modified susceptible-infected-removed (SIR) model has been proposed to explore rumor diffusion on complex social networks. We take variation of connectivity into consideration and assume the variation as noise. On the basis of related literature on virus networks, the noise is described as standard Brownian motion while stochastic differential equations (SDE) have been derived to characterize dynamics of rumor diffusion both on homogeneous networks and heterogeneous networks. Then, theoretical analysis on homogeneous networks has been demonstrated to investigate the solution of SDE model and the steady state of rumor diffusion. Simulations both on Barabási-Albert (BA) network and Watts-Strogatz (WS) network display that the addition of noise accelerates rumor diffusion and expands diffusion size, meanwhile, the spreading speed on BA network is much faster than on WS network under the same noise intensity. In addition, there exists a rumor diffusion threshold in statistical average meaning on homogeneous network which is absent on heterogeneous network. Finally, we find a positive correlation between peak value of infected individuals and noise intensity while a negative correlation between rumor lifecycle and noise intensity overall.

  16. Hydrometeorological network for flood monitoring and modeling

    Science.gov (United States)

    Efstratiadis, Andreas; Koussis, Antonis D.; Lykoudis, Spyros; Koukouvinos, Antonis; Christofides, Antonis; Karavokiros, George; Kappos, Nikos; Mamassis, Nikos; Koutsoyiannis, Demetris

    2013-08-01

    Due to its highly fragmented geomorphology, Greece comprises hundreds of small- to medium-size hydrological basins, in which often the terrain is fairly steep and the streamflow regime ephemeral. These are typically affected by flash floods, occasionally causing severe damages. Yet, the vast majority of them lack flow-gauging infrastructure providing systematic hydrometric data at fine time scales. This has obvious impacts on the quality and reliability of flood studies, which typically use simplistic approaches for ungauged basins that do not consider local peculiarities in sufficient detail. In order to provide a consistent framework for flood design and to ensure realistic predictions of the flood risk -a key issue of the 2007/60/EC Directive- it is essential to improve the monitoring infrastructures by taking advantage of modern technologies for remote control and data management. In this context and in the research project DEUCALION, we have recently installed and are operating, in four pilot river basins, a telemetry-based hydro-meteorological network that comprises automatic stations and is linked to and supported by relevant software. The hydrometric stations measure stage, using 50-kHz ultrasonic pulses or piezometric sensors, or both stage (piezometric) and velocity via acoustic Doppler radar; all measurements are being temperature-corrected. The meteorological stations record air temperature, pressure, relative humidity, wind speed and direction, and precipitation. Data transfer is made via GPRS or mobile telephony modems. The monitoring network is supported by a web-based application for storage, visualization and management of geographical and hydro-meteorological data (ENHYDRIS), a software tool for data analysis and processing (HYDROGNOMON), as well as an advanced model for flood simulation (HYDROGEIOS). The recorded hydro-meteorological observations are accessible over the Internet through the www-application. The system is operational and its

  17. A computational model of hemodynamic parameters in cortical capillary networks.

    Science.gov (United States)

    Safaeian, Navid; Sellier, Mathieu; David, Tim

    2011-02-21

    The analysis of hemodynamic parameters and functional reactivity of cerebral capillaries is still controversial. To assess the hemodynamic parameters in the cortical capillary network, a generic model was created using 2D voronoi tessellation in which each edge represents a capillary segment. This method is capable of creating an appropriate generic model of cerebral capillary network relating to each part of the brain cortex because the geometric model is able to vary the capillary density. The modeling presented here is based on morphometric parameters extracted from physiological data of the human cortex. The pertinent hemodynamic parameters were obtained by numerical simulation based on effective blood viscosity as a function of hematocrit and microvessel diameter, phase separation and plasma skimming effects. The hemodynamic parameters of capillary networks with two different densities (consistent with the variation of the morphometric data in the human cortical capillary network) were analyzed. The results show pertinent hemodynamic parameters for each model. The heterogeneity (coefficient variation) and the mean value of hematocrits, flow rates and velocities of the both network models were specified. The distributions of blood flow throughout the both models seem to confirm the hypothesis in which all capillaries in a cortical network are recruited at rest (normal condition). The results also demonstrate a discrepancy of the network resistance between two models, which are derived from the difference in the number density of capillary segments between the models. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. A modelling and reasoning framework for social networks policies

    Science.gov (United States)

    Governatori, Guido; Iannella, Renato

    2011-02-01

    Policy languages (such as privacy and rights) have had little impact on the wider community. Now that social networks have taken off, the need to revisit policy languages and realign them towards social networks requirements has become more apparent. One such language is explored as to its applicability to the social networks masses. We also argue that policy languages alone are not sufficient and thus they should be paired with reasoning mechanisms to provide precise and unambiguous execution models of the policies. To this end, we propose a computationally oriented model to represent, reason with and execute policies for social networks.

  19. Constitutive Modelling of INCONEL 718 using Artificial Neural Network

    Science.gov (United States)

    Abiriand Bhekisipho Twala, Olufunminiyi

    2017-08-01

    Artificial neural network is used to model INCONEL 718 in this paper. The model accounts for precipitate hardening in the alloy. The input variables for the neural network model are strain, strain rate, temperature and microstructure state. The output variable is the flow stress. The early stopping technique is combined with Bayesian regularization process in training the network. Sample and non-sample measurement data were taken from the literature. The model predictions of flow stress of the alloy are in good agreement with experimental measurements.

  20. Modeling Temporal Evolution and Multiscale Structure in Networks

    DEFF Research Database (Denmark)

    Herlau, Tue; Mørup, Morten; Schmidt, Mikkel Nørgaard

    2013-01-01

    -point model to account for the temporal evolution of each vertex. We demonstrate that our model is able to infer time-varying multiscale structure in synthetic as well as three real world time-evolving complex networks. Our modeling of the temporal evolution of hierarchies brings new insights......Many real-world networks exhibit both temporal evolution and multiscale structure. We propose a model for temporally correlated multifurcating hierarchies in complex networks which jointly capture both effects. We use the Gibbs fragmentation tree as prior over multifurcating trees and a change...

  1. Network Statistical Models for Language Learning Contexts: Exponential Random Graph Models and Willingness to Communicate

    Science.gov (United States)

    Gallagher, H. Colin; Robins, Garry

    2015-01-01

    As part of the shift within second language acquisition (SLA) research toward complex systems thinking, researchers have called for investigations of social network structure. One strand of social network analysis yet to receive attention in SLA is network statistical models, whereby networks are explained in terms of smaller substructures of…

  2. Modeling the propagation of mobile malware on complex networks

    Science.gov (United States)

    Liu, Wanping; Liu, Chao; Yang, Zheng; Liu, Xiaoyang; Zhang, Yihao; Wei, Zuxue

    2016-08-01

    In this paper, the spreading behavior of malware across mobile devices is addressed. By introducing complex networks to model mobile networks, which follows the power-law degree distribution, a novel epidemic model for mobile malware propagation is proposed. The spreading threshold that guarantees the dynamics of the model is calculated. Theoretically, the asymptotic stability of the malware-free equilibrium is confirmed when the threshold is below the unity, and the global stability is further proved under some sufficient conditions. The influences of different model parameters as well as the network topology on malware propagation are also analyzed. Our theoretical studies and numerical simulations show that networks with higher heterogeneity conduce to the diffusion of malware, and complex networks with lower power-law exponents benefit malware spreading.

  3. Random field Ising model and community structure in complex networks

    Science.gov (United States)

    Son, S.-W.; Jeong, H.; Noh, J. D.

    2006-04-01

    We propose a method to determine the community structure of a complex network. In this method the ground state problem of a ferromagnetic random field Ising model is considered on the network with the magnetic field Bs = +∞, Bt = -∞, and Bi≠s,t=0 for a node pair s and t. The ground state problem is equivalent to the so-called maximum flow problem, which can be solved exactly numerically with the help of a combinatorial optimization algorithm. The community structure is then identified from the ground state Ising spin domains for all pairs of s and t. Our method provides a criterion for the existence of the community structure, and is applicable equally well to unweighted and weighted networks. We demonstrate the performance of the method by applying it to the Barabási-Albert network, Zachary karate club network, the scientific collaboration network, and the stock price correlation network. (Ising, Potts, etc.)

  4. Dynamical complexity in the perception-based network formation model

    Science.gov (United States)

    Jo, Hang-Hyun; Moon, Eunyoung

    2016-12-01

    Many link formation mechanisms for the evolution of social networks have been successful to reproduce various empirical findings in social networks. However, they have largely ignored the fact that individuals make decisions on whether to create links to other individuals based on cost and benefit of linking, and the fact that individuals may use perception of the network in their decision making. In this paper, we study the evolution of social networks in terms of perception-based strategic link formation. Here each individual has her own perception of the actual network, and uses it to decide whether to create a link to another individual. An individual with the least perception accuracy can benefit from updating her perception using that of the most accurate individual via a new link. This benefit is compared to the cost of linking in decision making. Once a new link is created, it affects the accuracies of other individuals' perceptions, leading to a further evolution of the actual network. As for initial actual networks, we consider both homogeneous and heterogeneous cases. The homogeneous initial actual network is modeled by Erdős-Rényi (ER) random networks, while we take a star network for the heterogeneous case. In any cases, individual perceptions of the actual network are modeled by ER random networks with controllable linking probability. Then the stable link density of the actual network is found to show discontinuous transitions or jumps according to the cost of linking. As the number of jumps is the consequence of the dynamical complexity, we discuss the effect of initial conditions on the number of jumps to find that the dynamical complexity strongly depends on how much individuals initially overestimate or underestimate the link density of the actual network. For the heterogeneous case, the role of the highly connected individual as an information spreader is also discussed.

  5. Adaptive dynamical networks

    Science.gov (United States)

    Maslennikov, O. V.; Nekorkin, V. I.

    2017-10-01

    Dynamical networks are systems of active elements (nodes) interacting with each other through links. Examples are power grids, neural structures, coupled chemical oscillators, and communications networks, all of which are characterized by a networked structure and intrinsic dynamics of their interacting components. If the coupling structure of a dynamical network can change over time due to nodal dynamics, then such a system is called an adaptive dynamical network. The term ‘adaptive’ implies that the coupling topology can be rewired; the term ‘dynamical’ implies the presence of internal node and link dynamics. The main results of research on adaptive dynamical networks are reviewed. Key notions and definitions of the theory of complex networks are given, and major collective effects that emerge in adaptive dynamical networks are described.

  6. A solvable queueing network model for railway networks and its validation and applications for the Netherlands

    NARCIS (Netherlands)

    Huisman, Tijs; Boucherie, Richardus J.; van Dijk, N.M.

    2002-01-01

    The performance of new railway networks cannot be measured or simulated, as no detailed train schedules are available. Railway infrastructure and capacities are to be determined long before the actual traffic is known. This paper therefore proposes a solvable queueing network model to compute

  7. Stochastic modelling and control of communication networks

    NARCIS (Netherlands)

    Zuraniewski, P.W.

    2011-01-01

    The unprecedented growth of the Information Technologies sector observed within the past years creates an excellent opportunity to conduct new, exciting and interdisciplinary research. Increasing complexity of the communication networks calls for incorporating rigorously developed and reliable

  8. Analysis and Comparison of Typical Models within Distribution Network Design

    DEFF Research Database (Denmark)

    Jørgensen, Hans Jacob; Larsen, Allan; Madsen, Oli B.G.

    This paper investigates the characteristics of typical optimisation models within Distribution Network Design. During the paper fourteen models known from the literature will be thoroughly analysed. Through this analysis a schematic approach to categorisation of distribution network design models...... for educational purposes. Furthermore, the paper can be seen as a practical introduction to network design modelling as well as a being an art manual or recipe when constructing such a model....... are covered in the categorisation include fixed vs. general networks, specialised vs. general nodes, linear vs. nonlinear costs, single vs. multi commodity, uncapacitated vs. capacitated activities, single vs. multi modal and static vs. dynamic. The models examined address both strategic and tactical planning...

  9. Information Dynamics in Networks: Models and Algorithms

    Science.gov (United States)

    2016-09-13

    ICDCS). 29-JUN-15, Columbus, OH, USA. : , . Value-Based Network Externalities and Optimal Auction Design, Conference on Web and Internet Economics...NAME Total Number: NAME Total Number: PERCENT_SUPPORTEDNAME FTE Equivalent: Total Number: ...... ...... Inventions (DD882) Scientific Progress In...Value-based network externalities and optimal auction design. In Web and Internet Economics - 10th International Conference, WINE 2014, Beijing, China, December 14-17, pages 147–160, 2014. 6

  10. Home-Network Security Model in Ubiquitous Environment

    OpenAIRE

    Dong-Young Yoo; Jong-Whoi Shin; Jin-Young Choi

    2007-01-01

    Social interest and demand on Home-Network has been increasing greatly. Although various services are being introduced to respond to such demands, they can cause serious security problems when linked to the open network such as Internet. This paper reviews the security requirements to protect the service users with assumption that the Home-Network environment is connected to Internet and then proposes the security model based on the requirement. The proposed security mode...

  11. A Three-Dimensional Computational Model of Collagen Network Mechanics

    Science.gov (United States)

    Lee, Byoungkoo; Zhou, Xin; Riching, Kristin; Eliceiri, Kevin W.; Keely, Patricia J.; Guelcher, Scott A.; Weaver, Alissa M.; Jiang, Yi

    2014-01-01

    Extracellular matrix (ECM) strongly influences cellular behaviors, including cell proliferation, adhesion, and particularly migration. In cancer, the rigidity of the stromal collagen environment is thought to control tumor aggressiveness, and collagen alignment has been linked to tumor cell invasion. While the mechanical properties of collagen at both the single fiber scale and the bulk gel scale are quite well studied, how the fiber network responds to local stress or deformation, both structurally and mechanically, is poorly understood. This intermediate scale knowledge is important to understanding cell-ECM interactions and is the focus of this study. We have developed a three-dimensional elastic collagen fiber network model (bead-and-spring model) and studied fiber network behaviors for various biophysical conditions: collagen density, crosslinker strength, crosslinker density, and fiber orientation (random vs. prealigned). We found the best-fit crosslinker parameter values using shear simulation tests in a small strain region. Using this calibrated collagen model, we simulated both shear and tensile tests in a large linear strain region for different network geometry conditions. The results suggest that network geometry is a key determinant of the mechanical properties of the fiber network. We further demonstrated how the fiber network structure and mechanics evolves with a local formation, mimicking the effect of pulling by a pseudopod during cell migration. Our computational fiber network model is a step toward a full biomechanical model of cellular behaviors in various ECM conditions. PMID:25386649

  12. Hybrid network defense model based on fuzzy evaluation.

    Science.gov (United States)

    Cho, Ying-Chiang; Pan, Jen-Yi

    2014-01-01

    With sustained and rapid developments in the field of information technology, the issue of network security has become increasingly prominent. The theme of this study is network data security, with the test subject being a classified and sensitive network laboratory that belongs to the academic network. The analysis is based on the deficiencies and potential risks of the network's existing defense technology, characteristics of cyber attacks, and network security technologies. Subsequently, a distributed network security architecture using the technology of an intrusion prevention system is designed and implemented. In this paper, first, the overall design approach is presented. This design is used as the basis to establish a network defense model, an improvement over the traditional single-technology model that addresses the latter's inadequacies. Next, a distributed network security architecture is implemented, comprising a hybrid firewall, intrusion detection, virtual honeynet projects, and connectivity and interactivity between these three components. Finally, the proposed security system is tested. A statistical analysis of the test results verifies the feasibility and reliability of the proposed architecture. The findings of this study will potentially provide new ideas and stimuli for future designs of network security architecture.

  13. Neurocognitive networks: findings, models, and theory.

    Science.gov (United States)

    Meehan, Timothy P; Bressler, Steven L

    2012-11-01

    Through its early history, cognitive neuroscience largely followed a modular paradigm wherein high-level cognitive functions were mapped onto locally segregated brain regions. However, recent evidence drives a continuing shift away from modular theories of cognitive brain function, and toward theories which hold that cognition arises from the integrated activity of large-scale, distributed networks of brain regions. A growing consensus favors the fundamental concept of this new paradigm: the large-scale cognitive brain network, or neurocognitive network. This consensus was the motivation for Neurocognitive Networks 2010 (NCN 2010), a conference sponsored by the Cognitive Neuroscience Program of the National Science Foundation, organized by Drs. Steven Bressler and Craig Richter of Florida Atlantic University (FAU), and held at FAU in Boca Raton, FL on January 29-30, 2010. NCN 2010 gathered together some of today's leading investigators of neurocognitive networks. This paper serves to review their presentations as they relate to the paradigm of neurocognitive networks, as well as to compile the emergent themes, questions, and possible future research directions that arose from the conference. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Modeling of Bandwidth Aggregation over Heterogeneous Wireless Access Networks

    DEFF Research Database (Denmark)

    Popovska Avramova, Andrijana; Dittmann, Lars

    2012-01-01

    Motivated by the multihomming capability of the mobile devices and the fact that the heterogeneous wireless access networks overlap in coverage, mobile operators are looking for solutions that will benefit by simultaneous use of the available multiple access interfaces. Multipath or multilink...... applications. The analysis is performed on a multipath model developed with OPNET Modeler, which is an advanced research tool that supports modeling and integration of various kinds of built-in networks....

  15. When individual behaviour matters: homogeneous and network models in epidemiology

    OpenAIRE

    Bansal, Shweta; Grenfell, Bryan T.; Meyers, Lauren Ancel

    2007-01-01

    Heterogeneity in host contact patterns profoundly shapes population-level disease dynamics. Many epidemiological models make simplifying assumptions about the patterns of disease-causing interactions among hosts. In particular, homogeneous-mixing models assume that all hosts have identical rates of disease-causing contacts. In recent years, several network-based approaches have been developed to explicitly model heterogeneity in host contact patterns. Here, we use a network perspective to qua...

  16. Mathematics of epidemics on networks from exact to approximate models

    CERN Document Server

    Kiss, István Z; Simon, Péter L

    2017-01-01

    This textbook provides an exciting new addition to the area of network science featuring a stronger and more methodical link of models to their mathematical origin and explains how these relate to each other with special focus on epidemic spread on networks. The content of the book is at the interface of graph theory, stochastic processes and dynamical systems. The authors set out to make a significant contribution to closing the gap between model development and the supporting mathematics. This is done by: Summarising and presenting the state-of-the-art in modeling epidemics on networks with results and readily usable models signposted throughout the book; Presenting different mathematical approaches to formulate exact and solvable models; Identifying the concrete links between approximate models and their rigorous mathematical representation; Presenting a model hierarchy and clearly highlighting the links between model assumptions and model complexity; Providing a reference source for advanced undergraduate...

  17. Multi-mode clustering model for hierarchical wireless sensor networks

    Science.gov (United States)

    Hu, Xiangdong; Li, Yongfu; Xu, Huifen

    2017-03-01

    The topology management, i.e., clusters maintenance, of wireless sensor networks (WSNs) is still a challenge due to its numerous nodes, diverse application scenarios and limited resources as well as complex dynamics. To address this issue, a multi-mode clustering model (M2 CM) is proposed to maintain the clusters for hierarchical WSNs in this study. In particular, unlike the traditional time-trigger model based on the whole-network and periodic style, the M2 CM is proposed based on the local and event-trigger operations. In addition, an adaptive local maintenance algorithm is designed for the broken clusters in the WSNs using the spatial-temporal demand changes accordingly. Numerical experiments are performed using the NS2 network simulation platform. Results validate the effectiveness of the proposed model with respect to the network maintenance costs, node energy consumption and transmitted data as well as the network lifetime.

  18. An extended differentiated optical services model for WDM optical networks

    Science.gov (United States)

    Ouyang, Yong; Zeng, Qingji; Wei, Wei

    2004-04-01

    The need to provide QoS-guaranteed services in the WDM optical networks is becoming increasingly important because of a variety of candidate client networks (e.g., IP, ATM, SONET/SDH) and the requirement for QoS-delivery within the transport layers. This article addresses the QoS problem and presents a framework of QoS provisioning in the WDM optical network. We first characterize the QoS problem in the WDM optical network by comparing with that in the traditional networks. Then we propose a QoS service model in the optical domain called extended differentiated optical services (E-DoS) model based on a set of optical parameters that captures the quality, the reliability and the priority of an optical connection. Each component of the E-DoS model has been analyzed in detail in this article.

  19. Exponential random graph models for networks with community structure.

    Science.gov (United States)

    Fronczak, Piotr; Fronczak, Agata; Bujok, Maksymilian

    2013-09-01

    Although the community structure organization is an important characteristic of real-world networks, most of the traditional network models fail to reproduce the feature. Therefore, the models are useless as benchmark graphs for testing community detection algorithms. They are also inadequate to predict various properties of real networks. With this paper we intend to fill the gap. We develop an exponential random graph approach to networks with community structure. To this end we mainly built upon the idea of blockmodels. We consider both the classical blockmodel and its degree-corrected counterpart and study many of their properties analytically. We show that in the degree-corrected blockmodel, node degrees display an interesting scaling property, which is reminiscent of what is observed in real-world fractal networks. A short description of Monte Carlo simulations of the models is also given in the hope of being useful to others working in the field.

  20. Constraints and entropy in a model of network evolution

    Science.gov (United States)

    Tee, Philip; Wakeman, Ian; Parisis, George; Dawes, Jonathan; Kiss, István Z.

    2017-11-01

    Barabási-Albert's "Scale Free" model is the starting point for much of the accepted theory of the evolution of real world communication networks. Careful comparison of the theory with a wide range of real world networks, however, indicates that the model is in some cases, only a rough approximation to the dynamical evolution of real networks. In particular, the exponent γ of the power law distribution of degree is predicted by the model to be exactly 3, whereas in a number of real world networks it has values between 1.2 and 2.9. In addition, the degree distributions of real networks exhibit cut offs at high node degree, which indicates the existence of maximal node degrees for these networks. In this paper we propose a simple extension to the "Scale Free" model, which offers better agreement with the experimental data. This improvement is satisfying, but the model still does not explain why the attachment probabilities should favor high degree nodes, or indeed how constraints arrive in non-physical networks. Using recent advances in the analysis of the entropy of graphs at the node level we propose a first principles derivation for the "Scale Free" and "constraints" model from thermodynamic principles, and demonstrate that both preferential attachment and constraints could arise as a natural consequence of the second law of thermodynamics.

  1. Implicit methods for qualitative modeling of gene regulatory networks.

    Science.gov (United States)

    Garg, Abhishek; Mohanram, Kartik; De Micheli, Giovanni; Xenarios, Ioannis

    2012-01-01

    Advancements in high-throughput technologies to measure increasingly complex biological phenomena at the genomic level are rapidly changing the face of biological research from the single-gene single-protein experimental approach to studying the behavior of a gene in the context of the entire genome (and proteome). This shift in research methodologies has resulted in a new field of network biology that deals with modeling cellular behavior in terms of network structures such as signaling pathways and gene regulatory networks. In these networks, different biological entities such as genes, proteins, and metabolites interact with each other, giving rise to a dynamical system. Even though there exists a mature field of dynamical systems theory to model such network structures, some technical challenges are unique to biology such as the inability to measure precise kinetic information on gene-gene or gene-protein interactions and the need to model increasingly large networks comprising thousands of nodes. These challenges have renewed interest in developing new computational techniques for modeling complex biological systems. This chapter presents a modeling framework based on Boolean algebra and finite-state machines that are reminiscent of the approach used for digital circuit synthesis and simulation in the field of very-large-scale integration (VLSI). The proposed formalism enables a common mathematical framework to develop computational techniques for modeling different aspects of the regulatory networks such as steady-state behavior, stochasticity, and gene perturbation experiments.

  2. Stochastic S-system modeling of gene regulatory network.

    Science.gov (United States)

    Chowdhury, Ahsan Raja; Chetty, Madhu; Evans, Rob

    2015-10-01

    Microarray gene expression data can provide insights into biological processes at a system-wide level and is commonly used for reverse engineering gene regulatory networks (GRN). Due to the amalgamation of noise from different sources, microarray expression profiles become inherently noisy leading to significant impact on the GRN reconstruction process. Microarray replicates (both biological and technical), generated to increase the reliability of data obtained under noisy conditions, have limited influence in enhancing the accuracy of reconstruction . Therefore, instead of the conventional GRN modeling approaches which are deterministic, stochastic techniques are becoming increasingly necessary for inferring GRN from noisy microarray data. In this paper, we propose a new stochastic GRN model by investigating incorporation of various standard noise measurements in the deterministic S-system model. Experimental evaluations performed for varying sizes of synthetic network, representing different stochastic processes, demonstrate the effect of noise on the accuracy of genetic network modeling and the significance of stochastic modeling for GRN reconstruction . The proposed stochastic model is subsequently applied to infer the regulations among genes in two real life networks: (1) the well-studied IRMA network, a real-life in-vivo synthetic network constructed within the Saccharomyces cerevisiae yeast, and (2) the SOS DNA repair network in Escherichia coli.

  3. Metrics for evaluating performance and uncertainty of Bayesian network models

    Science.gov (United States)

    Bruce G. Marcot

    2012-01-01

    This paper presents a selected set of existing and new metrics for gauging Bayesian network model performance and uncertainty. Selected existing and new metrics are discussed for conducting model sensitivity analysis (variance reduction, entropy reduction, case file simulation); evaluating scenarios (influence analysis); depicting model complexity (numbers of model...

  4. System-level Modeling of Wireless Integrated Sensor Networks

    DEFF Research Database (Denmark)

    Virk, Kashif M.; Hansen, Knud; Madsen, Jan

    2005-01-01

    Wireless integrated sensor networks have emerged as a promising infrastructure for a new generation of monitoring and tracking applications. In order to efficiently utilize the extremely limited resources of wireless sensor nodes, accurate modeling of the key aspects of wireless sensor networks...... is necessary so that system-level design decisions can be made about the hardware and the software (applications and real-time operating system) architecture of sensor nodes. In this paper, we present a SystemC-based abstract modeling framework that enables system-level modeling of sensor network behavior...... by modeling the applications, real-time operating system, sensors, processor, and radio transceiver at the sensor node level and environmental phenomena, including radio signal propagation, at the sensor network level. We demonstrate the potential of our modeling framework by simulating and analyzing a small...

  5. Agent Based Modeling on Organizational Dynamics of Terrorist Network

    Directory of Open Access Journals (Sweden)

    Bo Li

    2015-01-01

    Full Text Available Modeling organizational dynamics of terrorist network is a critical issue in computational analysis of terrorism research. The first step for effective counterterrorism and strategic intervention is to investigate how the terrorists operate with the relational network and what affects the performance. In this paper, we investigate the organizational dynamics by employing a computational experimentation methodology. The hierarchical cellular network model and the organizational dynamics model are developed for modeling the hybrid relational structure and complex operational processes, respectively. To intuitively elucidate this method, the agent based modeling is used to simulate the terrorist network and test the performance in diverse scenarios. Based on the experimental results, we show how the changes of operational environments affect the development of terrorist organization in terms of its recovery and capacity to perform future tasks. The potential strategies are also discussed, which can be used to restrain the activities of terrorists.

  6. Towards a Social Networks Model for Online Learning & Performance

    Science.gov (United States)

    Chung, Kon Shing Kenneth; Paredes, Walter Christian

    2015-01-01

    In this study, we develop a theoretical model to investigate the association between social network properties, "content richness" (CR) in academic learning discourse, and performance. CR is the extent to which one contributes content that is meaningful, insightful and constructive to aid learning and by social network properties we…

  7. Energy Model of Networks-on-Chip and a Bus

    NARCIS (Netherlands)

    Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Kavaldjiev, N.K.; Becker, Jens E.; Becker, Jürgen; Nurmi, J.; Takala, J.; Hamalainen, T.D.

    2005-01-01

    A Network-on-Chip (NoC) is an energy-efficient onchip communication architecture for Multi-Processor Systemon-Chip (MPSoC) architectures. In earlier papers we proposed two Network-on-Chip architectures based on packet-switching and circuit-switching. In this paper we derive an energy model for both

  8. Modeling and optimization of an electric power distribution network ...

    African Journals Online (AJOL)

    EDNEPP) was solved by a mixed binary integer programming (MBIP) formulation of the network, where the steady-state operation of the network was modelled with non-linear mathematical expressions. The non-linear terms are linearized, using ...

  9. Modelling flow dynamics in water distribution networks using ...

    African Journals Online (AJOL)

    Computational approaches can be used to detect leakages in water distribution networks. One such approach is the Artificial Neural Networks (ANNs) technique. The advantage of ANNs is that they are robust and can be used to model complex linear and non-linear systems without making implicit assumptions. ANNs can ...

  10. Water distribution network modelling of a small community using ...

    African Journals Online (AJOL)

    In this study a network model was constructed for the hydraulic analysis and design of a small community (Sakwa) water distribution network in North Eastern geopolitical region of Nigeria using WaterCAD simulator. The analysis included a review of pressures, velocities and head loss gradients under steady state average ...

  11. An artificial neural network based fast radiative transfer model for ...

    Indian Academy of Sciences (India)

    In the present study, a fast radiative transfer model using neural networks is proposed to simulate radiances corresponding to the wavenumbers of INSAT-3D. Realistic atmospheric temperature and humidity profiles have been used for training the network. Spectral response functions of GOES-13, a satellite similar in ...

  12. Radio Channel Modelling for UAV Communication over Cellular Networks

    DEFF Research Database (Denmark)

    Amorim, Rafhael Medeiros de; Nguyen, Huan Cong; Mogensen, Preben Elgaard

    2017-01-01

    The main goal of this paper is to obtain models for path loss exponents and shadowing for the radio channel between airborne Unmanned Aerial Vehicles (UAVs) and cellular networks. In this pursuit, field measurements were conducted in live LTE networks at the 800 MHz frequency band, using a commer...

  13. Distribution Of Wealth In A Network Model Of The Economy

    OpenAIRE

    Tao Ma; Holden, John G.; Serota, R. A.

    2012-01-01

    We show, analytically and numerically, that wealth distribution in the Bouchaud-M\\'ezard network model of the economy is described by a three-parameter generalized inverse gamma distribution. In the mean-field limit of a network with any two agents linked, it reduces to the inverse gamma distribution.

  14. Water Distribution Network Modelling of a Small Community using ...

    African Journals Online (AJOL)

    Water Distribution Network Modelling of a Small Community using Watercad Simulator. ... Global Journal of Engineering Research ... with respect to pressure or available fire flow for the proposed service area and also that flow velocities are not excessive while head loss gradients in the network are within acceptable limits.

  15. Capacity allocation in wireless communication networks - models and analyses

    NARCIS (Netherlands)

    Litjens, Remco

    2003-01-01

    This monograph has concentrated on capacity allocation in cellular and Wireless Local Area Networks, primarily with a network operator’s perspective. In the introduc- tory chapter, a reference model has been proposed for the extensive suite of capacity allocation mechanisms that can be applied at

  16. Line and lattice networks under deterministic interference models

    NARCIS (Netherlands)

    Goseling, Jasper; Gastpar, Michael; Weber, Jos H.

    Capacity bounds are compared for four different deterministic models of wireless networks, representing four different ways of handling broadcast and superposition in the physical layer. In particular, the transport capacity under a multiple unicast traffic pattern is studied for a 1-D network of

  17. Energy Model of Networks-on-Chip and a Bus

    NARCIS (Netherlands)

    Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Kavaldjiev, N.K.; Becker, Jens E.; Becker, Jurgen

    A Network-on-Chip (NoC) is an energy-efficient onchip communication architecture for Multi-Processor Systemon- Chip (MPSoC) architectures. In earlier papers we proposed two Network-on-Chip architectures based on packet-switching and circuit-switching. In this paper we derive an energy model for both

  18. Modeling Verdict Outcomes Using Social Network Measures: The Watergate and Caviar Network Cases

    Science.gov (United States)

    2016-01-01

    Modelling criminal trial verdict outcomes using social network measures is an emerging research area in quantitative criminology. Few studies have yet analyzed which of these measures are the most important for verdict modelling or which data classification techniques perform best for this application. To compare the performance of different techniques in classifying members of a criminal network, this article applies three different machine learning classifiers–Logistic Regression, Naïve Bayes and Random Forest–with a range of social network measures and the necessary databases to model the verdicts in two real–world cases: the U.S. Watergate Conspiracy of the 1970’s and the now–defunct Canada–based international drug trafficking ring known as the Caviar Network. In both cases it was found that the Random Forest classifier did better than either Logistic Regression or Naïve Bayes, and its superior performance was statistically significant. This being so, Random Forest was used not only for classification but also to assess the importance of the measures. For the Watergate case, the most important one proved to be betweenness centrality while for the Caviar Network, it was the effective size of the network. These results are significant because they show that an approach combining machine learning with social network analysis not only can generate accurate classification models but also helps quantify the importance social network variables in modelling verdict outcomes. We conclude our analysis with a discussion and some suggestions for future work in verdict modelling using social network measures. PMID:26824351

  19. Non-consensus Opinion Models on Complex Networks

    Science.gov (United States)

    Li, Qian; Braunstein, Lidia A.; Wang, Huijuan; Shao, Jia; Stanley, H. Eugene; Havlin, Shlomo

    2013-04-01

    Social dynamic opinion models have been widely studied to understand how interactions among individuals cause opinions to evolve. Most opinion models that utilize spin interaction models usually produce a consensus steady state in which only one opinion exists. Because in reality different opinions usually coexist, we focus on non-consensus opinion models in which above a certain threshold two opinions coexist in a stable relationship. We revisit and extend the non-consensus opinion (NCO) model introduced by Shao et al. (Phys. Rev. Lett. 103:01870, 2009). The NCO model in random networks displays a second order phase transition that belongs to regular mean field percolation and is characterized by the appearance (above a certain threshold) of a large spanning cluster of the minority opinion. We generalize the NCO model by adding a weight factor W to each individual's original opinion when determining their future opinion (NCO W model). We find that as W increases the minority opinion holders tend to form stable clusters with a smaller initial minority fraction than in the NCO model. We also revisit another non-consensus opinion model based on the NCO model, the inflexible contrarian opinion (ICO) model (Li et al. in Phys. Rev. E 84:066101, 2011), which introduces inflexible contrarians to model the competition between two opinions in a steady state. Inflexible contrarians are individuals that never change their original opinion but may influence the opinions of others. To place the inflexible contrarians in the ICO model we use two different strategies, random placement and one in which high-degree nodes are targeted. The inflexible contrarians effectively decrease the size of the largest rival-opinion cluster in both strategies, but the effect is more pronounced under the targeted method. All of the above models have previously been explored in terms of a single network, but human communities are usually interconnected, not isolated. Because opinions propagate not

  20. Hybrid modeling and empirical analysis of automobile supply chain network

    Science.gov (United States)

    Sun, Jun-yan; Tang, Jian-ming; Fu, Wei-ping; Wu, Bing-ying

    2017-05-01

    Based on the connection mechanism of nodes which automatically select upstream and downstream agents, a simulation model for dynamic evolutionary process of consumer-driven automobile supply chain is established by integrating ABM and discrete modeling in the GIS-based map. Firstly, the rationality is proved by analyzing the consistency of sales and changes in various agent parameters between the simulation model and a real automobile supply chain. Second, through complex network theory, hierarchical structures of the model and relationships of networks at different levels are analyzed to calculate various characteristic parameters such as mean distance, mean clustering coefficients, and degree distributions. By doing so, it verifies that the model is a typical scale-free network and small-world network. Finally, the motion law of this model is analyzed from the perspective of complex self-adaptive systems. The chaotic state of the simulation system is verified, which suggests that this system has typical nonlinear characteristics. This model not only macroscopically illustrates the dynamic evolution of complex networks of automobile supply chain but also microcosmically reflects the business process of each agent. Moreover, the model construction and simulation of the system by means of combining CAS theory and complex networks supplies a novel method for supply chain analysis, as well as theory bases and experience for supply chain analysis of auto companies.

  1. When individual behaviour matters: homogeneous and network models in epidemiology.

    Science.gov (United States)

    Bansal, Shweta; Grenfell, Bryan T; Meyers, Lauren Ancel

    2007-10-22

    Heterogeneity in host contact patterns profoundly shapes population-level disease dynamics. Many epidemiological models make simplifying assumptions about the patterns of disease-causing interactions among hosts. In particular, homogeneous-mixing models assume that all hosts have identical rates of disease-causing contacts. In recent years, several network-based approaches have been developed to explicitly model heterogeneity in host contact patterns. Here, we use a network perspective to quantify the extent to which real populations depart from the homogeneous-mixing assumption, in terms of both the underlying network structure and the resulting epidemiological dynamics. We find that human contact patterns are indeed more heterogeneous than assumed by homogeneous-mixing models, but are not as variable as some have speculated. We then evaluate a variety of methodologies for incorporating contact heterogeneity, including network-based models and several modifications to the simple SIR compartmental model. We conclude that the homogeneous-mixing compartmental model is appropriate when host populations are nearly homogeneous, and can be modified effectively for a few classes of non-homogeneous networks. In general, however, network models are more intuitive and accurate for predicting disease spread through heterogeneous host populations.

  2. Destabilization of Terrorist Networks through Argument Driven Hypothesis Model

    DEFF Research Database (Denmark)

    Hussain, Dil Muhammad Akbar

    2007-01-01

    Social network analysis has been used for quite some time to analyze and understand the behavior of nodes in the network.  Theses nodes could be individuals or group of persons, events or organizations etc.  Infact these nodes could be any thing importantly, these nodes propagate and obviously ha......) to predict a path for its destabilization.  This network is selected to benchmark our proposed model framework.  The results obtained with various network analysis shows that it works better than other analysis measures for example based on degree, betweeness and closeness etc.        ...

  3. Mutual Interference Models for CDMA Mobile Communication Networks

    Directory of Open Access Journals (Sweden)

    K. Hrudkay

    2002-12-01

    Full Text Available Nowadays we are witnesses of a huge development one of the mostprogressive communication technology - mobile networks. The mainproblem in these networks is an elimination of the mutual interference,which, mainly in non-orthogonal CDMA networks, is the principalobstacle for reaching high transmission rates The aim of thiscontribution is to give simplified view to mutual interference modelsfor orthogonal and non-orthogonal CDMA networks. The contribution isintended mainly for PhD. students to help them to obtain an orientationin such a complicated areas, as the interference models for CDMAnetworks are.

  4. Neural network models: Insights and prescriptions from practical applications

    Energy Technology Data Exchange (ETDEWEB)

    Samad, T. [Honeywell Technology Center, Minneapolis, MN (United States)

    1995-12-31

    Neural networks are no longer just a research topic; numerous applications are now testament to their practical utility. In the course of developing these applications, researchers and practitioners have been faced with a variety of issues. This paper briefly discusses several of these, noting in particular the rich connections between neural networks and other, more conventional technologies. A more comprehensive version of this paper is under preparation that will include illustrations on real examples. Neural networks are being applied in several different ways. Our focus here is on neural networks as modeling technology. However, much of the discussion is also relevant to other types of applications such as classification, control, and optimization.

  5. Northern emporia and maritime networks. Modelling past communication using archaeological network analysis

    DEFF Research Database (Denmark)

    Sindbæk, Søren Michael

    2015-01-01

    Long-distance communication has emerged as a particular focus for archaeologicalexploration using network theory, analysis, and modelling. The promise is apparentlyobvious: communication in the past doubtlessly had properties of complex, dynamicnetworks, and archaeological datasets almost certainly...... preserve patterns of thisinteraction. Formal network analysis and modelling holds the potential to identify anddemonstrate such patterns, where traditional methods often prove inadequate. Thearchaeological study of communication networks in the past, however, calls for radically different analytical......,and use patterns. This point is demonstrated with reference to a study of Viking-period communication in the North Sea region...

  6. A Simplified Network Model for Travel Time Reliability Analysis in a Road Network

    Directory of Open Access Journals (Sweden)

    Kenetsu Uchida

    2017-01-01

    Full Text Available This paper proposes a simplified network model which analyzes travel time reliability in a road network. A risk-averse driver is assumed in the simplified model. The risk-averse driver chooses a path by taking into account both a path travel time variance and a mean path travel time. The uncertainty addressed in this model is that of traffic flows (i.e., stochastic demand flows. In the simplified network model, the path travel time variance is not calculated by considering all travel time covariance between two links in the network. The path travel time variance is calculated by considering all travel time covariance between two adjacent links in the network. Numerical experiments are carried out to illustrate the applicability and validity of the proposed model. The experiments introduce the path choice behavior of a risk-neutral driver and several types of risk-averse drivers. It is shown that the mean link flows calculated by introducing the risk-neutral driver differ as a whole from those calculated by introducing several types of risk-averse drivers. It is also shown that the mean link flows calculated by the simplified network model are almost the same as the flows calculated by using the exact path travel time variance.

  7. Transportation and dynamic networks: Models, theory, and applications to supply chains, electric power, and financial networks

    Science.gov (United States)

    Liu, Zugang

    Network systems, including transportation and logistic systems, electric power generation and distribution networks as well as financial networks, provide the critical infrastructure for the functioning of our societies and economies. The understanding of the dynamic behavior of such systems is also crucial to national security and prosperity. The identification of new connections between distinct network systems is the inspiration for the research in this dissertation. In particular, I answer two questions raised by Beckmann, McGuire, and Winsten (1956) and Copeland (1952) over half a century ago, which are, respectively, how are electric power flows related to transportation flows and does money flow like water or electricity? In addition, in this dissertation, I achieve the following: (1) I establish the relationships between transportation networks and three other classes of complex network systems: supply chain networks, electric power generation and transmission networks, and financial networks with intermediation. The establishment of such connections provides novel theoretical insights as well as new pricing mechanisms, and efficient computational methods. (2) I develop new modeling frameworks based on evolutionary variational inequality theory that capture the dynamics of such network systems in terms of the time-varying flows and incurred costs, prices, and, where applicable, profits. This dissertation studies the dynamics of such network systems by addressing both internal competition and/or cooperation, and external changes, such as varying costs and demands. (3) I focus, in depth, on electric power supply chains. By exploiting the relationships between transportation networks and electric power supply chains, I develop a large-scale network model that integrates electric power supply chains and fuel supply markets. The model captures both the economic transactions as well as the physical transmission constraints. The model is then applied to the New

  8. A DUAL NETWORK MODEL OF INTERLOCKING DIRECTORATES

    Directory of Open Access Journals (Sweden)

    Humphry Hung

    2003-01-01

    Full Text Available The article proposes an integrative framework for the study of interlocking directorates by using an approach that encompasses the concepts of multiple networks and resource endowment. This serves to integrate the traditional views of interorganizational linkages and intra-class cohesion. Through appropriate strategic analysis of relevant resource endowment of internal environment and external networks of organizations and corporate elites, this article argues that the selection of directors, if used effectively, can be adopted as a strategic device to enhance the corporation's overall performance.

  9. ARCHITECTURES AND ALGORITHMS FOR COGNITIVE NETWORKS ENABLED BY QUALITATIVE MODELS

    DEFF Research Database (Denmark)

    Balamuralidhar, P.

    2013-01-01

    Complexity of communication networks is ever increasing and getting complicated by their heterogeneity and dynamism. Traditional techniques are facing challenges in network performance management. Cognitive networking is an emerging paradigm to make networks more intelligent, thereby overcoming...... traditional limitations and potentially achieving better performance. The vision is that, networks should be able to monitor themselves, reason upon changes in self and environment, act towards the achievement of specific goals and learn from experience. The concept of a Cognitive Engine (CE) supporting...... cognitive functions, as part of network elements, enabling above said autonomic capabilities is gathering attention. Awareness of the self and the world is an important aspect of the cognitive engine to be autonomic. This is achieved through embedding their models in the engine, but the complexity...

  10. A Gaussian graphical model approach to climate networks

    Energy Technology Data Exchange (ETDEWEB)

    Zerenner, Tanja, E-mail: tanjaz@uni-bonn.de [Meteorological Institute, University of Bonn, Auf dem Hügel 20, 53121 Bonn (Germany); Friederichs, Petra; Hense, Andreas [Meteorological Institute, University of Bonn, Auf dem Hügel 20, 53121 Bonn (Germany); Interdisciplinary Center for Complex Systems, University of Bonn, Brühler Straße 7, 53119 Bonn (Germany); Lehnertz, Klaus [Department of Epileptology, University of Bonn, Sigmund-Freud-Straße 25, 53105 Bonn (Germany); Helmholtz Institute for Radiation and Nuclear Physics, University of Bonn, Nussallee 14-16, 53115 Bonn (Germany); Interdisciplinary Center for Complex Systems, University of Bonn, Brühler Straße 7, 53119 Bonn (Germany)

    2014-06-15

    Distinguishing between direct and indirect connections is essential when interpreting network structures in terms of dynamical interactions and stability. When constructing networks from climate data the nodes are usually defined on a spatial grid. The edges are usually derived from a bivariate dependency measure, such as Pearson correlation coefficients or mutual information. Thus, the edges indistinguishably represent direct and indirect dependencies. Interpreting climate data fields as realizations of Gaussian Random Fields (GRFs), we have constructed networks according to the Gaussian Graphical Model (GGM) approach. In contrast to the widely used method, the edges of GGM networks are based on partial correlations denoting direct dependencies. Furthermore, GRFs can be represented not only on points in space, but also by expansion coefficients of orthogonal basis functions, such as spherical harmonics. This leads to a modified definition of network nodes and edges in spectral space, which is motivated from an atmospheric dynamics perspective. We construct and analyze networks from climate data in grid point space as well as in spectral space, and derive the edges from both Pearson and partial correlations. Network characteristics, such as mean degree, average shortest path length, and clustering coefficient, reveal that the networks posses an ordered and strongly locally interconnected structure rather than small-world properties. Despite this, the network structures differ strongly depending on the construction method. Straightforward approaches to infer networks from climate data while not regarding any physical processes may contain too strong simplifications to describe the dynamics of the climate system appropriately.

  11. Quebec mental health services networks: models and implementation

    Directory of Open Access Journals (Sweden)

    Marie-Josée Fleury

    2005-06-01

    Full Text Available Purpose: In the transformation of health care systems, the introduction of integrated service networks is considered to be one of the main solutions for enhancing efficiency. In the last few years, a wealth of literature has emerged on the topic of services integration. However, the question of how integrated service networks should be modelled to suit different implementation contexts has barely been touched. To fill that gap, this article presents four models for the organization of mental health integrated networks. Data sources: The proposed models are drawn from three recently published studies on mental health integrated services in the province of Quebec (Canada with the author as principal investigator. Description: Following an explanation of the concept of integrated service network and a description of the Quebec context for mental health networks, the models, applicable in all settings: rural, urban or semi-urban, and metropolitan, and summarized in four figures, are presented. Discussion and conclusion: To apply the models successfully, the necessity of rallying all the actors of a system, from the strategic, tactical and operational levels, according to the type of integration involved: functional/administrative, clinical and physician-system is highlighted. The importance of formalizing activities among organizations and actors in a network and reinforcing the governing mechanisms at the local level is also underlined. Finally, a number of integration strategies and key conditions of success to operationalize integrated service networks are suggested.

  12. Modeling and simulation of the USAVRE network and radiology operations

    Science.gov (United States)

    Martinez, Ralph; Bradford, Daniel Q.; Hatch, Jay; Sochan, John; Chimiak, William J.

    1998-07-01

    The U.S. Army Medical Command, lead by the Brooke Army Medical Center, has embarked on a visionary project. The U.S. Army Virtual Radiology Environment (USAVRE) is a CONUS-based network that connects all the Army's major medical centers and Regional Medical Commands (RMC). The purpose of the USAVRE is to improve the quality, access, and cost of radiology services in the Army via the use of state-of-the-art medical imaging, computer, and networking technologies. The USAVRE contains multimedia viewing workstations; database archive systems are based on a distributed computing environment using Common Object Request Broker Architecture (CORBA) middleware protocols. The underlying telecommunications network is an ATM-based backbone network that connects the RMC regional networks and PACS networks at medical centers and RMC clinics. This project is a collaborative effort between Army, university, and industry centers with expertise in teleradiology and Global PACS applications. This paper describes a model and simulation of the USAVRE for performance evaluation purposes. As a first step the results of a Technology Assessment and Requirements Analysis (TARA) -- an analysis of the workload in Army radiology departments, their equipment and their staffing. Using the TARA data and other workload information, we have developed a very detailed analysis of the workload and workflow patterns of our Medical Treatment Facilities. We are embarking on modeling and simulation strategies, which will form the foundation for the VRE network. The workload analysis is performed for each radiology modality in a RMC site. The workload consists of the number of examinations per modality, type of images per exam, number of images per exam, and size of images. The frequency for store and forward cases, second readings, and interactive consultation cases are also determined. These parameters are translated into the model described below. The model for the USAVRE is hierarchical in nature

  13. Numerical analysis of modeling based on improved Elman neural network.

    Science.gov (United States)

    Jie, Shao; Li, Wang; WeiSong, Zhao; YaQin, Zhong; Malekian, Reza

    2014-01-01

    A modeling based on the improved Elman neural network (IENN) is proposed to analyze the nonlinear circuits with the memory effect. The hidden layer neurons are activated by a group of Chebyshev orthogonal basis functions instead of sigmoid functions in this model. The error curves of the sum of squared error (SSE) varying with the number of hidden neurons and the iteration step are studied to determine the number of the hidden layer neurons. Simulation results of the half-bridge class-D power amplifier (CDPA) with two-tone signal and broadband signals as input have shown that the proposed behavioral modeling can reconstruct the system of CDPAs accurately and depict the memory effect of CDPAs well. Compared with Volterra-Laguerre (VL) model, Chebyshev neural network (CNN) model, and basic Elman neural network (BENN) model, the proposed model has better performance.

  14. Numerical Analysis of Modeling Based on Improved Elman Neural Network

    Directory of Open Access Journals (Sweden)

    Shao Jie

    2014-01-01

    Full Text Available A modeling based on the improved Elman neural network (IENN is proposed to analyze the nonlinear circuits with the memory effect. The hidden layer neurons are activated by a group of Chebyshev orthogonal basis functions instead of sigmoid functions in this model. The error curves of the sum of squared error (SSE varying with the number of hidden neurons and the iteration step are studied to determine the number of the hidden layer neurons. Simulation results of the half-bridge class-D power amplifier (CDPA with two-tone signal and broadband signals as input have shown that the proposed behavioral modeling can reconstruct the system of CDPAs accurately and depict the memory effect of CDPAs well. Compared with Volterra-Laguerre (VL model, Chebyshev neural network (CNN model, and basic Elman neural network (BENN model, the proposed model has better performance.

  15. Neural network models of learning and categorization in multigame experiments

    Directory of Open Access Journals (Sweden)

    Davide eMarchiori

    2011-12-01

    Full Text Available Previous research has shown that regret-driven neural networks predict behavior in repeated completely mixed games remarkably well, substantially equating the performance of the most accurate established models of learning. This result prompts the question of what is the added value of modeling learning through neural networks. We submit that this modeling approach allows for models that are able to distinguish among and respond differently to different payoff structures. Moreover, the process of categorization of a game is implicitly carried out by these models, thus without the need of any external explicit theory of similarity between games. To validate our claims, we designed and ran two multigame experiments in which subjects faced, in random sequence, different instances of two completely mixed 2x2 games. Then, we tested on our experimental data two regret-driven neural network models, and compared their performance with that of other established models of learning and Nash equilibrium.

  16. SCYNet. Testing supersymmetric models at the LHC with neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Bechtle, Philip; Belkner, Sebastian; Hamer, Matthias [Universitaet Bonn, Bonn (Germany); Dercks, Daniel [Universitaet Hamburg, Hamburg (Germany); Keller, Tim; Kraemer, Michael; Sarrazin, Bjoern; Schuette-Engel, Jan; Tattersall, Jamie [RWTH Aachen University, Institute for Theoretical Particle Physics and Cosmology, Aachen (Germany)

    2017-10-15

    SCYNet (SUSY Calculating Yield Net) is a tool for testing supersymmetric models against LHC data. It uses neural network regression for a fast evaluation of the profile likelihood ratio. Two neural network approaches have been developed: one network has been trained using the parameters of the 11-dimensional phenomenological Minimal Supersymmetric Standard Model (pMSSM-11) as an input and evaluates the corresponding profile likelihood ratio within milliseconds. It can thus be used in global pMSSM-11 fits without time penalty. In the second approach, the neural network has been trained using model-independent signature-related objects, such as energies and particle multiplicities, which were estimated from the parameters of a given new physics model. (orig.)

  17. SCYNet: testing supersymmetric models at the LHC with neural networks

    Science.gov (United States)

    Bechtle, Philip; Belkner, Sebastian; Dercks, Daniel; Hamer, Matthias; Keller, Tim; Krämer, Michael; Sarrazin, Björn; Schütte-Engel, Jan; Tattersall, Jamie

    2017-10-01

    SCYNet (SUSY Calculating Yield Net) is a tool for testing supersymmetric models against LHC data. It uses neural network regression for a fast evaluation of the profile likelihood ratio. Two neural network approaches have been developed: one network has been trained using the parameters of the 11-dimensional phenomenological Minimal Supersymmetric Standard Model (pMSSM-11) as an input and evaluates the corresponding profile likelihood ratio within milliseconds. It can thus be used in global pMSSM-11 fits without time penalty. In the second approach, the neural network has been trained using model-independent signature-related objects, such as energies and particle multiplicities, which were estimated from the parameters of a given new physics model.

  18. Modelling the self-organization and collapse of complex networks

    Indian Academy of Sciences (India)

    Modelling the self-organization and collapse of complex networks. Sanjay Jain Department of Physics and Astrophysics, University of Delhi Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore Santa Fe Institute, Santa Fe, New Mexico.

  19. A model reduction method for biochemical reaction networks

    National Research Council Canada - National Science Library

    Rao, Shodhan; van der Schaft, Arjan; van Eunen, Karen; Bakker, Barbara; Jayawardhana, Bayu

    2014-01-01

    Background: In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics...

  20. Water distribution network modelling of a small community using ...

    African Journals Online (AJOL)

    Water distribution network modelling of a small community using watercad simulator. ... Global Journal of Engineering Research ... Pipes P-6, P-12, P-15 and P-19 expectedly have relatively low flow velocities due to the low average day ...

  1. Computational modeling of signal transduction networks: a pedagogical exposition.

    Science.gov (United States)

    Prasad, Ashok

    2012-01-01

    We give a pedagogical introduction to computational modeling of signal transduction networks, starting from explaining the representations of chemical reactions by differential equations via the law of mass action. We discuss elementary biochemical reactions such as Michaelis-Menten enzyme kinetics and cooperative binding, and show how these allow the representation of large networks as systems of differential equations. We discuss the importance of looking for simpler or reduced models, such as network motifs or dynamical motifs within the larger network, and describe methods to obtain qualitative behavior by bifurcation analysis, using freely available continuation software. We then discuss stochastic kinetics and show how to implement easy-to-use methods of rule-based modeling for stochastic simulations. We finally suggest some methods for comprehensive parameter sensitivity analysis, and discuss the insights that it could yield. Examples, including code to try out, are provided based on a paper that modeled Ras kinetics in thymocytes.

  2. Modelling and predicting biogeographical patterns in river networks

    Directory of Open Access Journals (Sweden)

    Sabela Lois

    2016-04-01

    Full Text Available Statistical analysis and interpretation of biogeographical phenomena in rivers is now possible using a spatially explicit modelling framework, which has seen significant developments in the past decade. I used this approach to identify a spatial extent (geostatistical range in which the abundance of the parasitic freshwater pearl mussel (Margaritifera margaritifera L. is spatially autocorrelated in river networks. I show that biomass and abundance of host fish are a likely explanation for the autocorrelation in mussel abundance within a 15-km spatial extent. The application of universal kriging with the empirical model enabled precise prediction of mussel abundance within segments of river networks, something that has the potential to inform conservation biogeography. Although I used a variety of modelling approaches in my thesis, I focus here on the details of this relatively new spatial stream network model, thus advancing the study of biogeographical patterns in river networks.

  3. Bayesian network models for error detection in radiotherapy plans.

    Science.gov (United States)

    Kalet, Alan M; Gennari, John H; Ford, Eric C; Phillips, Mark H

    2015-04-07

    The purpose of this study is to design and develop a probabilistic network for detecting errors in radiotherapy plans for use at the time of initial plan verification. Our group has initiated a multi-pronged approach to reduce these errors. We report on our development of Bayesian models of radiotherapy plans. Bayesian networks consist of joint probability distributions that define the probability of one event, given some set of other known information. Using the networks, we find the probability of obtaining certain radiotherapy parameters, given a set of initial clinical information. A low probability in a propagated network then corresponds to potential errors to be flagged for investigation. To build our networks we first interviewed medical physicists and other domain experts to identify the relevant radiotherapy concepts and their associated interdependencies and to construct a network topology. Next, to populate the network's conditional probability tables, we used the Hugin Expert software to learn parameter distributions from a subset of de-identified data derived from a radiation oncology based clinical information database system. These data represent 4990 unique prescription cases over a 5 year period. Under test case scenarios with approximately 1.5% introduced error rates, network performance produced areas under the ROC curve of 0.88, 0.98, and 0.89 for the lung, brain and female breast cancer error detection networks, respectively. Comparison of the brain network to human experts performance (AUC of 0.90 ± 0.01) shows the Bayes network model performs better than domain experts under the same test conditions. Our results demonstrate the feasibility and effectiveness of comprehensive probabilistic models as part of decision support systems for improved detection of errors in initial radiotherapy plan verification procedures.

  4. Modelling, Synthesis, and Configuration of Networks-on-Chips

    DEFF Research Database (Denmark)

    Stuart, Matthias Bo

    This thesis presents three contributions in two different areas of network-on-chip and system-on-chip research: Application modelling and identifying and solving different optimization problems related to two specific network-on-chip architectures. The contribution related to application modelling...... is an analytical method for deriving the worst-case traffic pattern caused by an application and the cache-coherence protocol in a cache-coherent shared-memory system. The contributions related to network-on-chip optimization problems consist of two parts: The development and evaluation of six heuristics...... for solving the network synthesis problem in the MANGO network-on-chip, and the identification and formalization of the ReNoC configuration problem together with three heuristics for solving it....

  5. A Neural Network Model for Prediction of Sound Quality

    DEFF Research Database (Denmark)

    Nielsen,, Lars Bramsløw

    An artificial neural network structure has been specified, implemented and optimized for the purpose of predicting the perceived sound quality for normal-hearing and hearing-impaired subjects. The network was implemented by means of commercially available software and optimized to predict results...... error on the test set. The overall concept proved functional, but further testing with data obtained from a new rating experiment is necessary to better assess the utility of this measure. The weights in the trained neural networks were analyzed to qualitatively interpret the relation between...... obtained in subjective sound quality rating experiments based on input data from an auditory model. Various types of input data and data representations from the auditory model were used as input data for the chosen network structure, which was a three-layer perceptron. This network was trained by means...

  6. Molecular modeling of amorphous, non-woven polymer networks.

    Science.gov (United States)

    Krausse, Constantin A; Milek, Theodor; Zahn, Dirk

    2015-10-01

    We outline a simple and efficient approach to generating molecular models of amorphous polymer networks. Similar to established techniques of preparing woven polymer networks from quenching high-temperature molecular simulation runs, we use a molecular dynamics simulations of a generic melt as starting points. This generic melt is however only used to describe parts of the polymers, namely the cross-linker units which positions are adopted from particle positions of the quenched melt. Specific degrees of network connectivity are tuned by geometric criteria for linker-linker connections and by suitable multi-body interaction potentials applied to the generic melt simulations. Using this technique we demonstrate adjusting fourfold linker coordination in amorphous polymer networks comprising 10-20% under-coordinated linkers. Graphical Abstract Molecular modeling of amorphous, non-woven polymer networks.

  7. Modeling and Analysis of New Products Diffusion on Heterogeneous Networks

    Directory of Open Access Journals (Sweden)

    Shuping Li

    2014-01-01

    Full Text Available We present a heterogeneous networks model with the awareness stage and the decision-making stage to explain the process of new products diffusion. If mass media is neglected in the decision-making stage, there is a threshold whether the innovation diffusion is successful or not, or else it is proved that the network model has at least one positive equilibrium. For networks with the power-law degree distribution, numerical simulations confirm analytical results, and also at the same time, by numerical analysis of the influence of the network structure and persuasive advertisements on the density of adopters, we give two different products propagation strategies for two classes of nodes in scale-free networks.

  8. Modeling pedestrian's conformity violation behavior: a complex network based approach.

    Science.gov (United States)

    Zhou, Zhuping; Hu, Qizhou; Wang, Wei

    2014-01-01

    Pedestrian injuries and fatalities present a problem all over the world. Pedestrian conformity violation behaviors, which lead to many pedestrian crashes, are common phenomena at the signalized intersections in China. The concepts and metrics of complex networks are applied to analyze the structural characteristics and evolution rules of pedestrian network about the conformity violation crossings. First, a network of pedestrians crossing the street is established, and the network's degree distributions are analyzed. Then, by using the basic idea of SI model, a spreading model of pedestrian illegal crossing behavior is proposed. Finally, through simulation analysis, pedestrian's illegal crossing behavior trends are obtained in different network structures and different spreading rates. Some conclusions are drawn: as the waiting time increases, more pedestrians will join in the violation crossing once a pedestrian crosses on red firstly. And pedestrian's conformity violation behavior will increase as the spreading rate increases.

  9. Optimization of recurrent neural networks for time series modeling

    DEFF Research Database (Denmark)

    Pedersen, Morten With

    1997-01-01

    series. The overall objective s are to improve training by application of second-order methods and to improve generalization ability by architecture optimization accomplished by pruning. The major topics covered in the thesis are: 1. The problem of training recurrent networks is analyzed from a numerical...... of solution obtained as well as computation time required. 3. A theoretical definition of the generalization error for recurrent networks is provided. This definition justifies a commonly adopted approach for estimating generalization ability. 4. The viability of pruning recurrent networks by the Optimal...... networks is proposed. The tool allows for assessment of the length of the effe ctive memory of previous inputs built up in the recurrent network during application. Time series modeling is also treated from a more general point of view, namely modeling of the joint probability distribution function...

  10. Message Integrity Model for Wireless Sensor Networks

    Science.gov (United States)

    Qleibo, Haider W.

    2009-01-01

    WSNs are susceptible to a variety of attacks. These attacks vary in the way they are performed and executed; they include but not limited to node capture, physical tampering, denial of service, and message alteration. It is of paramount importance to protect gathered data by WSNs and defend the network against illegal access and malicious…

  11. 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

  12. Reconstruction of social group networks from friendship networks using a tag-based model

    Science.gov (United States)

    Guan, Yuan-Pan; You, Zhi-Qiang; Han, Xiao-Pu

    2016-12-01

    Social group is a type of mesoscopic structure that connects human individuals in microscopic level and the global structure of society. In this paper, we propose a tag-based model considering that social groups expand along the edge that connects two neighbors with a similar tag of interest. The model runs on a real-world friendship network, and its simulation results show that various properties of simulated group network can well fit the empirical analysis on real-world social groups, indicating that the model catches the major mechanism driving the evolution of social groups and successfully reconstructs the social group network from a friendship network and throws light on digging of relationships between social functional organizations.

  13. Probabilistic Priority Message Checking Modeling Based on Controller Area Networks

    Science.gov (United States)

    Lin, Cheng-Min

    Although the probabilistic model checking tool called PRISM has been applied in many communication systems, such as wireless local area network, Bluetooth, and ZigBee, the technique is not used in a controller area network (CAN). In this paper, we use PRISM to model the mechanism of priority messages for CAN because the mechanism has allowed CAN to become the leader in serial communication for automobile and industry control. Through modeling CAN, it is easy to analyze the characteristic of CAN for further improving the security and efficiency of automobiles. The Markov chain model helps us to model the behaviour of priority messages.

  14. Network models in optimization and their applications in practice

    CERN Document Server

    Glover, Fred; Phillips, Nancy V

    2011-01-01

    Unique in that it focuses on formulation and case studies rather than solutions procedures covering applications for pure, generalized and integer networks, equivalent formulations plus successful techniques of network models. Every chapter contains a simple model which is expanded to handle more complicated developments, a synopsis of existing applications, one or more case studies, at least 20 exercises and invaluable references. An Instructor's Manual presenting detailed solutions to all the problems in the book is available upon request from the Wiley editorial department.

  15. Water Quality Modeling in Reservoirs Using Multivariate Linear Regression and Two Neural Network Models

    OpenAIRE

    Wei-Bo Chen; Wen-Cheng Liu

    2015-01-01

    In this study, two artificial neural network models (i.e., a radial basis function neural network, RBFN, and an adaptive neurofuzzy inference system approach, ANFIS) and a multilinear regression (MLR) model were developed to simulate the DO, TP, Chl a, and SD in the Mingder Reservoir of central Taiwan. The input variables of the neural network and the MLR models were determined using linear regression. The performances were evaluated using the RBFN, ANFIS, and MLR models based on statistical ...

  16. A network security situation prediction model based on wavelet neural network with optimized parameters

    Directory of Open Access Journals (Sweden)

    Haibo Zhang

    2016-08-01

    Full Text Available The security incidents ion networks are sudden and uncertain, it is very hard to precisely predict the network security situation by traditional methods. In order to improve the prediction accuracy of the network security situation, we build a network security situation prediction model based on Wavelet Neural Network (WNN with optimized parameters by the Improved Niche Genetic Algorithm (INGA. The proposed model adopts WNN which has strong nonlinear ability and fault-tolerance performance. Also, the parameters for WNN are optimized through the adaptive genetic algorithm (GA so that WNN searches more effectively. Considering the problem that the adaptive GA converges slowly and easily turns to the premature problem, we introduce a novel niche technology with a dynamic fuzzy clustering and elimination mechanism to solve the premature convergence of the GA. Our final simulation results show that the proposed INGA-WNN prediction model is more reliable and effective, and it achieves faster convergence-speed and higher prediction accuracy than the Genetic Algorithm-Wavelet Neural Network (GA-WNN, Genetic Algorithm-Back Propagation Neural Network (GA-BPNN and WNN.

  17. Spatial-temporal modeling of malware propagation in networks.

    Science.gov (United States)

    Chen, Zesheng; Ji, Chuanyi

    2005-09-01

    Network security is an important task of network management. One threat to network security is malware (malicious software) propagation. One type of malware is called topological scanning that spreads based on topology information. The focus of this work is on modeling the spread of topological malwares, which is important for understanding their potential damages, and for developing countermeasures to protect the network infrastructure. Our model is motivated by probabilistic graphs, which have been widely investigated in machine learning. We first use a graphical representation to abstract the propagation of malwares that employ different scanning methods. We then use a spatial-temporal random process to describe the statistical dependence of malware propagation in arbitrary topologies. As the spatial dependence is particularly difficult to characterize, the problem becomes how to use simple (i.e., biased) models to approximate the spatially dependent process. In particular, we propose the independent model and the Markov model as simple approximations. We conduct both theoretical analysis and extensive simulations on large networks using both real measurements and synthesized topologies to test the performance of the proposed models. Our results show that the independent model can capture temporal dependence and detailed topology information and, thus, outperforms the previous models, whereas the Markov model incorporates a certain spatial dependence and, thus, achieves a greater accuracy in characterizing both transient and equilibrium behaviors of malware propagation.

  18. Artificial neural network modeling of dissolved oxygen in reservoir.

    Science.gov (United States)

    Chen, Wei-Bo; Liu, Wen-Cheng

    2014-02-01

    The water quality of reservoirs is one of the key factors in the operation and water quality management of reservoirs. Dissolved oxygen (DO) in water column is essential for microorganisms and a significant indicator of the state of aquatic ecosystems. In this study, two artificial neural network (ANN) models including back propagation neural network (BPNN) and adaptive neural-based fuzzy inference system (ANFIS) approaches and multilinear regression (MLR) model were developed to estimate the DO concentration in the Feitsui Reservoir of northern Taiwan. The input variables of the neural network are determined as water temperature, pH, conductivity, turbidity, suspended solids, total hardness, total alkalinity, and ammonium nitrogen. The performance of the ANN models and MLR model was assessed through the mean absolute error, root mean square error, and correlation coefficient computed from the measured and model-simulated DO values. The results reveal that ANN estimation performances were superior to those of MLR. Comparing to the BPNN and ANFIS models through the performance criteria, the ANFIS model is better than the BPNN model for predicting the DO values. Study results show that the neural network particularly using ANFIS model is able to predict the DO concentrations with reasonable accuracy, suggesting that the neural network is a valuable tool for reservoir management in Taiwan.

  19. Extending a configuration model to find communities in complex networks

    Science.gov (United States)

    Jin, Di; He, Dongxiao; Hu, Qinghua; Baquero, Carlos; Yang, Bo

    2013-09-01

    Discovery of communities in complex networks is a fundamental data analysis task in various domains. Generative models are a promising class of techniques for identifying modular properties from networks, which has been actively discussed recently. However, most of them cannot preserve the degree sequence of networks, which will distort the community detection results. Rather than using a blockmodel as most current works do, here we generalize a configuration model, namely, a null model of modularity, to solve this problem. Towards decomposing and combining sub-graphs according to the soft community memberships, our model incorporates the ability to describe community structures, something the original model does not have. Also, it has the property, as with the original model, that it fixes the expected degree sequence to be the same as that of the observed network. We combine both the community property and degree sequence preserving into a single unified model, which gives better community results compared with other models. Thereafter, we learn the model using a technique of nonnegative matrix factorization and determine the number of communities by applying consensus clustering. We test this approach both on synthetic benchmarks and on real-world networks, and compare it with two similar methods. The experimental results demonstrate the superior performance of our method over competing methods in detecting both disjoint and overlapping communities.

  20. Innovative research of AD HOC network mobility model

    Science.gov (United States)

    Chen, Xin

    2017-08-01

    It is difficult for researchers of AD HOC network to conduct actual deployment during experimental stage as the network topology is changeable and location of nodes is unfixed. Thus simulation still remains the main research method of the network. Mobility model is an important component of AD HOC network simulation. It is used to describe the movement pattern of nodes in AD HOC network (including location and velocity, etc.) and decides the movement trail of nodes, playing as the abstraction of the movement modes of nodes. Therefore, mobility model which simulates node movement is an important foundation for simulation research. In AD HOC network research, mobility model shall reflect the movement law of nodes as truly as possible. In this paper, node generally refers to the wireless equipment people carry. The main research contents include how nodes avoid obstacles during movement process and the impacts of obstacles on the mutual relation among nodes, based on which a Node Self Avoiding Obstacle, i.e. NASO model is established in AD HOC network.

  1. Modified network simulation model with token method of bus access

    Directory of Open Access Journals (Sweden)

    L.V. Stribulevich

    2013-08-01

    Full Text Available Purpose. To study the characteristics of the local network with the marker method of access to the bus its modified simulation model was developed. Methodology. Defining characteristics of the network is carried out on the developed simulation model, which is based on the state diagram-layer network station with the mechanism of processing priorities, both in steady state and in the performance of control procedures: the initiation of a logical ring, the entrance and exit of the station network with a logical ring. Findings. A simulation model, on the basis of which can be obtained the dependencies of the application the maximum waiting time in the queue for different classes of access, and the reaction time usable bandwidth on the data rate, the number of network stations, the generation rate applications, the number of frames transmitted per token holding time, frame length was developed. Originality. The technique of network simulation reflecting its work in the steady condition and during the control procedures, the mechanism of priority ranking and handling was proposed. Practical value. Defining network characteristics in the real-time systems on railway transport based on the developed simulation model.

  2. A model reduction method for biochemical reaction networks.

    Science.gov (United States)

    Rao, Shodhan; van der Schaft, Arjan; van Eunen, Karen; Bakker, Barbara M; Jayawardhana, Bayu

    2014-05-03

    In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the complexes and reactions in the network. It does not rely on prior knowledge of the dynamic behaviour of the network and hence can be automated, as we demonstrate. The reduced network has fewer complexes, reactions, variables and parameters as compared to the original network, and yet the behaviour of a preselected set of significant metabolites in the reduced network resembles that of the original network. Moreover the reduced network largely retains the structure and kinetics of the original model. We apply our method to a yeast glycolysis model and a rat liver fatty acid beta-oxidation model. When the number of state variables in the yeast model is reduced from 12 to 7, the difference between metabolite concentrations in the reduced and the full model, averaged over time and species, is only 8%. Likewise, when the number of state variables in the rat-liver beta-oxidation model is reduced from 42 to 29, the difference between the reduced model and the full model is 7.5%. The method has improved our understanding of the dynamics of the two networks. We found that, contrary to the general disposition, the first few metabolites which were deleted from the network during our stepwise reduction approach, are not those with the shortest convergence times. It shows that our reduction approach performs differently from other approaches that are based on time-scale separation. The method can be used to facilitate fitting of the parameters or to embed a detailed model of interest in a more coarse

  3. An ART neural network model of discrimination shift learning

    NARCIS (Netherlands)

    Raijmakers, M.E.J.; Coffey, E.; Stevenson, C.; Winkel, J.; Berkeljon, A.; Taatgen, N.; van Rijn, H.

    2009-01-01

    We present an ART-based neural network model (adapted from [2]) of the development of discrimination-shift learning that models the trial-by-trial learning process in great detail. In agreement with the results of human participants (4-20 years of age) in [1] the model revealed two distinct learning

  4. Threat model framework and methodology for personal networks (PNs)

    DEFF Research Database (Denmark)

    Prasad, Neeli R.

    2007-01-01

    is to give a structured, convenient approach for building threat models. A framework for the threat model is presented with a list of requirements for methodology. The methodology will be applied to build a threat model for Personal Networks. Practical tools like UML sequence diagrams and attack trees have...

  5. Geometric and Network Model for Knowledge Structure and Mindspace

    OpenAIRE

    Chris Arney

    2012-01-01

    This paper describes an adaptive, complex network architecture for knowledge representation in virtual mindspace. Structures and processes for knowing, remembering, thinking, learning, deciding, and communicating describe a virtual geometric space (mathematical model) of a notional mind. This mindspace model can be visualized as a workspace and this paper provides a glimpse of a virtual model of the mind.

  6. Geometric and Network Model for Knowledge Structure and Mindspace

    Directory of Open Access Journals (Sweden)

    Chris Arney

    2012-02-01

    Full Text Available This paper describes an adaptive, complex network architecture for knowledge representation in virtual mindspace. Structures and processes for knowing, remembering, thinking, learning, deciding, and communicating describe a virtual geometric space (mathematical model of a notional mind. This mindspace model can be visualized as a workspace and this paper provides a glimpse of a virtual model of the mind.

  7. Bayesian Network Models for Local Dependence among Observable Outcome Variables

    Science.gov (United States)

    Almond, Russell G.; Mulder, Joris; Hemat, Lisa A.; Yan, Duanli

    2009-01-01

    Bayesian network models offer a large degree of flexibility for modeling dependence among observables (item outcome variables) from the same task, which may be dependent. This article explores four design patterns for modeling locally dependent observations: (a) no context--ignores dependence among observables; (b) compensatory context--introduces…

  8. Network and adaptive system of systems modeling and analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Lawton, Craig R.; Campbell, James E. Dr. (.; .); Anderson, Dennis James; Eddy, John P.

    2007-05-01

    This report documents the results of an LDRD program entitled ''Network and Adaptive System of Systems Modeling and Analysis'' that was conducted during FY 2005 and FY 2006. The purpose of this study was to determine and implement ways to incorporate network communications modeling into existing System of Systems (SoS) modeling capabilities. Current SoS modeling, particularly for the Future Combat Systems (FCS) program, is conducted under the assumption that communication between the various systems is always possible and occurs instantaneously. A more realistic representation of these communications allows for better, more accurate simulation results. The current approach to meeting this objective has been to use existing capabilities to model network hardware reliability and adding capabilities to use that information to model the impact on the sustainment supply chain and operational availability.

  9. Evolutionary re-wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species-specific gene expression and phenotypes

    Science.gov (United States)

    Sethi, Isha; Gluck, Christian; Zhou, Huiqing

    2017-01-01

    Abstract Although epidermal keratinocyte development and differentiation proceeds in similar fashion between humans and mice, evolutionary pressures have also wrought significant species-specific physiological differences. These differences between species could arise in part, by the rewiring of regulatory network due to changes in the global targets of lineage-specific transcriptional master regulators such as p63. Here we have performed a systematic and comparative analysis of the p63 target gene network within the integrated framework of the transcriptomic and epigenomic landscape of mouse and human keratinocytes. We determined that there exists a core set of ∼1600 genomic regions distributed among enhancers and super-enhancers, which are conserved and occupied by p63 in keratinocytes from both species. Notably, these DNA segments are typified by consensus p63 binding motifs under purifying selection and are associated with genes involved in key keratinocyte and skin-centric biological processes. However, the majority of the p63-bound mouse target regions consist of either murine-specific DNA elements that are not alignable to the human genome or exhibit no p63 binding in the orthologous syntenic regions, typifying an occupancy lost subset. Our results suggest that these evolutionarily divergent regions have undergone significant turnover of p63 binding sites and are associated with an underlying inactive and inaccessible chromatin state, indicative of their selective functional activity in the transcriptional regulatory network in mouse but not human. Furthermore, we demonstrate that this selective targeting of genes by p63 correlates with subtle, but measurable transcriptional differences in mouse and human keratinocytes that converges on major metabolic processes, which often exhibit species-specific trends. Collectively our study offers possible molecular explanation for the observable phenotypic differences between the mouse and human skin and broadly

  10. Constructing Neuronal Network Models in Massively Parallel Environments

    Directory of Open Access Journals (Sweden)

    Tammo Ippen

    2017-05-01

    Full Text Available Recent advances in the development of data structures to represent spiking neuron network models enable us to exploit the complete memory of petascale computers for a single brain-scale network simulation. In this work, we investigate how well we can exploit the computing power of such supercomputers for the creation of neuronal networks. Using an established benchmark, we divide the runtime of simulation code into the phase of network construction and the phase during which the dynamical state is advanced in time. We find that on multi-core compute nodes network creation scales well with process-parallel code but exhibits a prohibitively large memory consumption. Thread-parallel network creation, in contrast, exhibits speedup only up to a small number of threads but has little overhead in terms of memory. We further observe that the algorithms creating instances of model neurons and their connections scale well for networks of ten thousand neurons, but do not show the same speedup for networks of millions of neurons. Our work uncovers that the lack of scaling of thread-parallel network creation is due to inadequate memory allocation strategies and demonstrates that thread-optimized memory allocators recover excellent scaling. An analysis of the loop order used for network construction reveals that more complex tests on the locality of operations significantly improve scaling and reduce runtime by allowing construction algorithms to step through large networks more efficiently than in existing code. The combination of these techniques increases performance by an order of magnitude and harnesses the increasingly parallel compute power of the compute nodes in high-performance clusters and supercomputers.

  11. Constructing Neuronal Network Models in Massively Parallel Environments.

    Science.gov (United States)

    Ippen, Tammo; Eppler, Jochen M; Plesser, Hans E; Diesmann, Markus

    2017-01-01

    Recent advances in the development of data structures to represent spiking neuron network models enable us to exploit the complete memory of petascale computers for a single brain-scale network simulation. In this work, we investigate how well we can exploit the computing power of such supercomputers for the creation of neuronal networks. Using an established benchmark, we divide the runtime of simulation code into the phase of network construction and the phase during which the dynamical state is advanced in time. We find that on multi-core compute nodes network creation scales well with process-parallel code but exhibits a prohibitively large memory consumption. Thread-parallel network creation, in contrast, exhibits speedup only up to a small number of threads but has little overhead in terms of memory. We further observe that the algorithms creating instances of model neurons and their connections scale well for networks of ten thousand neurons, but do not show the same speedup for networks of millions of neurons. Our work uncovers that the lack of scaling of thread-parallel network creation is due to inadequate memory allocation strategies and demonstrates that thread-optimized memory allocators recover excellent scaling. An analysis of the loop order used for network construction reveals that more complex tests on the locality of operations significantly improve scaling and reduce runtime by allowing construction algorithms to step through large networks more efficiently than in existing code. The combination of these techniques increases performance by an order of magnitude and harnesses the increasingly parallel compute power of the compute nodes in high-performance clusters and supercomputers.

  12. Social Insects: A Model System for Network Dynamics

    Science.gov (United States)

    Charbonneau, Daniel; Blonder, Benjamin; Dornhaus, Anna

    Social insect colonies (ants, bees, wasps, and termites) show sophisticated collective problem-solving in the face of variable constraints. Individuals exchange information and materials such as food. The resulting network structure and dynamics can inform us about the mechanisms by which the insects achieve particular collective behaviors and these can be transposed to man-made and social networks. We discuss how network analysis can answer important questions about social insects, such as how effective task allocation or information flow is realized. We put forward the idea that network analysis methods are under-utilized in social insect research, and that they can provide novel ways to view the complexity of collective behavior, particularly if network dynamics are taken into account. To illustrate this, we present an example of network tasks performed by ant workers, linked by instances of workers switching from one task to another. We show how temporal network analysis can propose and test new hypotheses on mechanisms of task allocation, and how adding temporal elements to static networks can drastically change results. We discuss the benefits of using social insects as models for complex systems in general. There are multiple opportunities emergent technologies and analysis methods in facilitating research on social insect network. The potential for interdisciplinary work could significantly advance diverse fields such as behavioral ecology, computer sciences, and engineering.

  13. Language Networks as Models of Cognition: Understanding Cognition through Language

    Science.gov (United States)

    Beckage, Nicole M.; Colunga, Eliana

    Language is inherently cognitive and distinctly human. Separating the object of language from the human mind that processes and creates language fails to capture the full language system. Linguistics traditionally has focused on the study of language as a static representation, removed from the human mind. Network analysis has traditionally been focused on the properties and structure that emerge from network representations. Both disciplines could gain from looking at language as a cognitive process. In contrast, psycholinguistic research has focused on the process of language without committing to a representation. However, by considering language networks as approximations of the cognitive system we can take the strength of each of these approaches to study human performance and cognition as related to language. This paper reviews research showcasing the contributions of network science to the study of language. Specifically, we focus on the interplay of cognition and language as captured by a network representation. To this end, we review different types of language network representations before considering the influence of global level network features. We continue by considering human performance in relation to network structure and conclude with theoretical network models that offer potential and testable explanations of cognitive and linguistic phenomena.

  14. Regional Computation of TEC Using a Neural Network Model

    Science.gov (United States)

    Leandro, R. F.; Santos, M. C.

    2004-05-01

    One of the main sources of errors of GPS measurements is the ionosphere refraction. As a dispersive medium, the ionosphere allow its influence to be computed by using dual frequency receivers. In the case of single frequency receivers it is necessary to use models that tell us how big the ionospheric refraction is. The GPS broadcast message carries parameters of this model, namely Klobuchar model. Dual frequency receivers allow to estimate the influence of ionosphere in the GPS signal by the computation of TEC (Total Electron Content) values, that have a direct relationship with the magnitude of the delay caused by the ionosphere. One alternative is to create a regional model based on a network of dual frequency receivers. In this case, the regional behaviour of ionosphere is modelled in a way that it is possible to estimate the TEC values into or near this region. This regional model can be based on polynomials, for example. In this work we will present a Neural Network-based model to the regional computation of TEC. The advantage of using a Neural Network is that it is not necessary to have a great knowledge on the behaviour of the modelled surface due to the adaptation capability of neural networks training process, that is an iterative adjust of the synaptic weights in function of residuals, using the training parameters. Therefore, the previous knowledge of the modelled phenomena is important to define what kind of and how many parameters are needed to train the neural network so that reasonable results are obtained from the estimations. We have used data from the GPS tracking network in Brazil, and we have tested the accuracy of the new model to all locations where there is a station, accessing the efficiency of the model everywhere. TEC values were computed for each station of the network. After that the training parameters data set for the test station was formed, with the TEC values of all others (all stations, except the test one). The Neural Network was

  15. Modeling of axonal endoplasmic reticulum network by spastic paraplegia proteins.

    Science.gov (United States)

    Yalçın, Belgin; Zhao, Lu; Stofanko, Martin; O'Sullivan, Niamh C; Kang, Zi Han; Roost, Annika; Thomas, Matthew R; Zaessinger, Sophie; Blard, Olivier; Patto, Alex L; Sohail, Anood; Baena, Valentina; Terasaki, Mark; O'Kane, Cahir J

    2017-07-25

    Axons contain a smooth tubular endoplasmic reticulum (ER) network that is thought to be continuous with ER throughout the neuron; the mechanisms that form this axonal network are unknown. Mutations affecting reticulon or REEP proteins, with intramembrane hairpin domains that model ER membranes, cause an axon degenerative disease, hereditary spastic paraplegia (HSP). We show that Drosophila axons have a dynamic axonal ER network, which these proteins help to model. Loss of HSP hairpin proteins causes ER sheet expansion, partial loss of ER from distal motor axons, and occasional discontinuities in axonal ER. Ultrastructural analysis reveals an extensive ER network in axons, which shows larger and fewer tubules in larvae that lack reticulon and REEP proteins, consistent with loss of membrane curvature. Therefore HSP hairpin-containing proteins are required for shaping and continuity of axonal ER, thus suggesting roles for ER modeling in axon maintenance and function.

  16. PageRank model of opinion formation on social networks

    Science.gov (United States)

    Kandiah, Vivek; Shepelyansky, Dima L.

    2012-11-01

    We propose the PageRank model of opinion formation and investigate its rich properties on real directed networks of the Universities of Cambridge and Oxford, LiveJournal, and Twitter. In this model, the opinion formation of linked electors is weighted with their PageRank probability. Such a probability is used by the Google search engine for ranking of web pages. We find that the society elite, corresponding to the top PageRank nodes, can impose its opinion on a significant fraction of the society. However, for a homogeneous distribution of two opinions, there exists a bistability range of opinions which depends on a conformist parameter characterizing the opinion formation. We find that the LiveJournal and Twitter networks have a stronger tendency to a totalitarian opinion formation than the university networks. We also analyze the Sznajd model generalized for scale-free networks with the weighted PageRank vote of electors.

  17. A growing social network model in geographical space

    Science.gov (United States)

    Antonioni, Alberto; Tomassini, Marco

    2017-09-01

    In this work we propose a new model for the generation of social networks that includes their often ignored spatial aspects. The model is a growing one and links are created either taking space into account, or disregarding space and only considering the degree of target nodes. These two effects can be mixed linearly in arbitrary proportions through a parameter. We numerically show that for a given range of the combination parameter, and for given mean degree, the generated network class shares many important statistical features with those observed in actual social networks, including the spatial dependence of connections. Moreover, we show that the model provides a good qualitative fit to some measured social networks.

  18. Approaches to modeling gene regulatory networks: a gentle introduction.

    Science.gov (United States)

    Schlitt, Thomas

    2013-01-01

    This chapter is split into two main sections; first, I will present an introduction to gene networks. Second, I will discuss various approaches to gene network modeling which will include some examples for using different data sources. Computational modeling has been used for many different biological systems and many approaches have been developed addressing the different needs posed by the different application fields. The modeling approaches presented here are not limited to gene regulatory networks and occasionally I will present other examples. The material covered here is an update based on several previous publications by Thomas Schlitt and Alvis Brazma (FEBS Lett 579(8),1859-1866, 2005; Philos Trans R Soc Lond B Biol Sci 361(1467), 483-494, 2006; BMC Bioinformatics 8(suppl 6), S9, 2007) that formed the foundation for a lecture on gene regulatory networks at the In Silico Systems Biology workshop series at the European Bioinformatics Institute in Hinxton.

  19. Joint Modelling of Structural and Functional Brain Networks

    DEFF Research Database (Denmark)

    Andersen, Kasper Winther; Herlau, Tue; Mørup, Morten

    Functional and structural magnetic resonance imaging have become the most important noninvasive windows to the human brain. A major challenge in the analysis of brain networks is to establish the similarities and dissimilarities between functional and structural connectivity. We formulate a non......-parametric Bayesian network model which allows for joint modelling and integration of multiple networks. We demonstrate the model’s ability to detect vertices that share structure across networks jointly in functional MRI (fMRI) and diffusion MRI (dMRI) data. Using two fMRI and dMRI scans per subject, we establish...... significant structures that are consistently shared across subjects and data splits. This provides an unsupervised approach for modeling of structure-function relations in the brain and provides a general framework for multimodal integration....

  20. Modeling and Simulation Network Data Standards

    Science.gov (United States)

    2011-09-30

    12.1 Open Shortest Path First ( OSPF ) Protocol commonly used to find the shortest path between two nodes. User defined. 12.2 Border Gateway Protocol...Element Definition 12.7 Request for Comments – 1256 (RFC-1256) Router discovery protocol. 13.0 OSPF Sub-elements define OSPF parameters 13.1...resolution network analysis simulation tool OSPF open shortest path first OV operational view PEO-I Program Executive Office - Information

  1. Network Analysis and Modeling in Systems Biology

    OpenAIRE

    Bosque Chacón, Gabriel

    2017-01-01

    This thesis is dedicated to the study and comprehension of biological networks at the molecular level. The objectives were to analyse their topology, integrate it in a genotype-phenotype analysis, develop richer mathematical descriptions for them, study their community structure and compare different methodologies for estimating their internal fluxes. The work presented in this document moves around three main axes. The first one is the biological. Which organisms were studied in this ...

  2. Network Security Threats and Protection Models

    OpenAIRE

    Kumar, Amit; Malhotra, Santosh

    2015-01-01

    In a brave new age of global connectivity and e-commerce, interconnections via networks have heightened, creating for both individuals and organizations, a state of complete dependence upon vulnerable systems for storage and transfer of information. Never before, have so many people had power in their own hands. The power to deface websites, access personal mail accounts, and worse more the potential to bring down entire governments, and financial corporations through openly documented softwa...

  3. Stochastic modelling and control of communication networks

    OpenAIRE

    Zuraniewski, P.W.

    2011-01-01

    The unprecedented growth of the Information Technologies sector observed within the past years creates an excellent opportunity to conduct new, exciting and interdisciplinary research. Increasing complexity of the communication networks calls for incorporating rigorously developed and reliable methods for traffic control and management. Mathematics may offer extremely valuable tools to achieve these goals but transforming an engineering problem into the mathematical one requires a good unders...

  4. Bayesian network models for error detection in radiotherapy plans

    Science.gov (United States)

    Kalet, Alan M.; Gennari, John H.; Ford, Eric C.; Phillips, Mark H.

    2015-04-01

    The purpose of this study is to design and develop a probabilistic network for detecting errors in radiotherapy plans for use at the time of initial plan verification. Our group has initiated a multi-pronged approach to reduce these errors. We report on our development of Bayesian models of radiotherapy plans. Bayesian networks consist of joint probability distributions that define the probability of one event, given some set of other known information. Using the networks, we find the probability of obtaining certain radiotherapy parameters, given a set of initial clinical information. A low probability in a propagated network then corresponds to potential errors to be flagged for investigation. To build our networks we first interviewed medical physicists and other domain experts to identify the relevant radiotherapy concepts and their associated interdependencies and to construct a network topology. Next, to populate the network’s conditional probability tables, we used the Hugin Expert software to learn parameter distributions from a subset of de-identified data derived from a radiation oncology based clinical information database system. These data represent 4990 unique prescription cases over a 5 year period. Under test case scenarios with approximately 1.5% introduced error rates, network performance produced areas under the ROC curve of 0.88, 0.98, and 0.89 for the lung, brain and female breast cancer error detection networks, respectively. Comparison of the brain network to human experts performance (AUC of 0.90 ± 0.01) shows the Bayes network model performs better than domain experts under the same test conditions. Our results demonstrate the feasibility and effectiveness of comprehensive probabilistic models as part of decision support systems for improved detection of errors in initial radiotherapy plan verification procedures.

  5. Loops and autonomy promote evolvability of ecosystem networks.

    Science.gov (United States)

    Luo, Jianxi

    2014-09-29

    The structure of ecological networks, in particular food webs, determines their ability to evolve further, i.e. evolvability. The knowledge about how food web evolvability is determined by the structures of diverse ecological networks can guide human interventions purposefully to either promote or limit evolvability of ecosystems. However, the focus of prior food web studies was on stability and robustness; little is known regarding the impact of ecological network structures on their evolvability. To correlate ecosystem structure and evolvability, we adopt the NK model originally from evolutionary biology to generate and assess the ruggedness of fitness landscapes of a wide spectrum of model food webs with gradual variation in the amount of feeding loops and link density. The variation in network structures is controlled by linkage rewiring. Our results show that more feeding loops and lower trophic link density, i.e. higher autonomy of species, of food webs increase the potential for the ecosystem to generate heritable variations with improved fitness. Our findings allow the prediction of the evolvability of actual food webs according to their network structures, and provide guidance to enhancing or controlling the evolvability of specific ecosystems.

  6. Social Network Analyses and Nutritional Behavior: An Integrated Modeling Approach

    Directory of Open Access Journals (Sweden)

    Alistair McNair Senior

    2016-01-01

    Full Text Available Animals have evolved complex foraging strategies to obtain a nutritionally balanced diet and associated fitness benefits. Recent advances in nutrition research, combining state-space models of nutritional geometry with agent-based models of systems biology, show how nutrient targeted foraging behavior can also influence animal social interactions, ultimately affecting collective dynamics and group structures. Here we demonstrate how social network analyses can be integrated into such a modeling framework and provide a tangible and practical analytical tool to compare experimental results with theory. We illustrate our approach by examining the case of nutritionally mediated dominance hierarchies. First we show how nutritionally explicit agent-based models that simulate the emergence of dominance hierarchies can be used to generate social networks. Importantly the structural properties of our simulated networks bear similarities to dominance networks of real animals (where conflicts are not always directly related to nutrition. Finally, we demonstrate how metrics from social network analyses can be used to predict the fitness of agents in these simulated competitive environments. Our results highlight the potential importance of nutritional mechanisms in shaping dominance interactions in a wide range of social and ecological contexts. Nutrition likely influences social interaction in many species, and yet a theoretical framework for exploring these effects is currently lacking. Combining social network analyses with computational models from nutritional ecology may bridge this divide, representing a pragmatic approach for generating theoretical predictions for nutritional experiments.

  7. Developing Network Location Model in Uncertainty Mode (Robust Mode

    Directory of Open Access Journals (Sweden)

    AMINI Mousa

    2013-01-01

    Full Text Available In this research, facility location problem - network design under uncertainty robust mode has been discussed. In this regard a model will be developed, so that the uncertainty in parameters such as demand and problem’s various costs considered. Facility location- network design, unlike classical facility location models, which are assumed that network structure is pre-defined and specified- will also decide on the structure of the network. This has been in many actual applications such as road network, communication systems and etc and finding facility location and main network designing simultaneously has deemed important and the need for simultaneous design and optimization models to meet the mentioned items is felt. Different approaches have been developed in the uncertainty optimization literature. Amongst them, robust and stochastic optimizations are well- known. To deal with uncertainty and problem modeling, in this research robust optimization approach have been used. In addition, by using generated random samples, the proposed model has been tested and computational analysis is presented for various parameters.

  8. From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks.

    Science.gov (United States)

    Soh, Keng Cher; Miskovic, Ljubisa; Hatzimanikatis, Vassily

    2012-03-01

    Many important problems in cell biology arise from the dense nonlinear interactions between functional modules. The importance of mathematical modelling and computer simulation in understanding cellular processes is now indisputable and widely appreciated. Genome-scale metabolic models have gained much popularity and utility in helping us to understand and test hypotheses about these complex networks. However, there are some caveats that come with the use and interpretation of different types of metabolic models, which we aim to highlight here. We discuss and illustrate how the integration of thermodynamic and kinetic properties of the yeast metabolic networks in network analyses can help in understanding and utilizing this organism more successfully in the areas of metabolic engineering, synthetic biology and disease treatment. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  9. Generalized memory associativity in a network model for the neuroses

    Science.gov (United States)

    Wedemann, Roseli S.; Donangelo, Raul; de Carvalho, Luís A. V.

    2009-03-01

    We review concepts introduced in earlier work, where a neural network mechanism describes some mental processes in neurotic pathology and psychoanalytic working-through, as associative memory functioning, according to the findings of Freud. We developed a complex network model, where modules corresponding to sensorial and symbolic memories interact, representing unconscious and conscious mental processes. The model illustrates Freud's idea that consciousness is related to symbolic and linguistic memory activity in the brain. We have introduced a generalization of the Boltzmann machine to model memory associativity. Model behavior is illustrated with simulations and some of its properties are analyzed with methods from statistical mechanics.

  10. Constitutive models for rubber networks undergoing simultaneous crosslinking and scission.

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Aidan Patrick; Curro, John G.; Rottach, Dana R. (University of New Mexico, Albuquerque, NM); Grest, Gary Stephen; Budzien, Joanne L.; Lo, David Chi S.

    2006-01-01

    Constitutive models for chemically reacting networks are formulated based on a generalization of the independent network hypothesis. These models account for the coupling between chemical reaction and strain histories, and have been tested by comparison with microscopic molecular dynamics simulations. An essential feature of these models is the introduction of stress transfer functions that describe the interdependence between crosslinks formed and broken at various strains. Efforts are underway to implement these constitutive models into the finite element code Adagio. Preliminary results are shown that illustrate the effects of changing crosslinking and scission rates and history.

  11. ICA model order selection of task co-activation networks.

    Science.gov (United States)

    Ray, Kimberly L; McKay, D Reese; Fox, Peter M; Riedel, Michael C; Uecker, Angela M; Beckmann, Christian F; Smith, Stephen M; Fox, Peter T; Laird, Angela R

    2013-01-01

    Independent component analysis (ICA) has become a widely used method for extracting functional networks in the brain during rest and task. Historically, preferred ICA dimensionality has widely varied within the neuroimaging community, but typically varies between 20 and 100 components. This can be problematic when comparing results across multiple studies because of the impact ICA dimensionality has on the topology of its resultant components. Recent studies have demonstrated that ICA can be applied to peak activation coordinates archived in a large neuroimaging database (i.e., BrainMap Database) to yield whole-brain task-based co-activation networks. A strength of applying ICA to BrainMap data is that the vast amount of metadata in BrainMap can be used to quantitatively assess tasks and cognitive processes contributing to each component. In this study, we investigated the effect of model order on the distribution of functional properties across networks as a method for identifying the most informative decompositions of BrainMap-based ICA components. Our findings suggest dimensionality of 20 for low model order ICA to examine large-scale brain networks, and dimensionality of 70 to provide insight into how large-scale networks fractionate into sub-networks. We also provide a functional and organizational assessment of visual, motor, emotion, and interoceptive task co-activation networks as they fractionate from low to high model-orders.

  12. The new challenges of multiplex networks: Measures and models

    Science.gov (United States)

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2017-02-01

    What do societies, the Internet, and the human brain have in common? They are all examples of complex relational systems, whose emerging behaviours are largely determined by the non-trivial networks of interactions among their constituents, namely individuals, computers, or neurons, rather than only by the properties of the units themselves. In the last two decades, network scientists have proposed models of increasing complexity to better understand real-world systems. Only recently we have realised that multiplexity, i.e. the coexistence of several types of interactions among the constituents of a complex system, is responsible for substantial qualitative and quantitative differences in the type and variety of behaviours that a complex system can exhibit. As a consequence, multilayer and multiplex networks have become a hot topic in complexity science. Here we provide an overview of some of the measures proposed so far to characterise the structure of multiplex networks, and a selection of models aiming at reproducing those structural properties and quantifying their statistical significance. Focusing on a subset of relevant topics, this brief review is a quite comprehensive introduction to the most basic tools for the analysis of multiplex networks observed in the real-world. The wide applicability of multiplex networks as a framework to model complex systems in different fields, from biology to social sciences, and the colloquial tone of the paper will make it an interesting read for researchers working on both theoretical and experimental analysis of networked systems.

  13. Modeling Marine Electromagnetic Survey with Radial Basis Function Networks

    Directory of Open Access Journals (Sweden)

    Agus Arif

    2014-11-01

    Full Text Available A marine electromagnetic survey is an engineering endeavour to discover the location and dimension of a hydrocarbon layer under an ocean floor. In this kind of survey, an array of electric and magnetic receivers are located on the sea floor and record the scattered, refracted and reflected electromagnetic wave, which has been transmitted by an electric dipole antenna towed by a vessel. The data recorded in receivers must be processed and further analysed to estimate the hydrocarbon location and dimension. To conduct those analyses successfuly, a radial basis function (RBF network could be employed to become a forward model of the input-output relationship of the data from a marine electromagnetic survey. This type of neural networks is working based on distances between its inputs and predetermined centres of some basis functions. A previous research had been conducted to model the same marine electromagnetic survey using another type of neural networks, which is a multi layer perceptron (MLP network. By comparing their validation and training performances (mean-squared errors and correlation coefficients, it is concluded that, in this case, the MLP network is comparatively better than the RBF network[1].[1] This manuscript is an extended version of our previous paper, entitled Radial Basis Function Networks for Modeling Marine Electromagnetic Survey, which had been presented on 2011 International Conference on Electrical Engineering and Informatics, 17-19 July 2011, Bandung, Indonesia.

  14. A mixture copula Bayesian network model for multimodal genomic data

    Directory of Open Access Journals (Sweden)

    Qingyang Zhang

    2017-04-01

    Full Text Available Gaussian Bayesian networks have become a widely used framework to estimate directed associations between joint Gaussian variables, where the network structure encodes the decomposition of multivariate normal density into local terms. However, the resulting estimates can be inaccurate when the normality assumption is moderately or severely violated, making it unsuitable for dealing with recent genomic data such as the Cancer Genome Atlas data. In the present paper, we propose a mixture copula Bayesian network model which provides great flexibility in modeling non-Gaussian and multimodal data for causal inference. The parameters in mixture copula functions can be efficiently estimated by a routine expectation–maximization algorithm. A heuristic search algorithm based on Bayesian information criterion is developed to estimate the network structure, and prediction can be further improved by the best-scoring network out of multiple predictions from random initial values. Our method outperforms Gaussian Bayesian networks and regular copula Bayesian networks in terms of modeling flexibility and prediction accuracy, as demonstrated using a cell signaling data set. We apply the proposed methods to the Cancer Genome Atlas data to study the genetic and epigenetic pathways that underlie serous ovarian cancer.

  15. A mixture copula Bayesian network model for multimodal genomic data.

    Science.gov (United States)

    Zhang, Qingyang; Shi, Xuan

    2017-01-01

    Gaussian Bayesian networks have become a widely used framework to estimate directed associations between joint Gaussian variables, where the network structure encodes the decomposition of multivariate normal density into local terms. However, the resulting estimates can be inaccurate when the normality assumption is moderately or severely violated, making it unsuitable for dealing with recent genomic data such as the Cancer Genome Atlas data. In the present paper, we propose a mixture copula Bayesian network model which provides great flexibility in modeling non-Gaussian and multimodal data for causal inference. The parameters in mixture copula functions can be efficiently estimated by a routine expectation-maximization algorithm. A heuristic search algorithm based on Bayesian information criterion is developed to estimate the network structure, and prediction can be further improved by the best-scoring network out of multiple predictions from random initial values. Our method outperforms Gaussian Bayesian networks and regular copula Bayesian networks in terms of modeling flexibility and prediction accuracy, as demonstrated using a cell signaling data set. We apply the proposed methods to the Cancer Genome Atlas data to study the genetic and epigenetic pathways that underlie serous ovarian cancer.

  16. Applying Model Based Systems Engineering to NASA's Space Communications Networks

    Science.gov (United States)

    Bhasin, Kul; Barnes, Patrick; Reinert, Jessica; Golden, Bert

    2013-01-01

    System engineering practices for complex systems and networks now require that requirement, architecture, and concept of operations product development teams, simultaneously harmonize their activities to provide timely, useful and cost-effective products. When dealing with complex systems of systems, traditional systems engineering methodology quickly falls short of achieving project objectives. This approach is encumbered by the use of a number of disparate hardware and software tools, spreadsheets and documents to grasp the concept of the network design and operation. In case of NASA's space communication networks, since the networks are geographically distributed, and so are its subject matter experts, the team is challenged to create a common language and tools to produce its products. Using Model Based Systems Engineering methods and tools allows for a unified representation of the system in a model that enables a highly related level of detail. To date, Program System Engineering (PSE) team has been able to model each network from their top-level operational activities and system functions down to the atomic level through relational modeling decomposition. These models allow for a better understanding of the relationships between NASA's stakeholders, internal organizations, and impacts to all related entities due to integration and sustainment of existing systems. Understanding the existing systems is essential to accurate and detailed study of integration options being considered. In this paper, we identify the challenges the PSE team faced in its quest to unify complex legacy space communications networks and their operational processes. We describe the initial approaches undertaken and the evolution toward model based system engineering applied to produce Space Communication and Navigation (SCaN) PSE products. We will demonstrate the practice of Model Based System Engineering applied to integrating space communication networks and the summary of its

  17. Boolean network model predicts cell cycle sequence of fission yeast.

    Directory of Open Access Journals (Sweden)

    Maria I Davidich

    Full Text Available A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe is constructed solely on the basis of the known biochemical interaction topology. Simulating the model in the computer faithfully reproduces the known activity sequence of regulatory proteins along the cell cycle of the living cell. Contrary to existing differential equation models, no parameters enter the model except the structure of the regulatory circuitry. The dynamical properties of the model indicate that the biological dynamical sequence is robustly implemented in the regulatory network, with the biological stationary state G1 corresponding to the dominant attractor in state space, and with the biological regulatory sequence being a strongly attractive trajectory. Comparing the fission yeast cell-cycle model to a similar model of the corresponding network in S. cerevisiae, a remarkable difference in circuitry, as well as dynamics is observed. While the latter operates in a strongly damped mode, driven by external excitation, the S. pombe network represents an auto-excited system with external damping.

  18. A Cayley Tree Immune Network Model with Antibody Dynamics

    CERN Document Server

    Anderson, R W; Perelson, A S; Anderson, Russell W.; Neumann, Avidan U.; Perelson, Alan S.

    1993-01-01

    Abstract: A Cayley tree model of idiotypic networks that includes both B cell and antibody dynamics is formulated and analyzed. As in models with B cells only, localized states exist in the network with limited numbers of activated clones surrounded by virgin or near-virgin clones. The existence and stability of these localized network states are explored as a function of model parameters. As in previous models that have included antibody, the stability of immune and tolerant localized states are shown to depend on the ratio of antibody to B cell lifetimes as well as the rate of antibody complex removal. As model parameters are varied, localized steady-states can break down via two routes: dynamically, into chaotic attractors, or structurally into percolation attractors. For a given set of parameters, percolation and chaotic attractors can coexist with localized attractors, and thus there do not exist clear cut boundaries in parameter space that separate regions of localized attractors from regions of percola...

  19. Modeling the Merger of the Classified Networks of the DDN (Defense Data Network): BLACKER

    Science.gov (United States)

    1988-11-01

    Cain (1983) presented ’The DoD Internet Architecture Model" approach where a common internal host-to-host packet or datagram service is proposed for...The baseline model was a simulation similar to the model of *The DoD Internet Architecture Model" presented by Cerf and Cain. (1983) Parameters for...in each network can be redirected, what would be the optimal method for allocation? Third, what are the impacts of interdomain messages? What happens

  20. Multi-Topic Tracking Model for dynamic social network

    Science.gov (United States)

    Li, Yuhua; Liu, Changzheng; Zhao, Ming; Li, Ruixuan; Xiao, Hailing; Wang, Kai; Zhang, Jun

    2016-07-01

    The topic tracking problem has attracted much attention in the last decades. However, existing approaches rarely consider network structures and textual topics together. In this paper, we propose a novel statistical model based on dynamic bayesian network, namely Multi-Topic Tracking Model for Dynamic Social Network (MTTD). It takes influence phenomenon, selection phenomenon, document generative process and the evolution of textual topics into account. Specifically, in our MTTD model, Gibbs Random Field is defined to model the influence of historical status of users in the network and the interdependency between them in order to consider the influence phenomenon. To address the selection phenomenon, a stochastic block model is used to model the link generation process based on the users' interests to topics. Probabilistic Latent Semantic Analysis (PLSA) is used to describe the document generative process according to the users' interests. Finally, the dependence on the historical topic status is also considered to ensure the continuity of the topic itself in topic evolution model. Expectation Maximization (EM) algorithm is utilized to estimate parameters in the proposed MTTD model. Empirical experiments on real datasets show that the MTTD model performs better than Popular Event Tracking (PET) and Dynamic Topic Model (DTM) in generalization performance, topic interpretability performance, topic content evolution and topic popularity evolution performance.

  1. Enterprise Networks for Competences Exchange: A Simulation Model

    Science.gov (United States)

    Remondino, Marco; Pironti, Marco; Pisano, Paola

    A business process is a set of logically related tasks performed to achieve a defined business and related to improving organizational processes. Process innovation can happen at various levels: incrementally, redesign of existing processes, new processes. The knowledge behind process innovation can be shared, acquired, changed and increased by the enterprises inside a network. An enterprise can decide to exploit innovative processes it owns, thus potentially gaining competitive advantage, but risking, in turn, that other players could reach the same technological levels. Or it could decide to share it, in exchange for other competencies or money. These activities could be the basis for a network formation and/or impact the topology of an existing network. In this work an agent based model is introduced (E3), aiming to explore how a process innovation can facilitate network formation, affect its topology, induce new players to enter the market and spread onto the network by being shared or developed by new players.

  2. RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer.

    Science.gov (United States)

    Rao, Shuan; Sigl, Verena; Wimmer, Reiner Alois; Novatchkova, Maria; Jais, Alexander; Wagner, Gabriel; Handschuh, Stephan; Uribesalgo, Iris; Hagelkruys, Astrid; Kozieradzki, Ivona; Tortola, Luigi; Nitsch, Roberto; Cronin, Shane J; Orthofer, Michael; Branstetter, Daniel; Canon, Jude; Rossi, John; D'Arcangelo, Manolo; Botling, Johan; Micke, Patrick; Fleur, Linnea La; Edlund, Karolina; Bergqvist, Michael; Ekman, Simon; Lendl, Thomas; Popper, Helmut; Takayanagi, Hiroshi; Kenner, Lukas; Hirsch, Fred R; Dougall, William; Penninger, Josef M

    2017-10-15

    Lung cancer is the leading cause of cancer deaths. Besides smoking, epidemiological studies have linked female sex hormones to lung cancer in women; however, the underlying mechanisms remain unclear. Here we report that the receptor activator of nuclear factor-kB (RANK), the key regulator of osteoclastogenesis, is frequently expressed in primary lung tumors, an active RANK pathway correlates with decreased survival, and pharmacologic RANK inhibition reduces tumor growth in patient-derived lung cancer xenografts. Clonal genetic inactivation of KRasG12D in mouse lung epithelial cells markedly impairs the progression of KRasG12D -driven lung cancer, resulting in a significant survival advantage. Mechanistically, RANK rewires energy homeostasis in human and murine lung cancer cells and promotes expansion of lung cancer stem-like cells, which is blocked by inhibiting mitochondrial respiration. Our data also indicate survival differences in KRasG12D -driven lung cancer between male and female mice, and we show that female sex hormones can promote lung cancer progression via the RANK pathway. These data uncover a direct role for RANK in lung cancer and may explain why female sex hormones accelerate lung cancer development. Inhibition of RANK using the approved drug denosumab may be a therapeutic drug candidate for primary lung cancer. © 2017 Rao et al.; Published by Cold Spring Harbor Laboratory Press.

  3. Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells.

    Science.gov (United States)

    Wei, Ping; Wong, Wilson W; Park, Jason S; Corcoran, Ethan E; Peisajovich, Sergio G; Onuffer, James J; Weiss, Arthur; Lim, Wendell A

    2012-08-16

    Bacterial pathogens have evolved specific effector proteins that, by interfacing with host kinase signalling pathways, provide a mechanism to evade immune responses during infection. Although these effectors contribute to pathogen virulence, we realized that they might also serve as valuable synthetic biology reagents for engineering cellular behaviour. Here we exploit two effector proteins, the Shigella flexneri OspF protein and Yersinia pestis YopH protein, to rewire kinase-mediated responses systematically both in yeast and mammalian immune cells. Bacterial effector proteins can be directed to inhibit specific mitogen-activated protein kinase pathways selectively in yeast by artificially targeting them to pathway-specific complexes. Moreover, we show that unique properties of the effectors generate new pathway behaviours: OspF, which irreversibly inactivates mitogen-activated protein kinases, was used to construct a synthetic feedback circuit that shows novel frequency-dependent input filtering. Finally, we show that effectors can be used in T cells, either as feedback modulators to tune the T-cell response amplitude precisely, or as an inducible pause switch that can temporarily disable T-cell activation. These studies demonstrate how pathogens could provide a rich toolkit of parts to engineer cells for therapeutic or biotechnological applications.

  4. Robustness and Optimization of Complex Networks : Reconstructability, Algorithms and Modeling

    NARCIS (Netherlands)

    Liu, D.

    2013-01-01

    The infrastructure networks, including the Internet, telecommunication networks, electrical power grids, transportation networks (road, railway, waterway, and airway networks), gas networks and water networks, are becoming more and more complex. The complex infrastructure networks are crucial to our

  5. ARTIFICIAL NEURAL NETWORK FOR MODELS OF HUMAN OPERATOR

    Directory of Open Access Journals (Sweden)

    Martin Ruzek

    2017-12-01

    Full Text Available This paper presents a new approach to mental functions modeling with the use of artificial neural networks. The artificial neural networks seems to be a promising method for the modeling of a human operator because the architecture of the ANN is directly inspired by the biological neuron. On the other hand, the classical paradigms of artificial neural networks are not suitable because they simplify too much the real processes in biological neural network. The search for a compromise between the complexity of biological neural network and the practical feasibility of the artificial network led to a new learning algorithm. This algorithm is based on the classical multilayered neural network; however, the learning rule is different. The neurons are updating their parameters in a way that is similar to real biological processes. The basic idea is that the neurons are competing for resources and the criterion to decide which neuron will survive is the usefulness of the neuron to the whole neural network. The neuron is not using "teacher" or any kind of superior system, the neuron receives only the information that is present in the biological system. The learning process can be seen as searching of some equilibrium point that is equal to a state with maximal importance of the neuron for the neural network. This position can change if the environment changes. The name of this type of learning, the homeostatic artificial neural network, originates from this idea, as it is similar to the process of homeostasis known in any living cell. The simulation results suggest that this type of learning can be useful also in other tasks of artificial learning and recognition.

  6. Fast reconstruction of compact context-specific metabolic network models.

    Directory of Open Access Journals (Sweden)

    Nikos Vlassis

    2014-01-01

    Full Text Available Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning, which calls for fast algorithms. We present fastcore, a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X. fastcore takes as input a core set of reactions that are known to be active in the context of interest (e.g., cell or tissue, and it searches for a flux consistent subnetwork of the global network that contains all reactions from the core set and a minimal set of additional reactions. Our key observation is that a minimal consistent reconstruction can be defined via a set of sparse modes of the global network, and fastcore iteratively computes such a set via a series of linear programs. Experiments on liver data demonstrate speedups of several orders of magnitude, and significantly more compact reconstructions, over a rival method. Given its simplicity and its excellent performance, fastcore can form the backbone of many future metabolic network reconstruction algorithms.

  7. Clustering network layers with the strata multilayer stochastic block model.

    Science.gov (United States)

    Stanley, Natalie; Shai, Saray; Taylor, Dane; Mucha, Peter J

    2016-01-01

    Multilayer networks are a useful data structure for simultaneously capturing multiple types of relationships between a set of nodes. In such networks, each relational definition gives rise to a layer. While each layer provides its own set of information, community structure across layers can be collectively utilized to discover and quantify underlying relational patterns between nodes. To concisely extract information from a multilayer network, we propose to identify and combine sets of layers with meaningful similarities in community structure. In this paper, we describe the "strata multilayer stochastic block model" (sMLSBM), a probabilistic model for multilayer community structure. The central extension of the model is that there exist groups of layers, called "strata", which are defined such that all layers in a given stratum have community structure described by a common stochastic block model (SBM). That is, layers in a stratum exhibit similar node-to-community assignments and SBM probability parameters. Fitting the sMLSBM to a multilayer network provides a joint clustering that yields node-to-community and layer-to-stratum assignments, which cooperatively aid one another during inference. We describe an algorithm for separating layers into their appropriate strata and an inference technique for estimating the SBM parameters for each stratum. We demonstrate our method using synthetic networks and a multilayer network inferred from data collected in the Human Microbiome Project.

  8. Navy Network Dependability: Models, Metrics, and Tools

    Science.gov (United States)

    2010-01-01

    surveillance; TCDL = Tactical Common Data Link; UHF = ultra high frequency; UFO = ultra-high-frequency follow-on; WGS = Wideband Gapfiller Satellite. RAND...VOICE (DMR VALUES) UFO OE-82 UHF LOS VOICE (DMR VALUES) UHF SATCOM VOICE DMR UHF LOS VOICE DMR TVs ADMS KIV-7 COMSEC ADNS SW ADNS II HW ISNS SW ISNS HW...Data Link; UHF = ultra high frequency; UFO = ultra-high-frequency follow-on; WGS = Wideband Gapfiller Satellite. RAND MG1003-1.1 4 Navy Network

  9. Computer-Supported Modelling of Multi modal Transportation Networks Rationalization

    Directory of Open Access Journals (Sweden)

    Ratko Zelenika

    2007-09-01

    Full Text Available This paper deals with issues of shaping and functioning ofcomputer programs in the modelling and solving of multimoda Itransportation network problems. A methodology of an integrateduse of a programming language for mathematical modellingis defined, as well as spreadsheets for the solving of complexmultimodal transportation network problems. The papercontains a comparison of the partial and integral methods ofsolving multimodal transportation networks. The basic hypothesisset forth in this paper is that the integral method results inbetter multimodal transportation network rationalization effects,whereas a multimodal transportation network modelbased on the integral method, once built, can be used as the basisfor all kinds of transportation problems within multimodaltransport. As opposed to linear transport problems, multimodaltransport network can assume very complex shapes. This papercontains a comparison of the partial and integral approach totransp01tation network solving. In the partial approach, astraightforward model of a transp01tation network, which canbe solved through the use of the Solver computer tool within theExcel spreadsheet inteiface, is quite sufficient. In the solving ofa multimodal transportation problem through the integralmethod, it is necessmy to apply sophisticated mathematicalmodelling programming languages which supp01t the use ofcomplex matrix functions and the processing of a vast amountof variables and limitations. The LINGO programming languageis more abstract than the Excel spreadsheet, and it requiresa certain programming knowledge. The definition andpresentation of a problem logic within Excel, in a manner whichis acceptable to computer software, is an ideal basis for modellingin the LINGO programming language, as well as a fasterand more effective implementation of the mathematical model.This paper provides proof for the fact that it is more rational tosolve the problem of multimodal transportation networks by

  10. Forecast of consumer behaviour based on neural networks models comparison

    Directory of Open Access Journals (Sweden)

    Michael Štencl

    2012-01-01

    Full Text Available The aim of this article is comparison of accuracy level of forecasted values of several artificial neural network models. The comparison is performed on datasets of Czech household consumption values. Several statistical models often resolve this task with more or fewer restrictions. In previous work where models’ input conditions were not so strict and model with missing data was used (the time series didn’t contain many values we have obtained comparably good results with artificial neural networks. Two views – practical and theoretical, motivate the purpose of this study. Forecasting models for medium term prognosis of the main trends of Czech household consumption is part of the faculty research design grant MSM 6215648904/03/02 (Sub-task 5.3 which defines the practical purpose. Testing of nonlinear autoregressive artificial neural network model compared with feed-forward neural network and radial basis function neural network defines the theoretical purpose. The performance metrics of the models were evaluated using a combination of common error metrics, namely Correlation Coefficient and Mean Square Error, together with the number of epochs and/or main prediction error.

  11. Artificial neural networks modeling gene-environment interaction

    Directory of Open Access Journals (Sweden)

    Günther Frauke

    2012-05-01

    Full Text Available Abstract Background Gene-environment interactions play an important role in the etiological pathway of complex diseases. An appropriate statistical method for handling a wide variety of complex situations involving interactions between variables is still lacking, especially when continuous variables are involved. The aim of this paper is to explore the ability of neural networks to model different structures of gene-environment interactions. A simulation study is set up to compare neural networks with standard logistic regression models. Eight different structures of gene-environment interactions are investigated. These structures are characterized by penetrance functions that are based on sigmoid functions or on combinations of linear and non-linear effects of a continuous environmental factor and a genetic factor with main effect or with a masking effect only. Results In our simulation study, neural networks are more successful in modeling gene-environment interactions than logistic regression models. This outperfomance is especially pronounced when modeling sigmoid penetrance functions, when distinguishing between linear and nonlinear components, and when modeling masking effects of the genetic factor. Conclusion Our study shows that neural networks are a promising approach for analyzing gene-environment interactions. Especially, if no prior knowledge of the correct nature of the relationship between co-variables and response variable is present, neural networks provide a valuable alternative to regression methods that are limited to the analysis of linearly separable data.

  12. Biochemical Network Stochastic Simulator (BioNetS: software for stochastic modeling of biochemical networks

    Directory of Open Access Journals (Sweden)

    Elston Timothy C

    2004-03-01

    Full Text Available Abstract Background Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. Results We have developed the software package Biochemical Network Stochastic Simulator (BioNetS for efficientlyand accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solvesthe appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. Conclusions We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

  13. Stochastic population dynamic models as probability networks

    Science.gov (United States)

    M.E. and D.C. Lee. Borsuk

    2009-01-01

    The dynamics of a population and its response to environmental change depend on the balance of birth, death and age-at-maturity, and there have been many attempts to mathematically model populations based on these characteristics. Historically, most of these models were deterministic, meaning that the results were strictly determined by the equations of the model and...

  14. New approaches to model and study social networks

    Science.gov (United States)

    Lind, P. G.; Herrmann, H. J.

    2007-07-01

    We describe and develop three recent novelties in network research which are particularly useful for studying social systems. The first one concerns the discovery of some basic dynamical laws that enable the emergence of the fundamental features observed in social networks, namely the nontrivial clustering properties, the existence of positive degree correlations and the subdivision into communities. To reproduce all these features, we describe a simple model of mobile colliding agents, whose collisions define the connections between the agents which are the nodes in the underlying network, and develop some analytical considerations. The second point addresses the particular feature of clustering and its relationship with global network measures, namely with the distribution of the size of cycles in the network. Since in social bipartite networks it is not possible to measure the clustering from standard procedures, we propose an alternative clustering coefficient that can be used to extract an improved normalized cycle distribution in any network. Finally, the third point addresses dynamical processes occurring on networks, namely when studying the propagation of information in them. In particular, we focus on the particular features of gossip propagation which impose some restrictions in the propagation rules. To this end we introduce a quantity, the spread factor, which measures the average maximal fraction of nearest neighbours which get in contact with the gossip, and find the striking result that there is an optimal non-trivial number of friends for which the spread factor is minimized, decreasing the danger of being gossiped about.

  15. Modeling the Relationship Between Social Network Activity, Inactivity, and Growth

    CERN Document Server

    Ribeiro, Bruno

    2013-01-01

    Online Social Networks (OSNs) are multi-billion dollar enterprises. Surprisingly, little is known about the mechanisms that drive them to growth, stability, or death. This study sheds light on these mechanisms. We are particularly interested in OSNs where current subscribers can invite new users to join the network (e.g., Facebook, LinkedIn). Measuring the relationship between subscriber activity and network growth of a large OSN over five years, we formulate three hypotheses that together describe the observed OSN subscriber behavior. We then provide a model (and extensions) that simultaneously satisfies all three hypotheses. Our model provides deep insights into the dynamics of subscriber activity, inactivity, and network growth rates, even predicting four types of OSNs with respect to subscriber activity evolution. Finally, we present activity data of nearly thirty OSN websites, measured over five years, and show that the observed activity is well described by one of the four activity time series predicted...

  16. Metabolic robustness and network modularity: a model study.

    Science.gov (United States)

    Holme, Petter

    2011-02-02

    Several studies have mentioned network modularity-that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other-as a factor affecting metabolic robustness. In this paper we measure the relation between network modularity and several aspects of robustness directly in a model system of metabolism. By using a model for generating chemical reaction systems where one can tune the network modularity, we find that robustness increases with modularity for changes in the concentrations of metabolites, whereas it decreases with changes in the expression of enzymes. The same modularity scaling is true for the speed of relaxation after the perturbations. Modularity is not a general principle for making metabolism either more or less robust; this question needs to be addressed specifically for different types of perturbations of the system.

  17. WDM Systems and Networks Modeling, Simulation, Design and Engineering

    CERN Document Server

    Ellinas, Georgios; Roudas, Ioannis

    2012-01-01

    WDM Systems and Networks: Modeling, Simulation, Design and Engineering provides readers with the basic skills, concepts, and design techniques used to begin design and engineering of optical communication systems and networks at various layers. The latest semi-analytical system simulation techniques are applied to optical WDM systems and networks, and a review of the various current areas of optical communications is presented. Simulation is mixed with experimental verification and engineering to present the industry as well as state-of-the-art research. This contributed volume is divided into three parts, accommodating different readers interested in various types of networks and applications. The first part of the book presents modeling approaches and simulation tools mainly for the physical layer including transmission effects, devices, subsystems, and systems), whereas the second part features more engineering/design issues for various types of optical systems including ULH, access, and in-building system...

  18. A Reference Model for Semantic Peer-to-Peer Networks

    Science.gov (United States)

    Mawlood-Yunis, Abdul-Rahman; Weiss, Michael; Santoro, Nicola

    Today’s information systems are highly networked and need to operate in a global world. With this comes the problem of semantic heterogeneity of information representations. Semantic peer-to- peer networks have been proposed as a solution to this problem. They are based around two components: a peer-to-peer infrastructure for information exchange between information system, and the use of ontologies to define application semantics. However, progress in this area is hampered by a lack of commonality between these approaches, which makes their comparison and translation into practical implementations difficult. In this paper, we describe a reference model for semantic peer-to-peer networks in an effort to remedy this problem. The reference model will (1) enable the establishment of a common terminology for describing semantic peer-to-peer networks, and (2) pave the way for an emerging standardized API that will promote information system interoperability.

  19. Joint physical and numerical modeling of water distribution networks.

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, Adam; O' Hern, Timothy John; Orear, Leslie Jr.; Kajder, Karen C.; Webb, Stephen Walter; Cappelle, Malynda A.; Khalsa, Siri Sahib; Wright, Jerome L.; Sun, Amy Cha-Tien; Chwirka, J. Benjamin; Hartenberger, Joel David; McKenna, Sean Andrew; van Bloemen Waanders, Bart Gustaaf; McGrath, Lucas K.; Ho, Clifford Kuofei

    2009-01-01

    This report summarizes the experimental and modeling effort undertaken to understand solute mixing in a water distribution network conducted during the last year of a 3-year project. The experimental effort involves measurement of extent of mixing within different configurations of pipe networks, measurement of dynamic mixing in a single mixing tank, and measurement of dynamic solute mixing in a combined network-tank configuration. High resolution analysis of turbulence mixing is carried out via high speed photography as well as 3D finite-volume based Large Eddy Simulation turbulence models. Macroscopic mixing rules based on flow momentum balance are also explored, and in some cases, implemented in EPANET. A new version EPANET code was developed to yield better mixing predictions. The impact of a storage tank on pipe mixing in a combined pipe-tank network during diurnal fill-and-drain cycles is assessed. Preliminary comparison between dynamic pilot data and EPANET-BAM is also reported.

  20. Network modeling of PM10 concentration in Malaysia

    Science.gov (United States)

    Supian, Muhammad Nazirul Aiman Abu; Bakar, Sakhinah Abu; Razak, Fatimah Abdul

    2017-08-01

    Air pollution is not a new phenomenon in Malaysia. The Department of Environment (DOE) monitors the country's ambient air quality through a network of 51 stations. The air quality is measured using the Air Pollution Index (API) which is mainly recorded based on the concentration of particulate matter, PM10 readings. The Continuous Air Quality Monitoring (CAQM) stations are located in various places across the country. In this study, a network model of air quality based on PM10 concen tration for selected CAQM stations in Malaysia has been developed. The model is built using a graph formulation, G = (V, E) where vertex, V is a set of CAQM stations and edges, E is a set of correlation values for each pair of vertices. The network measurements such as degree distributions, closeness centrality, and betweenness centrality are computed to analyse the behaviour of the network. As a result, a rank of CAQM stations has been produced based on their centrality characteristics.