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ABSTRACT: The distribution of information is essential for a living system's ability to coordinate and adapt. Random walkers are often used to model this distribution process and, in doing so, one effectively assumes that information maintains its relevance over time. But the value of information in social and biological systems often decays and must continuously be updated. To capture the spatial dynamics of aging information, we introduce time walkers. A time walker moves like a random walker, but interacts with traces left by other walkers, some representing older information, some newer. The traces form a navigable information landscape which we visualize as a river network. We quantify the dynamical properties of time walkers, and the quality of the information left behind, on a two-dimensional lattice. We show that searching in this landscape is superior to random searching.
Physical Review Letters 01/2010; 104(4):040603. · 7.37 Impact Factor
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ABSTRACT: All metabolic networks contain metabolites, such as ATP and NAD, known as currency metabolites, which take part in many reactions. These are often removed in the study of these networks, but no consensus exists on what actually constitutes a currency metabolite, and it is also unclear how these highly connected nodes contribute to the global structure of the network.
In this article, we analyse how the Escherichia coli metabolic network responds to pruning in the form of sequential removal of metabolites with highest degree. As expected this leads to network fragmentation, but the process by which it occurs suggests modularity and long-range correlations within the network. We find that the pruned networks contain longer paths than the random expectation, and that the paths that survive the pruning also exhibit a lower cost (number of involved metabolites) compared with random paths in the full metabolic network. Finally we confirm that paths detected by pruning overlap with known metabolic pathways. We conclude that pruning reveals functional pathways in metabolic networks, where currency metabolites may be seen as ingredients in a well-balanced soup in which main metabolic production lines are immersed.
gerlee@nbi.dk
Supplementary data are available at Bioinformatics online.
Bioinformatics 10/2009; 25(24):3282-8. · 5.47 Impact Factor
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ABSTRACT: To investigate the role of information flow in group formation, we introduce a model of communication and social navigation. We let agents gather information in an idealized network society and demonstrate that heterogeneous groups can evolve without presuming that individuals have different interests. In our scenario, individuals' access to global information is constrained by local communication with the nearest neighbors on a dynamic network. The result is reinforced interests among like-minded agents in modular networks; the flow of information works as a glue that keeps individuals together. The model explains group formation in terms of limited information access and highlights global broadcasting of information as a way to counterbalance this fragmentation. To illustrate how the information constraints imposed by the communication structure affects future development of real-world systems, we extrapolate dynamics from the topology of four social networks.
Physical Review E 03/2009; 79(2 Pt 2):026111. · 2.26 Impact Factor
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Bioinformatics. 01/2009; 25:3282-3288.
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ABSTRACT: Social groups with widely different music tastes, political convictions, and religious beliefs emerge and disappear on scales from extreme subcultures to mainstream mass-cultures. Both the underlying social structure and the formation of opinions are dynamic and changes in one affect the other. Several positive feedback mechanisms have been proposed to drive the diversity in social and economic systems, but little effort has been devoted to pinpoint the interplay between a dynamically changing social network and the spread and gathering of information on the network. Here we analyze this phenomenon in terms of a social network-model that explicitly simulates the feedback between information assembly and emergence of social structures: changing beliefs are coupled to changing relationships because agents self-organize a dynamic network to facilitate their hunter-gatherer behavior in information space. Our analysis demonstrates that tribal organizations and modular social networks can emerge as a result of contact-seeking agents that reinforce their beliefs among like-minded. We also find that prestigious persons can streamline the social network into hierarchical structures around themselves.
09/2007;
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ABSTRACT: This paper introduces a model of self-organization between communication and topology in social networks, with a feedback between different communication habits and the topology. To study this feedback, we let agents communicate to build a perception of a network and use this information to create strategic links. We observe a narrow distribution of links when the communication is low and a system with a broad distribution of links when the communication is high. We also analyze the outcome of chatting, cheating, and lying, as strategies to get better access to information in the network. Chatting, although only adopted by a few agents, gives a global gain in the system. Contrary, a global loss is inevitable in a system with too many liars.
Physical Review E 08/2006; 74(1 Pt 2):016108. · 2.26 Impact Factor
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ABSTRACT: In this paper we quantify our limited information horizon, by measuring the information necessary to locate specific nodes in a network. To investigate different ways to overcome this horizon, and the interplay between communication and topology in social networks, we let agents communicate in a model society. Thereby they build a perception of the network that they can use to create strategic links to improve their standing in the network. We observe a narrow distribution of links when the communication is low and a network with a broad distribution of links when the communication is high.
05/2006;
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ABSTRACT: We model self-assembly of information in networks to investigate necessary conditions for building a global perception of a system by local communication. Our approach is to let agents chat in a model system to self-organize distant communication-pathways. We demonstrate that simple local rules allow agents to build a perception of the system, that is robust to dynamical changes and mistakes. We find that messages are most effectively forwarded in the presence of hubs, while transmission in hub-free networks is more robust against misinformation and failures.
04/2006;
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ABSTRACT: We investigate the searchability of complex systems in terms of their interconnectedness. Associating searchability with the number and size of branch points along the paths between the nodes, we find that scale-free networks are relatively difficult to search, and thus that the abundance of scale-free networks in nature and society may reflect an attempt to protect local areas in a highly interconnected network from nonrelated communication. In fact, starting from a random node, real-world networks with higher order organization like modular or hierarchical structure are even more difficult to navigate than random scale-free networks. The searchability at the node level opens the possibility for a generalized hierarchy measure that captures both the hierarchy in the usual terms of trees as in military structures, and the intrinsic hierarchical nature of topological hierarchies for scale-free networks as in the Internet.
Physical Review E 11/2005; 72(4 Pt 2):046117. · 2.26 Impact Factor
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ABSTRACT: We investigate and quantify the interplay between topology and the ability to send specific signals in complex networks. We find that in a majority of investigated real-world networks the ability to communicate is favored by the network topology at small distances, but disfavored at larger distances. We further suggest how the ability to locate specific nodes can be improved if information associated with the overall traffic in the network is available.
Physical Review Letters 07/2005; 94(23):238701. · 7.37 Impact Factor
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ABSTRACT: We study navigation with limited information in networks and demonstrate that many real-world networks have a structure which can be described as favoring communication at short distance at the cost of constraining communication at long distance. This feature, which is robust and more evident with limited than with complete information, reflects both topological and possibly functional design characteristics. For example, the characteristics of the networks studied derived from a city and from the Internet are manifested through modular network designs. We also observe that directed navigation in typical networks requires remarkably little information on the level of individual nodes. By studying navigation or specific signaling, we take a complementary approach to the common studies of information transfer devoted to broadcasting of information in studies of virus spreading and the like.
Physical Review E 07/2005; 71(6 Pt 2):066111. · 2.26 Impact Factor
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ABSTRACT: Traffic is constrained by the information involved in locating the receiver and the physical distance between sender and receiver. We here focus on the former, and investigate traffic in the perspective of information handling. We replot the road map of cities in terms of the information needed to locate specific addresses and create information city networks with roads mapped to nodes and intersections to links between nodes. These networks have the broad degree distribution found in many other complex networks. The mapping to an information city network makes it possible to quantify the information associated with locating specific addresses.
Physical Review Letters 02/2005; 94(2):028701. · 7.37 Impact Factor
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ABSTRACT: We propose that the ubiquitous scale free nature of many real world networks may emerge from a steady state process where nodes are created and merged randomly. The merging may be viewed as an optimization of efficiency by minimizing redundancy. Copyright EDP Sciences/Società Italiana di Fisica/Springer-Verlag 2005
Physics of Condensed Matter 01/2005; 43(3):369-372. · 1.53 Impact Factor
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ABSTRACT: We investigate and quantify the interplay between topology and ability to send specific signals in complex networks. We find that in a majority of investigated real-world networks the ability to communicate is favored by the network topology on small distances, but disfavored at larger distances. We further discuss how the ability to locate specific nodes can be improved if information associated to the overall traffic in the network is available.
01/2005;
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ABSTRACT: Signaling pathways and networks determine the ability to communicate in systems ranging from living cells to human society. We investigate how the network structure constrains communication in social-, man-made and biological networks. We find that human networks of governance and collaboration are predictable on teat-a-teat level, reflecting well defined pathways, but globally inefficient. In contrast, the Internet tends to have better overall communication abilities, more alternative pathways, and is therefore more robust. Between these extremes the molecular network of Saccharomyces cerevisea is more similar to the simpler social systems, whereas the pattern of interactions in the more complex Drosophilia melanogaster, resembles the robust Internet.
08/2004;
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ABSTRACT: We discuss merging-and-creation as a self-organizing process for scale-free topologies in networks. Three power-law classes characterized by the power-law exponents , 2 and are identified and the process is generalized to networks. In the network context the merging can be viewed as a consequence of optimization related to more efficient signaling.
Physica A: Statistical Mechanics and its Applications.
