A novel method of generating tunable underlying network topologies for social simulation

We propose a method of generating different scale-free networks, which has several input parameters in order to adjust the structure, so that they can serve as a basis for computer simulation of real-world phenomena. The topological structure of these networks was studied to determine what kind of networks can be produced and how can we give the appropriate values of parameters to get a desired structure.Comment: Originally presented at the 2013 IEEE 4th International Conference on Cognitive Infocommunications (CogInfoCom

The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells

BACKGROUND: Cell organization is governed and maintained via specific interactions among its constituent macromolecules. Comparison of the experimentally determined protein interaction networks in different model organisms has revealed little conservation of the specific edges linking ortholog proteins. Nevertheless, some topological characteristics of the graphs representing the networks - namely non-random degree distribution and high clustering coefficient - are shared by networks of distantly related organisms. Here we investigate the role of the topological features of the protein interaction network in promoting cell organization. METHODS: We have used a stochastic model, dubbed ProtNet representing a computer stylized cell to answer questions about the dynamic consequences of the topological properties of the static graphs representing protein interaction networks. RESULTS: By using a novel metrics of cell organization, we show that natural networks, differently from random networks, can promote cell self-organization. Furthermore the ensemble of protein complexes that forms in pseudocells, which self-organize according to the interaction rules of natural networks, are more robust to perturbations. CONCLUSIONS: The analysis of the dynamic properties of networks with a variety of topological characteristics lead us to conclude that self organization is a consequence of the high clustering coefficient, whereas the scale free degree distribution has little influence on this property

Small world networks and clustered small world networks with random connectivity

International audienceThe discovery of small world properties in real-world networks has revolutionized the way we analyze and study real-world systems. Mathematicians and physicists in particular have closely studied and developed several models to artificially generate networks with small world properties. The classical algorithms to produce these graphs artificially make use of the fact that with the introduction of some randomness in ordered graphs, small world graphs can be produced. In this paper, we present a novel algorithm to generate graphs with small world properties based on the idea that with the introduction of some order in a random graph, small world graphs can be generated. Our model starts with a randomly generated graph. We then replace each node of the random graph with cliques of different sizes. This ensures that the connectivity between the cliques is random but the clustering coefficient increases to a desired level. We further extend this model to incorporate the property of community structures (clusters) found readily in real-world networks such as social, biological and technological networks. These community structures are densely connected regions of nodes in a network that are loosely connected to each other. The model generates these clustered small world graphs by replacing nodes in the random graph with densely connected set of nodes. Experimentation shows that these two models generate small world and clustered small world graphs, respectively, as we were able to produce the desired properties of a small world network with high clustering coefficient and low average path lengths in both cases. Furthermore, we also calculated relative density and modularity to show that the clustered networks indeed had community structures