Random Networks with given Rich-club Coefficient

In complex networks it is common to model a network or generate a surrogate network based on the conservation of the network's degree distribution. We provide an alternative network model based on the conservation of connection density within a set of nodes. This density is measure by the rich-club coefficient. We present a method to generate surrogates networks with a given rich-club coefficient. We show that by choosing a suitable local linking term, the generated random networks can reproduce the degree distribution and the mixing pattern of real networks. The method is easy to implement and produces good models of real networks.Comment: revised version, new figure

The Information Coded in the Yeast Response Elements Accounts for Most of the Topological Properties of Its Transcriptional Regulation Network

The regulation of gene expression in a cell relies to a major extent on transcription factors, proteins which recognize and bind the DNA at specific binding sites (response elements) within promoter regions associated with each gene. We present an information theoretic approach to modeling transcriptional regulatory networks, in terms of a simple “sequence-matching” rule and the statistics of the occurrence of binding sequences of given specificity in random promoter regions. The crucial biological input is the distribution of the amount of information coded in these cognate response elements and the length distribution of the promoter regions. We provide an analysis of the transcriptional regulatory network of yeast Saccharomyces cerevisiae, which we extract from the available databases, with respect to the degree distributions, clustering coefficient, degree correlations, rich-club coefficient and the k-core structure. We find that these topological features are in remarkable agreement with those predicted by our model, on the basis of the amount of information coded in the interaction between the transcription factors and response elements

Detecting rich-club ordering in complex networks

Uncovering the hidden regularities and organizational principles of networks arising in physical systems ranging from the molecular level to the scale of large communication infrastructures is the key issue for the understanding of their fabric and dynamical properties [1-5]. The ``rich-club'' phenomenon refers to the tendency of nodes with high centrality, the dominant elements of the system, to form tightly interconnected communities and it is one of the crucial properties accounting for the formation of dominant communities in both computer and social sciences [4-8]. Here we provide the analytical expression and the correct null models which allow for a quantitative discussion of the rich-club phenomenon. The presented analysis enables the measurement of the rich-club ordering and its relation with the function and dynamics of networks in examples drawn from the biological, social and technological domains.Comment: 1 table, 3 figure

Structural constraints in complex networks

We present a link rewiring mechanism to produce surrogates of a network where both the degree distribution and the rich--club connectivity are preserved. We consider three real networks, the AS--Internet, the protein interaction and the scientific collaboration. We show that for a given degree distribution, the rich--club connectivity is sensitive to the degree--degree correlation, and on the other hand the degree--degree correlation is constrained by the rich--club connectivity. In particular, in the case of the Internet, the assortative coefficient is always negative and a minor change in its value can reverse the network's rich--club structure completely; while fixing the degree distribution and the rich--club connectivity restricts the assortative coefficient to such a narrow range, that a reasonable model of the Internet can be produced by considering mainly the degree distribution and the rich--club connectivity. We also comment on the suitability of using the maximal random network as a null model to assess the rich--club connectivity in real networks.Comment: To appear in New Journal of Physics (www.njp.org

On the influence of topological characteristics on robustness of complex networks

In this paper, we explore the relationship between the topological characteristics of a complex network and its robustness to sustained targeted attacks. Using synthesised scale-free, small-world and random networks, we look at a number of network measures, including assortativity, modularity, average path length, clustering coefficient, rich club profiles and scale-free exponent (where applicable) of a network, and how each of these influence the robustness of a network under targeted attacks. We use an established robustness coefficient to measure topological robustness, and consider sustained targeted attacks by order of node degree. With respect to scale-free networks, we show that assortativity, modularity and average path length have a positive correlation with network robustness, whereas clustering coefficient has a negative correlation. We did not find any correlation between scale-free exponent and robustness, or rich-club profiles and robustness. The robustness of small-world networks on the other hand, show substantial positive correlations with assortativity, modularity, clustering coefficient and average path length. In comparison, the robustness of Erdos-Renyi random networks did not have any significant correlation with any of the network properties considered. A significant observation is that high clustering decreases topological robustness in scale-free networks, yet it increases topological robustness in small-world networks. Our results highlight the importance of topological characteristics in influencing network robustness, and illustrate design strategies network designers can use to increase the robustness of scale-free and small-world networks under sustained targeted attacks

Rich-club and page-club coefficients for directed graphs

Rich-club and page-club coefficients and their null models are introduced for directed graphs. Null models allow for a quantitative discussion of the rich-club and page-club phenomena. These coefficients are computed for four directed real-world networks: Arxiv High Energy Physics paper citation network, Web network (released from Google), Citation network among US Patents, and Email network from a EU research institution. The results show a high correlation between rich-club and page-club ordering. For journal paper citation network, we identify both rich-club and page-club ordering, showing that {}"elite" papers are cited by other {}"elite" papers. Google web network shows partial rich-club and page-club ordering up to some point and then a narrow declining of the corresponding normalized coefficients, indicating the lack of rich-club ordering and the lack of page-club ordering, i.e. high in-degree (PageRank) pages purposely avoid sharing links with other high in-degree (PageRank) pages. For UC patents citation network, we identify page-club and rich-club ordering providing a conclusion that {}"elite" patents are cited by other {}"elite" patents. Finally, for e-mail communication network we show lack of both rich-club and page-club ordering. We construct an example of synthetic network showing page-club ordering and the lack of rich-club ordering.Comment: 18 pages, 6 figure

Rich-club vs rich-multipolarization phenomena in weighted networks

Large scale hierarchies characterize complex networks in different domains. Elements at their top, usually the most central or influential, may show multipolarization or tend to club forming tightly interconnected communities. The rich-club phenomenon quantified this tendency based on unweighted network representations. Here, we define this metric for weighted networks and discuss the appropriate normalization which preserves nodes' strengths and discounts structural strength-strength correlations if present. We find that in some real networks the results given by the weighted rich-club coefficient can be in sharp contrast to the ones in the unweighted approach. We also discuss that the scanning of the weighted subgraphs formed by the high-strength hubs is able to unveil features contrary to the average: the formation of local alliances in rich-multipolarized environments, or a lack of cohesion even in the presence of rich-club ordering. Beyond structure, this analysis matters for understanding correctly functionalities and dynamical processes relying on hub interconnectedness.Comment: 12 pages, 2 figure

Statistical significance of rich-club phenomena in complex networks

We propose that the rich-club phenomena in complex networks should be defined in the spirit of bootstrapping, in which a null model is adopted to assess the statistical significance of the rich-club detected. Our method can be served as a definition of rich-club phenomenon and is applied to analyzing three real networks and three model networks. The results improve significantly compared with previously reported results. We report a dilemma with an exceptional example, showing that there does not exist an omnipotent definition for the rich-club phenomenon.Comment: 3 Revtex pages + 5 figure