Tailored graph ensembles as proxies or null models for real networks II: results on directed graphs

We use mathematical methods from the theory of tailored random graphs to study systematically the effects of sampling on topological features of large biological signalling networks. Our aim in doing so is to increase our quantitative understanding of the relation between true biological networks and the imperfect and often biased samples of these networks that are reported in public data repositories and used by biomedical scientists. We derive exact explicit formulae for de...

First principle network models are crucial to make sense of the intricate topology of real complex networks. While modeling efforts have been quite successful in undirected networks, generative models for networks with asymmetric interactions are still not well developed and are unable to reproduce several basic topological properties. This is particularly disconcerting considering that real directed networks are the norm rather than the exception in many natural and human-ma...

We present a statistical mechanics approach for the description of complex networks. We first define an energy and an entropy associated to a degree distribution which have a geometrical interpretation. Next we evaluate the distribution which extremize the free energy of the network. We find two important limiting cases: a scale-free degree distribution and a finite-scale degree distribution. The size of the space of allowed simple networks given these distribution is evaluat...

Stochastic blockmodels are generative network models where the vertices are separated into discrete groups, and the probability of an edge existing between two vertices is determined solely by their group membership. In this paper, we derive expressions for the entropy of stochastic blockmodel ensembles. We consider several ensemble variants, including the traditional model as well as the newly introduced degree-corrected version [Karrer et al. Phys. Rev. E 83, 016107 (2011)]...

We survey and introduce concepts and tools located at the intersection of information theory and network biology. We show that Shannon's information entropy, compressibility and algorithmic complexity quantify different local and global aspects of synthetic and biological data. We show examples such as the emergence of giant components in Erdos-Renyi random graphs, and the recovery of topological properties from numerical kinetic properties simulating gene expression data. We...

In order to detect patterns in real networks, randomized graph ensembles that preserve only part of the topology of an observed network are systematically used as fundamental null models. However, their generation is still problematic. The existing approaches are either computationally demanding and beyond analytic control, or analytically accessible but highly approximate. Here we propose a solution to this long-standing problem by introducing an exact and fast method that a...

Complex network null models based on entropy maximization are becoming a powerful tool to characterize and analyze data from real systems. However, it is not easy to extract good and unbiased information from these models: A proper understanding of the nature of the underlying events represented in them is crucial. In this paper we emphasize this fact stressing how an accurate counting of configurations compatible with given constraints is fundamental to build good null model...

We present a method to construct a network null-model based on the maximum entropy principle and where the restrictions that the rich-club and the degree sequence impose are conserved. We show that the probability that two nodes share a link can be described with a simple probability function. The null-model closely approximates the assortative properties of the network.

Existing information-theoretic frameworks based on maximum entropy network ensembles are not able to explain the emergence of heterogeneity in complex networks. Here, we fill this gap of knowledge by developing a classical framework for networks based on finding an optimal trade-off between the information content of a compressed representation of the ensemble and the information content of the actual network ensemble. In this way not only we introduce a novel classical netwo...

In the paper, we study fluctuations over several ensembles of maximum-entropy random networks. We derive several fluctuation-dissipation relations characterizing susceptibilities of different networks to changes in external fields. In the case of networks with a given degree sequence, we argue that the scale-free topologies of real-world networks may arise as a result of self-organization of real systems into sparse structures with low susceptibility to random external pertur...