Randomizing networks using a naive "accept-all" edge-swap algorithm is generally biased. Building on recent results for nondirected graphs, we construct an ergodic detailed balance Markov chain with nontrivial acceptance probabilities for directed graphs, which converges to a strictly uniform measure and is based on edge swaps that conserve all in and out degrees. The acceptance probabilities can also be generalized to define Markov chains that target any alternative desired measure on the space of directed graphs in order to generate graphs with more sophisticated topological features. This is demonstrated by defining a process tailored to the production of directed graphs with specified degree-degree correlation functions. The theory is implemented numerically and tested on synthetic and biological network examples.

This book supports researchers who need to generate random networks, or who are interested in the theoretical study of random graphs. The coverage includes exponential random graphs (where the targeted probability of each network appearing in the ensemble is specified), growth algorithms (i.e. preferential attachment and the stub-joining configuration model), special constructions (e.g. geometric graphs and Watts Strogatz models) and graphs on structured spaces (e.g. multiplex networks). The presentation aims to be a complete starting point, including details of both theory and implementation, as well as discussions of the main strengths and weaknesses of each approach. It includes extensive references for readers wishing to go further. The material is carefully structured to be accessible to researchers from all disciplines while also containing rigorous mathematical analysis (largely based on the techniques of statistical mechanics) to support those wishing to further develop or implement the theory of random graph generation. This book is aimed at the graduate student or advanced undergraduate. It includes many worked examples, numerical simulations and exercises making it suitable for use in teaching. Explicit pseudocode algorithms are included to make the ideas easy to apply. Datasets are becoming increasingly large and network applications wider and more sophisticated. Testing hypotheses against properly specified control cases (null models) is at the heart of the ‘scientific method’. Knowledge on how to generate controlled and unbiased random graph ensembles is vital for anybody wishing to apply network science in their research.

We generate new mathematical tools with which to quantify the macroscopic topological structure of large directed networks. This is achieved via a statistical mechanical analysis of constrained maximum entropy ensembles of directed random graphs with prescribed joint distributions for in-and outdegrees and prescribed degree-degree correlation functions. We calculate exact and explicit formulae for the leading orders in the system size of the Shannon entropies and complexities of these ensembles, and for information-theoretic distances. The results are applied to data on gene regulation networks.

Networks observed in the real world often have many short loops. This violates the tree-like assumption that underpins the majority of random graph models and most of the methods used for their analysis. In this paper we sketch possible research routes to be explored in order to make progress on networks with many short loops, involving old and new random graph models and ideas for novel mathematical methods. We do not present conclusive solutions of problems, but aim to encourage and stimulate new activity and in what we believe to be an important but under-exposed area of research. We discuss in more detail the Strauss model, which can be seen as the 'harmonic oscillator' of 'loopy' random graphs, and a recent exactly solvable immunological model that involves random graphs with extensively many cliques and short loops.Résumé. Les réseaux observés dans la Nature ont souvent des cycles courts. Ceci contredit le postulat de hiérarchie sur lequel se base la majorité des modèles de réseaux aléatoires et la plupart des méthodes utilisées pour leur analyse. Dans cet article, nous esquissons des directions de recherches possibles, afin de progresser sur les réseaux contenant beaucoup de cycles courts, faisant appel à des modèles de réseaux aléatoires éprouvés ou nouveaux, et des idées pour de nouvelles méthodes mathématiques. Nous ne présentons pas de solutions définitives, mais notre but est d'encourager et de stimuler de nouveaux travaux dans ce que nous croyons être une direction de recherche importante, bien que insuffisamment explorée. Nous discutons en détail le modèle de Strauss, qui peut être interprété comme 'l'oscillateur harmonique' des réseaux aléatoires 'Ãȃ boucles', ainsi qu'un modèle immunologique soluble exactement qui implique des réseaux aléatoires avec de nombreux cliques et cycles courts.

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