No Arabic abstract
Many dynamical systems can be successfully analyzed by representing them as networks. Empirically measured networks and dynamic processes that take place in these situations show heterogeneous, non-Markovian, and intrinsically correlated topologies and dynamics. This makes their analysis particularly challenging. Randomized reference models (RRMs) have emerged as a general and versatile toolbox for studying such systems. Defined as random networks with given features constrained to match those of an input (empirical) network, they may for example be used to identify important features of empirical networks and their effects on dynamical processes unfolding in the network. RRMs are typically implemented as procedures that reshuffle an empirical network, making them very generally applicable. However, the effects of most shuffling procedures on network features remain poorly understood, rendering their use non-trivial and susceptible to misinterpretation. Here we propose a unified framework for classifying and understanding microcanonical RRMs (MRRMs) that sample networks with uniform probability. Focusing on temporal networks, we survey applications of MRRMs found in literature, and we use this framework to build a taxonomy of MRRMs that proposes a canonical naming convention, classifies them, and deduces their effects on a range of important network features. We furthermore show that certain classes of compatible MRRMs may be applied in sequential composition to generate new MRRMs from the existing ones surveyed in this article. We finally provide a tutorial showing how to apply a series of MRRMs to analyze how different network features affect a dynamic process in an empirical temporal network.
Many real-world complex systems are well represented as multilayer networks; predicting interactions in those systems is one of the most pressing problems in predictive network science. To address this challenge, we introduce two stochastic block models for multilayer and temporal networks; one of them uses nodes as its fundamental unit, whereas the other focuses on links. We also develop scalable algorithms for inferring the parameters of these models. Because our models describe all layers simultaneously, our approach takes full advantage of the information contained in the whole network when making predictions about any particular layer. We illustrate the potential of our approach by analyzing two empirical datasets---a temporal network of email communications, and a network of drug interactions for treating different cancer types. We find that modeling all layers simultaneously does result, in general, in more accurate link prediction. However, the most predictive model depends on the dataset under consideration; whereas the node-based model is more appropriate for predicting drug interactions, the link-based model is more appropriate for predicting email communication.
Dynamic networks exhibit temporal patterns that vary across different time scales, all of which can potentially affect processes that take place on the network. However, most data-driven approaches used to model time-varying networks attempt to capture only a single characteristic time scale in isolation --- typically associated with the short-time memory of a Markov chain or with long-time abrupt changes caused by external or systemic events. Here we propose a unified approach to model both aspects simultaneously, detecting short and long-time behaviors of temporal networks. We do so by developing an arbitrary-order mixed Markov model with change points, and using a nonparametric Bayesian formulation that allows the Markov order and the position of change points to be determined from data without overfitting. In addition, we evaluate the quality of the multiscale model in its capacity to reproduce the spreading of epidemics on the temporal network, and we show that describing multiple time scales simultaneously has a synergistic effect, where statistically significant features are uncovered that otherwise would remain hidden by treating each time scale independently.
We consider state-aggregation schemes for Markov chains from an information-theoretic perspective. Specifically, we consider aggregating the states of a Markov chain such that the mutual information of the aggregated states separated by T time steps is maximized. We show that for T = 1 this approach recovers the maximum-likelihood estimator of the degree-corrected stochastic block model as a particular case, thereby enabling us to explain certain features of the likelihood landscape of this popular generative network model from a dynamical lens. We further highlight how we can uncover coherent, long-range dynamical modules for which considering a time-scale T >> 1 is essential, using synthetic flows and real-world ocean currents, where we are able to recover the fundamental features of the surface currents of the oceans.
Time-stamped data are increasingly available for many social, economic, and information systems that can be represented as networks growing with time. The World Wide Web, social contact networks, and citation networks of scientific papers and online news articles, for example, are of this kind. Static methods can be inadequate for the analysis of growing networks as they miss essential information on the systems dynamics. At the same time, time-aware methods require the choice of an observation timescale, yet we lack principled ways to determine it. We focus on the popular community detection problem which aims to partition a networks nodes into meaningful groups. We use a multi-layer quality function to show, on both synthetic and real datasets, that the observation timescale that leads to optimal communities is tightly related to the systems intrinsic aging timescale that can be inferred from the time-stamped network data. The use of temporal information leads to drastically different conclusions on the community structure of real information networks, which challenges the current understanding of the large-scale organization of growing networks. Our findings indicate that before attempting to assess structural patterns of evolving networks, it is vital to uncover the timescales of the dynamical processes that generated them.
We introduce a new class of deterministic networks by associating networks with Diophantine equations, thus relating network topology to algebraic properties. The network is formed by representing integers as vertices and by drawing cliques between M vertices every time that M distinct integers satisfy the equation. We analyse the network generated by the Pythagorean equation $x^{2}+y^{2}= z^{2}$ showing that its degree distribution is well approximated by a power law with exponential cut-off. We also show that the properties of this network differ considerably from the features of scale-free networks generated through preferential attachment. Remarkably we also recover a power law for the clustering coefficient.