Elements in the Structure and Dynamics of Complex Networks - Böcker

Networks are convenient mathematical models to represent the structure of complex systems, from cells to societies. In the last decade, multilayer network science - the branch of the field dealing with units interacting in multiple distinct ways, simultaneously - was demonstrated to be an effective modeling and analytical framework for a wide spectrum of empirical systems, from biopolymers networks (such as interactome and metabolomes) to neuronal networks (such as connectomes), from social networks to urban and transportation networks. In this Element, a decade after one of the most seminal papers on this topic, the authors review the most salient features of multilayer network science, covering both theoretical aspects and direct applications to real-world coupled/interdependent systems, from the point of view of multilayer structure, dynamics and function. The authors discuss potential frontiers for this topic and the corresponding challenges in the field for the next future.

Community detection is one of the most important methodological fields of network science, and one which has attracted a significant amount of attention over the past decades. This area deals with the automated division of a network into fundamental building blocks, with the objective of providing a summary of its large-scale structure. Despite its importance and widespread adoption, there is a noticeable gap between what is arguably the state-of-the-art and the methods which are actually used in practice in a variety of fields. The Elements attempts to address this discrepancy by dividing existing methods according to whether they have a 'descriptive' or an 'inferential' goal. While descriptive methods find patterns in networks based on context-dependent notions of community structure, inferential methods articulate a precise generative model, and attempt to fit it to data. In this way, they are able to provide insights into formation mechanisms and separate structure from noise. This title is also available as open access on Cambridge Core.

Percolation theory is a well studied process utilized by networks theory to understand the resilience of networks under random or targeted attacks. Despite their importance, spatial networks have been less studied under the percolation process compared to the extensively studied non-spatial networks. In this Element, the authors will discuss the developments and challenges in the study of percolation in spatial networks ranging from the classical nearest neighbors lattice structures, through more generalized spatial structures such as networks with a distribution of edge lengths or community structure, and up to spatial networks of networks.

Many multiagent dynamics can be modeled as a stochastic process in which the agents in the system change their state over time in interaction with each other. The Gillespie algorithms are popular algorithms that exactly simulate such stochastic multiagent dynamics when each state change is driven by a discrete event, the dynamics is defined in continuous time, and the stochastic law of event occurrence is governed by independent Poisson processes. The first main part of this volume provides a tutorial on the Gillespie algorithms focusing on simulation of social multiagent dynamics occurring in populations and networks. The authors clarify why one should use the continuous-time models and the Gillespie algorithms in many cases, instead of easier-to-understand discrete-time models. The remainder of the Element reviews recent extensions of the Gillespie algorithms aiming to add more reality to the model (i.e., non-Poissonian cases) or to speed up the simulations. This title is also available as open access on Cambridge Core.

Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions - from molecules in gene regulatory networks to species in ecological networks - and the often-incomplete state of system knowledge, such as the unknown values of kinetic parameters for biochemical reactions. Boolean networks have emerged as a powerful tool for modeling these systems. This Element provides a methodological overview of Boolean network models of biological systems. After a brief introduction, the authors describe the process of building, analyzing, and validating a Boolean model. They then present the use of the model to make predictions about the system's response to perturbations and about how to control its behavior. The Element emphasizes the interplay between structural and dynamical properties of Boolean networks and illustrates them in three case studies from disparate levels of biological organization.

Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions - from molecules in gene regulatory networks to species in ecological networks - and the often-incomplete state of system knowledge, such as the unknown values of kinetic parameters for biochemical reactions. Boolean networks have emerged as a powerful tool for modeling these systems. This Element provides a methodological overview of Boolean network models of biological systems. After a brief introduction, the authors describe the process of building, analyzing, and validating a Boolean model. They then present the use of the model to make predictions about the system's response to perturbations and about how to control its behavior. The Element emphasizes the interplay between structural and dynamical properties of Boolean networks and illustrates them in three case studies from disparate levels of biological organization.

Higher-order networks describe the many-body interactions of a large variety of complex systems, ranging from the the brain to collaboration networks. Simplicial complexes are generalized network structures which allow us to capture the combinatorial properties, the topology and the geometry of higher-order networks. Having been used extensively in quantum gravity to describe discrete or discretized space-time, simplicial complexes have only recently started becoming the representation of choice for capturing the underlying network topology and geometry of complex systems. This Element provides an in-depth introduction to the very hot topic of network theory, covering a wide range of subjects ranging from emergent hyperbolic geometry and topological data analysis to higher-order dynamics. This Elements aims to demonstrate that simplicial complexes provide a very general mathematical framework to reveal how higher-order dynamics depends on simplicial network topology and geometry.

Complex networks datasets often come with the problem of missing information: interactions data that have not been measured or discovered, may be affected by errors, or are simply hidden because of privacy issues. This Element provides an overview of the ideas, methods and techniques to deal with this problem and that together define the field of network reconstruction. Given the extent of the subject, the authors focus on the inference methods rooted in statistical physics and information theory. The discussion is organized according to the different scales of the reconstruction task, that is, whether the goal is to reconstruct the macroscopic structure of the network, to infer its mesoscale properties, or to predict the individual microscopic connections.

Complex networks are typically not homogeneous, as they tend to display an array of structures at different scales. A feature that has attracted a lot of research is their modular organisation, i.e., networks may often be considered as being composed of certain building blocks, or modules. In this Element, the authors discuss a number of ways in which this idea of modularity can be conceptualised, focusing specifically on the interplay between modular network structure and dynamics taking place on a network. They discuss, in particular, how modular structure and symmetries may impact on network dynamics and, vice versa, how observations of such dynamics may be used to infer the modular structure. They also revisit several other notions of modularity that have been proposed for complex networks and show how these can be related to and interpreted from the point of view of dynamical processes on networks.

In many systems consisting of interacting subsystems, the complex interactions between elements can be represented using multilayer networks. However percolation, key to understanding connectivity and robustness, is not trivially generalised to multiple layers. This Element describes a generalisation of percolation to multilayer networks: weak multiplex percolation. A node belongs to a connected component if at least one of its neighbours in each layer is in this component. The authors fully describe the critical phenomena of this process. In two layers with finite second moments of the degree distributions the authors observe an unusual continuous transition with quadratic growth above the threshold. When the second moments diverge, the singularity is determined by the asymptotics of the degree distributions, creating a rich set of critical behaviours. In three or more layers the authors find a discontinuous hybrid transition which persists even in highly heterogeneous degree distributions, becoming continuous only when the powerlaw exponent reaches $1+1/(M-1)$ for $M$ layers.