Laplacian Dynamics and Multiscale Modular Structure in Networks

Most methods proposed to uncover communities in complex networks rely on their structural properties. Here we introduce the stability of a network partition, a measure of its quality defined in terms of the statistical properties of a dynamical process taking place on the graph. The time-scale of the process acts as an intrinsic parameter that uncovers community structures at different resolutions. The stability extends and unifies standard notions for community detection: modularity and spectral partitioning can be seen as limiting cases of our dynamic measure. Similarly, recently proposed multi-resolution methods correspond to linearisations of the stability at short times. The connection between community detection and Laplacian dynamics enables us to establish dynamically motivated stability measures linked to distinct null models. We apply our method to find multi-scale partitions for different networks and show that the stability can be computed efficiently for large networks with extended versions of current algorithms.Comment: New discussions on the selection of the most significant scales and the generalisation of stability to directed network

Laplacian Dynamics and Multiscale Modular Structure in Networks

Most methods proposed to uncover communities in complex networks rely on their structural properties. Here we introduce the stability of a network partition, a measure of its quality defined in terms of the statistical properties of a dynamical process taking place on the graph. The time-scale of the process acts as an intrinsic parameter that uncovers community structures at different resolutions. The stability extends and unifies standard notions for community detection: modularity and spectral partitioning can be seen as limiting cases of our dynamic measure. Similarly, recently proposed multi-resolution methods correspond to linearisations of the stability at short times. The connection between community detection and Laplacian dynamics enables us to establish dynamically motivated stability measures linked to distinct null models. We apply our method to find multi-scale partitions for different networks and show that the stability can be computed efficiently for large networks with extended versions of current algorithms.Comment: New discussions on the selection of the most significant scales and the generalisation of stability to directed network

Flow graphs: interweaving dynamics and structure

The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential because different dynamical processes may be affected very differently by network topology. A full characterization of such systems thus requires a formalization that encompasses both aspects simultaneously, rather than relying only on the topological adjacency matrix. To achieve this, we introduce the concept of flow graphs, namely weighted networks where dynamical flows are embedded into the link weights. Flow graphs provide an integrated representation of the structure and dynamics of the system, which can then be analyzed with standard tools from network theory. Conversely, a structural network feature of our choice can also be used as the basis for the construction of a flow graph that will then encompass a dynamics biased by such a feature. We illustrate the ideas by focusing on the mathematical properties of generic linear processes on complex networks that can be represented as biased random walks and also explore their dual consensus dynamics.Comment: 4 pages, 1 figur

Encoding dynamics for multiscale community detection: Markov time sweeping for the Map equation

The detection of community structure in networks is intimately related to finding a concise description of the network in terms of its modules. This notion has been recently exploited by the Map equation formalism (M. Rosvall and C.T. Bergstrom, PNAS, 105(4), pp.1118--1123, 2008) through an information-theoretic description of the process of coding inter- and intra-community transitions of a random walker in the network at stationarity. However, a thorough study of the relationship between the full Markov dynamics and the coding mechanism is still lacking. We show here that the original Map coding scheme, which is both block-averaged and one-step, neglects the internal structure of the communities and introduces an upper scale, the `field-of-view' limit, in the communities it can detect. As a consequence, Map is well tuned to detect clique-like communities but can lead to undesirable overpartitioning when communities are far from clique-like. We show that a signature of this behavior is a large compression gap: the Map description length is far from its ideal limit. To address this issue, we propose a simple dynamic approach that introduces time explicitly into the Map coding through the analysis of the weighted adjacency matrix of the time-dependent multistep transition matrix of the Markov process. The resulting Markov time sweeping induces a dynamical zooming across scales that can reveal (potentially multiscale) community structure above the field-of-view limit, with the relevant partitions indicated by a small compression gap.Comment: 10 pages, 6 figure

Modularity in signaling systems

Modularity is a property by which the behavior of a system does not change upon interconnection. It is crucial for understanding the behavior of a complex system from the behavior of the composing subsystems. Whether modularity holds in biology is an intriguing and largely debated question. In this paper, we discuss this question taking a control system theory view and focusing on signaling systems. In particular, we argue that, despite signaling systems being constituted of structural modules, such as covalent modification cycles, modularity does not hold in general. As in any engineering system, impedance-like effects, called retroactivity, appear at interconnections and alter the behavior of connected modules. We further argue that while signaling systems have evolved sophisticated ways to counter-act retroactivity and enforce modularity, retroactivity may also be exploited to finely control the information processing of signaling pathways. Testable predictions and experimental evidence are discussed with their implications

Protein multi-scale organization through graph partitioning and robustness analysis: Application to the myosin-myosin light chain interaction

Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models. We apply the method to four distinct conformations of myosin tail interacting protein, a protein from the molecular motor of the malaria parasite, and study properties that have been experimentally addressed such as the closing mechanism, the presence of conserved clusters, and the identification through computational mutational analysis of key residues for binding.Comment: 13 pages, 7 Postscript figure

Markov dynamics as a zooming lens for multiscale community detection: non clique-like communities and the field-of-view limit

In recent years, there has been a surge of interest in community detection algorithms for complex networks. A variety of computational heuristics, some with a long history, have been proposed for the identification of communities or, alternatively, of good graph partitions. In most cases, the algorithms maximize a particular objective function, thereby finding the `right' split into communities. Although a thorough comparison of algorithms is still lacking, there has been an effort to design benchmarks, i.e., random graph models with known community structure against which algorithms can be evaluated. However, popular community detection methods and benchmarks normally assume an implicit notion of community based on clique-like subgraphs, a form of community structure that is not always characteristic of real networks. Specifically, networks that emerge from geometric constraints can have natural non clique-like substructures with large effective diameters, which can be interpreted as long-range communities. In this work, we show that long-range communities escape detection by popular methods, which are blinded by a restricted `field-of-view' limit, an intrinsic upper scale on the communities they can detect. The field-of-view limit means that long-range communities tend to be overpartitioned. We show how by adopting a dynamical perspective towards community detection (Delvenne et al. (2010) PNAS:107: 12755-12760; Lambiotte et al. (2008) arXiv:0812.1770), in which the evolution of a Markov process on the graph is used as a zooming lens over the structure of the network at all scales, one can detect both clique- or non clique-like communities without imposing an upper scale to the detection. Consequently, the performance of algorithms on inherently low-diameter, clique-like benchmarks may not always be indicative of equally good results in real networks with local, sparser connectivity.Comment: 20 pages, 6 figure

Fast unfolding of communities in large networks

We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection method in terms of computation time. Moreover, the quality of the communities detected is very good, as measured by the so-called modularity. This is shown first by identifying language communities in a Belgian mobile phone network of 2.6 million customers and by analyzing a web graph of 118 million nodes and more than one billion links. The accuracy of our algorithm is also verified on ad-hoc modular networks. .Comment: 6 pages, 5 figures, 1 table; new version with new figures in order to clarify our method, where we look more carefully at the role played by the ordering of the nodes and where we compare our method with that of Wakita and Tsurum

Structured networks and coarse-grained descriptions: a dynamical perspective

This chapter discusses the interplay between structure and dynamics in complex networks. Given a particular network with an endowed dynamics, our goal is to find partitions aligned with the dynamical process acting on top of the network. We thus aim to gain a reduced description of the system that takes into account both its structure and dynamics. In the first part, we introduce the general mathematical setup for the types of dynamics we consider throughout the chapter. We provide two guiding examples, namely consensus dynamics and diffusion processes (random walks), motivating their connection to social network analysis, and provide a brief discussion on the general dynamical framework and its possible extensions. In the second part, we focus on the influence of graph structure on the dynamics taking place on the network, focussing on three concepts that allow us to gain insight into this notion. First, we describe how time scale separation can appear in the dynamics on a network as a consequence of graph structure. Second, we discuss how the presence of particular symmetries in the network give rise to invariant dynamical subspaces that can be precisely described by graph partitions. Third, we show how this dynamical viewpoint can be extended to study dynamics on networks with signed edges, which allow us to discuss connections to concepts in social network analysis, such as structural balance. In the third part, we discuss how to use dynamical processes unfolding on the network to detect meaningful network substructures. We then show how such dynamical measures can be related to seemingly different algorithm for community detection and coarse-graining proposed in the literature. We conclude with a brief summary and highlight interesting open future directions

Structured networks and coarse-grained descriptions: a dynamical perspective

This chapter discusses the interplay between structure and dynamics in complex networks. Given a particular network with an endowed dynamics, our goal is to find partitions aligned with the dynamical process acting on top of the network. We thus aim to gain a reduced description of the system that takes into account both its structure and dynamics. In the first part, we introduce the general mathematical setup for the types of dynamics we consider throughout the chapter. We provide two guiding examples, namely consensus dynamics and diffusion processes (random walks), motivating their connection to social network analysis, and provide a brief discussion on the general dynamical framework and its possible extensions. In the second part, we focus on the influence of graph structure on the dynamics taking place on the network, focussing on three concepts that allow us to gain insight into this notion. First, we describe how time scale separation can appear in the dynamics on a network as a consequence of graph structure. Second, we discuss how the presence of particular symmetries in the network give rise to invariant dynamical subspaces that can be precisely described by graph partitions. Third, we show how this dynamical viewpoint can be extended to study dynamics on networks with signed edges, which allow us to discuss connections to concepts in social network analysis, such as structural balance. In the third part, we discuss how to use dynamical processes unfolding on the network to detect meaningful network substructures. We then show how such dynamical measures can be related to seemingly different algorithm for community detection and coarse-graining proposed in the literature. We conclude with a brief summary and highlight interesting open future directions