Alignment and integration of complex networks by hypergraph-based spectral clustering

Complex networks possess a rich, multi-scale structure reflecting the dynamical and functional organization of the systems they model. Often there is a need to analyze multiple networks simultaneously, to model a system by more than one type of interaction or to go beyond simple pairwise interactions, but currently there is a lack of theoretical and computational methods to address these problems. Here we introduce a framework for clustering and community detection in such systems using hypergraph representations. Our main result is a generalization of the Perron-Frobenius theorem from which we derive spectral clustering algorithms for directed and undirected hypergraphs. We illustrate our approach with applications for local and global alignment of protein-protein interaction networks between multiple species, for tripartite community detection in folksonomies, and for detecting clusters of overlapping regulatory pathways in directed networks.Comment: 16 pages, 5 figures; revised version with minor corrections and figures printed in two-column format for better readability; algorithm implementation and supplementary information available at Google code at http://schype.googlecode.co

Hypergraph models of metabolism

In this paper, we employ a directed hypergraph model to investigate the extent to which environmental variability influences the set of available biochemical reactions within a living cell. Such an approach avoids the limitations of the usual complex network formalism by allowing for the multilateral relationships (i.e. connections involving more than two nodes) that naturally occur within many biological processes. More specifically, we extend the concept of network reciprocity to complex hyper-networks, thus enabling us to characterise a network in terms of the existence of mutual hyper-connections, which may be considered a proxy for metabolic network complexity. To demonstrate these ideas, we study 115 metabolic hyper-networks of bacteria, each of which can be classified into one of 6 increasingly varied habitats. In particular, we found that reciprocity increases significantly with increased environmental variability, supporting the view that organism adaptability leads to increased complexities in the resultant biochemical networks

Consistency of Spectral Hypergraph Partitioning under Planted Partition Model

Hypergraph partitioning lies at the heart of a number of problems in machine learning and network sciences. Many algorithms for hypergraph partitioning have been proposed that extend standard approaches for graph partitioning to the case of hypergraphs. However, theoretical aspects of such methods have seldom received attention in the literature as compared to the extensive studies on the guarantees of graph partitioning. For instance, consistency results of spectral graph partitioning under the stochastic block model are well known. In this paper, we present a planted partition model for sparse random non-uniform hypergraphs that generalizes the stochastic block model. We derive an error bound for a spectral hypergraph partitioning algorithm under this model using matrix concentration inequalities. To the best of our knowledge, this is the first consistency result related to partitioning non-uniform hypergraphs.Comment: 35 pages, 2 figures, 1 tabl

Multilayer Networks

In most natural and engineered systems, a set of entities interact with each other in complicated patterns that can encompass multiple types of relationships, change in time, and include other types of complications. Such systems include multiple subsystems and layers of connectivity, and it is important to take such "multilayer" features into account to try to improve our understanding of complex systems. Consequently, it is necessary to generalize "traditional" network theory by developing (and validating) a framework and associated tools to study multilayer systems in a comprehensive fashion. The origins of such efforts date back several decades and arose in multiple disciplines, and now the study of multilayer networks has become one of the most important directions in network science. In this paper, we discuss the history of multilayer networks (and related concepts) and review the exploding body of work on such networks. To unify the disparate terminology in the large body of recent work, we discuss a general framework for multilayer networks, construct a dictionary of terminology to relate the numerous existing concepts to each other, and provide a thorough discussion that compares, contrasts, and translates between related notions such as multilayer networks, multiplex networks, interdependent networks, networks of networks, and many others. We also survey and discuss existing data sets that can be represented as multilayer networks. We review attempts to generalize single-layer-network diagnostics to multilayer networks. We also discuss the rapidly expanding research on multilayer-network models and notions like community structure, connected components, tensor decompositions, and various types of dynamical processes on multilayer networks. We conclude with a summary and an outlook.Comment: Working paper; 59 pages, 8 figure