Spectral Graph Forge: Graph Generation Targeting Modularity

Community structure is an important property that captures inhomogeneities common in large networks, and modularity is one of the most widely used metrics for such community structure. In this paper, we introduce a principled methodology, the Spectral Graph Forge, for generating random graphs that preserves community structure from a real network of interest, in terms of modularity. Our approach leverages the fact that the spectral structure of matrix representations of a graph encodes global information about community structure. The Spectral Graph Forge uses a low-rank approximation of the modularity matrix to generate synthetic graphs that match a target modularity within user-selectable degree of accuracy, while allowing other aspects of structure to vary. We show that the Spectral Graph Forge outperforms state-of-the-art techniques in terms of accuracy in targeting the modularity and randomness of the realizations, while also preserving other local structural properties and node attributes. We discuss extensions of the Spectral Graph Forge to target other properties beyond modularity, and its applications to anonymization

Relations Between Adjacency and Modularity Graph Partitioning

In this paper the exact linear relation between the leading eigenvector of the unnormalized modularity matrix and the eigenvectors of the adjacency matrix is developed. Based on this analysis a method to approximate the leading eigenvector of the modularity matrix is given, and the relative error of the approximation is derived. A complete proof of the equivalence between normalized modularity clustering and normalized adjacency clustering is also given. Some applications and experiments are given to illustrate and corroborate the points that are made in the theoretical development.Comment: 11 page

Towards a robust algorithm to determine topological domains from colocalization data

One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing experimental data, in particular, from genome colocalization (Hi-C) matrices. Here we present an algorithm allowing to reveal the underlying hierarchical domain structure of a polymer conformation from analyzing the modularity of colocalization matrices. We also test this algorithm on several model polymer structures: equilibrium globules, random fractal globules and regular fractal (Peano) conformations. We define what we call a spectrum of cluster borders, and show that these spectra behave strikingly differently for equilibrium and fractal conformations, allowing us to suggest an additional criterion to identify fractal polymer conformations

Community Detection in Quantum Complex Networks

Determining community structure is a central topic in the study of complex networks, be it technological, social, biological or chemical, in static or interacting systems. In this paper, we extend the concept of community detection from classical to quantum systems---a crucial missing component of a theory of complex networks based on quantum mechanics. We demonstrate that certain quantum mechanical effects cannot be captured using current classical complex network tools and provide new methods that overcome these problems. Our approaches are based on defining closeness measures between nodes, and then maximizing modularity with hierarchical clustering. Our closeness functions are based on quantum transport probability and state fidelity, two important quantities in quantum information theory. To illustrate the effectiveness of our approach in detecting community structure in quantum systems, we provide several examples, including a naturally occurring light-harvesting complex, LHCII. The prediction of our simplest algorithm, semiclassical in nature, mostly agrees with a proposed partitioning for the LHCII found in quantum chemistry literature, whereas our fully quantum treatment of the problem uncovers a new, consistent, and appropriately quantum community structure.Comment: 16 pages, 4 figures, 1 tabl

Spectral redemption: clustering sparse networks

Spectral algorithms are classic approaches to clustering and community detection in networks. However, for sparse networks the standard versions of these algorithms are suboptimal, in some cases completely failing to detect communities even when other algorithms such as belief propagation can do so. Here we introduce a new class of spectral algorithms based on a non-backtracking walk on the directed edges of the graph. The spectrum of this operator is much better-behaved than that of the adjacency matrix or other commonly used matrices, maintaining a strong separation between the bulk eigenvalues and the eigenvalues relevant to community structure even in the sparse case. We show that our algorithm is optimal for graphs generated by the stochastic block model, detecting communities all the way down to the theoretical limit. We also show the spectrum of the non-backtracking operator for some real-world networks, illustrating its advantages over traditional spectral clustering.Comment: 11 pages, 6 figures. Clarified to what extent our claims are rigorous, and to what extent they are conjectures; also added an interpretation of the eigenvectors of the 2n-dimensional version of the non-backtracking matri