been adapted to modularity clustering. Section 4 details the single-level and multi-level refinement heuristics, and Section 5.3 compares them experimentally. Because the effectiveness of (particularly multi-level) refinement may depend on the coarsening algorithm, Section 5.4 examines various combinations of coarsening and refinement heuristics. Section 6 compares public implementations and benchmark results of modularity clustering heuristics, without a restriction to coarsening and refinement algorithms. While this is one of the most extensive comparisons in the literature, it is far from exhaustive, because implementations and sufficient experimental results have not been published for some proposed heurisarXiv:0812.4073v1

Abstract. Modular structure is ubiquitous in real-world complex networks, and its detection is important because it gives insights in the structure-functionality relationship. The standard approach is based on the optimization of a quality function, modularity, which is a relative quality measure for a partition of a network into modules. Recently some authors [1, 2] have pointed out that the optimization of modularity has a fundamental drawback: the existence of a resolution limit beyond which no modular structure can be detected even though these modules might have own entity. The reason is that several topological descriptions of the network coexist at different scales, which is, in general, a fingerprint of complex systems. Here we propose a method that allows for multiple resolution screening of the modular structure. The method has been validated using synthetic networks, discovering the predefined structures at all scales. Its application to two real social networks allows to find the exact splits reported in the literature, as well as the substructure beyond the actual split. PACS number: 89.75

Abstract. Community definitions usually focus on edges, inside and between the communities. However, the high density of edges within a community determines correlations between nodes going beyond nearest-neighbours, and which are indicated by the presence of motifs. We show how motifs can be used to define general classes of nodes, including communities, by extending the mathematical expression of Newman-Girvan modularity. We construct then a general framework and apply it to some synthetic and real networks. PACS number: 89.75 ‡ Author to whom any correspondence should be addressedMotif-based communities in complex networks 2

Abstract. The ubiquity of modular structure in real-world complex networks is being the focus of attention in many trials to understand the interplay between network topology and functionality. The best approaches to the identification of modular structure are based on the optimization of a quality function known as modularity. However this optimization is a hard task provided that the computational complexity of the problem is in the NP-hard class. Here we propose an exact method for reducing the size of weighted (directed and undirected) complex networks while maintaining invariant its modularity. This size reduction allows the heuristic algorithms that optimize modularity for a better exploration of the modularity landscape. We compare the modularity obtained in several real complex-networks by using the Extremal Optimization algorithm, before and after the size reduction, showing the improvement obtained. We speculate that the proposed analytical size reduction could be extended to an exact coarse graining of the network in the scope of real-space renormalization. PACS number: 89.75

In this paper, we present a measure associated with detection and inference of statistically anomalous clusters of a graph based on the likelihood test of observed and expected edges in a subgraph. This measure is adapted from spatial scan statistics for point sets and provides quantitative assessment for clusters. We discuss some important properties of this statistic and its relation to modularity and Bregman divergences. We apply a simple clustering algorithm to find clusters with large values of this measure in a variety of real-world data sets, and we illustrate its ability to identify statistically significant clusters of selected granularity. 1 Introduction. Numerous techniques have been proposed for identifying clusters in large networks, but it has proven difficult to

In this thesis, we explore techniques in statistics and persistent homology, which detect features among data sets such as graphs, triangulations and point cloud. We accompany our theorems with algorithms and experiments, to demonstrate their effectiveness in practice. We start with the derivation of graph scan statistics, a measure useful to assess the statistical significance of a subgraph in terms of edge density. We cluster graphs into densely-connected subgraphs based on this measure. We give algorithms for finding such clusterings and experiment on real-world data. We next study statistics on persistence, for piecewise-linear functions defined on the triangulations of topological spaces. We derive persistence pairing probabilities among vertices in the triangulation. We also provide upper bounds for total persistence in expectation. We continue by examining the elevation function defined on the triangulation of a surface. Its local maxima obtained by persistence pairing are useful in describing features of the triangulations of protein surfaces. We describe an algorithm to compute these local maxima, with a run-time ten-thousand times faster in practice than previous method. We connect such improvement with the total Gaussian curvature of the surfaces.

We investigate research and development collaborations under the EU Framework Programs (FPs) for Research and Technological Development. The collaborations in the FPs give rise to bipartite networks, with edges existing between projects and the organizations taking part in them. A version of the modularity measure, adapted to bipartite networks, is presented. Communities are found so as to maximize the bipartite modularity. Projects in the resulting communities are shown to be topically differentiated. 1