Modularity and community structure in networks

Many networks of interest in the sciences, including a variety of social and biological networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure has attracted considerable recent attention. One of the most sensitive detection methods is optimization of the quality function known as "modularity" over the possible divisions of a network, but direct application of this method using, for instance, simulated annealing is computationally costly. Here we show that the modularity can be reformulated in terms of the eigenvectors of a new characteristic matrix for the network, which we call the modularity matrix, and that this reformulation leads to a spectral algorithm for community detection that returns results of better quality than competing methods in noticeably shorter running times. We demonstrate the algorithm with applications to several network data sets.Comment: 7 pages, 3 figure

Fast Algorithm for Finding Maximum Distance with Space Subdivision in E2

Finding an exact maximum distance of two points in the given set is a fundamental computational problem which is solved in many applications. This paper presents a fast, simple to implement and robust algorithm for finding this maximum distance of two points in E2. This algorithm is based on a polar subdivision followed by division of remaining points into uniform grid. The main idea of the algorithm is to eliminate as many input points as possible before finding the maximum distance. The proposed algorithm gives the significant speed up compared to the standard algorithm

Faster ASV decomposition for orthogonal polyhedra using the Extreme Vertices Model (EVM)

The alternating sum of volumes (ASV) decomposition is a widely used technique for converting a B-Rep into a CSG model. The obtained CSG tree has convex primitives at its leaf nodes, while the contents of its internal nodes alternate between the set union and difference operators. This work first shows that the obtained CSG tree T can also be expressed as the regularized Exclusive-OR operation among all the convex primitives at the leaf nodes of T, regardless the structure and internal nodes of T. This is an important result in the case in which EVM represented orthogonal polyhedra are used because in this model the Exclusive-OR operation runs much faster than set union and difference operations. Therefore this work applies this result to EVM represented orthogonal polyhedra. It also presents experimental results that corroborate the theoretical results and includes some practical uses for the ASV decomposition of orthogonal polyhedra.Postprint (published version

Finding all equilibria in games of strategic complements

I present a simple and fast algorithm that finds all the pure-strategy Nash equilibria in games with strategic complementarities. This is the first non-trivial algorithm for finding all pure-strategy Nash equilibria

TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots

We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE guarantees to find the minimum free energy structure irrespectively of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequence that can be treated but comparison with state-of-the-art algorithms shows that TT2NE is a very powerful tool within its limits. Analysis of TT2NE's wrong predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea.fr/rna/tt2ne.php