Modeling the evolution of weighted networks

We present a general model for the growth of weighted networks in which the structural growth is coupled with the edges' weight dynamical evolution. The model is based on a simple weight-driven dynamics and a weights' reinforcement mechanism coupled to the local network growth. That coupling can be generalized in order to include the effect of additional randomness and non-linearities which can be present in real-world networks. The model generates weighted graphs exhibiting the statistical properties observed in several real-world systems. In particular, the model yields a non-trivial time evolution of vertices properties and scale-free behavior with exponents depending on the microscopic parameters characterizing the coupling rules. Very interestingly, the generated graphs spontaneously achieve a complex hierarchical architecture characterized by clustering and connectivity correlations varying as a function of the vertices' degree

Next Generation Cluster Editing

This work aims at improving the quality of structural variant prediction from the mapped reads of a sequenced genome. We suggest a new model based on cluster editing in weighted graphs and introduce a new heuristic algorithm that allows to solve this problem quickly and with a good approximation on the huge graphs that arise from biological datasets

Searching for network modules

When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a novel type of objective function for graph clustering, in the form of a multilinear polynomial whose coefficients are determined by network topology. It may be thought of as a potential function, to be maximized, taking its values on fuzzy clusterings or families of fuzzy subsets of nodes over which every node distributes a unit membership. When suitably parametrized, this potential is shown to attain its maximum when every node concentrates its all unit membership on some module. The output thus is a partition, while the original discrete optimization problem is turned into a continuous version allowing to conceive alternative search strategies. The instance of the problem being a pseudo-Boolean function assigning real-valued cluster scores to node subsets, modularity maximization is employed to exemplify a so-called quadratic form, in that the scores of singletons and pairs also fully determine the scores of larger clusters, while the resulting multilinear polynomial potential function has degree 2. After considering further quadratic instances, different from modularity and obtained by interpreting network topology in alternative manners, a greedy local-search strategy for the continuous framework is analytically compared with an existing greedy agglomerative procedure for the discrete case. Overlapping is finally discussed in terms of multiple runs, i.e. several local searches with different initializations.Comment: 10 page

Improved Parallel Algorithms for Spanners and Hopsets

We use exponential start time clustering to design faster and more work-efficient parallel graph algorithms involving distances. Previous algorithms usually rely on graph decomposition routines with strict restrictions on the diameters of the decomposed pieces. We weaken these bounds in favor of stronger local probabilistic guarantees. This allows more direct analyses of the overall process, giving: * Linear work parallel algorithms that construct spanners with $O(k)$ stretch and size $O(n^{1+1/k})$ in unweighted graphs, and size $O(n^{1+1/k} \log k)$ in weighted graphs. * Hopsets that lead to the first parallel algorithm for approximating shortest paths in undirected graphs with $O(m\;\mathrm{polylog}\;n)$ work

Euclidean Distances, soft and spectral Clustering on Weighted Graphs

We define a class of Euclidean distances on weighted graphs, enabling to perform thermodynamic soft graph clustering. The class can be constructed form the "raw coordinates" encountered in spectral clustering, and can be extended by means of higher-dimensional embeddings (Schoenberg transformations). Geographical flow data, properly conditioned, illustrate the procedure as well as visualization aspects.Comment: accepted for presentation (and further publication) at the ECML PKDD 2010 conferenc