Symmetries of Nonlinear PDEs on Metric Graphs and Branched Networks

This Special Issue focuses on recent progress in a new area of mathematical physics and applied analysis, namely, on nonlinear partial differential equations on metric graphs and branched networks. Graphs represent a system of edges connected at one or more branching points (vertices). The connection rule determines the graph topology. When the edges can be assigned a length and the wave functions on the edges are defined in metric spaces, the graph is called a metric graph. Evolution equations on metric graphs have attracted much attention as effective tools for the modeling of particle and wave dynamics in branched structures and networks. Since branched structures and networks appear in different areas of contemporary physics with many applications in electronics, biology, material science, and nanotechnology, the development of effective modeling tools is important for the many practical problems arising in these areas. The list of important problems includes searches for standing waves, exploring of their properties (e.g., stability and asymptotic behavior), and scattering dynamics. This Special Issue is a representative sample of the works devoted to the solutions of these and other problems

On Graph Stream Clustering with Side Information

Graph clustering becomes an important problem due to emerging applications involving the web, social networks and bio-informatics. Recently, many such applications generate data in the form of streams. Clustering massive, dynamic graph streams is significantly challenging because of the complex structures of graphs and computational difficulties of continuous data. Meanwhile, a large volume of side information is associated with graphs, which can be of various types. The examples include the properties of users in social network activities, the meta attributes associated with web click graph streams and the location information in mobile communication networks. Such attributes contain extremely useful information and has the potential to improve the clustering process, but are neglected by most recent graph stream mining techniques. In this paper, we define a unified distance measure on both link structures and side attributes for clustering. In addition, we propose a novel optimization framework DMO, which can dynamically optimize the distance metric and make it adapt to the newly received stream data. We further introduce a carefully designed statistics SGS(C) which consume constant storage spaces with the progression of streams. We demonstrate that the statistics maintained are sufficient for the clustering process as well as the distance optimization and can be scalable to massive graphs with side attributes. We will present experiment results to show the advantages of the approach in graph stream clustering with both links and side information over the baselines.Comment: Full version of SIAM SDM 2013 pape

A singular Riemannian geometry approach to Deep Neural Networks I. Theoretical foundations

Deep Neural Networks are widely used for solving complex problems in several scientific areas, such as speech recognition, machine translation, image analysis. The strategies employed to investigate their theoretical properties mainly rely on Euclidean geometry, but in the last years new approaches based on Riemannian geometry have been developed. Motivated by some open problems, we study a particular sequence of maps between manifolds, with the last manifold of the sequence equipped with a Riemannian metric. We investigate the structures induced trough pullbacks on the other manifolds of the sequence and on some related quotients. In particular, we show that the pullbacks of the final Riemannian metric to any manifolds of the sequence is a degenerate Riemannian metric inducing a structure of pseudometric space, we show that the Kolmogorov quotient of this pseudometric space yields a smooth manifold, which is the base space of a particular vertical bundle. We investigate the theoretical properties of the maps of such sequence, eventually we focus on the case of maps between manifolds implementing neural networks of practical interest and we present some applications of the geometric framework we introduced in the first part of the paper

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the representation, characterization, and description of small molecules and biomolecular complexes. Multicomponent persistent homology retains critical chemical and biological information during the topological simplification of biomolecular geometric complexity. Multi-level persistent homology enables a tailored topological description of inter- and/or intra-molecular interactions of interest. Electrostatic persistence incorporates partial charge information into topological invariants. These topological methods are paired with Wasserstein distance to characterize similarities between molecules and are further integrated with a variety of machine learning algorithms, including k-nearest neighbors, ensemble of trees, and deep convolutional neural networks, to manifest their descriptive and predictive powers for chemical and biological problems. Extensive numerical experiments involving more than 4,000 protein-ligand complexes from the PDBBind database and near 100,000 ligands and decoys in the DUD database are performed to test respectively the scoring power and the virtual screening power of the proposed topological approaches. It is demonstrated that the present approaches outperform the modern machine learning based methods in protein-ligand binding affinity predictions and ligand-decoy discrimination