Spectral Theory for Networks with Attractive and Repulsive Interactions

There is a wealth of applied problems that can be posed as a dynamical system defined on a network with both attractive and repulsive interactions. Some examples include: understanding synchronization properties of nonlinear oscillator;, the behavior of groups, or cliques, in social networks; the study of optimal convergence for consensus algorithm; and many other examples. Frequently the problems involve computing the index of a matrix, i.e. the number of positive and negative eigenvalues, and the dimension of the kernel. In this paper we consider one of the most common examples, where the matrix takes the form of a signed graph Laplacian. We show that the there are topological constraints on the index of the Laplacian matrix related to the dimension of a certain homology group. In certain situations, when the homology group is trivial, the index of the operator is rigid and is determined only by the topology of the network and is independent of the strengths of the interactions. In general these constraints give upper and lower bounds on the number of positive and negative eigenvalues, with the dimension of the homology group counting the number of eigenvalue crossings. The homology group also gives a natural decomposition of the dynamics into "fixed" degrees of freedom, whose index does not depend on the edge-weights, and an orthogonal set of "free" degrees of freedom, whose index changes as the edge weights change. We also present some numerical studies of this problem for large random matrices.Comment: 27 pages; 9 Figure

A graph theoretical analysis of the energy landscape of model polymers

In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and splitting of metastable states, have non trivial effects on such networks and must be taken into account. We do this by means of a recently proposed renormalization procedure. This method is applied to analyze the topology of the network of metastable states for different polypeptidic sequences in a minimalistic polymer model. A smaller spectral dimension emerges as a hallmark of stability of the global energy minimum and highlights a non-obvious link between dynamic and thermodynamic properties.Comment: 15 pages, 15 figure

Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues

We undertake an extensive numerical investigation of the graph spectra of thousands regular graphs, a set of random Erd\"os-R\'enyi graphs, the two most popular types of complex networks and an evolving genetic network by using novel conceptual and experimental tools. Our objective in so doing is to contribute to an understanding of the meaning of the Eigenvalues of a graph relative to its topological and information-theoretic properties. We introduce a technique for identifying the most informative Eigenvalues of evolving networks by comparing graph spectra behavior to their algorithmic complexity. We suggest that extending techniques can be used to further investigate the behavior of evolving biological networks. In the extended version of this paper we apply these techniques to seven tissue specific regulatory networks as static example and network of a na\"ive pluripotent immune cell in the process of differentiating towards a Th17 cell as evolving example, finding the most and least informative Eigenvalues at every stage.Comment: Forthcoming in 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Lecture Notes in Bioinformatics, 201