Topology Identification under Spatially Correlated Noise

This article addresses the problem of reconstructing the topology of a network of agents interacting via linear dynamics, while being excited by exogenous stochastic sources that are possibly correlated across the agents, from time-series measurements alone. It is shown, under the assumption that the correlations are affine in nature, such network of nodal interactions is equivalent to a network with added agents, represented by nodes that are latent, where no corresponding time-series measurements are available; however, here all exogenous excitements are spatially (that is, across agents) uncorrelated. Generalizing affine correlations, it is shown that, under polynomial correlations, the latent nodes in the expanded networks can be excited by clusters of noise sources, where the clusters are uncorrelated with each other. The clusters can be replaced with a single noise source if the latent nodes are allowed to have non-linear interactions. Finally, using the sparse plus low-rank matrix decomposition of the imaginary part of the inverse power spectral density matrix (IPSDM) of the time-series data, the topology of the network is reconstructed. Under non conservative assumptions, the correlation graph is retrieved.Comment: 14 pages, 5 figure

Graph Dynamical Networks for Unsupervised Learning of Atomic Scale Dynamics in Materials

Understanding the dynamical processes that govern the performance of functional materials is essential for the design of next generation materials to tackle global energy and environmental challenges. Many of these processes involve the dynamics of individual atoms or small molecules in condensed phases, e.g. lithium ions in electrolytes, water molecules in membranes, molten atoms at interfaces, etc., which are difficult to understand due to the complexity of local environments. In this work, we develop graph dynamical networks, an unsupervised learning approach for understanding atomic scale dynamics in arbitrary phases and environments from molecular dynamics simulations. We show that important dynamical information can be learned for various multi-component amorphous material systems, which is difficult to obtain otherwise. With the large amounts of molecular dynamics data generated everyday in nearly every aspect of materials design, this approach provides a broadly useful, automated tool to understand atomic scale dynamics in material systems.Comment: 25 + 7 pages, 5 + 3 figure

A nonuniform popularity-similarity optimization (nPSO) model to efficiently generate realistic complex networks with communities

The hidden metric space behind complex network topologies is a fervid topic in current network science and the hyperbolic space is one of the most studied, because it seems associated to the structural organization of many real complex systems. The Popularity-Similarity-Optimization (PSO) model simulates how random geometric graphs grow in the hyperbolic space, reproducing strong clustering and scale-free degree distribution, however it misses to reproduce an important feature of real complex networks, which is the community organization. The Geometrical-Preferential-Attachment (GPA) model was recently developed to confer to the PSO also a community structure, which is obtained by forcing different angular regions of the hyperbolic disk to have variable level of attractiveness. However, the number and size of the communities cannot be explicitly controlled in the GPA, which is a clear limitation for real applications. Here, we introduce the nonuniform PSO (nPSO) model that, differently from GPA, forces heterogeneous angular node attractiveness by sampling the angular coordinates from a tailored nonuniform probability distribution, for instance a mixture of Gaussians. The nPSO differs from GPA in other three aspects: it allows to explicitly fix the number and size of communities; it allows to tune their mixing property through the network temperature; it is efficient to generate networks with high clustering. After several tests we propose the nPSO as a valid and efficient model to generate networks with communities in the hyperbolic space, which can be adopted as a realistic benchmark for different tasks such as community detection and link prediction