Revealing networks from dynamics: an introduction

What can we learn from the collective dynamics of a complex network about its interaction topology? Taking the perspective from nonlinear dynamics, we briefly review recent progress on how to infer structural connectivity (direct interactions) from accessing the dynamics of the units. Potential applications range from interaction networks in physics, to chemical and metabolic reactions, protein and gene regulatory networks as well as neural circuits in biology and electric power grids or wireless sensor networks in engineering. Moreover, we briefly mention some standard ways of inferring effective or functional connectivity.Comment: Topical review, 48 pages, 7 figure

Sparsity in Bayesian Signal Estimation

In this chapter, we describe different methods to estimate an unknown signal from its linear measurements. We focus on the underdetermined case where the number of measurements is less than the dimension of the unknown signal. We introduce the concept of signal sparsity and describe how it could be used as prior information for either regularized least squares or Bayesian signal estimation. We discuss compressed sensing and sparse signal representation as examples where these sparse signal estimation methods could be applied

On the accuracy of solving confluent Prony systems

In this paper we consider several nonlinear systems of algebraic equations which can be called "Prony-type". These systems arise in various reconstruction problems in several branches of theoretical and applied mathematics, such as frequency estimation and nonlinear Fourier inversion. Consequently, the question of stability of solution with respect to errors in the right-hand side becomes critical for the success of any particular application. We investigate the question of "maximal possible accuracy" of solving Prony-type systems, putting stress on the "local" behavior which approximates situations with low absolute measurement error. The accuracy estimates are formulated in very simple geometric terms, shedding some light on the structure of the problem. Numerical tests suggest that "global" solution techniques such as Prony's algorithm and ESPRIT method are suboptimal when compared to this theoretical "best local" behavior

Differential Equation Models and Numerical Methods for Reverse Engineering Genetic Regulatory Networks

This dissertation develops and analyzes differential equation-based mathematical models and efficient numerical methods and algorithms for genetic regulatory network identification. The primary objectives of the dissertation are to design, analyze, and test a general variational framework and numerical methods for seeking its approximate solutions for reverse engineering genetic regulatory networks from microarray datasets using the approach based on differential equation modeling. In the proposed variational framework, no structure assumption on the genetic network is presumed, instead, the network is solely determined by the microarray profile of the network components and is identified through a well chosen variational principle which minimizes a biological energy functional. The variational principle serves not only as a selection criterion to pick up the right biological solution of the underlying differential equation model but also provide an effective mathematical characterization of the small-world property of genetic regulatory networks which has been observed in lab experiments. Five specific models within the variational framework and efficient numerical methods and algorithms for computing their solutions are proposed and analyzed in the dissertation. Model validations using both synthetic network datasets and real world subnetwork datasets of Saccharomyces cerevisiae (yeast) and E. Coli are done on all five proposed variational models and a performance comparison vs some existing genetic regulatory network identification methods is also provided. As microarray data is typically noisy, in order to take into account the noise effect in the mathematical models, we propose a new approach based on stochastic differential equation modeling and generalize the deterministic variational framework to a stochastic variational framework which relies on stochastic optimization. Numerical algorithms are also proposed for computing solutions of the stochastic variational models. To address the important issue of post-processing computed networks to reflect the small-world property of underlying genetic regulatory networks, a novel threshholding technique based on the Random Matrix Theory is proposed and tested on various synthetic network datasets

Fast and robust anchor calibration in range-based wireless localization

In this paper we investigate the anchor calibration problem where we want to find the anchor positions when the anchors are not able to range between each other. This is a problem of practical interest because in many systems, the anchors are not connected in a network but are just simple responders to range requests. The proposed calibration method is designed to be fast and simple using only a single range-capable device. For the estimation of the inter-anchor distances, we propose a Total Least Squares estimator as well as a L1 norm estimator. Real life experiments using publicly available hardware validate the proposed calibration technique and show the robustness of the algorithm to non-line-of-sight measurements