Network Inference from Consensus Dynamics

We consider the problem of identifying the topology of a weighted, undirected network $\mathcal G$ from observing snapshots of multiple independent consensus dynamics. Specifically, we observe the opinion profiles of a group of agents for a set of $M$ independent topics and our goal is to recover the precise relationships between the agents, as specified by the unknown network $\mathcal G$. In order to overcome the under-determinacy of the problem at hand, we leverage concepts from spectral graph theory and convex optimization to unveil the underlying network structure. More precisely, we formulate the network inference problem as a convex optimization that seeks to endow the network with certain desired properties -- such as sparsity -- while being consistent with the spectral information extracted from the observed opinions. This is complemented with theoretical results proving consistency as the number $M$ of topics grows large. We further illustrate our method by numerical experiments, which showcase the effectiveness of the technique in recovering synthetic and real-world networks.Comment: Will be presented at the 2017 IEEE Conference on Decision and Control (CDC

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53

Background: The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major challenges of using mathematical models to infer genetic regulation from microarray datasets is the lack of information for protein concentrations and activities. Most of the previous researches were based on an assumption that the mRNA levels of a gene are consistent with its protein activities, though it is not always the case. Therefore, a more sophisticated modelling framework together with the corresponding inference methods is needed to accurately estimate genetic regulation from "omics" datasets. Results: This work developed a novel approach, which is based on a nonlinear mathematical model, to infer genetic regulation from microarray gene expression data. By using the p53 network as a test system, we used the nonlinear model to estimate the activities of transcription factor (TF) p53 from the expression levels of its target genes, and to identify the activation/inhibition status of p53 to its target genes. The predicted top 317 putative p53 target genes were supported by DNA sequence analysis. A comparison between our prediction and the other published predictions of p53 targets suggests that most of putative p53 targets may share a common depleted or enriched sequence signal on their upstream non-coding region. Conclusions: The proposed quantitative model can not only be used to infer the regulatory relationship between TF and its down-stream genes, but also be applied to estimate the protein activities of TF from the expression levels of its target genes

A Bayesian inference framework to reconstruct transmission trees using epidemiological and genetic data

The accurate identification of the route of transmission taken by an infectious agent through a host population is critical to understanding its epidemiology and informing measures for its control. However, reconstruction of transmission routes during an epidemic is often an underdetermined problem: data about the location and timings of infections can be incomplete, inaccurate, and compatible with a large number of different transmission scenarios. For fast-evolving pathogens like RNA viruses, inference can be strengthened by using genetic data, nowadays easily and affordably generated. However, significant statistical challenges remain to be overcome in the full integration of these different data types if transmission trees are to be reliably estimated. We present here a framework leading to a bayesian inference scheme that combines genetic and epidemiological data, able to reconstruct most likely transmission patterns and infection dates. After testing our approach with simulated data, we apply the method to two UK epidemics of Foot-and-Mouth Disease Virus (FMDV): the 2007 outbreak, and a subset of the large 2001 epidemic. In the first case, we are able to confirm the role of a specific premise as the link between the two phases of the epidemics, while transmissions more densely clustered in space and time remain harder to resolve. When we consider data collected from the 2001 epidemic during a time of national emergency, our inference scheme robustly infers transmission chains, and uncovers the presence of undetected premises, thus providing a useful tool for epidemiological studies in real time. The generation of genetic data is becoming routine in epidemiological investigations, but the development of analytical tools maximizing the value of these data remains a priority. Our method, while applied here in the context of FMDV, is general and with slight modification can be used in any situation where both spatiotemporal and genetic data are available

Online Resource Inference in Network Utility Maximization Problems

The amount of transmitted data in computer networks is expected to grow considerably in the future, putting more and more pressure on the network infrastructures. In order to guarantee a good service, it then becomes fundamental to use the network resources efficiently. Network Utility Maximization (NUM) provides a framework to optimize the rate allocation when network resources are limited. Unfortunately, in the scenario where the amount of available resources is not known a priori, classical NUM solving methods do not offer a viable solution. To overcome this limitation we design an overlay rate allocation scheme that attempts to infer the actual amount of available network resources while coordinating the users rate allocation. Due to the general and complex model assumed for the congestion measurements, a passive learning of the available resources would not lead to satisfying performance. The coordination scheme must then perform active learning in order to speed up the resources estimation and quickly increase the system performance. By adopting an optimal learning formulation we are able to balance the tradeoff between an accurate estimation, and an effective resources exploitation in order to maximize the long term quality of the service delivered to the users

Distributed Constrained Recursive Nonlinear Least-Squares Estimation: Algorithms and Asymptotics

This paper focuses on the problem of recursive nonlinear least squares parameter estimation in multi-agent networks, in which the individual agents observe sequentially over time an independent and identically distributed (i.i.d.) time-series consisting of a nonlinear function of the true but unknown parameter corrupted by noise. A distributed recursive estimator of the \emph{consensus} + \emph{innovations} type, namely $\mathcal{CIWNLS}$, is proposed, in which the agents update their parameter estimates at each observation sampling epoch in a collaborative way by simultaneously processing the latest locally sensed information~(\emph{innovations}) and the parameter estimates from other agents~(\emph{consensus}) in the local neighborhood conforming to a pre-specified inter-agent communication topology. Under rather weak conditions on the connectivity of the inter-agent communication and a \emph{global observability} criterion, it is shown that at every network agent, the proposed algorithm leads to consistent parameter estimates. Furthermore, under standard smoothness assumptions on the local observation functions, the distributed estimator is shown to yield order-optimal convergence rates, i.e., as far as the order of pathwise convergence is concerned, the local parameter estimates at each agent are as good as the optimal centralized nonlinear least squares estimator which would require access to all the observations across all the agents at all times. In order to benchmark the performance of the proposed distributed $\mathcal{CIWNLS}$ estimator with that of the centralized nonlinear least squares estimator, the asymptotic normality of the estimate sequence is established and the asymptotic covariance of the distributed estimator is evaluated. Finally, simulation results are presented which illustrate and verify the analytical findings.Comment: 28 pages. Initial Submission: Feb. 2016, Revised: July 2016, Accepted: September 2016, To appear in IEEE Transactions on Signal and Information Processing over Networks: Special Issue on Inference and Learning over Network

An Empirical Bayes Approach for Distributed Estimation of Spatial Fields

In this paper we consider a network of spatially distributed sensors which collect measurement samples of a spatial field, and aim at estimating in a distributed way (without any central coordinator) the entire field by suitably fusing all network data. We propose a general probabilistic model that can handle both partial knowledge of the physics generating the spatial field as well as a purely data-driven inference. Specifically, we adopt an Empirical Bayes approach in which the spatial field is modeled as a Gaussian Process, whose mean function is described by means of parametrized equations. We characterize the Empirical Bayes estimator when nodes are heterogeneous, i.e., perform a different number of measurements. Moreover, by exploiting the sparsity of both the covariance and the (parametrized) mean function of the Gaussian Process, we are able to design a distributed spatial field estimator. We corroborate the theoretical results with two numerical simulations: a stationary temperature field estimation in which the field is described by a partial differential (heat) equation, and a data driven inference in which the mean is parametrized by a cubic spline