Robust Network Topology Inference and Processing of Graph Signals

The abundance of large and heterogeneous systems is rendering contemporary data more pervasive, intricate, and with a non-regular structure. With classical techniques facing troubles to deal with the irregular (non-Euclidean) domain where the signals are defined, a popular approach at the heart of graph signal processing (GSP) is to: (i) represent the underlying support via a graph and (ii) exploit the topology of this graph to process the signals at hand. In addition to the irregular structure of the signals, another critical limitation is that the observed data is prone to the presence of perturbations, which, in the context of GSP, may affect not only the observed signals but also the topology of the supporting graph. Ignoring the presence of perturbations, along with the couplings between the errors in the signal and the errors in their support, can drastically hinder estimation performance. While many GSP works have looked at the presence of perturbations in the signals, much fewer have looked at the presence of perturbations in the graph, and almost none at their joint effect. While this is not surprising (GSP is a relatively new field), we expect this to change in the upcoming years. Motivated by the previous discussion, the goal of this thesis is to advance toward a robust GSP paradigm where the algorithms are carefully designed to incorporate the influence of perturbations in the graph signals, the graph support, and both. To do so, we consider different types of perturbations, evaluate their disruptive impact on fundamental GSP tasks, and design robust algorithms to address them.Comment: Dissertatio

Netter: re-ranking gene network inference predictions using structural network properties

Background: Many algorithms have been developed to infer the topology of gene regulatory networks from gene expression data. These methods typically produce a ranking of links between genes with associated confidence scores, after which a certain threshold is chosen to produce the inferred topology. However, the structural properties of the predicted network do not resemble those typical for a gene regulatory network, as most algorithms only take into account connections found in the data and do not include known graph properties in their inference process. This lowers the prediction accuracy of these methods, limiting their usability in practice. Results: We propose a post-processing algorithm which is applicable to any confidence ranking of regulatory interactions obtained from a network inference method which can use, inter alia, graphlets and several graph-invariant properties to re-rank the links into a more accurate prediction. To demonstrate the potential of our approach, we re-rank predictions of six different state-of-the-art algorithms using three simple network properties as optimization criteria and show that Netter can improve the predictions made on both artificially generated data as well as the DREAM4 and DREAM5 benchmarks. Additionally, the DREAM5 E. coli. community prediction inferred from real expression data is further improved. Furthermore, Netter compares favorably to other post-processing algorithms and is not restricted to correlation-like predictions. Lastly, we demonstrate that the performance increase is robust for a wide range of parameter settings. Netter is available at http://bioinformatics. intec. ugent. be. Conclusions: Network inference from high-throughput data is a long-standing challenge. In this work, we present Netter, which can further refine network predictions based on a set of user-defined graph properties. Netter is a flexible system which can be applied in unison with any method producing a ranking from omics data. It can be tailored to specific prior knowledge by expert users but can also be applied in general uses cases. Concluding, we believe that Netter is an interesting second step in the network inference process to further increase the quality of prediction

Exact detection of direct links in networks of interacting dynamical units

Authors NR, EB-M, CG, and MSB acknowledge the Scottish Universities Physics Alliance (SUPA). EB-M and MSB also acknowledge the Engineering and Physical Science Research Council (EPSRC) project Ref. EP/I032 606/1. ACM and CM acknowledge the LINC project (FP7-PEOPLE-2011-ITN, grant no. 289447). ACM also aknowledges PEDECIBA and CSIC(Uruguay). CM also acknowledges grant FIS2012–37655-C02–01 from the Spanish MCI, grant 2009 SGR 1168, and the ICREA Academia programme from the Generalitat de Catalunya.Peer reviewedPublisher PD

Large scale probabilistic available bandwidth estimation

The common utilization-based definition of available bandwidth and many of the existing tools to estimate it suffer from several important weaknesses: i) most tools report a point estimate of average available bandwidth over a measurement interval and do not provide a confidence interval; ii) the commonly adopted models used to relate the available bandwidth metric to the measured data are invalid in almost all practical scenarios; iii) existing tools do not scale well and are not suited to the task of multi-path estimation in large-scale networks; iv) almost all tools use ad-hoc techniques to address measurement noise; and v) tools do not provide enough flexibility in terms of accuracy, overhead, latency and reliability to adapt to the requirements of various applications. In this paper we propose a new definition for available bandwidth and a novel framework that addresses these issues. We define probabilistic available bandwidth (PAB) as the largest input rate at which we can send a traffic flow along a path while achieving, with specified probability, an output rate that is almost as large as the input rate. PAB is expressed directly in terms of the measurable output rate and includes adjustable parameters that allow the user to adapt to different application requirements. Our probabilistic framework to estimate network-wide probabilistic available bandwidth is based on packet trains, Bayesian inference, factor graphs and active sampling. We deploy our tool on the PlanetLab network and our results show that we can obtain accurate estimates with a much smaller measurement overhead compared to existing approaches.Comment: Submitted to Computer Network