A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology

An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment

Telecommunications Networks

This book guides readers through the basics of rapidly emerging networks to more advanced concepts and future expectations of Telecommunications Networks. It identifies and examines the most pressing research issues in Telecommunications and it contains chapters written by leading researchers, academics and industry professionals. Telecommunications Networks - Current Status and Future Trends covers surveys of recent publications that investigate key areas of interest such as: IMS, eTOM, 3G/4G, optimization problems, modeling, simulation, quality of service, etc. This book, that is suitable for both PhD and master students, is organized into six sections: New Generation Networks, Quality of Services, Sensor Networks, Telecommunications, Traffic Engineering and Routing

Curve Shortening Flow for Spatial Random Permutations

Motivated by mean-curvature type droplet shrinking in the hydrodynamic scaling limit for the Ising model on a 2-dimensional lattice at zero temperature, we analyse a similar microscopic model based on spatial random permutations. This naturally leads to interacting particle systems and the derivation of their hydrodynamic equations. In the progress, we deal with non-gradient systems and non-product stationary measures

Differential Models, Numerical Simulations and Applications

This Special Issue includes 12 high-quality articles containing original research findings in the fields of differential and integro-differential models, numerical methods and efficient algorithms for parameter estimation in inverse problems, with applications to biology, biomedicine, land degradation, traffic flows problems, and manufacturing systems

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available