Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections

In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped with information about their spatial relationships. The semantics of such models is expressed through colored Petri nets to implement regulation rules, combined with topological collections to implement the spatial information. Some constraints are put on the the representation of spatial information in order to preserve the possibility of an enumerative and exhaustive state space exploration. This paper presents the modelling framework, its semantics, as well as a prototype implementation that allowed preliminary experimentation on some applications.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Inversion of multiconfiguration complex EMI data with minimum gradient support regularization: A case study

Frequency-domain electromagnetic instruments allow the collection of data in different configurations, that is, varying the intercoil spacing, the frequency, and the height above the ground. Their handy size makes these tools very practical for near-surface characterization in many fields of applications, for example, precision agriculture, pollution assessments, and shallow geological investigations. To this end, the inversion of either the real (in-phase) or the imaginary (quadrature) component of the signal has already been studied. Furthermore, in many situations, a regularization scheme retrieving smooth solutions is blindly applied, without taking into account the prior available knowledge. The present work discusses an algorithm for the inversion of the complex signal in its entirety, as well as a regularization method that promotes the sparsity of the reconstructed electrical conductivity distribution. This regularization strategy incorporates a minimum gradient support stabilizer into a truncated generalized singular value decomposition scheme. The results of the implementation of this sparsity-enhancing regularization at each step of a damped Gauss-Newton inversion algorithm (based on a nonlinear forward model) are compared with the solutions obtained via a standard smooth stabilizer. An approach for estimating the depth of investigation, that is, the maximum depth that can be investigated by a chosen instrument configuration in a particular experimental setting is also discussed. The effectiveness and limitations of the whole inversion algorithm are demonstrated on synthetic and real data sets

HP-multigrid as smoother algorithm for higher order discontinuous Galerkin discretizations of advection dominated flows. Part I. Multilevel Analysis

The hp-Multigrid as Smoother algorithm (hp-MGS) for the solution of higher order accurate space-(time) discontinuous Galerkin discretizations of advection dominated flows is presented. This algorithm combines p-multigrid with h-multigrid at all p-levels, where the h-multigrid acts as smoother in the p-multigrid. The performance of the hp-MGS algorithm is further improved using semi-coarsening in combination with a new semi-implicit Runge-Kutta method as smoother. A detailed multilevel analysis of the hp-MGS algorithm is presented to obtain more insight into the theoretical performance of the algorithm. As model problem a fourth order accurate space-time discontinuous Galerkin discretization of the advection-diffusion equation is considered. The multilevel analysis shows that the hp-MGS algorithm has excellent convergence rates, both for low and high cell Reynolds numbers and on highly stretched meshes

On the impact of the GOP size in a temporal H.264/AVC-to-SVC transcoder in baseline and main profile

Scalable video coding is a recent extension of the advanced video coding H.264/AVC standard developed jointly by ISO/IEC and ITU-T, which allows adapting the bitstream easily by dropping parts of it named layers. This adaptation makes it possible for a single bitstream to meet the requirements for reliable delivery of video to diverse clients over heterogeneous networks using temporal, spatial or quality scalability, combined or separately. Since the scalable video coding design requires scalability to be provided at the encoder side, existing content cannot benefit from it. Efficient techniques for converting contents without scalability to a scalable format are desirable. In this paper, an approach for temporal scalability transcoding from H.264/AVC to scalable video coding in baseline and main profile is presented and the impact of the GOP size is analyzed. Independently of the GOP size chosen, time savings of around 63 % for baseline profile and 60 % for main profile are achieved while maintaining the coding efficiency