Efficient Parallel Statistical Model Checking of Biochemical Networks

We consider the problem of verifying stochastic models of biochemical networks against behavioral properties expressed in temporal logic terms. Exact probabilistic verification approaches such as, for example, CSL/PCTL model checking, are undermined by a huge computational demand which rule them out for most real case studies. Less demanding approaches, such as statistical model checking, estimate the likelihood that a property is satisfied by sampling executions out of the stochastic model. We propose a methodology for efficiently estimating the likelihood that a LTL property P holds of a stochastic model of a biochemical network. As with other statistical verification techniques, the methodology we propose uses a stochastic simulation algorithm for generating execution samples, however there are three key aspects that improve the efficiency: first, the sample generation is driven by on-the-fly verification of P which results in optimal overall simulation time. Second, the confidence interval estimation for the probability of P to hold is based on an efficient variant of the Wilson method which ensures a faster convergence. Third, the whole methodology is designed according to a parallel fashion and a prototype software tool has been implemented that performs the sampling/verification process in parallel over an HPC architecture

Category Theory and Model-Driven Engineering: From Formal Semantics to Design Patterns and Beyond

There is a hidden intrigue in the title. CT is one of the most abstract mathematical disciplines, sometimes nicknamed "abstract nonsense". MDE is a recent trend in software development, industrially supported by standards, tools, and the status of a new "silver bullet". Surprisingly, categorical patterns turn out to be directly applicable to mathematical modeling of structures appearing in everyday MDE practice. Model merging, transformation, synchronization, and other important model management scenarios can be seen as executions of categorical specifications. Moreover, the paper aims to elucidate a claim that relationships between CT and MDE are more complex and richer than is normally assumed for "applied mathematics". CT provides a toolbox of design patterns and structural principles of real practical value for MDE. We will present examples of how an elementary categorical arrangement of a model management scenario reveals deficiencies in the architecture of modern tools automating the scenario.Comment: In Proceedings ACCAT 2012, arXiv:1208.430

Complexity-entropy analysis at different levels of organization in written language

Written language is complex. A written text can be considered an attempt to convey a meaningful message which ends up being constrained by language rules, context dependence and highly redundant in its use of resources. Despite all these constraints, unpredictability is an essential element of natural language. Here we present the use of entropic measures to assert the balance between predictability and surprise in written text. In short, it is possible to measure innovation and context preservation in a document. It is shown that this can also be done at the different levels of organization of a text. The type of analysis presented is reasonably general, and can also be used to analyze the same balance in other complex messages such as DNA, where a hierarchy of organizational levels are known to exist

Clusters of firms in space and time

The use of the K-functions (Ripley, 1977) has become recently popular in the analysis of the spatial pattern of firms. It was first introduced in the economic literature by Arbia and Espa (1996) and then popularized by Marcon and Puech (2003), Quah and Simpson (2003), Duranton and Overman (2005) and Arbia et al. (2008). In particular in Arbia et al. (2008) we used Ripley’s K-functions as instruments to study the inter-sectoral co-agglomeration pattern of firms in a single moment of time. All this researches have followed a static approach, disregarding the time dimension. Temporal dynamics, on the other hand, play a crucial role in understanding the economic and social phenomena, particularly when referring to the analysis of the individual choices leading to the observed clusters of economic activities. With respect to the contributions previously appeared in the literature, this paper uncovers the process of firm demography by studying the dynamics of localization through space-time K-functions. The empirical part of the paper will focus on the study of the long run localization of firms in the area of Rome (Italy), by concentrating on the ICT sector data collected by the Italian Industrial Union in the period 1920- 2005.Agglomeration, Non-parametric measures; Space-time K-functions, Spatial clusters, Spatial econometrics.

Towards Distributed Petascale Computing

In this chapter we will argue that studying such multi-scale multi-science systems gives rise to inherently hybrid models containing many different algorithms best serviced by different types of computing environments (ranging from massively parallel computers, via large-scale special purpose machines to clusters of PC's) whose total integrated computing capacity can easily reach the PFlop/s scale. Such hybrid models, in combination with the by now inherently distributed nature of the data on which the models `feed' suggest a distributed computing model, where parts of the multi-scale multi-science model are executed on the most suitable computing environment, and/or where the computations are carried out close to the required data (i.e. bring the computations to the data instead of the other way around). We presents an estimate for the compute requirements to simulate the Galaxy as a typical example of a multi-scale multi-physics application, requiring distributed Petaflop/s computational power.Comment: To appear in D. Bader (Ed.) Petascale, Computing: Algorithms and Applications, Chapman & Hall / CRC Press, Taylor and Francis Grou