Checking Dynamic Consistency of Conditional Hyper Temporal Networks via Mean Payoff Games (Hardness and (pseudo) Singly-Exponential Time Algorithm)

In this work we introduce the \emph{Conditional Hyper Temporal Network (CHyTN)} model, which is a natural extension and generalization of both the \CSTN and the \HTN model. Our contribution goes as follows. We show that deciding whether a given \CSTN or CHyTN is dynamically consistent is \coNP-hard. Then, we offer a proof that deciding whether a given CHyTN is dynamically consistent is \PSPACE-hard, provided that the input instances are allowed to include both multi-head and multi-tail hyperarcs. In light of this, we continue our study by focusing on CHyTNs that allow only multi-head or only multi-tail hyperarcs, and we offer the first deterministic (pseudo) singly-exponential time algorithm for the problem of checking the dynamic-consistency of such CHyTNs, also producing a dynamic execution strategy whenever the input CHyTN is dynamically consistent. Since \CSTN{s} are a special case of CHyTNs, this provides as a byproduct the first sound-and-complete (pseudo) singly-exponential time algorithm for checking dynamic-consistency in CSTNs. The proposed algorithm is based on a novel connection between CSTN{s}/CHyTN{s} and Mean Payoff Games. The presentation of the connection between \CSTN{s}/CHyTNs and \MPG{s} is mediated by the \HTN model. In order to analyze the algorithm, we introduce a refined notion of dynamic-consistency, named $\epsilon$-dynamic-consistency, and present a sharp lower bounding analysis on the critical value of the reaction time $\hat{\varepsilon}$ where a \CSTN/CHyTN transits from being, to not being, dynamically consistent. The proof technique introduced in this analysis of $\hat{\varepsilon}$ is applicable more generally when dealing with linear difference constraints which include strict inequalities.Comment: arXiv admin note: text overlap with arXiv:1505.0082

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

Design and Development of Software Tools for Bio-PEPA

This paper surveys the design of software tools for the Bio-PEPA process algebra. Bio-PEPA is a high-level language for modelling biological systems such as metabolic pathways and other biochemical reaction networks. Through providing tools for this modelling language we hope to allow easier use of a range of simulators and model-checkers thereby freeing the modeller from the responsibility of developing a custom simulator for the problem of interest. Further, by providing mappings to a range of different analysis tools the Bio-PEPA language allows modellers to compare analysis results which have been computed using independent numerical analysers, which enhances the reliability and robustness of the results computed.

Biochemical network matching and composition

This paper looks at biochemical network matching and compositio

BioDiVinE: A Framework for Parallel Analysis of Biological Models

In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study

BigraphER: rewriting and analysis engine for bigraphs

BigraphER is a suite of open-source tools providing an effi- cient implementation of rewriting, simulation, and visualisation for bigraphs, a universal formalism for modelling interacting systems that evolve in time and space and first introduced by Milner. BigraphER consists of an OCaml library that provides programming interfaces for the manipulation of bigraphs, their constituents and reaction rules, and a command-line tool capable of simulating Bigraphical Reactive Systems (BRSs) and computing their transition systems. Other features are native support for both bigraphs and bigraphs with sharing, stochastic reaction rules, rule priorities, instantiation maps, parameterised controls, predicate checking, graphical output and integration with the probabilistic model checker PRISM