Bisimulation of Labeled State-to-Function Transition Systems of Stochastic Process Languages

Labeled state-to-function transition systems, FuTS for short, admit multiple transition schemes from states to functions of finite support over general semirings. As such they constitute a convenient modeling instrument to deal with stochastic process languages. In this paper, the notion of bisimulation induced by a FuTS is proposed and a correspondence result is proven stating that FuTS-bisimulation coincides with the behavioral equivalence of the associated functor. As generic examples, the concrete existing equivalences for the core of the process algebras ACP, PEPA and IMC are related to the bisimulation of specific FuTS, providing via the correspondence result coalgebraic justification of the equivalences of these calculi.Comment: In Proceedings ACCAT 2012, arXiv:1208.430

Investigating modularity in the analysis of process algebra models of biochemical systems

Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in a formalism which allows the problem to be tackled compositionally. In this paper we consider the extent to which the compositional structure which is inherent in process algebra models of biochemical systems can be exploited during model solution. In essence this means using the compositional structure to guide decomposed solution and analysis. Unfortunately the dynamic behaviour of biochemical systems exhibits strong interdependencies between the components of the model making decomposed solution a difficult task. Nevertheless we believe that if such decomposition based on process algebras could be established it would demonstrate substantial benefits for systems biology modelling. In this paper we present our preliminary investigations based on a case study of the pheromone pathway in yeast, modelling in the stochastic process algebra Bio-PEPA

Bisimulation of Labelled State-to-Function Transition Systems Coalgebraically

Labeled state-to-function transition systems, FuTS for short, are characterized by transitions which relate states to functions of states over general semirings, equipped with a rich set of higher-order operators. As such, FuTS constitute a convenient modeling instrument to deal with process languages and their quantitative extensions in particular. In this paper, the notion of bisimulation induced by a FuTS is addressed from a coalgebraic point of view. A correspondence result is established stating that FuTS-bisimilarity coincides with behavioural equivalence of the associated functor. As generic examples, the equivalences underlying substantial fragments of major examples of quantitative process algebras are related to the bisimilarity of specific FuTS. The examples range from a stochastic process language, PEPA, to a language for Interactive Markov Chains, IML, a (discrete) timed process language, TPC, and a language for Markov Automata, MAL. The equivalences underlying these languages are related to the bisimilarity of their specific FuTS. By the correspondence result coalgebraic justification of the equivalences of these calculi is obtained. The specific selection of languages, besides covering a large variety of process interaction models and modelling choices involving quantities, allows us to show different classes of FuTS, namely so-called simple FuTS, combined FuTS, nested FuTS, and general FuTS

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.

Amalgamation of Transition Sequences in the PEPA Formalism

This report presents a proposed formal approach towards reduction of sequences in PEPA components. By performing the described amalgamation procedure we may remove, from the Markov chain underlying an initial PEPA model, those states for which detailed local balance equations cannot be formulated. This transformation may lead to a simpler model with product form solution. Some classes of reduced models preserve those performance measures which we are interested in and, moreover, the steady state solution vector is much easier to find from the computational point of view

Fluid passage-time calculation in large Markov models

Recent developments in the analysis of large Markov models facilitate the fast approximation of transient characteristics of the underlying stochastic process. So-called fluid analysis makes it possible to consider previously intractable models whose underlying discrete state space grows exponentially as model components are added. In this work, we show how fluid approximation techniques may be used to extract passage-time measures from performance models. We focus on two types of passage measure: passage-times involving individual components; as well as passage-times which capture the time taken for a population of components to evolve. Specifically, we show that for models of sufficient scale, passage-time distributions can be well approximated by a deterministic fluid-derived passage-time measure. Where models are not of sufficient scale, we are able to generate approximate bounds for the entire cumulative distribution function of these passage-time random variables, using moment-based techniques. Finally, we show that for some passage-time measures involving individual components the cumulative distribution function can be directly approximated by fluid techniques

Extended Differential Aggregations in Process Algebra for Performance and Biology

We study aggregations for ordinary differential equations induced by fluid semantics for Markovian process algebra which can capture the dynamics of performance models and chemical reaction networks. Whilst previous work has required perfect symmetry for exact aggregation, we present approximate fluid lumpability, which makes nearby processes perfectly symmetric after a perturbation of their parameters. We prove that small perturbations yield nearby differential trajectories. Numerically, we show that many heterogeneous processes can be aggregated with negligible errors.Comment: In Proceedings QAPL 2014, arXiv:1406.156