Abstracting Asynchronous Multi-Valued Networks: An Initial Investigation

Multi-valued networks provide a simple yet expressive qualitative state based modelling approach for biological systems. In this paper we develop an abstraction theory for asynchronous multi-valued network models that allows the state space of a model to be reduced while preserving key properties of the model. The abstraction theory therefore provides a mechanism for coping with the state space explosion problem and supports the analysis and comparison of multi-valued networks. We take as our starting point the abstraction theory for synchronous multi-valued networks which is based on the finite set of traces that represent the behaviour of such a model. The problem with extending this approach to the asynchronous case is that we can now have an infinite set of traces associated with a model making a simple trace inclusion test infeasible. To address this we develop a decision procedure for checking asynchronous abstractions based on using the finite state graph of an asynchronous multi-valued network to reason about its trace semantics. We illustrate the abstraction techniques developed by considering a detailed case study based on a multi-valued network model of the regulation of tryptophan biosynthesis in Escherichia coli.Comment: Presented at MeCBIC 201

Verifying Modal Workflow Specifications Using Constraint Solving

International audienceNowadaysworkflowsareextensivelyusedbycompaniestoimproveorganizationalefficiencyandproductivity.Thispaperfocusesontheverificationofmodalworkflowspecificationsusingconstraintsolvingasacomputationaltool.ItsmaincontributionconsistsindevelopinganinnovativeformalframeworkbasedonconstraintsystemstomodelexecutionsofworkflowPetrinetsandtheirstructuralproperties,aswellastoverifytheirmodalspecifications.Finally,animplementationandpromisingexperimentalresultsconstituteapracticalcontribution

Extensions to the CEGAR approach on Petri nets

Formal verification is becoming more prevalent and often compulsory in the safety-critical system and software development processes. Reachability analysis can provide information about safety and invariant properties of the developed system. However, checking the reachability is a computationally hard problem, especially in the case of asynchronous or infinite state systems. Petri nets are widely used for the modeling and verification of such systems. In this paper we examine a recently published approach for the reachability checking of Petri net markings. We give proofs concerning the completeness and the correctness properties of the algorithm, and we introduce algorithmic improvements. We also extend the algorithm to handle new classes of problems: submarking coverability and reachability of Petri nets with inhibitor arcs

Synthesis of Bounded Choice-Free Petri Nets

This paper describes a synthesis algorithm tailored to the construction of choice-free Petri nets from finite persistent transition systems. With this goal in mind, a minimised set of simplified systems of linear inequalities is distilled from a general region-theoretic approach, leading to algorithmic improvements as well as to a partial characterisation of the class of persistent transition systems that have a choice-free Petri net realisation

Abstracting Asynchronous Multi-Valued Networks

Multi-valued networks (MVNs) provide a simple yet expressive qualitative state based modelling approach for biological systems. In this paper we develop an abstraction theory for asynchronous MVNs that allows the state space of a model to be reduced while preserving key properties. The abstraction theory therefore provides a mechanism for coping with the state space explosion problem and supports the analysis and comparison of MVNs. We take as our starting point the abstraction theory for synchronous MVNs which uses the under- approximation approach of trace set inclusion. We show this definition of asynchronous abstraction allows the sound inference of analysis properties and preserves other interesting model properties. One problem that arises in the asynchronous case is that the trace set of an MVN can be infinite making a simple trace set inclusion check infeasible. To address this we develop a decision procedure for checking asynchronous abstractions based on using the finite state graph of an asynchronous MVN to reason about its trace semantics and formally show that this decision procedure is correct. We illustrate the abstraction techniques developed by considering two detailed case studies in which asynchronous abstractions are identified and validated for existing asynchronous MVN models taken from the literature