MathMC: A mathematica-based tool for CSL model checking of deterministic and stochastic Petri nets

Deterministic and Stochastic Petri Nets (DSPNs) are a widely used high-level formalism for modeling discreteevent systems where events may occur either without consuming time, after a deterministic time, or after an exponentially distributed time. CSL (Continuous Stochastic Logic) is a (branching) temporal logic developed to express probabilistic properties in continuous time Markov chains (CTMCs). In this paper we present a Mathematica-based tool that implements recent developments for model checking CSL style properties on DSPNs. Furthermore, as a consequence of the type of process underlying DSPNs (a superset of Markovian processes), we are also able to check CSL properties of Generalized Stochastic Petri Nets (GSPNs) and labeled CTMCs

Model-checking branching-time properties of probabilistic automata and probabilistic one-counter automata

This paper studies the problem of model-checking of probabilistic automaton and probabilistic one-counter automata against probabilistic branching-time temporal logics (PCTL and PCTL$^*$). We show that it is undecidable for these problems. We first show, by reducing to emptiness problem of probabilistic automata, that the model-checking of probabilistic finite automata against branching-time temporal logics are undecidable. And then, for each probabilistic automata, by constructing a probabilistic one-counter automaton with the same behavior as questioned probabilistic automata the undecidability of model-checking problems against branching-time temporal logics are derived, herein.Comment: Comments are welcom

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Variations of model checking

The logic ATCTL is a convenient logic to specify properties with actions and real-time. It is intended as a property language for Lightweight UML models [12], which consist mainly of simplified class diagrams and statecharts. ATCTL combines two known extensions of CTL, namely ACTL and TCTL. The reason to extend CTL with both actions and real time is that in LUML state¿transition diagrams, we specify states, actions and real time, and our properties refer to all of these elements. The analyst therefore needs a property language that contains constructs for all these elements. ATCTL can be reduced to ACTL as well as to TCTL, and therefore also to CTL. This gives us a choice of tools for model checking; we have used is Kronos [13], a TCTL model checker

A Monte Carlo model checker for probabilistic LTL with numerical constraints

We define the syntax and semantics of a new temporal logic called probabilistic LTL with numerical constraints (PLTLc). We introduce an efficient model checker for PLTLc properties. The efficiency of the model checker is through approximation using Monte Carlo sampling of finite paths through the model’s state space (simulation outputs) and parallel model checking of the paths. Our model checking method can be applied to any model producing quantitative output – continuous or stochastic, including those with complex dynamics and those with an infinite state space. Furthermore, our offline approach allows the analysis of observed (real-life) behaviour traces. We find in this paper that PLTLc properties with constraints over free variables can replace full model checking experiments, resulting in a significant gain in efficiency. This overcomes one disadvantage of model checking experiments which is that the complexity depends on system granularity and number of variables, and quickly becomes infeasible. We focus on models of biochemical networks, and specifically in this paper on intracellular signalling pathways; however our method can be applied to a wide range of biological as well as technical systems and their models. Our work contributes to the emerging field of synthetic biology by proposing a rigourous approach for the structured formal engineering of biological systems

Tableaux for Policy Synthesis for MDPs with PCTL* Constraints

Markov decision processes (MDPs) are the standard formalism for modelling sequential decision making in stochastic environments. Policy synthesis addresses the problem of how to control or limit the decisions an agent makes so that a given specification is met. In this paper we consider PCTL*, the probabilistic counterpart of CTL*, as the specification language. Because in general the policy synthesis problem for PCTL* is undecidable, we restrict to policies whose execution history memory is finitely bounded a priori. Surprisingly, no algorithm for policy synthesis for this natural and expressive framework has been developed so far. We close this gap and describe a tableau-based algorithm that, given an MDP and a PCTL* specification, derives in a non-deterministic way a system of (possibly nonlinear) equalities and inequalities. The solutions of this system, if any, describe the desired (stochastic) policies. Our main result in this paper is the correctness of our method, i.e., soundness, completeness and termination.Comment: This is a long version of a conference paper published at TABLEAUX 2017. It contains proofs of the main results and fixes a bug. See the footnote on page 1 for detail