Bisimilarity and Behaviour-Preserving Reconfigurations of Open Petri Nets

We propose a framework for the specification of behaviour-preserving reconfigurations of systems modelled as Petri nets. The framework is based on open nets, a mild generalisation of ordinary Place/Transition nets suited to model open systems which might interact with the surrounding environment and endowed with a colimit-based composition operation. We show that natural notions of bisimilarity over open nets are congruences with respect to the composition operation. The considered behavioural equivalences differ for the choice of the observations, which can be single firings or parallel steps. Additionally, we consider weak forms of such equivalences, arising in the presence of unobservable actions. We also provide an up-to technique for facilitating bisimilarity proofs. The theory is used to identify suitable classes of reconfiguration rules (in the double-pushout approach to rewriting) whose application preserves the observational semantics of the net.Comment: To appear in "Logical Methods in Computer Science", 41 page

Modelling epistasis in genetic disease using Petri nets, evolutionary computation and frequent itemset mining

Petri nets are useful for mathematically modelling disease-causing genetic epistasis. A Petri net model of an interaction has the potential to lead to biological insight into the cause of a genetic disease. However, defining a Petri net by hand for a particular interaction is extremely difficult because of the sheer complexity of the problem and degrees of freedom inherent in a Petri net’s architecture. We propose therefore a novel method, based on evolutionary computation and data mining, for automatically constructing Petri net models of non-linear gene interactions. The method comprises two main steps. Firstly, an initial partial Petri net is set up with several repeated sub-nets that model individual genes and a set of constraints, comprising relevant common sense and biological knowledge, is also defined. These constraints characterise the class of Petri nets that are desired. Secondly, this initial Petri net structure and the constraints are used as the input to a genetic algorithm. The genetic algorithm searches for a Petri net architecture that is both a superset of the initial net, and also conforms to all of the given constraints. The genetic algorithm evaluation function that we employ gives equal weighting to both the accuracy of the net and also its parsimony. We demonstrate our method using an epistatic model related to the presence of digital ulcers in systemic sclerosis patients that was recently reported in the literature. Our results show that although individual “perfect” Petri nets can frequently be discovered for this interaction, the true value of this approach lies in generating many different perfect nets, and applying data mining techniques to them in order to elucidate common and statistically significant patterns of interaction

Petri Nets Modeling of Dead-End Refinement Problems in a 3D Anisotropic hp-Adaptive Finite Element Method

We consider two graph grammar based Petri nets models for anisotropic refinements of three dimensional hexahedral grids. The first one detects possible dead-end problems during the graph grammar based anisotropic refinements of the mesh. The second one employs an enhanced graph grammar model that is actually dead-end free. We apply the resulting algorithm to the simulation of resistivity logging measurements for estimating the location of underground oil and/or gas formations. The graph grammar based Petri net models allow to fix the self-adaptive mesh refinement algorithm and finish the adaptive computations with the required accuracy needed by the numerical solution

Connector algebras for C/E and P/T nets interactions

A quite fourishing research thread in the recent literature on component based system is concerned with the algebraic properties of different classes of connectors. In a recent paper, an algebra of stateless connectors was presented that consists of five kinds of basic connectors, namely symmetry, synchronization, mutual exclusion, hiding and inaction, plus their duals and it was shown how they can be freely composed in series and in parallel to model sophisticated "glues". In this paper we explore the expressiveness of stateful connectors obtained by adding one-place buffers or unbounded buffers to the stateless connectors. The main results are: i) we show how different classes of connectors exactly correspond to suitable classes of Petri nets equipped with compositional interfaces, called nets with boundaries; ii) we show that the difference between strong and weak semantics in stateful connectors is reflected in the semantics of nets with boundaries by moving from the classic step semantics (strong case) to a novel banking semantics (weak case), where a step can be executed by taking some "debit" tokens to be given back during the same step; iii) we show that the corresponding bisimilarities are congruences (w.r.t. composition of connectors in series and in parallel); iv) we show that suitable monoidality laws, like those arising when representing stateful connectors in the tile model, can nicely capture concurrency aspects; and v) as a side result, we provide a basic algebra, with a finite set of symbols, out of which we can compose all P/T nets, fulfilling a long standing quest

Applying Algebraic Approaches for Modeling Workflows and their Transformations in Mobile Networks

In emergency scenarios we can obtain a more effective coordination among team members, each of them equipped with hand-held devices, through the use of workflow management software. Team members constitute a Mobile Ad-hoc NETwork (MANET), whose topology both influences and is influenced by the workflow. In this paper we propose an algebraic approach for modeling workflow progress as well as its modifications as required by topology transformations. The approach is based on Algebraic Higher-Order Nets and sees both workflows and topologies as tokens, allowing their concurrent modification

An LTL Semantics of Business Workflows with Recovery

We describe a business workflow case study with abnormal behavior management (i.e. recovery) and demonstrate how temporal logics and model checking can provide a methodology to iteratively revise the design and obtain a correct-by construction system. To do so we define a formal semantics by giving a compilation of generic workflow patterns into LTL and we use the bound model checker Zot to prove specific properties and requirements validity. The working assumption is that such a lightweight approach would easily fit into processes that are already in place without the need for a radical change of procedures, tools and people's attitudes. The complexity of formalisms and invasiveness of methods have been demonstrated to be one of the major drawback and obstacle for deployment of formal engineering techniques into mundane projects

Thermodynamic graph-rewriting

We develop a new thermodynamic approach to stochastic graph-rewriting. The ingredients are a finite set of reversible graph-rewriting rules called generating rules, a finite set of connected graphs P called energy patterns and an energy cost function. The idea is that the generators define the qualitative dynamics, by showing which transformations are possible, while the energy patterns and cost function specify the long-term probability $\pi$ of any reachable graph. Given the generators and energy patterns, we construct a finite set of rules which (i) has the same qualitative transition system as the generators; and (ii) when equipped with suitable rates, defines a continuous-time Markov chain of which $\pi$ is the unique fixed point. The construction relies on the use of site graphs and a technique of `growth policy' for quantitative rule refinement which is of independent interest. This division of labour between the qualitative and long-term quantitative aspects of the dynamics leads to intuitive and concise descriptions for realistic models (see the examples in S4 and S5). It also guarantees thermodynamical consistency (AKA detailed balance), otherwise known to be undecidable, which is important for some applications. Finally, it leads to parsimonious parameterizations of models, again an important point in some applications