Encoding Higher Level Extensions of Petri Nets in Answer Set Programming

Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require simulation based reasoning. To answer such questions, we need formalisms to build pathway models, add extensions, simulate, and reason with them. We chose Petri Nets and Answer Set Programming (ASP) as suitable formalisms, since Petri Net models are similar to biological pathway diagrams; and ASP provides easy extension and strong reasoning abilities. We found that certain aspects of biological pathways, such as locations and substance types, cannot be represented succinctly using regular Petri Nets. As a result, we need higher level constructs like colored tokens. In this paper, we show how Petri Nets with colored tokens can be encoded in ASP in an intuitive manner, how additional Petri Net extensions can be added by making small code changes, and how this work furthers our long term research goals. Our approach can be adapted to other domains with similar modeling needs

1-Safe Petri nets and special cube complexes: equivalence and applications

Nielsen, Plotkin, and Winskel (1981) proved that every 1-safe Petri net $N$ unfolds into an event structure $\mathcal{E}_N$. By a result of Thiagarajan (1996 and 2002), these unfoldings are exactly the trace regular event structures. Thiagarajan (1996 and 2002) conjectured that regular event structures correspond exactly to trace regular event structures. In a recent paper (Chalopin and Chepoi, 2017, 2018), we disproved this conjecture, based on the striking bijection between domains of event structures, median graphs, and CAT(0) cube complexes. On the other hand, in Chalopin and Chepoi (2018) we proved that Thiagarajan's conjecture is true for regular event structures whose domains are principal filters of universal covers of (virtually) finite special cube complexes. In the current paper, we prove the converse: to any finite 1-safe Petri net $N$ one can associate a finite special cube complex ${X}_N$ such that the domain of the event structure $\mathcal{E}_N$ (obtained as the unfolding of $N$) is a principal filter of the universal cover $\widetilde{X}_N$ of $X_N$. This establishes a bijection between 1-safe Petri nets and finite special cube complexes and provides a combinatorial characterization of trace regular event structures. Using this bijection and techniques from graph theory and geometry (MSO theory of graphs, bounded treewidth, and bounded hyperbolicity) we disprove yet another conjecture by Thiagarajan (from the paper with S. Yang from 2014) that the monadic second order logic of a 1-safe Petri net is decidable if and only if its unfolding is grid-free. Our counterexample is the trace regular event structure $\mathcal{\dot E}_Z$ which arises from a virtually special square complex $\dot Z$. The domain of $\mathcal{\dot E}_Z$ is grid-free (because it is hyperbolic), but the MSO theory of the event structure $\mathcal{\dot E}_Z$ is undecidable

A counterexample to Thiagarajan's conjecture on regular event structures

We provide a counterexample to a conjecture by Thiagarajan (1996 and 2002) that regular event structures correspond exactly to event structures obtained as unfoldings of finite 1-safe Petri nets. The same counterexample is used to disprove a closely related conjecture by Badouel, Darondeau, and Raoult (1999) that domains of regular event structures with bounded $\natural$-cliques are recognizable by finite trace automata. Event structures, trace automata, and Petri nets are fundamental models in concurrency theory. There exist nice interpretations of these structures as combinatorial and geometric objects. Namely, from a graph theoretical point of view, the domains of prime event structures correspond exactly to median graphs; from a geometric point of view, these domains are in bijection with CAT(0) cube complexes. A necessary condition for both conjectures to be true is that domains of regular event structures (with bounded $\natural$-cliques) admit a regular nice labeling. To disprove these conjectures, we describe a regular event domain (with bounded $\natural$-cliques) that does not admit a regular nice labeling. Our counterexample is derived from an example by Wise (1996 and 2007) of a nonpositively curved square complex whose universal cover is a CAT(0) square complex containing a particular plane with an aperiodic tiling. We prove that other counterexamples to Thiagarajan's conjecture arise from aperiodic 4-way deterministic tile sets of Kari and Papasoglu (1999) and Lukkarila (2009). On the positive side, using breakthrough results by Agol (2013) and Haglund and Wise (2008, 2012) from geometric group theory, we prove that Thiagarajan's conjecture is true for regular event structures whose domains occur as principal filters of hyperbolic CAT(0) cube complexes which are universal covers of finite nonpositively curved cube complexes

Using Colored Stochastic Petri Net (CS-PN) software for protocol specification, validation, and evaluation

The specification, verification, validation, and evaluation, which make up the different steps of the CS-PN software are outlined. The colored stochastic Petri net software is applied to a Wound/Wait protocol decomposable into two principal modules: request or couple (transaction, granule) treatment module and wound treatment module. Each module is specified, verified, validated, and then evaluated separately, to deduce a verification, validation and evaluation of the complete protocol. The colored stochastic Petri nets tool is shown to be a natural extension of the stochastic tool, adapted to distributed systems and protocols, because the color conveniently takes into account the numerous sites, transactions, granules and messages

Petri net equivalence

Determining whether two Petri nets are equivalent is an interesting problem from both practical and theoretical standpoints. Although it is undecidable in the general case, for many interesting nets the equivalence problem is solvable. This paper explores, mostly from a theoretical point of view, some of the issues of Petri net equivalence, including both reachability sets and languages. Some new definitions of reachability set equivalence are described which allow the markings of some places to be treated identically or ignored, analogous to the Petri net languages in which multiple transitions may be labeled with the same symbol or with the empty string. The complexity of some decidable Petri net equivalence problems is analyzed

An Operational Petri Net Semantics for the Join-Calculus

We present a concurrent operational Petri net semantics for the join-calculus, a process calculus for specifying concurrent and distributed systems. There often is a gap between system specifications and the actual implementations caused by synchrony assumptions on the specification side and asynchronously interacting components in implementations. The join-calculus is promising to reduce this gap by providing an abstract specification language which is asynchronously distributable. Classical process semantics establish an implicit order of actually independent actions, by means of an interleaving. So does the semantics of the join-calculus. To capture such independent actions, step-based semantics, e.g., as defined on Petri nets, are employed. Our Petri net semantics for the join-calculus induces step-behavior in a natural way. We prove our semantics behaviorally equivalent to the original join-calculus semantics by means of a bisimulation. We discuss how join specific assumptions influence an existing notion of distributability based on Petri nets.Comment: In Proceedings EXPRESS/SOS 2012, arXiv:1208.244

Modeling the fraud-like investment founds by Petri nets

In this paper we model the fraud-like investment founds using place-transition Petri nets. We will also classify the business using regression line in order to find the possible fraud-like investment founds. In these regression lines we compute analytical the mark of a place in function of some other elements of the Petri net, and next we express this value in function of the same elements using regression. From the identity of the coefficients we find a ratio between two weights of arcs. We make also a program where the marks and transitions are implemented as classes for Petri nets, and, using the heritage mechanism we extend the Petri net to Petri net with priorities.Petri nets, fraud-like investment founds, objects programming.