Modular organisation of interaction networks based on asymptotic dynamics

This paper investigates questions related to the modularity in discrete models of biological interaction networks. We develop a theoretical framework based on the analysis of their asymptotic dynamics. More precisely, we exhibit formal conditions under which agents of interaction networks can be grouped into modules. As a main result, we show that the usual decomposition in strongly connected components fulfils the conditions of being a modular organisation. Furthermore, we point out that our framework enables a finer analysis providing a decomposition in elementary modules

Indefinite waitings in MIRELA systems

MIRELA is a high-level language and a rapid prototyping framework dedicated to systems where virtual and digital objects coexist in the same environment and interact in real time. Its semantics is given in the form of networks of timed automata, which can be checked using symbolic methods. This paper shows how to detect various kinds of indefinite waitings in the components of such systems. The method is experimented using the PRISM model checker.Comment: In Proceedings ESSS 2015, arXiv:1506.0325

Efficient Reachability Graph Representation of Petri Nets With Unbounded Counters

AbstractIn this paper, we define a class of Petri nets, called Petri nets with counters, that can be seen as place/transition Petri nets enriched with a vector of integer variables on which linear operations may be applied. Their semantics usually leads to huge or infinite reachability graphs. Then, a more compact representation for this semantics is defined as a symbolic state graph whose nodes possibly encode infinitely many values for the variables. Both representations are shown behaviourally equivalent

Proceedings of SUMo and CompoNet 2011

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Efficient reachability graph representation of Petri nets with unbounded counters

International audienceIn this paper, we define a class of Petri nets, called Petri nets with counters, that can be seen as place/transition Petri nets enriched with a vector of integer variables on which linear operations may be applied. Their semantics usually leads to huge or infinite reachability graphs. Then, a more compact representation for this semantics is defined as a symbolic state graph whose nodes possibly encode infinitely many values for the variables. Both representations are shown behaviourally equivalent

A modular, qualitative modelling of regulatory networks using Petri nets

International audienceAdvances in high-throughput technologies have enabled the de-lineation of large networks of interactions that control cellular processes. To understand behavioural properties of these complex networks, mathematical and computational tools are required. The multi-valued logical formalism, initially defined by R. Thomas and co-workers, proved well adapted to account for the qualitative knowledge available on regulatory interactions, and also to perform analyses of their dynamical properties. In this context, we present two representations of logical models in terms of Petri nets. In a first step, we briefly show how logical models of regulatory networks can be transposed into standard (place/transition) Petri nets, and discuss the capabilities of such representation. In the second part, we focus on logical regulatory modules and their composition, demonstrating that a high-level Petri net representation greatly facilitates the modelling of interconnected modules. Doing so, we introduce an explicit means to integrate signals from various interconnected modules, taking into account their spatial distribution. This provides a flexible modelling framework to handle regulatory networks that operate at both intra-and intercellular levels. As an illustration, we describe a simplified model of the segment-polarity module involved in the segmentation of the Drosophila embryo

Dynamic exploration of multi-agent systems with timed periodic tasks

We formalise and study multi-agent timed models MAPTs (Multi-Agent with timed Periodic Tasks), where each agent is associated to a regular timed schema upon which all possibles actions of the agent rely. MAPTs allow for an accelerated semantics and a layered structure of the state space, so that it is possible to explore the latter dynamically and use heuristics to greatly reduce the computation time needed to address reachability problems. We apply MAPTs to explore state spaces of autonomous vehicles and compare it with other approaches in terms of expressivity, abstraction level and computation time

Complexity of Membership and Non-Emptiness Problems in Unbounded Memory Automata

We study the complexity relationship between three models of unbounded memory automata: nu-automata (?-A), Layered Memory Automata (LaMA)and History-Register Automata (HRA). These are all extensions of finite state automata with unbounded memory over infinite alphabets. We prove that the membership problem is NP-complete for all of them, while they fall into different classes for what concerns non-emptiness. The problem of non-emptiness is known to be Ackermann-complete for HRA, we prove that it is PSPACE-complete for ?-A

General parameterised refinement and recursion for the M-net calculus

AbstractThe algebra of M-nets, a high-level class of labelled Petri nets, was introduced in order to cope with the size problem of the low-level Petri box calculus, especially when applied as semantical domain for parallel programming languages. General, unrestricted and parameterised refinement and recursion operators, allowing to represent the (possibly recursive and concurrent) procedure call mechanism, are introduced into the M-net calculus

Incremental and unifying modelling formalism for biological interaction networks

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