10,274 research outputs found
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
Representing Conversations for Scalable Overhearing
Open distributed multi-agent systems are gaining interest in the academic
community and in industry. In such open settings, agents are often coordinated
using standardized agent conversation protocols. The representation of such
protocols (for analysis, validation, monitoring, etc) is an important aspect of
multi-agent applications. Recently, Petri nets have been shown to be an
interesting approach to such representation, and radically different approaches
using Petri nets have been proposed. However, their relative strengths and
weaknesses have not been examined. Moreover, their scalability and suitability
for different tasks have not been addressed. This paper addresses both these
challenges. First, we analyze existing Petri net representations in terms of
their scalability and appropriateness for overhearing, an important task in
monitoring open multi-agent systems. Then, building on the insights gained, we
introduce a novel representation using Colored Petri nets that explicitly
represent legal joint conversation states and messages. This representation
approach offers significant improvements in scalability and is particularly
suitable for overhearing. Furthermore, we show that this new representation
offers a comprehensive coverage of all conversation features of FIPA
conversation standards. We also present a procedure for transforming AUML
conversation protocol diagrams (a standard human-readable representation), to
our Colored Petri net representation
A review of information flow diagrammatic models for product-service systems
A product-service system (PSS) is a combination of products and services to
create value for both customers and manufacturers. Modelling a PSS based on
function orientation offers a useful way to distinguish system inputs and
outputs with regards to how data are consumed and information is used, i.e.
information flow. This article presents a review of diagrammatic information
flow tools, which are designed to describe a system through its functions. The
origin, concept and applications of these tools are investigated, followed by an
analysis of information flow modelling with regards to key PSS properties. A
case study of selection laser melting technology implemented as PSS will then be
used to show the application of information flow modelling for PSS design. A
discussion based on the usefulness of the tools in modelling the key elements of
PSS and possible future research directions are also presented
Learning Petri net models of non-linear gene interactions
Understanding how an individual's genetic make-up influences their risk of disease is a problem of paramount importance. Although machine-learning techniques are able to uncover the relationships between genotype and disease, the problem of automatically building the best biochemical model or “explanation” of the relationship has received less attention. In this paper, I describe a method based on random hill climbing that automatically builds Petri net models of non-linear (or multi-factorial) disease-causing gene–gene interactions. Petri nets are a suitable formalism for this problem, because they are used to model concurrent, dynamic processes analogous to biochemical reaction networks. I show that this method is routinely able to identify perfect Petri net models for three disease-causing gene–gene interactions recently reported in the literature
Two polygraphic presentations of Petri nets
This document gives an algebraic and two polygraphic translations of Petri
nets, all three providing an easier way to describe reductions and to identify
some of them. The first one sees places as generators of a commutative monoid
and transitions as rewriting rules on it: this setting is totally equivalent to
Petri nets, but lacks any graphical intuition. The second one considers places
as 1-dimensional cells and transitions as 2-dimensional ones: this translation
recovers a graphical meaning but raises many difficulties since it uses
explicit permutations. Finally, the third translation sees places as
degenerated 2-dimensional cells and transitions as 3-dimensional ones: this is
a setting equivalent to Petri nets, equipped with a graphical interpretation.Comment: 28 pages, 24 figure
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
Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections
In this paper, we aim at modelling and analyzing the regulation processes in
multi-cellular biological systems, in particular tissues.
The modelling framework is based on interconnected logical regulatory
networks a la Rene Thomas equipped with information about their spatial
relationships. The semantics of such models is expressed through colored Petri
nets to implement regulation rules, combined with topological collections to
implement the spatial information.
Some constraints are put on the the representation of spatial information in
order to preserve the possibility of an enumerative and exhaustive state space
exploration.
This paper presents the modelling framework, its semantics, as well as a
prototype implementation that allowed preliminary experimentation on some
applications.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
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
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