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4. Analysis of Discrete Models for Ecosystem Ecology

Author

Di Giusto, Cinzia, Gaucherel, Cédric, Klaudel, Hanna, Pommereau, Franck, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Roque, Ana, editor, Tomczyk, Arkadiusz, editor, De Maria, Elisabetta, editor, Putze, Felix, editor, Moucek, Roman, editor, Fred, Ana, editor, and Gamboa, Hugo, editor

Published
2020
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5. Model Checking Contest @ Petri Nets, Report on the 2013 edition

Author

Kordon, Fabrice, Linard, Alban, Beccuti, Marco, Buchs, Didier, Fronc, Łukasz, Hillah, Lom-Messan, Hulin-Hubard, Francis, Legond-Aubry, Fabrice, Lohmann, Niels, Marechal, Alexis, Paviot-Adet, Emmanuel, Pommereau, Franck, Rodríguez, César, Rohr, Christian, Thierry-Mieg, Yann, Wimmel, Harro, and Wolf, Karsten

Subjects
Computer Science - Software Engineering
Abstract

This document presents the results of the Model Checking Contest held at Petri Nets 2013 in Milano. This contest aimed at a fair and experimental evaluation of the performances of model checking techniques applied to Petri nets. This is the third edition after two successful editions in 2011 and 2012. The participating tools were compared on several examinations (state space generation and evaluation of several types of formul{\ae} -- reachability, LTL, CTL for various classes of atomic propositions) run on a set of common models (Place/Transition and Symmetric Petri nets). After a short overview of the contest, this paper provides the raw results from the contest, model per model and examination per examination. An HTML version of this report is also provided (http://mcc.lip6.fr)., Comment: one main report (422 pages) and two annexes (1386 and 1740 pages)

Published
2013

6. Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections

Author

Giavitto, Jean-Louis, Klaudel, Hanna, and Pommereau, Franck

Subjects
Computer Science - Computational Engineering, Finance, and Science, J3, I.6.5, I.6.4, D.2.2
Abstract

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:1011.0051

Published
2010
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7. Formal Modelling and Analysis of Distributed Storage Systems

Author

de la Houssaye, Jordan, Pommereau, Franck, Deniel, Philippe, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Koutny, Maciej, editor, Kleijn, Jetty, editor, and Penczek, Wojciech, editor

Published
2017
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8. Scalable Fine-Grained Metric-Based Remeshing Algorithm for Manycore/NUMA Architectures

Author

Rakotoarivelo, Hoby, Ledoux, Franck, Pommereau, Franck, Le-Goff, Nicolas, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Rivera, Francisco F., editor, Pena, Tomás F., editor, and Cabaleiro, José C., editor

Published
2017
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9. Faster Simulation of (Coloured) Petri Nets Using Parallel Computing

Author

Pommereau, Franck, de la Houssaye, Jordan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, van der Aalst, Wil, editor, and Best, Eike, editor

Published
2017
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11. ABCD: A User-Friendly Language for Formal Modelling and Analysis

Author

Pommereau, Franck, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Kordon, Fabrice, editor, and Moldt, Daniel, editor

Published
2016
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12. SNAKES: A Flexible High-Level Petri Nets Library (Tool Paper)

Author

Pommereau, Franck, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Devillers, Raymond, editor, and Valmari, Antti, editor

Published
2015
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15. Towards a Certified Petri Net Model-Checker

Author

Fronc, Lukasz, Pommereau, Franck, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, and Yang, Hongseok, editor

Published
2011
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16. Modeling and Analysis of Security Protocols Using Role Based Specifications and Petri Nets

Author

Bouroulet, Roland, Devillers, Raymond, Klaudel, Hanna, Pelz, Elisabeth, Pommereau, Franck, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, van Hee, Kees M., editor, and Valk, Rüdiger, editor

Published
2008
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17. Towards Efficient Verification of Systems with Dynamic Process Creation

Author

Klaudel, Hanna, Koutny, Maciej, Pelz, Elisabeth, Pommereau, Franck, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Fitzgerald, John S., editor, Haxthausen, Anne E., editor, and Yenigun, Husnu, editor

Published
2008
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18. Causal Time Calculus

Author

Pommereau, Franck, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Larsen, Kim Guldstrand, editor, and Niebert, Peter, editor

Published
2004
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19. Petri Nets as Executable Specifications of High-Level Timed Parallel Systems

Author

Pommereau, Franck, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Bubak, Marian, editor, van Albada, Geert Dick, editor, Sloot, Peter M. A., editor, and Dongarra, Jack, editor

Published
2004
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20. An Algebra of Non-safe Petri Boxes

Author

Devillers, Raymond, Klaudel, Hanna, Koutny, Maciej, Pommereau, Franck, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Kirchner, Hélène, editor, and Ringeissen, Christophe, editor

Published
2002
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22. Reset Petri Net Unfolding Semantics for Ecosystem Hypergraphs

Author

Aguirre-Samboní, Giann Karlo, Gaucherel, Cédric, Haar, Stefan, Pommereau, Franck, Laboratoire Méthodes Formelles (LMF), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Modeling and Exploitation of Interaction and Concurrency (MEXICO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Méthodes Formelles (LMF), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Informatique, BioInformatique, Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay, and This work was supported by the LABEX DIGICOSME grant ESCAPE, reference DIGICOSME RD 242-ESCAPE-15203.

Subjects
[INFO.INFO-FL]Computer Science [cs]/Formal Languages and Automata Theory [cs.FL]
Abstract

International audience

Published
2022

23. EDEN Framework for Interactive Analysis of Ecosystems Models

Author

Pommereau, Franck, Thomas, Colin, Gaucherel, Cédric, Informatique, BioInformatique, Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)

Subjects
Interactive analysis, Formal modelling, [INFO.INFO-FL]Computer Science [cs]/Formal Languages and Automata Theory [cs.FL], Ecosystems
Abstract

International audience; Understanding ecosystems is crucial, in particular to take conservation actions. One way to do so is formal modelling and analysis. In this paper, we present the eden (Ecological Discrete-Event Networks) framework that provides ecologists with discrete modelling languages and dedicated analysis tools. These tools are based on well-known techniques in computer science, like symbolic state-spaces or model-checking, but used in quite a different way. Indeed, most formal analysis techniques provide yes/no answers to well-defined questions, possibly with a witness execution, which is good to assess whether a system exhibits or not a given property. However, most questions in ecology are not stated as “Does the system have such behaviour?” but rather as “Why does the system sometimes has such behaviour and how can we prevent it from happening?” Moreover, these questions are often hard to express formally. With eden, we propose an exploratory way to build progressively a representation of this behaviour that is suitable to answer such questions. The question itself being formalised on the way, together with the model exploration. This approach is based on a hybrid representation of the state-space that can be incrementally split into a graph of components (symbolic sets of states) linked by transitions. The goal is thus to provide the users with a human-readable representation of the state-space that can be fine-tuned with respect to the questions of interest, resulting in an object that constitutes by itself the expected explanation. While eden is rather specific to ecology, we advocate that its analysis method and tools could be beneficial for other domains.

Published
2022

30. Qualitative Modeling for Bridging Expert-Knowledge and Social-Ecological Dynamics of an East African Savanna

Author

Cosme, Maximilien, Hély, Christelle, Pommereau, Franck, Pasquariello, Paolo, Tiberi, Christel, Treydte, Anna C., Gaucherel, Cédric, Cosme, Maximilien, Hély, Christelle, Pommereau, Franck, Pasquariello, Paolo, Tiberi, Christel, Treydte, Anna C., and Gaucherel, Cédric

Abstract

Sub-Saharan social-ecological systems are undergoing changes in environmental conditions, including modifications in rainfall pattern and biodiversity loss. Consequences of such changes depend on complex causal chains which call for integrated management strategies whose efficiency could benefit from ecosystem dynamic modeling. However, ecosystem models often require lots of quantitative information for estimating parameters, which is often unavailable. Alternatively, qualitative modeling frameworks have proved useful for explaining ecosystem responses to perturbations, while only requiring qualitative information about social-ecological interactions and events and providing more general predictions due to their validity for wide ranges of parameter values. In this paper, we propose the Ecological Discrete-Event Network (EDEN), an innovative qualitative dynamic modeling framework based on if-then rules generating non-deterministic dynamics. Based on expert knowledge, observations, and literature, we use EDEN to assess the effect of permanent changes in surface water and herbivores diversity on vegetation and socio-economic transitions in an East African savanna. Results show that water availability drives changes in vegetation and socio-economic transitions, while herbivore functional groups have highly contrasted effects depending on the group. This first use of EDEN in a savanna context is promising for bridging expert knowledge and ecosystem modeling.

Published
2022
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36. Some slide-cascades in social-ecological systems viewed by spatially explicit and multi-scale models

Author

Leloup, Maxime, Cosme, Maximilien, Pommereau, Franck, and Gaucherel, Cédric

Subjects
Discrete-event system, Slide-cascade, Process-based model, Burkina Faso, Petri nets, Foresight, Food security, Decision maker
Abstract

Food security is a key aspect of a sustainable society, and some threats as climate change and food riots may unsettle any social-ecological system such as the Dano’s region in Burkina Faso. Some facets of food security such as food production and food distribution are inherently spatial, and taking space into account may refine our region understanding. We developed both spatialized and non-spatialized discrete event models to address food security dynamics in the Dano socialecological system. The comparison of these two models allowed estimating the influence of spatialization in modelling dynamics. Results showed that water cycle and soil components are critical features of the landscape’s food security. Space refined the region’s understanding in highlighting unexpected slide-cascades the system is exposed to and revealing high sensitivity of the region’s food security to dam water presence. As food security spreading in space, to explicit spatial processes in models appears critical to get a proper understanding of most processes in social ecological systems.

Published
2021
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45. Algebras of coloured Petri nets

Author

Pommereau Franck

Abstract

This document surveys my research work about a framework of composable coloured Petri nets. This framework is organised around a core model of coloured Petri nets that can be extended with various features: control flow, synchronous communication, exceptions, threads, functions and time. Extensions are made in such a way that the underlying model of coloured Petri net is preserved and the usual analysis tools and techniques can still be used. However, specific verifications issues arise from the proposed approaches; we discuss these issues and propose solutions to enable for efficient verification. An implementation of the framework is also presented, as well as applications to the modelling and verification of security protocols, and to the modelling and analysis of biological regulatory networks in the context of developmental processes.

Published
2019
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