Skip to main content

Drawing the Line: Basin Boundaries in Safe Petri Nets

  • Conference paper
  • First Online:
Computational Methods in Systems Biology (CMSB 2020)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 12314))

Included in the following conference series:

Abstract

Attractors of network dynamics represent the long-term behaviours of the modelled system. Understanding the basin of an attractor, comprising all those states from which the evolution will eventually lead into that attractor, is therefore crucial for understanding the response and differentiation capabilities of a dynamical system. Building on our previous results [2] allowing to find attractors via Petri net Unfoldings, we exploit further the unfolding technique for a backward exploration of the state space, starting from a known attractor, and show how all strong or weak basins of attractions can be explicitly computed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Which Cousot et al.  [6] have recently use as theoretical foundation for capturing which entity of a program is responsible of a given behavior.

  2. 2.

    Note that infinite-state Petri nets do not have finite complete prefixes in our sense.

References

  1. Abadi, M., Lamport, L.: The existence of refinement mappings. Theor. Comput. Sci. 82(2), 253–284 (1991)

    Article  MathSciNet  Google Scholar 

  2. Chatain, T., Haar, S., Jezequel, L., Paulevé, L., Schwoon, S.: Characterization of reachable attractors using Petri Net Unfoldings. In: Mendes, P., Dada, J.O., Smallbone, K. (eds.) CMSB 2014. LNCS, vol. 8859, pp. 129–142. Springer, Cham (2014). https://doi.org/10.1007/978-3-319-12982-2_10

    Chapter  Google Scholar 

  3. Chatain, T., Haar, S., Kolcák, J., Paulevé, L., Thakkar, A.: Concurrency in Boolean networks. Natural Comput. (2019, to appear)

    Google Scholar 

  4. Thomas Chatain and Loïc Paulevé. Goal-driven unfolding of petri nets. In Roland Meyer and Uwe Nestmann, editors, 28th International Conference on Concurrency Theory, CONCUR 2017, 5–8 September 2017, Berlin, Germany, LIPIcs, vol. 85, pp. 18:1–18:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2017)

    Google Scholar 

  5. Cohen, D.P.A., Martignetti, L., Robine, S., Barillot, E., Zinovyev, A., Calzone, L.: Mathematical modelling of molecular pathways enabling tumour cell invasion and migration. PLoS Comput. Biol. 11(11), e1004571 (2015)

    Article  Google Scholar 

  6. Deng, C., Cousot, P.: Responsibility analysis by abstract interpretation. In: Chang, B.-Y.E. (ed.) SAS 2019. LNCS, vol. 11822, pp. 368–388. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32304-2_18

    Chapter  Google Scholar 

  7. Diekert, V., Rozenberg, G. (eds.): The Book of Traces. World Scientific (1995)

    Google Scholar 

  8. Esparza, J., Heljanko, K.: Unfoldings - A Partial-Order Approach to Model Checking. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-77426-6

    Book  MATH  Google Scholar 

  9. Esparza, J., Römer, S., Vogler, W.: An improvement of McMillan’s unfolding algorithm. FMSD 20, 285–310 (2002)

    MATH  Google Scholar 

  10. Fitime, L.F., Roux, O., Guziolowski, C., Paulevé, L.: Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming. Algorithm Molecular Biol. 12(1), 19 (2017)

    Article  Google Scholar 

  11. Fueyo, S., Monteiro, P.T., Naldi, A., Dorier, J., Remy, É, Chaouiya, C.: Reversed dynamics to uncover basins of attraction of asynchronous logical models. F1000Research 30(6) (2017)

    Google Scholar 

  12. Godefroid, P. (ed.): Partial-Order Methods for the Verification of Concurrent Systems. LNCS, vol. 1032. Springer, Heidelberg (1996). https://doi.org/10.1007/3-540-60761-7

    Book  MATH  Google Scholar 

  13. Goubault, É., Raussen, M.: Dihomotopy as a tool in state space analysis tutorial. In: Rajsbaum, S. (ed.) LATIN 2002. LNCS, vol. 2286, pp. 16–37. Springer, Heidelberg (2002). https://doi.org/10.1007/3-540-45995-2_8

    Chapter  Google Scholar 

  14. Khomenk, V.: Punf. http://homepages.cs.ncl.ac.uk/victor.khomenko/tools/punf/

  15. Klarner, H., Siebert, H., Nee, S., Heinitz, F.: Basins of attraction, commitment sets and phenotypes of Boolean networks. IEEE/ACM Trans. Comput. Biol. Bioinform. 17, 115–1124 (2018)

    Google Scholar 

  16. Mandon, H., Su, C., Haar, S., Pang, J., Paulevé, L.: Sequential reprogramming of Boolean networks made practical. In: Bortolussi, L., Sanguinetti, G. (eds.) CMSB 2019. LNCS, vol. 11773, pp. 3–19. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-31304-3_1

    Chapter  Google Scholar 

  17. Mandon, H., Su, C., Pang, J., Paul, S., Haar, S., Paulevé, L.: Algorithms for the sequential reprogramming of Boolean networks. IEEE/ACM Trans. Computat. Biol. Bioinform. (2019, to appear)

    Google Scholar 

  18. McMillan, K.L.: Using unfoldings to avoid the state explosion problem in the verification of asynchronous circuits. In: CAV, pp. 164–177 (1992)

    Google Scholar 

  19. Mendes, N.D., Henriques, R., Remy, E., Carneiro, J., Monteiro, P.T., Chaouiya, C.: Estimating attractor reachability in asynchronous logical models. Front. Physiol. 9 (2018)

    Google Scholar 

  20. Murata, T.: Petri nets: properties, analysis and applications. Proc. IEEE 77(4), 541–580 (1989)

    Article  Google Scholar 

  21. Nielsen, M., Plotkin, G.D., Winskel, G.: Petri nets, event structures and domains, Part I. Theor. Comput. Sci. 13, 85–108 (1981)

    Article  Google Scholar 

  22. Schwoon, S.: Mole. http://www.lsv.ens-cachan.fr/~schwoon/tools/mole/

  23. Vogler, W.: Fairness and partial order semantics. Inf. Process. Lett. 55(1), 33–39 (1995)

    Article  MathSciNet  Google Scholar 

Download references

Acknowledgments

This research was supported by Agence Nationale de la Recherche (ANR) with the ANR-FNR project AlgoReCell (ANR-16-CE12-0034); Labex DigiCosme (project ANR-11-LABEX-0045-DIGICOSME) operated by ANR as part of the program “Investissement d’Avenir” Idex Paris-Saclay (ANR-11-IDEX-0003-02).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stefan Haar .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Haar, S., Paulevé, L., Schwoon, S. (2020). Drawing the Line: Basin Boundaries in Safe Petri Nets. In: Abate, A., Petrov, T., Wolf, V. (eds) Computational Methods in Systems Biology. CMSB 2020. Lecture Notes in Computer Science(), vol 12314. Springer, Cham. https://doi.org/10.1007/978-3-030-60327-4_17

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-60327-4_17

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-60326-7

  • Online ISBN: 978-3-030-60327-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics