Skip to main content

Computing Cumulative Rewards Using Fast Adaptive Uniformisation

  • Conference paper
Computational Methods in Systems Biology (CMSB 2013)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8130))

Included in the following conference series:

  • 1610 Accesses

Abstract

The computation of transient probabilities for continuous-time Markov chains often employs uniformisation, also known as the Jensen’s method. The fast adaptive uniformisation method introduced by Mateescu approximates the probability by neglecting insignificant states, and has proven to be effective for quantitative analysis of stochastic models arising in chemical and biological applications. However, this method has only been formulated for the analysis of properties at a given point of time t. In this paper, we extend fast adaptive uniformisation to handle expected reward properties which reason about the model behaviour until time t, for example, the expected number of chemical reactions that have occurred until t. To show the feasibility of the approach, we integrate the method into the probabilistic model checker PRISM and apply it to a range of biological models, demonstrating superior performance compared to existing techniques.

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

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Aziz, A., Sanwal, K., Singhal, V., Brayton, R.K.: Model-checking continuous-time Markov chains. ACM TCS 1(1), 162–170 (2000)

    Article  MathSciNet  Google Scholar 

  2. Baier, C., Haverkort, B., Hermanns, H., Katoen, J.P.: Performance evaluation and model checking join forces. Commun. ACM 53(9), 76–85 (2010)

    Article  Google Scholar 

  3. Baier, C., Haverkort, B.R., Hermanns, H., Katoen, J.P.: Model-checking algorithms for continuous-time Markov chains. IEEE TSE 29(6), 524–541 (2003)

    Google Scholar 

  4. Clark, G., Courtney, T., Daly, D., Deavours, D., Derisavi, S., Doyle, J.M., Sanders, W.H., Webster, P.: The MÖBIUS modeling tool. In: PNPM, pp. 241–250 (2001)

    Google Scholar 

  5. Dannenberg, F., Kwiatkowska, M., Thachuk, C., Turberfield, A.J.: DNA walker circuits: Computational potential, design, and verification. In: Soloveichik, D., Yurke, B. (eds.) DNA 2013. LNCS, vol. 8141, pp. 31–45. Springer, Heidelberg (2013)

    Google Scholar 

  6. Didier, F., Henzinger, T.A., Mateescu, M., Wolf, V.: SABRE: A tool for stochastic analysis of biochemical reaction networks. In: QEST, pp. 193–194 (2010)

    Google Scholar 

  7. Evans, T.W., Gillespie, C.S., Wilkinson, D.J.: The SBML discrete stochastic models test suite. Bioinformatics 24(2), 285–286 (2008)

    Article  Google Scholar 

  8. Fox, B.L., Glynn, P.W.: Computing Poisson probabilities. Comm. ACM 31(4), 440–445 (1988)

    Article  MathSciNet  Google Scholar 

  9. Heath, J., Kwiatkowska, M., Norman, G., Parker, D., Tymchyshyn, O.: Probabilistic model checking of complex biological pathways. Theoretical Computer Science 319(3), 239–257 (2008)

    Article  MathSciNet  Google Scholar 

  10. Jensen, A.: Markoff chains as an aid in the study of Markoff processes. Skand. Aktuarietidskr. 36, 87–91 (1953)

    MathSciNet  Google Scholar 

  11. Katoen, J.P., Zapreev, I.S., Hahn, E.M., Hermanns, H., Jansen, D.N.: The ins and outs of the probabilistic model checker MRMC. PEVA 68(2), 90–104 (2011)

    Google Scholar 

  12. Kwiatkowska, M., Norman, G., Pacheco, A.: Model checking expected time and expected reward formulae with random time bounds. CMA 51, 305–316 (2006)

    MathSciNet  MATH  Google Scholar 

  13. Kwiatkowska, M., Norman, G., Parker, D.: Stochastic model checking. In: Bernardo, M., Hillston, J. (eds.) SFM 2007. LNCS, vol. 4486, pp. 220–270. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  14. Kwiatkowska, M., Norman, G., Parker, D.: PRISM 4.0: Verification of probabilistic real-time systems. In: Gopalakrishnan, G., Qadeer, S. (eds.) CAV 2011. LNCS, vol. 6806, pp. 585–591. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  15. Lakin, M., Parker, D., Cardelli, L., Kwiatkowska, M., Phillips, A.: Design and analysis of DNA strand displacement devices using probabilistic model checking. Journal of the Royal Society Interface 9(72), 1470–1485 (2012)

    Article  Google Scholar 

  16. Mateescu, M., Wolf, V., Didier, F., Henzinger, T.A.: Fast adaptive uniformisation of the chemical master equation. IET Syst. Biol. 4(6), 441–452 (2010)

    Article  Google Scholar 

  17. Mateescu, M.: Propagation Models for Biochemical Reaction Networks. Ph.D. thesis, EPFL (2011)

    Google Scholar 

  18. van Moorsel, A.P.A., Sanders, W.H.: Adaptive uniformization. ORSA Communications in Statistics: Stochastic Models 10(3), 619–648 (1994)

    Article  MATH  Google Scholar 

  19. Schwarick, M., Heiner, M., Rohr, C.: MARCIE - model checking and reachability analysis done efficiently. In: QEST, pp. 91–100 (2011)

    Google Scholar 

  20. Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science 314(5805), 1585–1588 (2006)

    Article  Google Scholar 

  21. Wickham, S.F.J., Bath, J., Katsuda, Y., Endo, M., Hidaka, K., Sugiyama, H., Turberfield, A.J.: A DNA-based molecular motor that can navigate a network of tracks. Nature Nanotechnology 7(3), 169–173 (2012)

    Article  Google Scholar 

  22. Wickham, S.F.J., Endo, M., Katsuda, Y., Hidaka, K., Bath, J., Sugiyama, H., Turberfield, A.J.: Direct observation of stepwise movement of a synthetic molecular transporter. Nature Nanotechnology 6(3), 166–169 (2011)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Dannenberg, F., Hahn, E.M., Kwiatkowska, M. (2013). Computing Cumulative Rewards Using Fast Adaptive Uniformisation. In: Gupta, A., Henzinger, T.A. (eds) Computational Methods in Systems Biology. CMSB 2013. Lecture Notes in Computer Science(), vol 8130. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-40708-6_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-40708-6_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-40707-9

  • Online ISBN: 978-3-642-40708-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics