Skip to main content

On the Formal Analysis of HMM Using Theorem Proving

  • Conference paper
Formal Methods and Software Engineering (ICFEM 2014)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 8829))

Included in the following conference series:

Abstract

Hidden Markov Models (HMMs) have been widely utilized for modeling time series data in various engineering and biological systems. The analyses of these models are usually conducted using computer simulations and paper-and-pencil proof methods and, more recently, using probabilistic model-checking. However, all these methods either do not guarantee accurate analysis or are not scalable (for instance, they can hardly handle the computation when some parameters become very huge). As an alternative, we propose to use higher-order logic theorem proving to reason about properties of discrete HMMs by applying automated verification techniques. This paper presents some foundational formalizations in this regard, namely an extended-real numbers based formalization of finite-state Discrete-Time Markov chains and HMMs along with the verification of some of their fundamental properties. The distinguishing feature of our work is that it facilitates automatic verification of systems involving HMMs. For illustration purposes, we utilize our results for the formal analysis of a DNA sequence.

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 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Affeldt, R., Hagiwara, M.: Formalization of Shannon’s Theorems in SSReflect-Coq. In: Beringer, L., Felty, A. (eds.) ITP 2012. LNCS, vol. 7406, pp. 233–249. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  2. C. Baier and J. Katoen. Principles of Model Checking. MIT Press (2008)

    Google Scholar 

  3. Bhattacharya, R.N., Waymire, E.C.: Stochastic Processes with Applications. John Wiley & Sons (1990)

    Google Scholar 

  4. ChIP-Seq Tool Set (2012), http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi

  5. Chung, K.L.: Markov chains with stationary transition probabilities. Springer, Heidelberg (1960)

    Book  MATH  Google Scholar 

  6. Coq (2014), http://coq.inria.fr/

  7. Daniel, N.: Electrocardiogram Signal Processing using Hidden Markov Models. Ph.D. Thesis, Czech Technical University, Czech Republic (2003)

    Google Scholar 

  8. Eddy, S.R.: What is a Hidden Markov Model? Nature Biotechnology 22(10), 1315–1316 (2004)

    Google Scholar 

  9. Frédéric, S., Delorenzi, M.: MAMOT: Hidden Markov Modeling Tool. Bioinformatics 24(11), 1399–1400 (2008)

    Article  Google Scholar 

  10. Gordon, M.J.C.: Mechanizing Programming Logics in Higher-0rder Logic. In: Current Trends in Hardware Verification and Automated Theorem Proving, pp. 387–439. Springer, Heidelberg (1989)

    Chapter  Google Scholar 

  11. HMMER (2013), http://hmmer.janelia.org/

  12. HMMTool (2013), http://iri.columbia.edu/climate/forecast/stochastictools/

  13. Hölzl, J., Heller, A.: Three Chapters of Measure Theory in Isabelle/HOL. In: van Eekelen, M., Geuvers, H., Schmaltz, J., Wiedijk, F. (eds.) ITP 2011. LNCS, vol. 6898, pp. 135–151. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  14. L. Liu (2013), http://hvg.ece.concordia.ca/projects/prob-it/dtmc_hmm.html

  15. Liu, L., Hasan, O., Tahar, S.: Formalization of finite-state discrete-time markov chains in HOL. In: Bultan, T., Hsiung, P.-A. (eds.) ATVA 2011. LNCS, vol. 6996, pp. 90–104. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  16. MacDonald, I.L., Zucchini, W.: Hidden Markov and Other Models for Discrete-valued Time Series. Chapman & Hall, London (1997)

    Google Scholar 

  17. Mhamdi, T., Hasan, O., Tahar, S.: On the Formalization of the Lebesgue Integration Theory in HOL. In: Kaufmann, M., Paulson, L.C. (eds.) ITP 2010. LNCS, vol. 6172, pp. 387–402. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  18. MRMC (2013), http://www.mrmc-tool.org/trac/

  19. Norris, J.R.: Markov Chains. Cambridge University Press (1999)

    Google Scholar 

  20. PRISM (2013), http://www.prismmodelchecker.org

  21. Robertson, A.W., Kirshner, S., Smyth, P.: Downscaling of Daily Rainfall Occurrence over Northeast Brazil using a Hidden Markov Model. Journal of Climate 17, 4407–4424 (2004)

    Article  Google Scholar 

  22. Rutten, J., Kwaiatkowska, M., Norman, G., Parker, D.: Mathematical Techniques for Analyzing Concurrent and Probabilisitc Systems. CRM Monograph Series, vol. 23. American Mathematical Society (2004)

    Google Scholar 

  23. Sen, K., Viswanathan, M., Agha, G.: VESTA: A Statistical Model-Checker and Analyzer for Probabilistic Systems. In: IEEE International Conference on the Quantitative Evaluation of Systems, pp. 251–252 (2005)

    Google Scholar 

  24. YMER (2013), http://www.tempastic.org/ymer/

  25. Zhang, L., Hermanns, H., Jansen, D.N.: Logic and Model Checking for Hidden Markov Models. In: Wang, F. (ed.) FORTE 2005. LNCS, vol. 3731, pp. 98–112. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  26. Zhang, L.J.: Logic and Model Checking for Hidden Markov Models. Master Thesis, Universität des Saarlandes, Germany (2004)

    Google Scholar 

  27. Zoubin, G.: An Introduction to Hidden Markov Models and Bayesian Networks. International Journal of Pattern Recognition and Artificial Intelligence 15(1), 9–42 (2001)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Liu, L., Aravantinos, V., Hasan, O., Tahar, S. (2014). On the Formal Analysis of HMM Using Theorem Proving. In: Merz, S., Pang, J. (eds) Formal Methods and Software Engineering. ICFEM 2014. Lecture Notes in Computer Science, vol 8829. Springer, Cham. https://doi.org/10.1007/978-3-319-11737-9_21

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-11737-9_21

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-11736-2

  • Online ISBN: 978-3-319-11737-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics