A new method for inferring hidden markov models from noisy time sequences

PloS One
David KellyKaroline Wiesner

Abstract

We present a new method for inferring hidden Markov models from noisy time sequences without the necessity of assuming a model architecture, thus allowing for the detection of degenerate states. This is based on the statistical prediction techniques developed by Crutchfield et al. and generates so called causal state models, equivalent in structure to hidden Markov models. The new method is applicable to any continuous data which clusters around discrete values and exhibits multiple transitions between these values such as tethered particle motion data or Fluorescence Resonance Energy Transfer (FRET) spectra. The algorithms developed have been shown to perform well on simulated data, demonstrating the ability to recover the model used to generate the data under high noise, sparse data conditions and the ability to infer the existence of degenerate states. They have also been applied to new experimental FRET data of Holliday Junction dynamics, extracting the expected two state model and providing values for the transition rates in good agreement with previous results and with results obtained using existing maximum likelihood based methods. The method differs markedly from previous Markov-model reconstructions in being able to u...Continue Reading

References

Jul 10, 1989·Physical Review Letters·J P Crutchfield, K Young
Jun 14, 2000·Current Opinion in Structural Biology·C BustamanteD Smith
Dec 24, 2002·Nature Structural Biology·Sean A McKinneyTaekjip Ha
Nov 5, 2003·Nature Biotechnology·Elizabeth A Jares-Erijman, Thomas M Jovin
Jan 30, 2004·Biochemical Society Transactions·S A McKinneyT Ha
Sep 28, 2004·Physical Review Letters·Cosma Rohilla ShaliziRobert Haslinger
Apr 13, 2005·Proceedings of the National Academy of Sciences of the United States of America·Sean A McKinneyTaekjip Ha
Jun 13, 2006·Biophysical Journal·Sean A McKinneyTaekjip Ha
Jul 20, 2006·Journal of the Royal Society, Interface·James P Crutchfield, Olof Görnerup
Jan 9, 2007·Biophysical Journal·G I Mashanov, J E Molloy
Jan 25, 2007·ACS Chemical Biology·Peter V Cornish, Taekjip Ha
Feb 6, 2007·Biophysical Journal·John F BeausangPhilip C Nelson
Jan 8, 2008·Proceedings of the National Academy of Sciences of the United States of America·Chun-Biu LiTamiki Komatsuzaki
May 21, 2008·Artificial Life·Olof Görnerup, James P Crutchfield
Jul 8, 2008·Angewandte Chemie·Jan VogelsangPhilip Tinnefeld
Jul 10, 2009·Nucleic Acids Research·Niels LaurensGijs J L Wuite
Dec 1, 2009·Current Opinion in Chemical Biology·Jovencio Hilario, Stephen C Kowalczykowski
Apr 8, 2010·Biophysical Journal·Hergen BrutzerRalf Seidel
Jul 16, 2010·Methods in Enzymology·Evangelos SisamakisClaus A M Seidel
Nov 4, 2010·Biophysical Journal·Seamus J HoldenAchillefs N Kapanidis

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Citations

Feb 14, 2013·Acta Crystallographica. Section A, Foundations of Crystallography·D P VarnJ P Crutchfield
Jan 5, 2014·PloS One·Sebastian L B KönigRoland K O Sigel
Sep 1, 2012·Chembiochem : a European Journal of Chemical Biology·Søren Preus, L Marcus Wilhelmsson
May 16, 2014·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Christopher C Strelioff, James P Crutchfield
Apr 19, 2017·Physical Review. E·Cina Aghamohammadi, James P Crutchfield
Jun 7, 2018·Frontiers in Computational Neuroscience·Elham Bayat MokhtariEmily F Stone
Jul 29, 2017·Scientific Reports·Cina AghamohammadiJames P Crutchfield
Apr 2, 2018·The Journal of Chemical Physics·Sonja Schmid, Thorsten Hugel
Jan 10, 2021·Biophysical Journal·Zeliha KilicSteve Pressé
Jan 16, 2021·Physical Review Letters·Thomas J ElliottMile Gu
Dec 21, 2018·The Journal of Physical Chemistry. B·Ioannis SgouralisSteve Pressé
Aug 31, 2021·Physical Review Letters·Mauro FaccinJean-Charles Delvenne

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Methods Mentioned

BETA
Fluorescence
FRET

Software Mentioned

HaMMy
Solis
Matlab
CSSR

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