Identification of hidden markov models for ion channel currents-Part I: Colored background noise

IEEE Transactions on Signal Processing

Volumn 46, Issue 7, 1998, Pages 1901-1915

  Venkataramanan, Lalitha ^a   Walsh, John L ^a   Kuc, Roman ^a   Sigworth, Fred J ^a  

^a Yale University   (United States)

Author keywords

Colored noise; Hidden markov model; Ion channel

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; ELECTRIC CURRENTS; MARKOV PROCESSES; MATHEMATICAL MODELS; SIGNAL TO NOISE RATIO; SPURIOUS SIGNAL NOISE; VECTORS;

COLORED BACKGROUND NOISE; HIDDEN MARKOV MODELS (HMM); ION CHANNELS;

SIGNAL PROCESSING;

EID: 0032122144     PISSN: 1053587X     EISSN: None     Source Type: Journal    
DOI: 10.1109/78.700963     Document Type: Article

References (30)

1. E. Neher and B. Sakmann, "The patch clamp technique," Sci. Amer., pp. 44-51, Mar. 1992.
2. D. Colquhoun and A. G. Hawkes, "The principles of stochastic interpretation of ion-channel mechanisms," in Single-Channel Recording, B. Sakmann and E. Neher, Eds. New York: Plenum, 1995.
3. J. D. Becker et al., "Analyzing ion channels with hidden Markov models," Pflugers Arch., vol. 426, pp. 328-332, 1994.
4. S. H. Chung, J. Moore, L. Xia, L. S. Premkumar, and P. W. Gage, "Characterization of single channel currents using digital signal processing techniques based on hidden Markov models," Phil. Trans. R. Soc. Land. B, vol. 329, pp. 265-285, 1990.
5. S. H. Chung, V. Krishnamurthy, and J. B. Moore, "Adaptive processing techniques based on hidden Markov models for characterizing very small channel currents buried in noise and deterministic interferences," Phil. Trans. R. Soc. Land. B, vol. 334, pp. 357-384, 1991.
6. D. R. Fredkin and J. A. Rice, "Maximum likelihood estimation and identification from single-channel recordings," in Proc. R. Soc. Land. B, 1992, vol. 249, pp. 125-132.
7. D. R. Fredkin and J. A. Rice, "Bayesian restoration of single channel patch clamp recordings," Biometrika, vol. 48, pp. 427448, 1992.
8. F. Qin, J. Chen, A. Auerbach, and F. Sachs, "Extracting channel kinetic parameters using hidden Markov techniques," presented at the 38th Anna. Meeting Biophys. Soc., New Orleans, LA, 1994.
9. L. R. Rabiner and B. H. Juang, "An introduction to hidden Markov models," IEEE Acoust., Speech, Signal Processing Mag., pp. 4-16, Jan. 1986.
10. S. E. Levinson, L. R. Rabiner, and M. M. Sondhi, "An introduction to the application of the theory of probabilistic functions of a Markov process to automatic speech recognition," Bell Syst. Tech. J., vol. 62, pp. 1035-1074, 1983.
11. R. A. Levis and J. L. Rae, "The use of quartz patch pipettes for low noise single channel recording," Biophys. J., vol. 65, pp. 1666-1677, 1993.
12. F. J. Sigworth, "Electronic design of the patch clamp," in Single-Channel Recording, B. Sakmann and E. Neher, Eds. New York: Plenum, 1995.
13. C. J. Wellekens, "Explicit time correlation in hidden Markov models for speech recognition," in Proc. ICASSP, 19, pp. 384-387.
14. V. Krishnamurthy and L. B. White, "Blind equalization of FIR channels with Markov inputs," in Proc. IFAC Int. Conf. Adaptive Syst. Contr. Signal Process., 19.
15. J. L. Walsh, "Extraction of single channel current from correlated noise via a hidden Markov model," M.D. dissertation, Sch. Medicine, Yale Univ., New Haven, CT, 1992.
16. A. B. Poritz, "Hidden Markov models: A guided tour," Proc. ICASSP, 19, pp. 7-13.
17. S. M. Sine, T. Claudio, and F. J. Sigworth, "Activation of Torpedo acetylcholine receptors expressed in mouse fibroblasts. Single channel current kinetics reveal distinct agonist binding affinities," J. General Physiol., vol. 96, pp. 39537, 1990.
18. S. M. Kay and S. L. Marple, "Spectrum analysis-a modern perspective," Proc. IEEE. vol. 69, pp. 1380-1419, 1981.
19. A. A. Giordano and F. M. Hsu, Least Squares Estimation with Applications to Digital Signal Processing. New York: Wiley, 1985.
20. V. Krishnamurthy and A. Logothetis, "Iterative and recursive estimators for hidden Markov errors-in-variables models," IEEE Trans. Signal Processing, vol. 44, pp. 629-639, 1996.
21. L. E. Baum, T. Pétrie, G. Soûles, and N. Weiss, "A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains," Ann. Math. Statist., vol. 41, pp. 164-171, 1970.
22. L. A. Liporace, "Maximum likelihood estimation for multivariate observations of Markov sources," IEEE Trans. Inform. Theory, vol. 28, pp. 729-734, 1982.
23. D. Colquhoun and F. J. Sigworth, "Fitting and statistical analysis of single-channel records," in Single-Channel Recording, B. Sakmann and E. Neher, Eds. New York: Plenum, 1995.
24. G. E. P. Box and G. M. Jenkins, Time Series Analysis: Forecasting and Control. San Francisco, CA: Holden-Day, 1970.
25. V. Krishnamurthy, J. B. Moore, and S. H. Chung, "Hidden Markov model signal processing in presence of unknown deterministic interferences," IEEE Trans. Automat. Contr., vol. 38, pp. 146-152, 1993.
26. S. H. Heinemann and F. J. Sigworth, "Open channel noise VI. Analysis of amplitude histograms to determine rapid kinetic parameters," Biophys. J., vol. 60, pp. 577-587, 1991.
27. F. J. Sigworth, D. W. Urry, and U. K. Prasad, "Open channel noise III. High-resolution recordings show rapid current fluctuations in Gramicidin A and four chemical analogues," Biophys. J., vol. 52, pp. 1055-1064, 1987.
28. S. H. Heinemann and F. J. Sigworth, "Fluctuations of ionic currents and ion channel proteins," in Thermodynamics of Membrane Receptors and Channels. Boca Raton, FL: CRC, 1993.
29. T. W. Anderson, An Introduction to Multivariate Statistical Analysis, 2nd ed. New York: Wiley, 1984, Wiley Series in Probability and Mathematical Statistics, 1984.
30. L. E. Baum, "An inequality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes," Inequalities, vol. 3, 1972.