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A new constant memory recursion for hidden Markov models.

Francesco Bartolucci1, Silvia Pandolfi

  • 1Department of Economics, Finance and Statistics, University of Perugia , Perugia, Italy .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 29, 2013
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Summary
This summary is machine-generated.

We developed a new recursion for hidden Markov (HM) models, enabling efficient state estimation and decoding. This method significantly reduces memory requirements compared to existing algorithms, even for long time-series data.

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Area of Science:

  • Statistics
  • Machine Learning
  • Time Series Analysis

Background:

  • Hidden Markov (HM) models are widely used for analyzing sequential data.
  • Traditional estimation algorithms like Baum-Welch have memory limitations that scale with data length.
  • Existing methods may require numerical adjustments (renormalizations) and complex decoding procedures (e.g., Viterbi).

Purpose of the Study:

  • To develop a novel recursion for hidden Markov models (HM) based on Bartolucci and Besag (2002).
  • To implement an estimation algorithm with memory requirements independent of the observed data series length.
  • To enable direct global decoding of latent states without Viterbi, reducing computational complexity.

Main Methods:

  • Developed a new recursion to compute the conditional distribution of latent states.
  • Implemented an estimation algorithm leveraging this recursion, achieving constant memory usage.
  • Compared the proposed algorithm with Baum-Welch and the Churbanov-Winters-Hilt linear memory algorithm via simulations.

Main Results:

  • The proposed algorithm requires memory independent of the time-series length.
  • It avoids numerical renormalization issues common in other methods.
  • Direct global decoding is achieved, outperforming Viterbi in memory efficiency.

Conclusions:

  • The novel recursion provides a memory-efficient approach for HM model estimation and decoding.
  • This method offers advantages over Baum-Welch and Viterbi, particularly for large datasets.
  • Simulations confirm the computational and memory benefits for continuous time-series data.