The Infinite Hidden Markov Model for Single Molecule experiments
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Implements the infinite Hidden Markov Model for diverse single-molecule experiments.

This project contains Matlab scripts that implement the infinite Hidden Markov Model (iHMM) [1, 2] for specific datasets from single-molecule experiments.

The code can be used out of the box for similar applications or serve as a guide to develop new emission models. Applying the scripts to one of the datasets provided would be a good tutorial on analyzing the output of non-parametric HMMs.

[1] Van Gael, J. et al. Beam sampling for the infinite Hidden Markov Model. Proceedings of the 25th International Conference of Machine Learning, 2008.
[2] Teh, YW. Hierarchical Dirichlet Process. Journal of the American Statistical Association. Vol. 101, No. 476, p. 1566, 2006.

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Sergio Bacallado

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SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.

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