JUMP-Means: Small-Variance Asymptotics for Markov Jump Processes
Jonathan Huggins, Karthik Narasimhan, Ardavan Saeedi, Vikash Mansinghka
Abstract
Markov jump processes (MJPs) are used to model a wide range of phenomenon from disease progression to RNA path folding. However, existing methods suffer from a number of shortcomings: degenerate trajectories in the case of ML estimation of parametric models and poor inferential performance in the case of nonparametric models. We take a small-variance asymptotics (SVA) approach to overcome these limitations. We derive the small-variance asymptotics for parametric and nonparametric MJPs for both directly observed and hidden state models. In the parametric case we obtain a novel objective function which leads to non-degenerate trajectories. To derive the nonparametric version we introduce the gamma-gamma process, a novel extension to the gamma-exponential process. We propose algorithms for each of these formulations, which we call \emphJUMP-means. Our experiments demonstrate that JUMP-means is competitive with or outperforms widely used MJP inference approaches in terms of both speed and reconstruction accuracy.
BibTeX
@InProceedings{pmlr-v37-hugginsa15,
title = {JUMP-Means: Small-Variance Asymptotics for Markov Jump Processes},
author = {Huggins, Jonathan and Narasimhan, Karthik and Saeedi, Ardavan and Mansinghka, Vikash},
booktitle = {Proceedings of the 32nd International Conference on Machine Learning},
pages = {693--701},
year = {2015},
editor = {Bach, Francis and Blei, David},
volume = {37},
series = {Proceedings of Machine Learning Research},
address = {Lille, France},
month = {07--09 Jul},
publisher = {PMLR},
pdf = {http://proceedings.mlr.press/v37/hugginsa15.pdf},
url = {https://proceedings.mlr.press/v37/hugginsa15.html},
abstract = {Markov jump processes (MJPs) are used to model a wide range of phenomenon from disease progression to RNA path folding. However, existing methods suffer from a number of shortcomings: degenerate trajectories in the case of ML estimation of parametric models and poor inferential performance in the case of nonparametric models. We take a small-variance asymptotics (SVA) approach to overcome these limitations. We derive the small-variance asymptotics for parametric and nonparametric MJPs for both directly observed and hidden state models. In the parametric case we obtain a novel objective function which leads to non-degenerate trajectories. To derive the nonparametric version we introduce the gamma-gamma process, a novel extension to the gamma-exponential process. We propose algorithms for each of these formulations, which we call \emphJUMP-means. Our experiments demonstrate that JUMP-means is competitive with or outperforms widely used MJP inference approaches in terms of both speed and reconstruction accuracy.}
}