Bartolucci Francesco, Pandolfi Silvia
Department of Economics, Finance and Statistics, University of Perugia , Perugia, Italy .
J Comput Biol. 2014 Feb;21(2):99-117. doi: 10.1089/cmb.2013.0096. Epub 2013 Oct 25.
We develop the recursion for hidden Markov (HM) models proposed by Bartolucci and Besag (2002), and we show how it may be used to implement an estimation algorithm for these models that requires an amount of memory not depending on the length of the observed series of data. This recursion allows us to obtain the conditional distribution of the latent state at every occasion, given the previous state and the observed data. With respect to the estimation algorithm based on the well-known Baum-Welch recursions, which requires an amount of memory that increases with the sample size, the proposed algorithm also has the advantage of not requiring dummy renormalizations to avoid numerical problems. Moreover, it directly allows us to perform global decoding of the latent sequence of states, without the need of a Viterbi method and with a consistent reduction of the memory requirement with respect to the latter. The proposed approach is compared, in terms of computing time and memory requirement, with the algorithm based on the Baum-Welch recursions and with the so-called linear memory algorithm of Churbanov and Winters-Hilt. The comparison is also based on a series of simulations involving an HM model for continuous time-series data.
我们推导了由巴托卢奇和贝萨格(2002年)提出的隐马尔可夫(HM)模型的递推公式,并展示了如何利用它来实现一种针对这些模型的估计算法,该算法所需的内存量不依赖于观测数据序列的长度。这种递推使我们能够在给定先前状态和观测数据的情况下,获得每次时刻潜在状态的条件分布。与基于著名的鲍姆 - 韦尔奇递推的估计算法相比,后者所需的内存量会随着样本量的增加而增加,本文提出的算法还具有无需虚拟重归一化来避免数值问题的优点。此外,它直接使我们能够对潜在状态序列进行全局解码,无需维特比方法,并且相对于后者内存需求持续减少。在计算时间和内存需求方面,我们将所提出的方法与基于鲍姆 - 韦尔奇递推的算法以及丘尔巴诺夫和温特斯 - 希尔特的所谓线性内存算法进行了比较。该比较还基于一系列涉及连续时间序列数据的HM模型的模拟。