Hierarchical Hidden Markov Models (HHMMs) are sophisticated stochastic models that enable us to capture a hierarchical context characterization of sequence data. However, existing HHMM parameter estimation methods require large computations of time complexity O(TN~(2D)) at least for model inference, where D is the depth of the hierarchy, N is the number of states in each level, and T is the sequence length. In this paper, we propose a new inference method of HHMMs for which the time complexity is O(TN~(D+1)). A key idea of our algorithm is application of the forward-backward algorithm to state activation probabilities. The notion of a state activation, which offers a simple formalization of the hierarchical transition behavior of HHMMs, enables us to conduct model inference efficiently. We present some experiments to demonstrate that our proposed method works more efficiently to estimate HHMM parameters than do some existing methods such as the flattening method and Gibbs sampling method.
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