This paper discusses a probabilistic model-based approach to clus(cid:173) tering sequences, using hidden Markov models (HMMs) . The prob(cid:173) lem can be framed as a generalization of the standard mixture model approach to clustering in feature space. Two primary issues are addressed. First, a novel parameter initialization procedure is proposed, and second, the more difficult problem of determining the number of clusters K, from the data, is investigated. Experi(cid:173) mental results indicate that the proposed techniques are useful for revealing hidden cluster structure in data sets of sequences.

Most of existing methods for DNA motif discovery consider only a single set of sequences to find an over-represented motif. In contrast, we consider multiple sets of sequences where we group sets associated with the same motif into a cluster, assuming that each set involves a single motif. Clustering sets of sequences yields clusters of coherent motifs, improving signal-to-noise ratio or enabling us to identify multiple motifs. We present a probabilistic model for DNA motif discovery where we identify multiple motifs through searching for patterns which are shared across multiple sets of sequences. Our model infers cluster-indicating latent variables and learns motifs simultaneously, where these two tasks interact with each other.

Most of existing methods for DNA motif discovery consider only a single set of sequences to find an over-represented motif. In contrast, we consider multiple sets of sequences where we group sets associated with the same motif into a cluster, assuming that each set involves a single motif. Clustering sets of sequences yields clusters of coherent motifs, improving signal-to-noise ratio or enabling us to identify multiple motifs. We present a probabilistic model for DNA motif discovery where we identify multiple motifs through searching for patterns which are shared across multiple sets of sequences. Our model infers cluster-indicating latent variables and learns motifs simultaneously, where these two tasks interact with each other.

This paper discusses a probabilistic model-based approach to clustering sequences, using hidden Markov models (HMMs). The problem can be framed as a generalization of the standard mixture model approach to clustering in feature space. Two primary issues are addressed. First, a novel parameter initialization procedure is proposed, and second, the more difficult problem of determining the number of clusters K, from the data, is investigated. Experimental results indicate that the proposed techniques are useful for revealing hidden cluster structure in data sets of sequences.

This paper discusses a probabilistic model-based approach to clustering sequences, using hidden Markov models (HMMs). The problem can be framed as a generalization of the standard mixture model approach to clustering in feature space. Two primary issues are addressed. First, a novel parameter initialization procedure is proposed, and second, the more difficult problem of determining the number of clusters K, from the data, is investigated. Experimental results indicate that the proposed techniques are useful for revealing hidden cluster structure in data sets of sequences.

This paper discusses a probabilistic model-based approach to clustering sequences,using hidden Markov models (HMMs) . The problem can be framed as a generalization of the standard mixture model approach to clustering in feature space. Two primary issues are addressed. First, a novel parameter initialization procedure is proposed, and second, the more difficult problem of determining the number of clusters K, from the data, is investigated. Experimental resultsindicate that the proposed techniques are useful for revealing hidden cluster structure in data sets of sequences.