Multiple word alignment with profile hidden Markov models

Abstract

Profile hidden Markov models (Profile HMMs) are specific types of hidden Markov models used in biological sequence analysis. We propose the use of Profile HMMs for word-related tasks. We test their applicability to the tasks of multiple cognate alignment and cognate set matching, and find that they work well in general for both tasks. On the latter task, the Profile HMM method outperforms average and minimum edit distance. Given the success for these two tasks, we further discuss the potential applications of Profile HMMs to any task where consideration of a set of words is necessary.