Faster Recovery of Approximate Periods over Edit Distance

07/27/2018

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by   Tomasz Kociumaka, et al.

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The approximate period recovery problem asks to compute all approximate word-periods of a given word S of length n: all primitive words P (|P|=p) which have a periodic extension at edit distance smaller than τ_p from S, where τ_p = n/(3.75+ϵ)· p for some ϵ>0. Here, the set of periodic extensions of P consists of all finite prefixes of P^∞. We improve the time complexity of the fastest known algorithm for this problem of Amir et al. [Theor. Comput. Sci., 2018] from O(n^4/3) to O(n n). Our tool is a fast algorithm for Approximate Pattern Matching in Periodic Text. We consider only verification for the period recovery problem when the candidate approximate word-period P is explicitly given up to cyclic rotation; the algorithm of Amir et al. reduces the general problem in O(n) time to a logarithmic number of such more specific instances.