Faster Pattern Matching under Edit Distance [article]

Panagiotis Charalampopoulos, Tomasz Kociumaka, Philip Wellnitz
2022 arXiv   pre-print
We consider the approximate pattern matching problem under the edit distance. Given a text T of length n, a pattern P of length m, and a threshold k, the task is to find the starting positions of all substrings of T that can be transformed to P with at most k edits. More than 20 years ago, Cole and Hariharan [SODA'98, J. Comput.'02] gave an 𝒪(n+k^4 · n/ m)-time algorithm for this classic problem, and this runtime has not been improved since. Here, we present an algorithm that runs in time
more » ... 3.5√(log m log k)· n/m), thus breaking through this long-standing barrier. In the case where n^1/4+ε≤ k ≤ n^2/5-ε for some arbitrarily small positive constant ε, our algorithm improves over the state-of-the-art by polynomial factors: it is polynomially faster than both the algorithm of Cole and Hariharan and the classic 𝒪(kn)-time algorithm of Landau and Vishkin [STOC'86, J. Algorithms'89]. We observe that the bottleneck case of the alternative 𝒪(n+k^4 · n/m)-time algorithm of Charalampopoulos, Kociumaka, and Wellnitz [FOCS'20] is when the text and the pattern are (almost) periodic. Our new algorithm reduces this case to a new dynamic problem (Dynamic Puzzle Matching), which we solve by building on tools developed by Tiskin [SODA'10, Algorithmica'15] for the so-called seaweed monoid of permutation matrices. Our algorithm relies only on a small set of primitive operations on strings and thus also applies to the fully-compressed setting (where text and pattern are given as straight-line programs) and to the dynamic setting (where we maintain a collection of strings under creation, splitting, and concatenation), improving over the state of the art.
arXiv:2204.03087v1 fatcat:wgqepmoesna7fbhlchkp6m6tna