2026-07-25T22:56:47Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:21091 2024-09-23T09:13:16Z ddc:004 open_access

Pattern Matching with Mismatches and Wildcards Bathie, Gabriel Charalampopoulos, Panagiotis Starikovskaya, Tatiana pattern matching wildcards mismatches Hamming distance In this work, we address the problem of approximate pattern matching with wildcards. Given a pattern P of length m containing D wildcards, a text T of length n, and an integer k, our objective is to identify all fragments of T within Hamming distance k from P. Our primary contribution is an algorithm with runtime 𝒪(n + (D+k)(G+k)⋅ n/m) for this problem. Here, G ≤ D represents the number of maximal wildcard fragments in P. We derive this algorithm by elaborating in a non-trivial way on the ideas presented by [Charalampopoulos, Kociumaka, and Wellnitz, FOCS'20] for pattern matching with mismatches (without wildcards). Our algorithm improves over the state of the art when D, G, and k are small relative to n. For instance, if m = n/2, k = G = n^{2/5}, and D = n^{3/5}, our algorithm operates in 𝒪(n) time, surpassing the Ω(n^{6/5}) time requirement of all previously known algorithms. In the case of exact pattern matching with wildcards (k = 0), we present a much simpler algorithm with runtime 𝒪(n + DG ⋅ n/m) that clearly illustrates our main technical innovation: the utilisation of positions of P that do not belong to any fragment of P with a density of wildcards much larger than D/m as anchors for the sought (approximate) occurrences. Notably, our algorithm outperforms the best-known 𝒪(n log m)-time FFT-based algorithms of [Cole and Hariharan, STOC'02] and [Clifford and Clifford, IPL'04] if DG = o(m log m). We complement our algorithmic results with a structural characterization of the k-mismatch occurrences of P. We demonstrate that in a text of length 𝒪(m), these occurrences can be partitioned into 𝒪((D+k)(G+k)) arithmetic progressions. Additionally, we construct an infinite family of examples with Ω((D+k)k) arithmetic progressions of occurrences, leveraging a combinatorial result on progression-free sets [Elkin, SODA'10]. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Gabriel Bathie and Panagiotis Charalampopoulos and Tatiana Starikovskaya 2024 Is Part Of LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.ESA.2024.20 urn:nbn:de:0030-drops-210910 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.20 eng https://creativecommons.org/licenses/by/4.0/legalcode