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Faster Algorithms for Longest Common Substring Charalampopoulos, Panagiotis Kociumaka, Tomasz Pissis, Solon P. Radoszewski, Jakub longest common substring k mismatches wavelet tree In the classic longest common substring (LCS) problem, we are given two strings S and T, each of length at most n, over an alphabet of size σ, and we are asked to find a longest string occurring as a fragment of both S and T. Weiner, in his seminal paper that introduced the suffix tree, presented an 𝒪(n log σ)-time algorithm for this problem [SWAT 1973]. For polynomially-bounded integer alphabets, the linear-time construction of suffix trees by Farach yielded an 𝒪(n)-time algorithm for the LCS problem [FOCS 1997]. However, for small alphabets, this is not necessarily optimal for the LCS problem in the word RAM model of computation, in which the strings can be stored in 𝒪(n log σ/log n) space and read in 𝒪(n log σ/log n) time. We show that, in this model, we can compute an LCS in time 𝒪(n log σ / √{log n}), which is sublinear in n if σ = 2^{o(√{log n})} (in particular, if σ = 𝒪(1)), using optimal space 𝒪(n log σ/log n). We then lift our ideas to the problem of computing a k-mismatch LCS, which has received considerable attention in recent years. In this problem, the aim is to compute a longest substring of S that occurs in T with at most k mismatches. Flouri et al. showed how to compute a 1-mismatch LCS in 𝒪(n log n) time [IPL 2015]. Thankachan et al. extended this result to computing a k-mismatch LCS in 𝒪(n log^k n) time for k = 𝒪(1) [J. Comput. Biol. 2016]. We show an 𝒪(n log^{k-1/2} n)-time algorithm, for any constant integer k > 0 and irrespective of the alphabet size, using 𝒪(n) space as the previous approaches. We thus notably break through the well-known n log^k n barrier, which stems from a recursive heavy-path decomposition technique that was first introduced in the seminal paper of Cole et al. [STOC 2004] for string indexing with k errors. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Panagiotis Charalampopoulos and Tomasz Kociumaka and Solon P. Pissis and Jakub Radoszewski 2021 Is Part Of LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.ESA.2021.30 urn:nbn:de:0030-drops-146114 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2021.30 eng https://creativecommons.org/licenses/by/4.0/legalcode