Locally Maximal Common Factors as a Tool for Efficient Dynamic String Algorithms

There has been recent interest in dynamic string algorithms, i.e. string problems where the input changes dynamically. One such problem is the longest common factor (LCF) problem. It is well known that the LCF of two strings S and D of length n over a fixed constant-sized alphabet Sigma can be computed in time linear in n. Recently, a new challenge was introduced - finding the LCF of two strings in a dynamic setting. The problem is the fully dynamic one sided LCF (FDOS-LCF) problem. In the FDOS-LCF problem we get q consecutive queries of the form , where each such query means: "replace D[i] by alpha, alpha in Sigma and output the LCF of S and (the updated) D. The goal is to initially preprocess S and D so that we do not need O(n) time to compute an LCF for each such query. The state-of-the-art is an algorithm that preprocesses the two strings S and D in time O(n log^4 n). Subsequently, the algorithm answers in time O(log^3 n) a single query of the form: Given a position i on D and a letter alpha, return an LCF of S and D\u27, where D\u27 is the string resulting from D after substituting D[i] with alpha. That algorithm is not extendable to multiple queries. In this paper we present a tool - Locally Maximal Common Factors (LMCF) - that proves to be quite useful in solving some restricted versions of the FDOS-LCF problem . The versions we solve are the Decremental FDOS-LCS problem, where every change is of the form , omega !in Sigma, and the Periodic FDOS-LCS problem, where S is a periodic string with period length p. For the decremental problem we provide an algorithm with linear time preprocessing and O(log log n) time per query. For the periodic problem our preprocessing time is linear and the query time is O(p log log n)

Dynamic Longest Common Substring in Polylogarithmic Time

The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings S and T, each of length at most n, that undergo substitutions of letters, in order to be able to return a longest common substring after each substitution. Recently, Amir et al. [ESA 2019] presented a solution for this problem that needs only ??(n^(2/3)) time per update. This brought the challenge of determining whether there exists a faster solution with polylogarithmic update time, or (as is the case for other dynamic problems), we should expect a polynomial (conditional) lower bound. We answer this question by designing a significantly faster algorithm that processes each substitution in amortized log^?(1) n time with high probability. Our solution relies on exploiting the local consistency of the parsing of a collection of dynamic strings due to Gawrychowski et al. [SODA 2018], and on maintaining two dynamic trees with labeled bicolored leaves, so that after each update we can report a pair of nodes, one from each tree, of maximum combined weight, which have at least one common leaf-descendant of each color. We complement this with a lower bound of ?(log n/ log log n) for the update time of any polynomial-size data structure that maintains the LCS of two dynamic strings, even allowing amortization and randomization

Longest common substring made fully dynamic

Given two strings S and T, each of length at most n, the longest common substring (LCS) problem is to find a longest substring common to S and T. This is a classical problem in computer science with an O(n)-time solution. In the fully dynamic setting, edit operations are allowed in either of the two strings, and the problem is to find an LCS after each edit. We present the first solution to this problem requiring sublinear time in n per edit operation. In particular, we show how to find an LCS after each edit operation in Õ(n2/3) time, after Õ(n)-time and space preprocessing. 1 This line of research has been recently initiated in a somewhat restricted dynamic variant by Amir et al. [SPIRE 2017]. More specifically, they presented an Õ(n)-sized data structure that returns an LCS of the two strings after a single edit operation (that is reverted afterwards) in Õ(1) time. At CPM 2018, three papers (Abedin et al., Funakoshi et al., and Urabe et al.) studied analogously restricted dynamic variants of problems on strings. We show that the techniques we develop can be applied to obtain fully dynamic algorithms for all of these variants. The only previously known sublinear-time dynamic algorithms for problems on strings were for maintaining a dynamic collection of strings for comparison queries and for pattern matching, with the most recent advances made by Gawrychowski et al. [SODA 2018] and by Clifford et al. [STACS 2018]. As an intermediate problem we consider computing the solution for a string with a given set of k edits, which leads us, in particular, to answering internal queries on a string. The input to such a query is specified by a substring (or substrings) of a given string. Data structures for answering internal string queries that were proposed by Kociumaka et al. [SODA 2015] and by Gagie et al. [CCCG 2013] are used, along with new ones, based on ingredients such as the suffix tree, heavy-path decomposition, orthogonal range queries, difference covers, and string periodicity

Fully-Functional Suffix Trees and Optimal Text Searching in BWT-runs Bounded Space

Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts is r, the number of runs in their Burrows-Wheeler Transforms (BWTs). One of the earliest indexes for repetitive collections, the Run-Length FM-index, used O(r) space and was able to efficiently count the number of occurrences of a pattern of length m in the text (in loglogarithmic time per pattern symbol, with current techniques). However, it was unable to locate the positions of those occurrences efficiently within a space bounded in terms of r. In this paper we close this long-standing problem, showing how to extend the Run-Length FM-index so that it can locate the occ occurrences efficiently within O(r) space (in loglogarithmic time each), and reaching optimal time, O(m + occ), within O(r log log w ({\sigma} + n/r)) space, for a text of length n over an alphabet of size {\sigma} on a RAM machine with words of w = {\Omega}(log n) bits. Within that space, our index can also count in optimal time, O(m). Multiplying the space by O(w/ log {\sigma}), we support count and locate in O(dm log({\sigma})/we) and O(dm log({\sigma})/we + occ) time, which is optimal in the packed setting and had not been obtained before in compressed space. We also describe a structure using O(r log(n/r)) space that replaces the text and extracts any text substring of length ` in almost-optimal time O(log(n/r) + ` log({\sigma})/w). Within that space, we similarly provide direct access to suffix array, inverse suffix array, and longest common prefix array cells, and extend these capabilities to full suffix tree functionality, typically in O(log(n/r)) time per operation.Comment: submitted version; optimal count and locate in smaller space: O(r log log_w(n/r + sigma)