Related papers: Elastic-Degenerate String Comparison
A string $S[1,n]$ is a power (or tandem repeat) of order $k$ and period $n/k$ if it can decomposed into $k$ consecutive equal-length blocks of letters. Powers and periods are fundamental to string processing, and algorithms for their…
Given a string $T$ with length $n$ whose characters are drawn from an ordered alphabet of size $\sigma$, its longest Lyndon subsequence is a longest subsequence of $T$ that is a Lyndon word. We propose algorithms for finding such a…
String Edit Distance is a more-than-classical problem whose behavior in the dynamic setting, where the strings are updated over time, is well studied. A single-character substitution, insertion, or deletion can be processed in time…
This paper gives new results for synchronization strings, a powerful combinatorial object that allows to efficiently deal with insertions and deletions in various communication settings: $\bullet$ We give a deterministic, linear time…
In this paper we are interested in indexing texts for substring matching queries with one edit error. That is, given a text $T$ of $n$ characters over an alphabet of size $\sigma$, we are asked to build a data structure that answers the…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…
The set of all $ q $-ary strings that do not contain repeated substrings of length $ \leqslant\! 3 $ (i.e., that do not contain substrings of the form $ a a $, $ a b a b $, and $ a b c a b c $) constitutes a code correcting an arbitrary…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
The Longest Common Subsequence (LCS) Problem asks for the longest sequence of (non-contiguous) matches between two given strings of characters. Using extensive Monte Carlo simulations, we find a finite size scaling law of the form E(L)/N =C…
We present time-space trade-offs for computing the Euclidean minimum spanning tree of a set $S$ of $n$ point-sites in the plane. More precisely, we assume that $S$ resides in a random-access memory that can only be read. The edges of the…
Simon's congruence $\sim_k$ is defined as follows: two words are $\sim_k$-equivalent if they have the same set of subsequences of length at most $k$. We propose an algorithm which computes, given two words $s$ and $t$, the largest $k$ for…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
We consider the problem of computing a shortest solid cover of an indeterminate string. An indeterminate string may contain non-solid symbols, each of which specifies a subset of the alphabet that could be present at the corresponding…
We address the separability problem for straight-line string constraints. The separability problem for languages of a class C by a class S asks: given two languages A and B in C, does there exist a language I in S separating A and B (i.e.,…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
The Cover Suffix Tree (CST) of a string $T$ is the suffix tree of $T$ with additional explicit nodes corresponding to halves of square substrings of $T$. In the CST an explicit node corresponding to a substring $C$ of $T$ is annotated with…