Related papers: Computing Abelian regularities on RLE strings

In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…

For $0<\delta <1$ a $\delta$-subrepetition in a word is a factor which exponent is less than~2 but is not less than $1+\delta$ (the exponent of the factor is the ratio of the factor length to its minimal period). The $\delta$-subrepetition…

Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…

A weighted string, also known as a position weight matrix, is a sequence of probability distributions over some alphabet. We revisit the Weighted Shortest Common Supersequence (WSCS) problem, introduced by Amir et al. [SPIRE 2011], that is,…

We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…

Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…

Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…

We investigate abelian repetitions in Sturmian words. We exploit a bijection between factors of Sturmian words and subintervals of the unitary segment that allows us to study the periods of abelian repetitions by using classical results of…

We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…

Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…

Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT), and for this problem various in-memory…

Kosaraju in ``Computation of squares in a string'' briefly described a linear-time algorithm for computing the minimal squares starting at each position in a word. Using the same construction of suffix trees, we generalize his result and…

The notion of Abelian complexity of infinite words was recently used by the three last authors to investigate various Abelian properties of words. In particular, using van der Waerden's theorem, they proved that if a word avoids Abelian…

Let $(\Gamma,+)$ be an Abelian group of order $n^2$ and MS$_{\Gamma}(n)$ be an $n\times n$ array whose entries are all elements of $\Gamma$. Then MS$_{\Gamma}(n)$ is a $\Gamma$-magic square if all row, column, main and backward main…

Two finite words $u,v$ are 2-binomially equivalent if, for all words $x$ of length at most 2, the number of occurrences of $x$ as a (scattered) subword of $u$ is equal to the number of occurrences of $x$ in $v$. This notion is a refinement…

A longest common extension (LCE) query on a string computes the length of the longest common suffix or prefix at two given positions. A dynamic LCE algorithm maintains a data structure that allows efficient LCE queries on a string that can…

The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…

In this note, we consider the problem of counting and verifying abelian border arrays of binary words. We show that the number of valid abelian border arrays of length \(n\) is \(2^{n-1}\). We also show that verifying whether a given array…

Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…

Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…