Related papers: Efficiently Testing Simon's Congruence

Piecewise testable languages are a subclass of the regular languages. There are many equivalent ways of defining them; Simon's congruence $\sim_k$ is one of the most classical approaches. Two words are $\sim_k$-equivalent if they have the…

Simon's congruence, denoted \sim_n, relates words having the same subwords of length up to n. We show that, over a k-letter alphabet, the number of words modulo \sim_n is in 2^{\Theta(n^{k-1} log n)}.

Determining the index of the Simon congruence is a long outstanding open problem. Two words $u$ and $v$ are called Simon congruent if they have the same set of scattered factors, which are parts of the word in the correct order but not…

For a word $S$, let $f(S)$ be the largest integer $m$ such that there are two disjoints identical (scattered) subwords of length $m$. Let $f(n, \Sigma) = \min \{f(S): S \text{is of length} n, \text{over alphabet} \Sigma \}$. Here, it is…

Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…

Two words $w_1$ and $w_2$ are said to be $k$-binomial equivalent if every non-empty word $x$ of length at most $k$ over the alphabet of $w_1$ and $w_2$ appears as a scattered factor of $w_1$ exactly as many times as it appears as a…

A subsequence of a word $w$ is a word $u$ such that $u = w[i_1] w[i_2] , \dots w[i_{|u|}]$, for some set of indices $1 \leq i_1 < i_2 < \dots < i_k \leq |w|$. A word $w$ is $k$-subsequence universal over an alphabet $\Sigma$ if every word…

Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…

We consider the problem of dictionary matching in a stream. Given a set of strings, known as a dictionary, and a stream of characters arriving one at a time, the task is to report each time some string in our dictionary occurs in the…

The $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately…

A synchronizing word of a deterministic finite complete automaton is a word whose action maps every state to a single one. Finding a shortest or a short synchronizing word is a central computational problem in the theory of synchronizing…

Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…

The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in…

Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…

We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…

Longest Common Subsequence ($LCS$) deals with the problem of measuring similarity of two strings. While this problem has been analyzed for decades, the recent interest stems from a practical observation that considering single characters is…

A locally testable semigroup S is a semigroup with the property that for some nonnegative integer k, called the order or level of local testability, two words u and v in some set of generators for semigroup S are equal in the semigroup if…

Squares (fragments of the form $xx$, for some string $x$) are arguably the most natural type of repetition in strings. The basic algorithmic question concerning squares is to check if a given string of length $n$ is square-free, that is,…

We investigate the order of the variance of the optimal alignments score of two independent iid binary random words having the same length. The letters are equiprobable, but the scoring function is such that one letter has a larger score…

In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…