Related papers: Subsequence Covers of Words
A {\em subsequence} of a word $w$ is a word $u$ that can be obtained by deleting some letters from $w$ while maintaining the relative order of the remaining letters, e.g., $\mathtt{lala}$ is a subsequence of $\mathtt{alfalfa}$. A word, over…
An \emph{indeterminate string} $x = x[1..n]$ on an alphabet $\Sigma$ is a sequence of nonempty subsets of $\Sigma$; $x$ is said to be \emph{regular} if every subset is of size one. A proper substring $u$ of regular $x$ is said to be a…
The subword complexity of a word $w$ over a finite alphabet $\mathcal{A}$ is a function that assigns for each positive integer $n$, the number of distinct subwords of length $n$ in $w$. The subword complexity of a word is a good measure of…
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…
The avoidability, or unavoidability of patterns in words over finite alphabets has been studied extensively. A word (pattern) over a finite set is said to be unavoidable if, for all but finitely many words, there exists a morphism mapping…
In this paper we provide an overview of a series of recent results regarding algorithms for searching for subsequences in words or for the analysis of the sets of subsequences occurring in a word.
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…
We present a new recursive generation algorithm for prefix normal words. These are binary strings with the property that no substring has more 1s than the prefix of the same length. The new algorithm uses two operations on binary strings,…
Anchors (Ribeiro et al., 2018) is a post-hoc, rule-based interpretability method. For text data, it proposes to explain a decision by highlighting a small set of words (an anchor) such that the model to explain has similar outputs when they…
We consider the complexities of substitutive sequences over a binary alphabet. By studying various types of special words, we show that, knowing some initial values, its complexity can be completely formulated via a recurrence formula…
Quasiperiodicity in strings was introduced almost 30 years ago as an extension of string periodicity. The basic notions of quasiperiodicity are cover and seed. A cover of a text $T$ is a string whose occurrences in $T$ cover all positions…
Given a sequence $S$ of length $n$, a letter-duplicated subsequence is a subsequence of $S$ in the form of $x_1^{d_1}x_2^{d_2}\cdots x_k^{d_k}$ with $x_i\in\Sigma$, $x_j\neq x_{j+1}$ and $d_i\geq 2$ for all $i$ in $[k]$ and $j$ in $[k-1]$.…
Grammar-based compression is a popular and powerful approach to compressing repetitive texts but until recently its relatively poor time-space trade-offs during real-life construction made it impractical for truly massive datasets such as…
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 give the first approximation algorithm for mixed packing and covering semidefinite programs (SDPs) with polylogarithmic dependence on width. Mixed packing and covering SDPs constitute a fundamental algorithmic primitive with recent…
A word $u$ is a subsequence of another word $w$ if $u$ can be obtained from $w$ by deleting some of its letters. The word $w$ with alph$(w)=\Sigma$ is called $k$-subsequence universal if the set of subsequences of length $k$ of $w$ contains…
Given a class C of word languages, the C-separation problem asks for an algorithm that, given as input two regular languages, decides whether there exists a third language in C containing the first language, while being disjoint from the…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
In this paper we introduce and study a new complexity measure for finite words. For positive integer $d$ special scattered subwords, called super-$d$-subwords, in which the gaps are of length at least $(d-1)$, are defined. We give methods…
Finding the common subsequences of $L$ multiple strings has many applications in the area of bioinformatics, computational linguistics, and information retrieval. A well-known result states that finding a Longest Common Subsequence (LCS)…