Related papers: Minimizers in Semi-Dynamic Strings
Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $\Sigma$. Further let $w\geq 2$ and $k\geq 1$ be…
Minimizers are sampling schemes with numerous applications in computational biology. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a linear order $\rho$ on strings of length $k$ (also…
Minimizer schemes, or just minimizers, are a very important computational primitive in sampling and sketching biological strings. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a total order…
The minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers $w$ and $k$, it selects the…
The rank and select operations over a string of length n from an alphabet of size $\sigma$ have been used widely in the design of succinct data structures. In many applications, the string itself need be maintained dynamically, allowing…
A string $w$ is called a minimal absent word (MAW) for a string $S$ if $w$ does not occur as a substring in $S$ and all proper substrings of $w$ occur in $S$. MAWs are well-studied combinatorial string objects that have potential…
Given a string $S$ over an alphabet $\Sigma$, the 'string indexing problem' is to preprocess $S$ to subsequently support efficient pattern matching queries, i.e., given a pattern string $P$ report all the occurrences of $P$ in $S$. In this…
A substring $u$ of a string $T$ is called a minimal unique substring (MUS) of $T$ if $u$ occurs exactly once in $T$ and any proper substring of $u$ occurs at least twice in $T$. A string $w$ is called a minimal absent word (MAW) of $T$ if…
String attractors [STOC 2018] are combinatorial objects recently introduced to unify all known dictionary compression techniques in a single theory. A set $\Gamma\subseteq [1..n]$ is a $k$-attractor for a string $S\in[1..\sigma]^n$ if and…
We consider the problem of storing a dynamic string $S$ over an alphabet $\Sigma=\{\,1,\ldots,\sigma\,\}$ in compressed form. Our representation supports insertions and deletions of symbols and answers three fundamental queries:…
A string $w$ is called a minimal absent word (MAW) for another string $T$ if $w$ does not occur in $T$ but the proper substrings of $w$ occur in $T$. For example, let $\Sigma = \{\mathtt{a, b, c}\}$ be the alphabet. Then, the set of MAWs…
In bioinformatics, minimizers have become an inescapable method for handling $k$-mers (words of fixed size $k$) extracted from DNA or RNA sequencing, whether for sampling, storage, querying or partitioning. According to some fixed order on…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
Maximizing submodular functions under cardinality constraints lies at the core of numerous data mining and machine learning applications, including data diversification, data summarization, and coverage problems. In this work, we study this…
A Random Access query to a string $T\in [0..\sigma)^n$ asks for the character $T[i]$ at a given position $i\in [0..n)$. In $O(n\log\sigma)$ bits of space, this fundamental task admits constant-time queries. While this is optimal in the…
Given a string $w$, another string $v$ is said to be a subsequence of $w$ if $v$ can be obtained from $w$ by removing some of its letters; on the other hand, $v$ is called an absent subsequence of $w$ if $v$ is not a subsequence of $w$. The…
A string $w$ is called a minimal absent word (MAW) for another string $T$ if $w$ does not occur (as a substring) in $T$ and any proper substring of $w$ occurs in $T$. State-of-the-art data structures for reporting the set $\mathsf{MAW}(T)$…
Let $S$ be a string of length $n$. In this paper we introduce the notion of \emph{string attractor}: a subset of the string's positions $[1,n]$ such that every distinct substring of $S$ has an occurrence crossing one of the attractor's…
The random access problem for compressed strings is to build a data structure that efficiently supports accessing the character in position $i$ of a string given in compressed form. Given a grammar of size $n$ compressing a string of size…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…