Related papers: RePair in Compressed Space and Time
Compressed indexing enables powerful queries over massive and repetitive textual datasets using space proportional to the compressed input. While theoretical advances have led to highly efficient index structures, their practical…
We present an algorithm for computing the Lyndon factorization of a string that is given in grammar compressed form, namely, a Straight Line Program (SLP). The algorithm runs in $O(n^4 + mn^3h)$ time and $O(n^2)$ space, where $m$ is the…
We consider the problem of preprocessing two strings $S$ and $T$, of lengths $m$ and $n$, respectively, in order to be able to efficiently answer the following queries: Given positions $i,j$ in $S$ and positions $a,b$ in $T$, return the…
The $k$-mismatch problem consists in computing the Hamming distance between a pattern $P$ of length $m$ and every length-$m$ substring of a text $T$ of length $n$, if this distance is no more than $k$. In many real-world applications, any…
It was recently proved that any SLP generating a given string $w$ can be transformed in linear time into an equivalent balanced SLP of the same asymptotic size. We show that this result also holds for RLSLPs, which are SLPs extended with…
The $r$-index (Gagie et al., JACM 2020) represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude. Its space usage, $\mathcal{O}(r)$ where $r$ is the number of…
We give two algorithms for output-sparse matrix multiplication (OSMM), the problem of multiplying two $n \times n$ matrices $A, B$ when their product $AB$ is promised to have at most $O(n^{\delta})$ many non-zero entries for a given value…
We propose a method to improve traditional character-based PPM text compression algorithms. Consider a text file as a sequence of alternating words and non-words, the basic idea of our algorithm is to encode non-words and prefixes of words…
We present an efficient algorithm for computing the LZ78 factorization of a text, where the text is represented as a straight line program (SLP), which is a context free grammar in the Chomsky normal form that generates a single string.…
In a seminal paper on finding large matchings in sparse random graphs, Karp and Sipser proposed two algorithms for this task. The second algorithm has been intensely studied, but due to technical difficulties, the first algorithm has…
We study the support recovery problem for compressed sensing, where the goal is to reconstruct the a high-dimensional $K$-sparse signal $\mathbf{x}\in\mathbb{R}^N$, from low-dimensional linear measurements with and without noise. Our key…
The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high…
In this paper, we present the following results: (1) We propose a new \emph{dynamic compressed index} of $O(w)$ space, that supports searching for a pattern $P$ in the current text in $O(|P| f(M,w) + \log w \log |P| \log^* M (\log N + \log…
Given $m$ documents of total length $n$, we consider the problem of finding a longest string common to at least $d \geq 2$ of the documents. This problem is known as the \emph{longest common substring (LCS) problem} and has a classic $O(n)$…
The LZ-End parsing [Kreft & Navarro, 2011] of an input string yields compression competitive with the popular Lempel-Ziv 77 scheme, but also allows for efficient random access. Kempa and Kosolobov showed that the parsing can be computed in…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
This paper deals with the two fundamental problems concerning the handling of large n-gram language models: indexing, that is compressing the n-gram strings and associated satellite data without compromising their retrieval speed; and…
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…
In this work, we study the limits of compressed data structures, i.e., structures that support various queries on an input text $T\in\Sigma^n$ using space proportional to the size of $T$ in compressed form. Nearly all fundamental queries…
In this paper we further investigate the well-studied problem of finding a perfect matching in a regular bipartite graph. The first non-trivial algorithm, with running time $O(mn)$, dates back to K\"{o}nig's work in 1916 (here $m=nd$ is the…