Related papers: String Attractors
Repetitiveness measures reveal profound characteristics of datasets, and give rise to compressed data structures and algorithms working in compressed space. Alas, the computation of some of these measures is NP-hard, and straight-forward…
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…
We raise the question of approximating the compressibility of a string with respect to a fixed compression scheme, in sublinear time. We study this question in detail for two popular lossless compression schemes: run-length encoding (RLE)…
In this paper, we describe string attractors of all factors of episturmian sequences and show that their size is equal to the number of distinct letters contained in the factor.
The Shortest Superstring Problem (SSP) consists, for a set of strings S = {s_1,...,s_n}, to find a minimum length string that contains all s_i, 1 <= i <= k, as substrings. This problem is proved to be NP-Complete and APX-hard. Guaranteed…
Succinct representations of a graph have been objects of central study in computer science for decades. In this paper, we study the operation called \emph{Distance Preserving Graph Contractions}, which was introduced by Bernstein et al.…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
Repetitiveness measures quantify how much repetitive structure a string contains and serve as parameters for compressed representations and indexing data structures. We study the measure $\chi$, defined as the size of the smallest…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
A superstring of a set of strings correspond to a string which contains all the other strings as substrings. The problem of finding the Shortest Linear Superstring is a well-know and well-studied problem in stringology. We present here a…
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"…
Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
A suffixient set is a novel combinatorial object that captures the essential information of repetitive strings in a way that, provided with a random access mechanism, supports various forms of pattern matching. In this paper, we study the…
Given a string $S$ of $n$ integers in $[0,\sigma)$, a range minimum query RMQ$(i, j)$ asks for the index of the smallest integer in $S[i \dots j]$. It is well known that the problem can be solved with a succinct data structure of size $2n +…
Grammar based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. In this paper, we present a novel…