Related papers: Finger Search in Grammar-Compressed Strings
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
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 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…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
The edit distance problem is a classical fundamental problem in computer science in general, and in combinatorial pattern matching in particular. The standard dynamic programming solution for this problem computes the edit-distance between…
We consider the problem of decompressing the Lempel--Ziv 77 representation of a string $S$ of length $n$ using a working space as close as possible to the size $z$ of the input. The folklore solution for the problem runs in $O(n)$ time but…
The FAR FROM MOST STRING PROBLEM (FFMSP) is a string selection problem. The objective is to find a string whose distance to other strings in a certain input set is above a given threshold for as many of those strings as possible. This…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…
Suppose that we are given a string $s$ of length $n$ over an alphabet $\{0,1,\ldots,n^{O(1)}\}$ and $\delta$ is the string complexity of $s$, a known compression measure. We describe an index on $s$ with $O(\delta\log\frac{n}{\delta})$…
Given a source of iid samples of edges of an input graph $G$ with $n$ vertices and $m$ edges, how many samples does one need to compute a constant factor approximation to the maximum matching size in $G$? Moreover, is it possible to obtain…
We consider the problem of computing the q-gram profile of a string \str of size $N$ compressed by a context-free grammar with $n$ production rules. We present an algorithm that runs in $O(N-\alpha)$ expected time and uses $O(n+q+\kq)$…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression…
This thesis concerns sequential-access data compression, i.e., by algorithms that read the input one or more times from beginning to end. In one chapter we consider adaptive prefix coding, for which we must read the input character by…
The area of sublinear algorithms have recently received a lot of attention. In this setting, one has to choose specific access model for the input, as the algorithm does not have time to pre-process or even to see the whole input. A…
A predecessor (successor) search finds the largest element $x^-$ smaller than the input string $x$ (the smallest element $x^+$ larger than or equal to $x$, respectively) out of a given set $S$; in this paper, we consider the static case…
In the particular case we have insertions/deletions at the tail of a given set S of $n$ one-dimensional elements, we present a simpler and more concrete algorithm than that presented in [Anderson, 2007] achieving the same (but also…