相关论文: Optimal searching of gapped repeats in a word
A gapped repeat is a factor of the form $uvu$ where $u$ and $v$ are nonempty words. The period of the gapped repeat is defined as $|u|+|v|$. The gapped repeat is maximal if it cannot be extended to the left or to the right by at least one…
For $\alpha\geq 1$, an $\alpha$-gapped repeat in a word $w$ is a factor $uvu$ of $w$ such that $|uv|\leq \alpha |u|$; the two factors $u$ in such a repeat are called arms, while the factor $v$ is called gap. Such a repeat is called maximal…
For $0<\delta <1$ a $\delta$-subrepetition in a word is a factor which exponent is less than~2 but is not less than $1+\delta$ (the exponent of the factor is the ratio of the factor length to its minimal period). The $\delta$-subrepetition…
Two recent lower bounds on the compressibility of repetitive sequences, $\delta \le \gamma$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $\sigma$ can be represented within the…
A border of a string is a non-empty prefix of the string that is also a suffix of the string, and a string is unbordered if it has no border other than itself. Loptev, Kucherov, and Starikovskaya [CPM 2015] conjectured the following: If we…
We show that the number of all maximal $\alpha$-gapped repeats and palindromes of a word of length $n$ is at most $3(\pi^2/6 + 5/2) \alpha n$ and $7 (\pi^2 / 6 + 1/2) \alpha n - 5 n - 1$, respectively.
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
Much research in stringology focuses on structures that can, in a way, ``grasp'' repeats (substrings that occur multiple times) as, for example, the so-called runs, a.k.a. maximal repetitions, compactly describe all tandem repeats. In this…
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…
In this paper we initiate the study of computing a maximal (not necessarily maximum) repeating pattern in a single input string, where the corresponding problems have been studied (e.g., a maximal common subsequence) only in two or more…
For any functions $f(x)$, $g(x)$ from $\mathbb {N}$ to $\mathbb {R}$ we call repeats $uvu$ such that $g(|u|)\le |v|\le f(|u|)$ as {\it $f,g$-gapped repeats}. We study the possible number of $f,g$-gapped repeats in words of fixed length~$n$.…
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 observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…
We study the problem of computing a longest increasing subsequence in a sequence $S$ of $n$ distinct elements in the presence of persistent comparison errors. In this model, every comparison between two elements can return the wrong result…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
A border of a string is a non-empty proper prefix of the string that is also a suffix. A string is unbordered if it has no border. The longest unbordered factor is a fundamental notion in stringology, closely related to string periodicity.…
We refine a uniform algebraic approach for deriving upper bounds on reset thresholds of synchronizing automata. We express the condition that an automaton is synchronizing in terms of linear algebra, and obtain upper bounds for the reset…
The cornerstone of any algorithm computing all repetitions in a string of length n in O(n) time is the fact that the number of runs (or maximal repetitions) is O(n). We give a simple proof of this result. As a consequence of our approach,…
In Gapped String Indexing, the goal is to compactly represent a string $S$ of length $n$ such that for any query consisting of two strings $P_1$ and $P_2$, called patterns, and an integer interval $[\alpha, \beta]$, called gap range, we can…
We study word reconstruction problems. Improving a previous result by P. Fleischmann, M. Lejeune, F. Manea, D. Nowotka and M. Rigo, we prove that, for any unknown word $w$ of length $n$ over an alphabet of cardinality $k$, $w$ can be…