Related papers: Elastic-Degenerate String Comparison
The problem of detecting and measuring the repetitiveness of one-dimensional strings has been extensively studied in data compression and text indexing. Our understanding of these issues has been significantly improved by the introduction…
We show that equivalence of deterministic top-down tree-to-string transducers is decidable, thus solving a long standing open problem in formal language theory. We also present efficient algorithms for subclasses: polynomial time for total…
An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$…
It is well-known that checking whether a given string $w$ matches a given regular expression $r$ can be done in quadratic time $O(|w|\cdot |r|)$ and that this cannot be improved to a truly subquadratic running time of $O((|w|\cdot…
We consider the following model for sampling pairs of strings: $s_1$ is a uniformly random bitstring of length $n$, and $s_2$ is the bitstring arrived at by applying substitutions, insertions, and deletions to each bit of $s_1$ with some…
In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…
Effective String Theory (EST) offers a robust non-perturbative framework for describing confinement in Yang-Mills theory by treating the confining flux tube between a static quark-antiquark pair as a thin, vibrating string. While EST…
To understand an emergent spacetime is to understand the emergence of locality. Entanglement entropy is a powerful diagnostic of locality, because locality leads to a large amount of short distance entanglement. Two dimensional string…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
Pattern matching on graphs has been widely studied lately due to its importance in genomics applications. Unfortunately, even the simplest problem of deciding if a string appears as a subpath of a graph admits a quadratic lower bound under…
A two-dimensional string is simply a two-dimensional array. We continue the study of the combinatorial properties of repetitions in such strings over the binary alphabet, namely the number of distinct tandems, distinct quartics, and runs.…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
The evolution of a closed bosonic string is envisaged in the time-dependent background of its massless modes. A duality transformation is implemented on the spatial component of string coordinates to obtain a dual string. It is shown that…
The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…