相关论文: Hairpin Completion Distance Lower Bound

Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…

In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…

In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…

String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…

We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…

An elastic-degenerate (ED) string $T$ is a sequence of $n$ sets $T[1],\ldots,T[n]$ containing $m$ strings in total whose cumulative length is $N$. We call $n$, $m$, and $N$ the length, the cardinality and the size of $T$, respectively. The…

Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are…

We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…

We study the fundamental problem of approximating the edit distance of two strings. After an extensive line of research led to the development of a constant-factor approximation algorithm in almost-linear time, recent years have witnessed a…

In CPM 2017, Amir et al. introduce a problem, named \emph{approximate string cover} (\textbf{ACP}), motivated by many aplications including coding and automata theory, formal language theory, combinatorics and molecular biology. A…

We present an algorithm for approximating the edit distance $\operatorname{ed}(x, y)$ between two strings $x$ and $y$ in time parameterized by the degree to which one of the strings $x$ satisfies a natural pseudorandomness property. The…

We introduce the following natural generalization of trace reconstruction, parameterized by a deletion probability $\delta \in (0,1)$ and length $n$: There is a length $n$ string of probabilities, $S=p_1,\ldots,p_n,$ and each "trace" is…

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…

The edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…

We study edit distance computation with preprocessing: the preprocessing algorithm acts on each string separately, and then the query algorithm takes as input the two preprocessed strings. This model is inspired by scenarios where we would…

We show that the edit distance between two run-length encoded strings of compressed lengths $m$ and $n$ respectively, can be computed in $\mathcal{O}(mn\log(mn))$ time. This improves the previous record by a factor of…

Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…

Given a context free language $\mathcal{L(G)}$ over alphabet $\Sigma$ and a string $s \in \Sigma^*$, {\em the language edit distance} problem seeks the minimum number of edits (insertions, deletions and substitutions) required to convert…

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…

Approximate Pattern Matching is among the most fundamental string-processing tasks. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to identify the fragments of $T$ that are at distance at most…