Related papers: Faster STR-EC-LCS Computation
In this paper, we explore worst-case solutions for the problems of single and multiple matching on strings in the word RAM model with word length w. In the first problem, we have to build a data structure based on a pattern p of length m…
Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple…
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…
Consider two random strings having the same length and generated by an iid sequence taking its values uniformly in a fixed finite alphabet. Artificially place a long constant block into one of the strings, where a constant block is a…
In the problem of the longest common substring with $k$ mismatches we are given two strings $X, Y$ and must find the maximal length $\ell$ such that there is a length-$\ell$ substring of $X$ and a length-$\ell$ substring of $Y$ that differ…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
The Shortest Common Superstring (SCS) problem asks for the shortest string that contains each of a given set of strings as a substring. Its reverse-complement variant, the Shortest Common Superstring problem with Reverse Complements…
In the Minimum Consistent Subset (MCS) problem, we are presented with a connected simple undirected graph $G=(V,E)$, consisting of a vertex set $V$ of size $n$ and an edge set $E$. Each vertex in $V$ is assigned a color from the set…
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…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
Given two positions $i$ and $j$ in a string $T$ of length $N$, a longest common extension (LCE) query asks for the length of the longest common prefix between suffixes beginning at $i$ and $j$. A compressed LCE data structure is a data…
In this paper, we study edit distance (ED) and longest common subsequence (LCS) in the asymmetric streaming model, introduced by Saks and Seshadhri [SS13]. As an intermediate model between the random access model and the streaming model,…
Correlation Clustering is a fundamental and widely-studied problem in unsupervised learning and data mining. The input is a graph and the goal is to construct a clustering minimizing the number of inter-cluster edges plus the number of…
The problem of identification of statistically significant patterns in a sequence of data has been applied to many domains such as intrusion detection systems, financial models, web-click records, automated monitoring systems, computational…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
We revisit the fundamental problem of dictionary look-up with mismatches. Given a set (dictionary) of $d$ strings of length $m$ and an integer $k$, we must preprocess it into a data structure to answer the following queries: Given a query…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
Let us consider the Multiple String Matching Problem. In this problem, we consider a long string, denoted by $t$, of length $n$. This string is referred to as a text. We also consider a sequence of $m$ strings, denoted by $S$, which we…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…