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The longest common substring with $k$-mismatches problem is to find, given two strings $S_1$ and $S_2$, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance between $A_1$ and $A_2$ is $\le k$. We introduce a…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
The Longest Common Subsequence (LCS) is the problem of finding a subsequence among a set of strings that has two properties of being common to all and is the longest. The LCS has applications in computational biology and text editing, among…
The 2-LCPS problem, first introduced by Chowdhury et al. [Fundam. Inform., 129(4):329-340, 2014], asks one to compute (the length of) a longest palindromic common subsequence between two given strings $A$ and $B$. We show that the 2-LCPS…
There are efficient dynamic programming solutions to the computation of the Edit Distance from $S\in[1..\sigma]^n$ to $T\in[1..\sigma]^m$, for many natural subsets of edit operations, typically in time within $O(nm)$ in the worst-case over…
In the decremental $(1+\epsilon)$-approximate Single-Source Shortest Path (SSSP) problem, we are given a graph $G=(V,E)$ with $n = |V|, m = |E|$, undergoing edge deletions, and a distinguished source $s \in V$, and we are asked to process…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…
In this work, we consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s1 and s2 over an alphabet A, a set C_s of strings, and a function Co…
This paper addresses the Poisson $\pi$ps sampling problem, a topic of significant academic interest in various domains and with practical data mining applications, such as influence maximization. The problem includes a set $\mathcal{S}$ of…
Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…
In this paper, we introduce zip-tries, which are simple, dynamic, memory-efficient data structures for strings. Zip-tries support search and update operations for $k$-length strings in $\mathcal{O}(k+\log n)$ time in the standard RAM model…
It is widely assumed that $O(m+\lg \sigma)$ is the best one can do for finding a pattern of length $m$ in a compacted trie storing strings over an alphabet of size $\sigma$, if one insists on linear-size data structures and deterministic…
The palindromic fingerprint of a string $S[1\ldots n]$ is the set $PF(S) = \{(i,j)~|~ S[i\ldots j] \textit{ is a maximal }\\ \textit{palindrome substring of } S\}$. In this work, we consider the problem of string reconstruction from a…
Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
In this paper we introduce a new family of string processing problems. We are given two or more strings and we are asked to compute a factor common to all strings that preserves a specific property and has maximal length. Here we consider…
The interval subset sum problem (ISSP) is a generalization of the well-known subset sum problem. Given a set of intervals $\left\{[a_{i,1},a_{i,2}]\right\}_{i=1}^n$ and a target integer $T,$ the ISSP is to find a set of integers, at most…