Related papers: Variants of Constrained Longest Common Subsequence
We show that Closest Substring, one of the most important problems in the field of biological sequence analysis, is W[1]-hard when parameterized by the number k of input strings (and remains so, even over a binary alphabet). This problem 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…
In the Shortest Superstring problem we are given a set of strings $S=\{s_1, \ldots, s_n\}$ and integer $\ell$ and the question is to decide whether there is a superstring $s$ of length at most $\ell$ containing all strings of $S$ as…
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…
We revisit the longest common extension (LCE) problem, that is, preprocess a string $T$ into a compact data structure that supports fast LCE queries. An LCE query takes a pair $(i,j)$ of indices in $T$ and returns the length of the longest…
Motivated by comparative genomics, Chen et al. [9] introduced the Maximum Duo-preservation String Mapping (MDSM) problem in which we are given two strings $s_1$ and $s_2$ from the same alphabet and the goal is to find a mapping $\pi$…
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,…
In the Manhattan Sequence Consensus problem (MSC problem) we are given $k$ integer sequences, each of length $l$, and we are to find an integer sequence $x$ of length $l$ (called a consensus sequence), such that the maximum Manhattan…
This paper reformulates the problem of finding a longest common increasing subsequence of the two given input sequences in a very succinct way. An extremely simple linear space algorithm based on the new formula can find a longest common…
The Data Clustering (DC) problem is of central importance for the area of Machine Learning (ML), given its usefulness to represent data structural similarities from input spaces. Differently from Supervised Machine Learning (SML), which…
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…
Lately, there is a growing interest in dynamic string matching problems. Specifically, the dynamic Longest Common Factor problem has been researched and some interesting results has been reached. In this paper we examine another classic…
In this article, we study the problem of finding the longest common separable pattern between several permutations. We give a polynomial-time algorithm when the number of input permutations is fixed and show that the problem is NP-hard for…
Given a sequence of n numbers, the Maximum Consecutive Subsums Problem (MCSP) asks for the maximum consecutive sum of lengths l for each l = 1,...,n. No algorithm is known for this problem which is significantly better than the naive…
We introduce subsequence covers (s-covers, in short), a new type of covers of a word. A word $C$ is an s-cover of a word $S$ if the occurrences of $C$ in $S$ as subsequences cover all the positions in $S$. The s-covers seem to be…
We give a sublinear quantum algorithm for the longest common substring (LCS) problem on the run-length encoded (RLE) inputs, under the assumption that the prefix-sums of the runs are given. Our algorithm costs $\tilde{O}(n^{5/6})\cdot…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
Restricted Syndrome Decoding (ResSD) is a variant of linear code decoding problem where each of the error's entries must belong to a fixed small set of values. This problem underlies the security of CROSS, a post-quantum signature scheme…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…