Related papers: The complexity of Shortest Common Supersequence fo…
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…
In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
The Shortest Path Reconfiguration problem has as input a graph G (with unit edge lengths) with vertices s and t, and two shortest st-paths P and Q. The question is whether there exists a sequence of shortest st-paths that starts with P and…
We study geometric variations of the discriminating code problem. In the \emph{discrete version} of the problem, a finite set of points $P$ and a finite set of objects $S$ are given in $\mathbb{R}^d$. The objective is to choose a subset…
In this paper we are dealing with the issue of finding possibly short synchronizing words in automata with weight assigned to each letter in the alphabet $\Sigma$. First we discuss some complexity problems, and then we present new…
We investigate the asymptotic standard deviation of the Longest Common Subsequence (LCS) of two independent i.i.d. sequences of length n. The first sequence is drawn from a three letter alphabet {0,1,a}, whilst the second sequence is…
We consider the learning and communication complexity of subsequence containment. In the learning problem, we seek to learn a classifier that positively labels a binary string $x$ if it contains a fixed binary string $y$ as a subsequence.…
The exponential-time hypothesis (ETH) states that 3-SAT is not solvable in subexponential time, i.e. not solvable in O(c^n) time for arbitrary c > 1, where n denotes the number of variables. Problems like k-SAT can be viewed as special…
We examine the open problem of finding the shortest string that contains each of the n! permutations of n symbols as contiguous substrings (i.e., the shortest superpermutation on n symbols). It has been conjectured that the shortest…
Park et al. [TCS 2020] observed that the similarity between two (numerical) strings can be captured by the Cartesian trees: The Cartesian tree of a string is a binary tree recursively constructed by picking up the smallest value of the…
Bounded context switching (BCS) is an under-approximate method for finding violations to safety properties in shared memory concurrent programs. Technically, BCS is a reachability problem that is known to be NP-complete. Our contribution is…
A PSCA$(v, t, \lambda)$ is a multiset of permutations of the $v$-element alphabet $\{0, \dots, v-1\}$ such that every sequence of $t$ distinct elements of the alphabet appears in the specified order in exactly $\lambda$ of the permutations.…
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…
We generalise a multiple string pattern matching algorithm, recently proposed by Fredriksson and Grabowski [J. Discr. Alg. 7, 2009], to deal with arbitrary dictionaries on an alphabet of size $s$. If $r_m$ is the number of words of length…
Covers are a kind of quasiperiodicity in strings. A string $C$ is a cover of another string $T$ if any position of $T$ is inside some occurrence of $C$ in $T$. The shortest and longest cover arrays of $T$ have the lengths of the shortest…
Let C be a finite set of N elements and R = r_1,r_2,..., r_m a family of M subsets of C. A subset X of R verifies the Consecutive Ones Property (C1P) if there exists a permutation P of C such that each r_i in X is an interval of P. A…
This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including…
A finite deterministic (semi)automaton $\mathcal{A} =(Q,\Sigma,\delta)$ is $k$-compressible if there is some word $w\in \Sigma^+$ such that the image of its state set $Q$ under the natural action of $w$ is reduced by at least $k$ states.…
In the spanning-tree congestion problem ($\mathsf{STC}$), we are given a graph $G$, and the objective is to compute a spanning tree of $G$ that minimizes the maximum edge congestion. While $\mathsf{STC}$ is known to be $\mathbb{NP}$-hard,…