Related papers: The complexity of Shortest Common Supersequence fo…

In this paper we consider the following problems: how many different subsets of Sigma^n can occur as set of all length-n factors of a finite word? If a subset is representable, how long a word do we need to represent it? How many such…

In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…

Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…

In a typical regular expression (regex) crossword puzzle, you are given two nonempty lists $R_1,\ldots,R_m$ and $C_1,\ldots,C_n$ of regular expressions over some alphabet, and your goal is to fill in an $m\times n$ grid with letters from…

This paper shows that a simple algorithm produces the {\em all-prefixes-LCSs-graph} in $O(mn)$ time for two input sequences of size $m$ and $n$. Given any prefix $p$ of the first input sequence and any prefix $q$ of the second input…

This paper studies the problem of, given the structure of a linear-time invariant system and a set of possible inputs, finding the smallest subset of input vectors that ensures system's structural controllability. We refer to this problem…

In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…

The Minimum Consistent Subset (MCS) problem arises naturally in the context of supervised clustering and instance selection. In supervised clustering, one aims to infer a meaningful partitioning of data using a small labeled subset.…

The Surjective Constraint Satisfaction Problem (SCSP) is the problem of deciding whether there exists a surjective assignment to a set of variables subject to some specified constraints, where a surjective assignment is an assignment…

Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…

We study the problems of finding a shortest synchronizing word and its length for a given prefix code. This is done in two different settings: when the code is defined by an arbitrary decoder recognizing its star and when the code is…

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…

In a connected simple graph G = (V,E), each vertex of V is colored by a color from the set of colors C={c1, c2,..., c_{\alpha}}$. We take a subset S of V, such that for every vertex v in V\S, at least one vertex of the same color is present…

We study extremal and algorithmic questions of subset and careful synchronization in monotonic automata. We show that several synchronization problems that are hard in general automata can be solved in polynomial time in monotonic automata,…

Let S be a finite set of words over an alphabet Sigma. The set S is said to be complete if every word w over the alphabet Sigma is a factor of some element of S*, i.e. w belongs to Fact(S*). Otherwise if S is not complete, we are interested…

Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $\Sigma$. Further let $w\geq 2$ and $k\geq 1$ be…

Let $X_1, X_2, ..., X_s$ and $Y_1, Y_2, ..., Y_t$ be strings over an alphabet $\Sigma$, where $s$ and $t$ are positive integers. The longest common subsequence and substring problem for multiple strings $X_1, X_2, ..., X_s$ and $Y_1, Y_2,…

Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…

A weakly consecutive sequence (WCS) is a permutation $\sigma$ of $\{1, \ldots, k\}$ such that if an integer $d$ divides $\sigma(i)$, then $d$ also divides $\sigma(i \pm d)$ insofar as these are defined. The structure of weakly consecutive…

In this paper, we revisit the much studied LCS problem for two given sequences. Based on the algorithm of Iliopoulos and Rahman for solving the LCS problem, we have suggested 3 new improved algorithms. We first reformulate the problem in a…