Related papers: Arc-preserving subsequences of arc-annotated seque…

Let $\Sigma$ be an alphabet. For two strings $X$, $Y$, and a constrained string $P$ over the alphabet $\Sigma$, the constrained longest common subsequence and substring problem for two strings $X$ and $Y$ with respect to $P$ is to find a…

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…

One of the most fundamental method for comparing two given strings $A$ and $B$ is the longest common subsequence (LCS), where the task is to find (the length) of an LCS of $A$ and $B$. In this paper, we deal with the STR-IC-LCS problem…

This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…

The paper suggests the use of Multi-Valued Decision Diagrams (MDDs) as the supporting data structure for a generic global constraint. We give an algorithm for maintaining generalized arc consistency (GAC) on this constraint that amortizes…

The Longest Common Increasing Subsequence problem (LCIS) is a natural variant of the celebrated Longest Common Subsequence (LCS) problem. For LCIS, as well as for LCS, there is an $O(n^2)$-time algorithm and a SETH-based conditional lower…

In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…

Given a set of $t$ words of length $n$ over a $k$-letter alphabet, it is proved that there exists a common subsequence among two of them of length at least $\frac{n}{k}+cn^{1-1/(t-k-2)}$, for some $c>0$ depending on $k$ and $t$. This is…

The recently introduced longest common substring with $k$-mismatches ($k$-LCF) problem is to find, given two sequences $S_1$ and $S_2$ of length $n$ each, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance…

Noncrossing arc diagrams are combinatorial models for permutations that encode information about lattice congruences of the weak order and about the associated discrete geometry. In this paper, we consider two related, analogous models for…

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…

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…

Encoding data structures store enough information to answer the queries they are meant to support but not enough to recover their underlying datasets. In this paper we give the first encoding data structure for the challenging problem of…

One of the most critical problems in the field of string algorithms is the longest common subsequence problem (LCS). The problem is NP-hard for an arbitrary number of strings but can be solved in polynomial time for a fixed number of…

We propose an end-to-end recurrent encoder-decoder based sequence learning approach for printed text Optical Character Recognition (OCR). In contrast to present day existing state-of-art OCR solution which uses connectionist temporal…

This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…

Considering the optimal alignment of two i.i.d. random sequences of length $n$, we show that when the scoring function is chosen randomly, almost surely the empirical distribution of aligned letter pairs in all optimal alignments converges…

In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the…

In this note, we first introduce a new problem called the longest common subsequence and substring problem. Let $X$ and $Y$ be two strings over an alphabet $\Sigma$. The longest common subsequence and substring problem for $X$ and $Y$ is to…

The characterization of all the Constraint Satisfaction Problems of bounded width, proposed by Feder and Vardi [SICOMP'98], was confirmed in [Bulatov'09] and independently in [FOCS'09, JACM'14]. Both proofs are based on the…