Related papers: Approximating LCS and Alignment Distance over Mult…

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…

We investigate the scheduling of $n$ jobs divided into $c$ classes on $m$ identical parallel machines. For every class there is a setup time which is required whenever a machine switches from the processing of one class to another class.…

Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…

The similarity between a pair of time series, i.e., sequences of indexed values in time order, is often estimated by the dynamic time warping (DTW) distance, instead of any in the well-studied family of measures including the longest common…

Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…

The Longest Common Subsequence (LCS) Problem asks for the longest sequence of (non-contiguous) matches between two given strings of characters. Using extensive Monte Carlo simulations, we find a finite size scaling law of the form E(L)/N =C…

Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…

This paper is about the old Wahba problem in its more general form, which we call "simultaneous rotation and correspondence search". In this generalization we need to find a rotation that best aligns two partially overlapping $3$D point…

Approximating the length of the longest increasing sequence (LIS) of an array is a well-studied problem. We study this problem in the data stream model, where the algorithm is allowed to make a single left-to-right pass through the array…

Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which…

Finding the length of the longest increasing subsequence (LIS) is a classic algorithmic problem. Let $n$ denote the size of the array. Simple $O(n\log n)$ algorithms are known for this problem. We develop a polylogarithmic time randomized…

We give a near-optimal quantum algorithm for the longest common substring (LCS) problem between two run-length encoded (RLE) strings, with the assumption that the prefix-sums of the run-lengths are given. Our algorithm costs…

It is common to reject undesired outputs of Large Language Models (LLMs); however, current methods to do so require an excessive amount of computation to re-sample after a rejection, or distort the distribution of outputs by constraining…

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…

Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…

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,…

The edit distance (ED) and longest common subsequence (LCS) are two fundamental problems which quantify how similar two strings are to one another. In this paper, we consider these problems in the asymmetric streaming model introduced by…

Finding analytically the statistics of the longest common subsequence (LCS) of a pair of random sequences drawn from c alphabets is a challenging problem in computational evolutionary biology. We present exact asymptotic results for the…

This note provides very simple, efficient algorithms for computing the number of distinct longest common subsequences of two input strings and for computing the number of LCS embeddings.

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…