Related papers: Longest Common Subsequence on Weighted Sequences

In [1] a syndrome counting based upper bound on the minimum distance of regular binary LDPC codes is given. In this paper we extend the bound to the case of irregular and generalized LDPC codes over GF(q). The comparison to the lower bound…

In this paper, we consider a variant of the classical algorithmic problem of checking whether a given word $v$ is a subsequence of another word $w$. More precisely, we consider the problem of deciding, given a number $p$ (defining 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…

A sequence $S=s_{1}s_{2}..._{n}$ is \emph{nonrepetitive} if no two adjacent blocks of $S$ are identical. In 1906 Thue proved that there exist arbitrarily long nonrepetitive sequences over 3-element set of symbols. We study a generalization…

Let $(X_k)_{k\geq 1}$ and $(Y_k)_{k\geq 1}$ be two independent sequences of i.i.d. random variables, with values in a finite and totally ordered alphabet $\mathcal{A}_m:=\{1,\dots,m\}$, and having respective probability mass function…

The expected length of longest common subsequences is a problem that has been in the literature for at least twenty five years. Determining the limiting constants \gamma_k appears to be quite difficult, and the current best bounds leave…

We propose an $\widetilde{O}(n + 1/\eps)$-time FPTAS (Fully Polynomial-Time Approximation Scheme) for the classical Partition problem. This is the best possible (up to a polylogarithmic factor) assuming SETH (Strong Exponential Time…

The central conjecture of parameterized complexity states that FPT is not equal to W[1], and is generally regarded as the parameterized counterpart to P != NP. We revisit the issue of the plausibility of FPT != W[1], focusing on two…

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…

The Longest Common Substring (LCS) and Longest Palindromic Substring (LPS) are classical problems in computer science, representing fundamental challenges in string processing. Both problems can be solved in linear time using a classical…

The largest common embeddable subtree problem asks for the largest possible tree embeddable into two input trees and generalizes the classical maximum common subtree problem. Several variants of the problem in labeled and unlabeled rooted…

We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…

In a simple pattern matching problem one has a pattern $w$ and a text $t$, which are words over a finite alphabet $\Sigma$. One may ask whether $w$ occurs in $t$, and if so, where? More generally, we may have a set $P$ of patterns and a set…

Everywhere-$\delta$-dense graphs are defined as graphs on $n$ vertices in which every vertex has degree at least $\delta n$ for some constant $\delta > 0$. Approximation schemes are vital for handling NP-hard optimization problems, but for…

In this work, we study the limits of compressed data structures, i.e., structures that support various queries on an input text $T\in\Sigma^n$ using space proportional to the size of $T$ in compressed form. Nearly all fundamental queries…

A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…

Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…

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…

Let $X=(X_i)_{i\ge 1}$ and $Y=(Y_i)_{i\ge 1}$ be two sequences of independent and identically distributed (iid) random variables taking their values, uniformly, in a common totally ordered finite alphabet. Let LCI$_n$ be the length of the…

Sequence representations supporting queries $access$, $select$ and $rank$ are at the core of many data structures. There is a considerable gap between the various upper bounds and the few lower bounds known for such representations, and how…