Related papers: Longest Common Subsequence on Weighted Sequences
Many problems in bioinformatics are about finding strings that approximately represent a collection of given strings. We look at more general problems where some input strings can be classified as outliers. The Close to Most Strings problem…
A longest common extension (LCE) query on a string computes the length of the longest common suffix or prefix at two given positions. A dynamic LCE algorithm maintains a data structure that allows efficient LCE queries on a string that can…
Let $G$ be an abelian group, let $S$ be a sequence of terms $s_1,s_2,...,s_{n}\in G$ not all contained in a coset of a proper subgroup of $G$, and let $W$ be a sequence of $n$ consecutive integers. Let $$W\odot S=\{w_1s_1+...+w_ns_n:\;w_i…
We give a number of approximation metatheorems for monotone maximization problems expressible in the first-order logic, in substantially more general settings than the previously known. We obtain * constant-factor approximation algorithm in…
In this paper, we will find a pseudopolynomial algorithm to solve $Qm \mid \mid L_{\max}$ and then we will prove that it is impossible to get any constant-factor approximation in polynomial time, and thus also impossible to have a PTAS for…
For a class $\mathcal{H}$ of graphs, #Sub$(\mathcal{H})$ is the counting problem that, given a graph $H\in \mathcal{H}$ and an arbitrary graph $G$, asks for the number of subgraphs of $G$ isomorphic to $H$. It is known that if $\mathcal{H}$…
The detailed behaviour of a system is often represented as a labelled transition system (LTS) and the abstract behaviour as a stuttering-insensitive semantic congruence. Numerous congruences have been presented in the literature. On the…
We investigate the variance of the length of the longest common subsequences of two independent random words of size $n$, where the letters of one word are i.i.d. uniformly drawn from $\{\alpha_1, \alpha_2, \cdots, \alpha_m\}$, while the…
In the Shortest Common Superstring problem, one needs to find the shortest superstring for a set of strings. This problem is APX-hard, and many approximation algorithms were proposed, with the current best approximation factor of 2.466.…
We study a natural generalization of the maximum weight many-to-one matching problem. We are given an undirected bipartite graph $G= (A \cup P, E)$ with weights on the edges in $E$, and with lower and upper quotas on the vertices in $P$. We…
In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
We consider the expected length of the longest common subsequence between two random words of lengths $n$ and $(1-\varepsilon)kn$ over $k$-symbol alphabet. It is well-known that this quantity is asymptotic to $\gamma_{k,\varepsilon} n$ for…
The strong exponential-time hypothesis (SETH) is a commonly used conjecture in the field of complexity theory. It states that CNF formulas cannot be analyzed for satisfiability with a speedup over exhaustive search. This hypothesis and its…
Given a string $T$ with length $n$ whose characters are drawn from an ordered alphabet of size $\sigma$, its longest Lyndon subsequence is a longest subsequence of $T$ that is a Lyndon word. We propose algorithms for finding such a…
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…
Consider a finite set of sources, each producing i.i.d. observations that follow a unique probability distribution on a finite alphabet. We study the problem of matching a finite set of observed sequences to the set of sources under the…
In the longest common substring problem, we are given two strings of length $n$ and must find a substring of maximal length that occurs in both strings. It is well known that the problem can be solved in linear time, but the solution is not…
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…
In the Weighted Triangle-Free 2-Matching problem (WTF2M), we are given an undirected edge-weighted graph. Our goal is to compute a maximum-weight subgraph that is a 2-matching (i.e., no node has degree more than $2$) and triangle-free…
A generalized Davenport-Schinzel sequence is one over a finite alphabet that contains no subsequences isomorphic to a fixed forbidden subsequence. One of the fundamental problems in this area is bounding (asymptotically) the maximum length…