Related papers: Longest Common Subsequence on Weighted Sequences
We consider the lossless compression bound of any individual data sequence. If we fit the data by a parametric model, the entropy quantity $nH({\hat \theta}_n)$ obtained by plugging in the maximum likelihood estimate is an underestimate of…
The concept of NP-completeness has been proposed for half a century, and it is conjectured that there are no subexponential-time algorithms for NP-hard problems, which is known as the Exponential Time Hypothesis (ETH). As a pivotal…
In this paper we address the longest common extension (LCE) problem: to compute the length $\ell$ of the longest common prefix between any two suffixes of $T\in \Sigma^n$ with $ \Sigma = \{0, \ldots \sigma-1\} $. We present two fast and…
In this paper, we study the problem of designing prefix-free encoding schemes having minimum average code length that can be decoded efficiently under a decode cost model that captures memory hierarchy induced cost functions. We also study…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
A border of a string is a non-empty proper prefix of the string that is also a suffix. A string is unbordered if it has no border. The longest unbordered factor is a fundamental notion in stringology, closely related to string periodicity.…
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…
For two strings u, v over some alphabet A, we investigate the problem of embedding u into w as a subsequence under the presence of generalised gap constraints. A generalised gap constraint is a triple (i, j, C_{i, j}), where 1 <= i < j <=…
We prove that for every integer $n > 0$ and for every alphabet $\Sigma_k$ of size $k \geq 3$, there exists a necklace of length $n$ whose Burrows-Wheeler Transform (BWT) is completely unclustered, i.e., it consists of exactly $n$ runs with…
In this article, we study the problem of finding the longest common separable pattern between several permutations. We give a polynomial-time algorithm when the number of input permutations is fixed and show that the problem is NP-hard for…
In this paper, we study a series of algorithmic problems related to the subsequences occurring in the strings of a given language, under the assumption that this language is succinctly represented by a grammar generating it, or an automaton…
An important objective in scheduling literature is to minimize the sum of weighted flow times. We are given a set of jobs where each job is characterized by a release time, a processing time, and a weight. Our goal is to find a preemptive…
A quasi-complementary sequence set (QCSS) refers to a set of two-dimensional matrices with low non-trivial aperiodic auto- and cross- correlation sums. For multicarrier code-division multiple-access applications, the availability of large…
We present a practical algorithm for the cyclic longest common subsequence (CLCS) problem that runs in O(mn) time, where m and n are the lengths of the two input strings. While this is not necessarily an asymptotic improvement over the…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
A non-empty word $w$ is a \emph{border} of a word $u$ if $\vert w\vert<\vert u\vert$ and $w$ is both a prefix and a suffix of $u$. A word $u$ is \emph{privileged} if $\vert u\vert\leq 1$ or if $u$ has a privileged border $w$ that appears…
We introduce and study a discrete multi-period extension of the classical knapsack problem, dubbed generalized incremental knapsack. In this setting, we are given a set of $n$ items, each associated with a non-negative weight, and $T$ time…
A large family of words must contain two words that are similar. We investigate several problems where the measure of similarity is the length of a common subsequence. We construct a family of n^{1/3} permutations on n letters, such that…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
The weak saturation number $\mathrm{wsat}(n,F)$ is the minimum number of edges in a graph on $n$ vertices such that all the missing edges can be activated sequentially so that each new edge creates a copy of $F$. A usual approach to prove a…