Related papers: Efficient Seeds Computation Revisited
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
We first describe three algorithms for computing the Lyndon array that have been suggested in the literature, but for which no structured exposition has been given. Two of these algorithms execute in quadratic time in the worst case, the…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
A $k$-matching cover of a graph $G$ is a union of $k$ matchings of $G$ which covers $V(G)$. A matching cover of $G$ is optimal if it consists of the fewest matchings of $G$. In this paper, we present an algorithm for finding an optimal…
A linear time algorithm to find a set of nearest elements in a mesh.
Packing and covering linear programs belong to the narrow class of linear programs that are efficiently solvable in parallel and distributed models of computation, yet are a powerful modeling tool for a wide range of fundamental problems in…
An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
This work considers a number of optimization problems and reductive relations between them. The two main problems we are interested in are the \emph{Optimal Decision Tree} and \emph{Set Cover}. We study these two fundamental tasks under…
Binary segmentation is the classic greedy algorithm which recursively splits a sequential data set by optimizing some loss or likelihood function. Binary segmentation is widely used for changepoint detection in data sets measured over space…
Let $P$ and $S$ be two disjoint sets of $n$ and $m$ points in the plane, respectively. We consider the problem of computing a Steiner tree whose Steiner vertices belong to $S$, in which each point of $P$ is a leaf, and whose longest edge…
In this paper we investigate the problem of partitioning an input string T in such a way that compressing individually its parts via a base-compressor C gets a compressed output that is shorter than applying C over the entire T at once.…
A tree-packing is a collection of spanning trees of a graph. It has been a useful tool for computing the minimum cut in static, dynamic, and distributed settings. In particular, [Thorup, Comb. 2007] used them to obtain his dynamic min-cut…
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…
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of target alignments, an associated…
In many applications, it is necessary to determine the string similarity. Edit distance[WF74] approach is a classic method to determine Field Similarity. A well known dynamic programming algorithm [GUS97] is used to calculate edit distance…
We propose an algorithm with expected complexity of $\bigO(n\log n)$ arithmetic operations to solve a special shortest vector problem arising in computer-and-forward design, where $n$ is the dimension of the channel vector. This algorithm…
This note presents an elementary version of Sims's algorithm for computing strong generators of a given perm group, together with a proof of correctness and some notes about appropriate low-level data structures. Upper and lower bounds on…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…