Related papers: Linear Time Inference of Strings from Cover Arrays…
In this note, we give an algorithm that computes the linearwidth of input $n$-vertex graphs in time $O^*(2^n)$, which improves a trivial $O^*(2^m)$-time algorithm, where $n$ and $m$ the number of vertices and edges, respectively.
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
In this work, we analyze a sublinear-time algorithm for selecting a few rows and columns of a matrix for low-rank approximation purposes. The algorithm is based on an initial uniformly random selection of rows and columns, followed by a…
In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$. Our algorithm runs in linear time using only a stack in addition to the…
In this paper we introduce a method to detect words or phrases in a given sequence of alphabets without knowing the lexicon. Our linear time unsupervised algorithm relies entirely on statistical relationships among alphabets in the input…
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 this paper, we will show that the width of simplices defined by systems of linear inequalities can be computed in polynomial time if some minors of their constraint matrices are bounded. Additionally, we present some…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
We prove new necessary and sufficient conditions to carry out a compact linearization approach for a general class of binary quadratic problems subject to assignment constraints as it has been proposed by Liberti in 2007. The new conditions…
Alphabetic codes and binary search trees are combinatorial structures that abstract search procedures in ordered sets endowed with probability distributions. In this paper, we design new linear-time algorithms to construct alphabetic codes,…
A factorization $f_1, \ldots, f_m$ of a string $w$ of length $n$ is called a repetition factorization of $w$ if $f_i$ is a repetition, i.e., $f_i$ is a form of $x^kx'$, where $x$ is a non-empty string, $x'$ is a (possibly-empty) proper…
A factor $u$ of a word $w$ is a cover of $w$ if every position in $w$ lies within some occurrence of $u$ in $w$. A word $w$ covered by $u$ thus generalizes the idea of a repetition, that is, a word composed of exact concatenations of $u$.…
Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…
A binary string representation of prime occurrences is a sequence of bits, where $1$ entries encode positions of prime numbers. This is a convenient representation for analysis of prime distribution, since it allows for application of a…
We present efficient computational solutions to the problems of checking equality, performing multiplication, and computing minimal representatives of elements of free bands. A band is any semigroup satisfying the identity $x ^ 2 \approx x$…
In this article we mainly study linear codes over $\mathbb{F}_{2^n}$ and their binary subfield codes. We construct linear codes over $\mathbb{F}_{2^n}$ whose defining sets are the certain subsets of $\mathbb{F}_{2^n}^m$ obtained from…