Related papers: Lyndon Array Construction during Burrows-Wheeler I…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
In this short note, we first associate a new simple undirected graph with a given word over an ordered alphabet of $n$-letters. We will call it the Lyndon graph of that word. Then, we introduce the concept of the Lyndon-word representable…
We present the first worst-case linear time algorithm that directly computes the parameterized suffix and LCP arrays for constant sized alphabets. Previous algorithms either required quadratic time or the parameterized suffix tree to be…
Finding the length of the longest increasing subsequence (LIS) is a classic algorithmic problem. Let $n$ denote the size of the array. Simple $O(n\log n)$ algorithms are known for this problem. We develop a polylogarithmic time randomized…
Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…
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…
Many constraints restricting the result of some computations over an integer sequence can be compactly represented by register automata. We improve the propagation of the conjunction of such constraints on the same sequence by synthesising…
We present a new algorithm for the 2D Sliding Window Discrete Fourier Transform (SWDFT). Our algorithm avoids repeating calculations in overlapping windows by storing them in a tree data-structure based on the ideas of the Cooley- Tukey…
We present a simple algorithm for computing the document array given a string collection and its suffix array as input. Our algorithm runs in linear time using constant additional space for strings from constant alphabets.
The suffix trees are fundamental data structures for various kinds of string processing. The suffix tree of a string $T$ of length $n$ has $O(n)$ nodes and edges, and the string label of each edge is encoded by a pair of positions in $T$.…
Lyndon words are extensively studied in combinatorics on words -- they play a crucial role on upper bounding the number of runs a word can have [Bannai+, SIAM J. Comput.'17]. We can determine Lyndon words, factorize a word into Lyndon words…
The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the…
We survey some results on linear-time algorithms for systolic arrays. In particular, we show how the greatest common divisor (GCD) of two polynomials of degree n over a finite field can be computed in time O(n) on a linear systolic array of…
The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the…
We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…
We investigate properties of the bijective Burrows-Wheeler transform (BBWT). We show that for any string $w$, a bidirectional macro scheme of size $O(r_B)$ can be induced from the BBWT of $w$, where $r_B$ is the number of maximal character…
We present a sublinear randomized algorithm to compute a sparse Fourier transform for nonequispaced data. Suppose a signal S is known to consist of N equispaced samples, of which only L<N are available. If the ratio p=L/N is not close to 1,…
We introduce the Non-commutative Subset Convolution - a convolution of functions useful when working with determinant-based algorithms. In order to compute it efficiently, we take advantage of Clifford algebras, a generalization of…
In this paper, we propose a data structure, a quadruple neighbor list (QN-list, for short), to support real time queries of all longest increasing subsequence (LIS) and LIS with constraints over sequential data streams. The QN-List built by…
The Burrows-Wheeler Transform (BWT) is an invertible text transformation that permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the main component of popular lossless compression programs (such as…