Related papers: In-Place BWT and Lyndon Array Construction in Cons…
Given a string $T$, it is known that its suffix tree can be represented using the compact directed acyclic word graph (CDAWG) with $e_T$ arcs, taking overall $O(e_T+e_{{\overline{T}}})$ words of space, where ${\overline{T}}$ is the reverse…
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…
Motivated by applications to string processing, we introduce variants of the Lyndon factorization called inverse Lyndon factorizations. Their factors, named inverse Lyndon words, are in a class that strictly contains anti-Lyndon words, that…
The Burrows-Wheeler Transform (BWT) has been an essential tool in text compression and indexing. First introduced in 1994, it went on to provide the backbone for the first encoding of the classic suffix tree data structure in space close to…
In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use…
The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array…
We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…
We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input parameter, and tries to make the best use of it by splitting…
We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of…
We propose a novel method for the construction of orthogonal arrays. The algorithm makes use of the Kronecker Product operator in association with unit column vectors to generate new orthogonal arrays from existing orthogonal arrays. The…
We deal with the problem of maintaining the suffix tree indexing structure for a fully-online collection of multiple strings, where a new character can be prepended to any string in the collection at any time. The only previously known…
In-place associative integer sorting technique was proposed for integer lists which requires only constant amount of additional memory replacing bucket sort, distribution counting sort and address calculation sort family of algorithms.…
Recent work by Elmasry et al. (STACS 2015) and Asano et al. (ISAAC 2014), reconsidered classical fundamental graph algorithms focusing on improving the space complexity. We continue this line of work focusing on space. Our first result is a…
Lyndon words have been largely investigated and showned to be a useful tool to prove interesting combinatorial properties of words. In this paper we state new properties of both Lyndon and inverse Lyndon factorizations of a word $w$, with…
In this paper, we resolve a long-standing question in self-stabilization by demonstrating that it is indeed possible to construct a spanning tree in a semi-uniform network using constant memory per node. We introduce a self-stabilizing…
We consider space-saving versions of several important operations on univariate polynomials, namely power series inversion and division, division with remainder, multi-point evaluation, and interpolation. Now-classical results show that…
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several area in science and…
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…