Related papers: Burrows-Wheeler transform and LCP array constructi…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
Ordering the collection of states of a given automaton starting from an order of the underlying alphabet is a natural move towards a computational treatment of the language accepted by the automaton. Along this path, Wheeler \emph{graphs}…
A new array based data structure named black-white array (BWA) is introduced as an effective and efficient alternative to the list or tree based data structures for dynamic data set. It consists of two sub-arrays, one white and one black of…
The notion of Wheeler languages is rooted in the Burrows-Wheeler transform (BWT), one of the most central concepts in data compression and indexing. The BWT has been generalized to finite automata, the so-called Wheeler automata, by Gagie…
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…
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 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…
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 $b$…
We propose a novel algorithm for computing the Walsh-Hadamard Transform (WHT) which consists entirely of Haar wavelet transforms. We prove that the algorithm, which we call the Cascading Haar Wavelet (CHW) algorithm, shares precisely the…
The wavelet tree (Grossi et al. [SODA, 2003]) and wavelet matrix (Claude et al. [Inf. Syst., 47:15--32, 2015]) are compact indices for texts over an alphabet $[0,\sigma)$ that support rank, select and access queries in $O(\lg \sigma)$ time.…
The notions of synchronizing and partitioning sets are recently introduced variants of locally consistent parsings with great potential in problem-solving. In this paper we propose a deterministic algorithm that constructs for a given…
Given a graph $G$, the longest path problem asks to compute a simple path of $G$ with the largest number of vertices. This problem is the most natural optimization version of the well known and well studied Hamiltonian path problem, and…
In this paper, we propose several improvements on the block-coordinate Frank-Wolfe (BCFW) algorithm from Lacoste-Julien et al. (2013) recently used to optimize the structured support vector machine (SSVM) objective in the context of…
A self-index is a compressed data structure that supports locate queries -- reporting all positions where a given pattern occurs in a string while maintaining the string in compressed form. While many self-indexes have been proposed,…
Blind estimation of intersymbol interference channels based on the Baum-Welch (BW) algorithm, a specific implementation of the expectation-maximization (EM) algorithm for training hidden Markov models, is robust and does not require labeled…
For a partial word $w$ the longest common compatible prefix of two positions $i,j$, denoted $lccp(i,j)$, is the largest $k$ such that $w[i,i+k-1]\uparrow w[j,j+k-1]$, where $\uparrow$ is the compatibility relation of partial words (it is…
Suffix arrays and LCP arrays are one of the most fundamental data structures widely used for various kinds of string processing. We consider two problems for a read-only string of length $N$ over an integer alphabet $[1, \dots, \sigma]$ for…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
We show that counting Euler tours in undirected bounded tree-width graphs is tractable even in parallel - by proving a $\#SAC^1$ upper bound. This is in stark contrast to #P-completeness of the same problem in general graphs. Our main…
We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer…