Related papers: Optimal-Time Text Indexing in BWT-runs Bounded Spa…
The proliferation of interconnected devices in the Internet of Things (IoT) has led to an exponential increase in data, commonly known as Big IoT Data. Efficient retrieval of this heterogeneous data demands a robust indexing mechanism for…
In pattern matching on strings, a locate query asks for an enumeration of all the occurrences of a given pattern in a given text. The r-index [Gagie et al., 2018] is a recently presented compressed self index that stores the text and…
We study the classic problem of scheduling $n$ precedence constrained unit-size jobs on $m = O(1)$ machines so as to minimize the makespan. In a recent breakthrough, Levey and Rothvoss \cite{LR16} developed a $(1+\epsilon)$-approximation…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
We consider the approximate pattern matching problem under edit distance. In this problem we are given a pattern $P$ of length $w$ and a text $T$ of length $n$ over some alphabet $\Sigma$, and a positive integer $k$. The goal is to find all…
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…
Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…
We consider the dynamic range minimum problem on the ultra-wide word RAM model of computation. This model extends the classic $w$-bit word RAM model with special ultrawords of length $w^2$ bits that support standard arithmetic and boolean…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…
Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset…
We propose a new approach for calculating the Lempel-Ziv factorization of a string, based on run length encoding (RLE). We present a conceptually simple off-line algorithm based on a variant of suffix arrays, as well as an on-line algorithm…
An occurrence of a repeated substring $u$ in a string $S$ is called a net occurrence if extending the occurrence to the left or to the right decreases the number of occurrences to 1. The net frequency (NF) of a repeated substring $u$ in a…
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…
Classically, the edit distance of two length-$n$ strings can be computed in $O(n^2)$ time, whereas an $O(n^{2-\epsilon})$-time procedure would falsify the Orthogonal Vectors Hypothesis. If the edit distance does not exceed $k$, the running…
We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT.…
We study a document retrieval problem in the new framework where $D$ text documents are organized in a {\em category tree} with a pre-defined number $h$ of categories. This situation occurs e.g. with taxomonic trees in biology or subject…
Shannon's entropy is a clear lower bound for statistical compression. The situation is not so well understood for dictionary-based compression. A plausible lower bound is $b$, the least number of phrases of a general bidirectional parse of…