Related papers: Constructing Suffixient Arrays Revisited
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…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
Two strings of equal length are said to parameterized match if there is a bijection that maps the characters of one string to those of the other string, so that two strings become identical. The parameterized pattern matching problem is,…
An initializable array is an array that supports the read and write operations for any element and the initialization of the entire array. This paper proposes a simple in-place algorithm to implement an initializable array of length $N$…
Introduced about thirty years ago in the field of Data Compression, the Burrows-Wheeler Transform (BWT) is a string transformation that, besides being a booster of the performance of memoryless compressors, plays a fundamental role in the…
We study the IS-algorithm, a well-known linear-time algorithm for computing the suffix array of a word. This algorithm relies on transforming the input word $w$ into another word, called the reduced word of $w$, that will be at least twice…
Suffix tree construction algorithms based on suffix links are popular because they are simple to implement, can operate online in linear time, and because the suffix links are often convenient for pattern matching. We present an approach…
The Suffix Array $SA_S[1\ldots n]$ of an $n$-length string $S$ is a lexicographically sorted array of the suffixes of $S$. The suffix array is one of the most well known and widely used data structures in string algorithms. We present a…
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…
Indexing labeled graphs for pattern matching is a central challenge of pangenomics. Equi et al. (Algorithmica, 2022) developed the Elastic Founder Graph ($\mathsf{EFG}$) representing an alignment of $m$ sequences of length $n$, drawn from…
The Burrows-Wheeler transform (BWT) is a string transformation that enhances string indexing and compressibility. Cotumaccio and Prezza [SODA '21] extended this transformation to nondeterministic finite automata (NFAs) through…
Indexing highly repetitive strings (i.e., strings with many repetitions) for fast queries has become a central research topic in string processing, because it has a wide variety of applications in bioinformatics and natural language…
In this paper, we present the first study of the computational complexity of converting an automata-based text index structure, called the Compact Directed Acyclic Word Graph (CDAWG), of size $e$ for a text $T$ of length $n$ into other text…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
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…
The focus of this thesis is the study and construction of covering arrays, relying on maximal period sequences and other tools from finite fields. A covering array of strength $t$, denoted $\mathrm{CA}(N; t, k,v)$, is an $N\times k$ array…
We consider the problem of constructing a sparse suffix tree (or suffix array) for $b$ suffixes of a given text $T$ of size $n$, using only $O(b)$ words of space during construction time. Breaking the naive bound of $\Omega(nb)$ time for…
The size of the \textit{smallest suffixient set} of positions of a string recently emerged as a new measure of string \textit{repetitiveness} -- a measure reflecting how much of repetitive content the string contains. We study how to…
We revisit the classic border tree data structure [Gu, Farach, Beigel, SODA 1994] that answers the following prefix-suffix queries on a string $T$ of length $n$ over an integer alphabet $\Sigma=[0,\sigma)$: for any $i,j \in [0,n)$ return…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…