Related papers: Space-Efficient Construction of Compressed Suffix …
The Burrows-Wheeler transform (BWT) is a well studied text transformation widely used in data compression and text indexing. The BWT of two strings can also provide similarity measures between them, based on the observation that the more…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
We present an extension of the in-place BWT algorithm of Crochemore et al. [8] that enables the construction of the Lyndon array using O(1) extra space. Our approach incrementally maintains the lexicographic ranks of the suffixes during the…
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…
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 directed acyclic word graph (DAWG) of a string $y$ of length $n$ is the smallest (partial) DFA which recognizes all suffixes of $y$ with only $O(n)$ nodes and edges. In this paper, we show how to construct the DAWG for the input string…
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…
It is shown that every tree of size $n$ over a fixed set of $\sigma$ different ranked symbols can be decomposed (in linear time as well as in logspace) into $O\big(\frac{n}{\log_\sigma n}\big) = O\big(\frac{n \log \sigma}{\log n}\big)$ many…
We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction of a set of suffixes $B$ using only $O(|B|)$ words of space. The second problem is the…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
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 show that both the Lempel Ziv 77- and the 78-factorization of a text of length $n$ on an integer alphabet of size $\sigma$ can be computed in $O(n \lg \lg \sigma)$ time (linear time if we allow randomization) using $O(n \lg \sigma)$ bits…
Existing parallel algorithms for wavelet tree construction have a work complexity of $O(n\log\sigma)$. This paper presents parallel algorithms for the problem with improved work complexity. Our first algorithm is based on parallel integer…
The rank and select operations over a string of length n from an alphabet of size $\sigma$ have been used widely in the design of succinct data structures. In many applications, the string itself need be maintained dynamically, allowing…
Given a string of length $n$ that is composed of $r$ runs of letters from the alphabet $\{0,1,\ldots,\sigma{-}1\}$ such that $2 \le \sigma \le r$, we describe a data structure that, provided $r \le n / \log^{\omega(1)} n$, stores the string…
We present linear-space data structures for several frequency queries on trees, namely: path mode, path least frequent element, and path $\alpha$-minority queries. We present the first linear-space data structures, requiring $O(n…
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…
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in $O (r)$ space and $O ((r + L) \log (m + n))$ time, where $m$ and $n$ are the…
We show how to construct a dynamic ordered dictionary, supporting insert/delete/rank/select on a set of $n$ elements from a universe of size $U$, that achieves the optimal amortized expected time complexity of $O(1 + \log n / \log \log U)$,…
In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…