Related papers: Bijective BWT based compression schemes
In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$. Our algorithm runs in linear time using only a stack in addition to the…
The sensitivity of a string compression algorithm $C$ asks how much the output size $C(T)$ for an input string $T$ can increase when a single character edit operation is performed on $T$. This notion enables one to measure the robustness of…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…
A string $w$ is called a minimal absent word (MAW) for another string $T$ if $w$ does not occur (as a substring) in $T$ and any proper substring of $w$ occurs in $T$. State-of-the-art data structures for reporting the set $\mathsf{MAW}(T)$…
The string repetitiveness measures $\chi$ (the size of a smallest suffixient set of a string) and $r$ (the number of runs in the Burrows--Wheeler Transform) are related. Recently, we have shown that the bound $\chi \leq 2r$, proved by…
Motivated by applications in polymer-based data storage we introduced the new problem of characterizing the code rate and designing constant-weight binary $B_2$-sequences. Binary $B_2$-sequences are collections of binary strings of length…
The Burrows Wheeler transform has applications in data compression as well as full text indexing. Despite its important applications and various existing algorithmic approaches the construction of the transform for large data sets is still…
Second-order M{\o}ller-Plesset perturbation theory (MP2) often breaks down catastrophically in small-gap systems, leaving much to be desired in its performance for myriad chemical applications such as noncovalent interactions,…
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…
Compression algorithms and streaming algorithms are both powerful tools for dealing with massive data sets, but many of the best compression algorithms -- e.g., those based on the Burrows-Wheeler Transform -- at first seem incompatible with…
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 revisit a graph width parameter that we dub bipartite treewidth (btw). Bipartite treewidth can be seen as a common generalization of treewidth and the odd cycle transversal number, and is closely related to odd-minors. Intuitively, a…
We study weighted pseudorandom generators (WPRGs) and derandomizations for read-once branching programs (ROBPs). Denote $n$ and $w$ as the length and the width of a ROBP. We have the following results. For standard ROBPs, we give an…
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…
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…
Motivated by the duplication-correcting problem for data storage in live DNA, we study the construction of constant-weight codes in $\ell_1$-metric. By using packings and group divisible designs in combinatorial design theory, we give…
We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds…
Given a weighted bipartite graph $G = (L, R, E, w)$, the maximum weight matching (MWM) problem seeks to find a matching $M \subseteq E$ that maximizes the total weight $\sum_{e \in M} w(e)$. This paper presents a novel algorithm with a time…
Let $T [1..n]$ be a text over an alphabet of size $\sigma \in \mathrm{polylog} (n)$, let $r^*$ be the sum of the numbers of runs in the Burrows-Wheeler Transforms of $T$ and its reverse, and let $z$ be the number of phrases in the LZ77…