相关论文: An Optimal-Time RLBWT Construction in BWT-runs Bou…

A weight based dynamic compression method has recently been proposed, which is especially suitable for the encoding of files with locally skewed distributions. Its main idea is to assign larger weights to closer to be encoded symbols by…

Let $S_{T}(k)$ denote the set of distinct substrings of length $k$ in a string $T$, then the $k$-th substring complexity is defined by its cardinality $|S_{T}(k)|$. Recently, $\delta = \max \{ |S_{T}(k)| / k : k \ge 1 \}$ is shown to be a…

Given a string $T$ of length $N$, the goal of grammar compression is to construct a small context-free grammar generating only $T$. Among existing grammar compression methods, RePair (recursive paring) [Larsson and Moffat, 1999] is notable…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…

The Positional Burrows-Wheeler Transform (PBWT) is a fundamental data structure for the efficient representation and analysis of large-scale haplotype panels. For a panel of $h$ sequences $\{S_1, \dots, S_h\}$ over $m$ sites, a key…

Re-Pair is an effective grammar-based compression scheme achieving strong compression rates in practice. Let $n$, $\sigma$, and $d$ be the text length, alphabet size, and dictionary size of the final grammar, respectively. In their original…

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…

Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…

Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…

The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…

Re-Pair is a grammar compression scheme with favorably good compression rates. The computation of Re-Pair comes with the cost of maintaining large frequency tables, which makes it hard to compute Re-Pair on large scale data sets. As a…

Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…

We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…

Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…

Re-Pair is an efficient grammar compressor that operates by recursively replacing high-frequency character pairs with new grammar symbols. The most space-efficient linear-time algorithm computing Re-Pair uses $(1+\epsilon)n+\sqrt n$ words…

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…

A factorization $f_1, \ldots, f_m$ of a string $w$ of length $n$ is called a repetition factorization of $w$ if $f_i$ is a repetition, i.e., $f_i$ is a form of $x^kx'$, where $x$ is a non-empty string, $x'$ is a (possibly-empty) proper…

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…

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…

A Random Access query to a string $T\in [0..\sigma)^n$ asks for the character $T[i]$ at a given position $i\in [0..n)$. In $O(n\log\sigma)$ bits of space, this fundamental task admits constant-time queries. While this is optimal in the…