Related papers: Inverting Parameterized Burrows-Wheeler Transform

We prove that for every integer $n > 0$ and for every alphabet $\Sigma_k$ of size $k \geq 3$, there exists a necklace of length $n$ whose Burrows-Wheeler Transform (BWT) is completely unclustered, i.e., it consists of exactly $n$ runs with…

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…

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…

In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…

We propose a novel transformer-based styled handwritten text image generation approach, HWT, that strives to learn both style-content entanglement as well as global and local writing style patterns. The proposed HWT captures the long and…

We study the impact that string reversal can have on several repetitiveness measures. First, we exhibit an infinite family of strings where the number, $r$, of runs in the run-length encoding of the Burrows--Wheeler transform (BWT) can…

The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…

Variation graphs, which represent genetic variation within a population, are replacing sequences as reference genomes. Path indexes are one of the most important tools for working with variation graphs. They generalize text indexes to…

Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…

The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…

Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…

Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…

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 parameterized matching problem is a variant of string matching, which is to search for all parameterized occurrences of a pattern $P$ in a text $T$. In considering matching algorithms, the combinatorial natures of strings, especially…

The Universal Transformer (UT) is a variant of the Transformer that shares parameters across its layers. Empirical evidence shows that UTs have better compositional generalization than Vanilla Transformers (VTs) in formal language tasks.…

The Balanced-Pairwise-Affinities (BPA) feature transform is designed to upgrade the features of a set of input items to facilitate downstream matching or grouping related tasks. The transformed set encodes a rich representation of high…

We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…

In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…

Inverted indexes are vital in providing fast key-word-based search. For every term in the document collection, a list of identifiers of documents in which the term appears is stored, along with auxiliary information such as term frequency,…

The notion of Wheeler languages is rooted in the Burrows-Wheeler transform (BWT), one of the most central concepts in data compression and indexing. The BWT has been generalized to finite automata, the so-called Wheeler automata, by Gagie…