Related papers: A Bijective String Sorting Transform
In this paper we investigate the problem of partitioning an input string T in such a way that compressing individually its parts via a base-compressor C gets a compressed output that is shorter than applying C over the entire T at once.…
We first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $\sigma$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n /…
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…
Compression of inverted lists with methods that support fast intersection operations is an active research topic. Most compression schemes rely on encoding differences between consecutive positions with techniques that favor small numbers.…
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…
Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH)…
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…
Sorted data is usually easier to compress than unsorted permutations of the same data. This motivates a simple compression scheme: specify the sorted permutation of the data along with a representation of the sorted data compressed…
The synthesis of string transformation programs from input-output examples utilizes various techniques, all based on an inductive bias that comprises a restricted set of basic operators to be combined. A new algorithm, Transduce, is…
Bidirectional compression algorithms work by substituting repeated substrings by references that, unlike in the famous LZ77-scheme, can point to either direction. We present such an algorithm that is particularly suited for an external…
Visual data compression is shifting from human-centered reconstruction to machine-oriented representation coding. In this setting, an image is often mapped to a compact semantic embedding, which is then compressed and transmitted for…
Compression of integer sets and sequences has been extensively studied for settings where elements follow a uniform probability distribution. In addition, methods exist that exploit clustering of elements in order to achieve higher…
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…
Recurrent neural networks have a strong inductive bias towards learning temporally compressed representations, as the entire history of a sequence is represented by a single vector. By contrast, Transformers have little inductive bias…
Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems. We describe issues with this approach that were not widely known, and…
Most existing Neural Machine Translation models use groups of characters or whole words as their unit of input and output. We propose a model with a hierarchical char2word encoder, that takes individual characters both as input and output.…
We formulate and explain the extended Burrows-Wheeler transform of Mantaci et al from the viewpoint of permutations on a chain taken as a union of partial order-preserving mappings. In so doing we establish a link with syntactic semigroups…
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…
We consider the problem of {\em restructuring} compressed texts without explicit decompression. We present algorithms which allow conversions from compressed representations of a string $T$ produced by any grammar-based compression…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…