Related papers: Relative Suffix Trees
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main…
We present a new universal source code for distributions of unlabeled binary and ordinal trees that achieves optimal compression to within lower order terms for all tree sources covered by existing universal codes. At the same time, it…
Computing over compressed data combines the space saving of data compression with efficient support for queries directly on the compressed representation. Such data structures are widely applied in text indexing and have been successfully…
In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…
Extractive compression is a challenging natural language processing problem. This work contributes by formulating neural extractive compression as a parse tree transduction problem, rather than a sequence transduction task. Motivated by…
The Simplex Tree (ST) is a recently introduced data structure that can represent abstract simplicial complexes of any dimension and allows efficient implementation of a large range of basic operations on simplicial complexes. In this paper,…
The task of calculating similarities between strings held by different organizations without revealing these strings is an increasingly important problem in areas such as health informatics, national censuses, genomics, and fraud detection.…
Measuring the complexity of tree structures can be beneficial in areas that use tree data structures for storage, communication, and processing purposes. This complexity can then be used to compress tree data structures to their…
We propose a new linear-size data structure which provides a fast access to all palindromic substrings of a string or a set of strings. This structure inherits some ideas from the construction of both the suffix trie and suffix tree. Using…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
The {\em wavelet tree} is a flexible data structure that permits representing sequences $S[1,n]$ of symbols over an alphabet of size $\sigma$, within compressed space and supporting a wide range of operations on $S$. When $\sigma$ is…
The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
This paper introduces a data structure, called simplex tree, to represent abstract simplicial complexes of any dimension. All faces of the simplicial complex are explicitly stored in a trie whose nodes are in bijection with the faces of the…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
Succinct data structures give space-efficient representations of large amounts of data without sacrificing performance. They rely one cleverly designed data representations and algorithms. We present here the formalization in Coq/SSReflect…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…