Related papers: Compressing Suffix Trees by Path Decompositions
The Suffix Array is a classic text index enabling on-line pattern matching queries via simple binary search. The main drawback of the Suffix Array is that it takes linear space in the text's length, even if the text itself is extremely…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…
The suffix array and the suffix tree are the two most fundamental data structures for string processing. For a length-$n$ text, however, they use $\Theta(n \log n)$ bits of space, which is often too costly. To address this, Grossi and…
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 $T$…
The Burrows-Wheeler Transform (BWT) has been an essential tool in text compression and indexing. First introduced in 1994, it went on to provide the backbone for the first encoding of the classic suffix tree data structure in space close to…
We present a compressed representation of tries based on top tree compression [ICALP 2013] that works on a standard, comparison-based, pointer machine model of computation and supports efficient prefix search queries. Namely, we show how to…
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…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to 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 $b$…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
Tries are popular data structures for storing a set of strings, where common prefixes are represented by common root-to-node paths. Over fifty years of usage have produced many variants and implementations to overcome some of their…
We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let $n$ be the text length and $\sigma$ be the alphabet size.…
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…
The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…
Suffix trees and suffix arrays are two of the most widely used data structures for text indexing. Each uses linear space and can be constructed in linear time for polynomially sized alphabets. However, when it comes to answering queries…
The well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…
Consider an input text string T[1,N] drawn from an unbounded alphabet. We study partial computation in suffix-based problems for Data Compression and Text Indexing such as (I) retrieve any segment of K<=N consecutive symbols from the…