Related papers: Fast and Small Subsampled R-indexes
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In this paper we consider the basic variant where the pattern is…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
Suppose that we are given a string $s$ of length $n$ over an alphabet $\{0,1,\ldots,n^{O(1)}\}$ and $\delta$ is the string complexity of $s$, a known compression measure. We describe an index on $s$ with $O(\delta\log\frac{n}{\delta})$…
Indexing highly repetitive collections has become a relevant problem with the emergence of large repositories of versioned documents, among other applications. These collections may reach huge sizes, but are formed mostly of documents that…
We describe the first self-indexes able to count and locate pattern occurrences in optimal time within a space bounded by the size of the most popular dictionary compressors. To achieve this result we combine several recent findings,…
We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction of a set of suffixes $B$ using only $O(|B|)$ words of space. The second problem is the…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…
We consider the problem of creating document representations in which inter-document similarity measurements correspond to semantic similarity. We first present a novel subspace-based framework for formalizing this task. Using this…
Given a string $S$ of $n$ integers in $[0,\sigma)$, a range minimum query RMQ$(i, j)$ asks for the index of the smallest integer in $S[i \dots j]$. It is well known that the problem can be solved with a succinct data structure of size $2n +…
In this work, we study the limits of compressed data structures, i.e., structures that support various queries on an input text $T\in\Sigma^n$ using space proportional to the size of $T$ in compressed form. Nearly all fundamental queries…
We introduce the first self-index based on the Lempel-Ziv 1977 compression format (LZ77). It is particularly competitive for highly repetitive text collections such as sequence databases of genomes of related species, software repositories,…
Self-supervised learning (SSL) has allowed substantial progress in Automatic Speech Recognition (ASR) performance in low-resource settings. In this context, it has been demonstrated that larger self-supervised feature extractors are crucial…
A central task in string processing is text indexing, where the goal is to preprocess a text (a string of length $n$) into an efficient index (a data structure) supporting queries about the text. Cole, Gottlieb, and Lewenstein (STOC 2004)…
While several self-indexes for highly repetitive texts exist, developing a practical self-index applicable to real world repetitive texts remains a challenge. ESP-index is a grammar-based self-index on the notion of edit-sensitive parsing…
In recent years, RDF has gained popularity as a format for the standardized publication and exchange of information in the Web of Data. In this paper we introduce RDFCSA, a data structure that is able to self-index an RDF dataset in small…
Let $\D = $$ \{d_1,d_2,...d_D\}$ be a given set of $D$ string documents of total length $n$, our task is to index $\D$, such that the $k$ most relevant documents for an online query pattern $P$ of length $p$ can be retrieved efficiently. We…
An optimal index solving top-k document retrieval [Navarro and Nekrich, SODA12] takes O(m + k) time for a pattern of length m, but its space is at least 80n bytes for a collection of n symbols. We reduce it to 1.5n to 3n bytes, with…
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…
Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…