Related papers: A Faster Grammar-Based Self-Index
Internal Pattern Matching (IPM) queries on a text $T$, given two fragments $X$ and $Y$ of $T$ such that $|Y|<2|X|$, ask to compute all exact occurrences of $X$ within $Y$. IPM queries have been introduced by Kociumaka, Radoszewski, Rytter,…
The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…
To handle vast amounts of data, it is natural and popular to compress vectors and matrices. When we compress a vector from size $N$ down to size $n \ll N$, it certainly makes it easier to store and transmit efficiently, but does it also…
XML document markup is highly repetitive and therefore well compressible using dictionary-based methods such as DAGs or grammars. In the context of selectivity estimation, grammar-compressed trees were used before as synopsis for structural…
Unlike in statistical compression, where Shannon's entropy is a definitive lower bound, no such clear measure exists for the compressibility of repetitive sequences. Since statistical entropy does not capture repetitiveness, ad-hoc measures…
Grammar compression is, next to Lempel-Ziv (LZ77) and run-length Burrows-Wheeler transform (RLBWT), one of the most flexible approaches to representing and processing highly compressible strings. The main idea is to represent a text as a…
Indexing data is a fundamental problem in computer science. Recently, various papers apply machine learning to this problem. For a fixed integer $\varepsilon$, a \emph{learned index} is a function $h : \mathcal{U} \rightarrow [0, n]$ where…
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets…
It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…
The $r$-index (Gagie et al., JACM 2020) represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude. Its space usage, $\mathcal{O}(r)$ where $r$ is the number of…
We introduce fast-decodable indexing schemes for edit distance which can be used to speed up edit distance computations to near-linear time if one of the strings is indexed by an indexing string $I$. In particular, for every length $n$ and…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
In this paper we describe a data structure that supports pattern matching queries on a dynamically arriving text over an alphabet ofconstant size. Each new symbol can be prepended to $T$ in O(1) worst-case time. At any moment, we can report…
The $r$-index represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude in query time. Its space usage, $O(r)$ where $r$ is the number of runs in the…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
Many services today massively and continuously produce log files of different and varying formats. These logs are important since they contain information about the application activities, which is necessary for improvements by analyzing…
The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in…
It was recently proved that any Straight-Line Program (SLP) generating a given string can be transformed in linear time into an equivalent balanced SLP of the same asymptotic size. We generalize this proof to a general class of grammars we…
A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…
In this paper, we propose a new \emph{dynamic compressed index} of $O(w)$ space for a dynamic text $T$, where $w = O(\min(z \log N \log^*M, N))$ is the size of the signature encoding of $T$, $z$ is the size of the Lempel-Ziv77 (LZ77)…