Related papers: Succincter Text Indexing with Wildcards
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…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
We consider the problem of supporting Rank() and Select() operations on a bit vector of length m with n 1 bits. The problem is considered in the succinct index model, where the bit vector is stored in "read-only" memory and an additional…
Most of the attention in statistical compression is given to the space used by the compressed sequence, a problem completely solved with optimal prefix codes. However, in many applications, the storage space used to represent the prefix…
Pattern matching with wildcards is the problem of finding all factors of a text $t$ of length $n$ that match a pattern $x$ of length $m$, where wildcards (characters that match everything) may be present. In this paper we present a number…
We introduce the first index that can be built in $o(n)$ time for a text of length $n$, and can also be queried in $o(q)$ time for a pattern of length $q$. On an alphabet of size $\sigma$, our index uses $O(n\sqrt{\log n\log\sigma})$ bits,…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
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…
In this paper we propose a variant of the induced suffix sorting algorithm by Nong (TOIS, 2013) that computes simultaneously the Lyndon array and the suffix array of a text in $O(n)$ time using $\sigma + O(1)$ words of working space, where…
We propose to design data structures called succinct geometric indexes of negligible space (more precisely, o(n) bits) that, by taking advantage of the n points in the data set permuted and stored elsewhere as a sequence, to support…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
We consider the problem of designing a succinct data structure for {\it path graphs} (which are a proper subclass of chordal graphs and a proper superclass of interval graphs) on $n$ vertices while supporting degree, adjacency, and…
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…
It is widely assumed that $O(m+\lg \sigma)$ is the best one can do for finding a pattern of length $m$ in a compacted trie storing strings over an alphabet of size $\sigma$, if one insists on linear-size data structures and deterministic…
The index coding problem is concerned with broadcasting encoded information to a collection of receivers in a way that enables each receiver to discover its required data based on its side information, which comprises the data required by…
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…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…