Related papers: Faster run-length compressed suffix arrays
We present an extension of the in-place BWT algorithm of Crochemore et al. [8] that enables the construction of the Lyndon array using O(1) extra space. Our approach incrementally maintains the lexicographic ranks of the suffixes during the…
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…
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 $O(\delta\log\frac{n}{\delta})$…
We study how the application of injective morphisms affects the number $r$ of equal-letter runs in the Burrows-Wheeler Transform (BWT). This parameter has emerged as a key repetitiveness measure in compressed indexing. We focus on the…
Given a set of pattern strings $\mathcal{P}=\{P_1, P_2,\ldots P_k\}$ and a text string $S$, the classic dictionary matching problem is to report all occurrences of each pattern in $S$. We study the dictionary problem in the compressed…
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…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the…
With the rapid growing of data and number of applications, there is a crucial need of dictionary based reversible transformation techniques to increase the efficiency of the compression algorithms and hence contribute towards the…
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…
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…
We consider a sliding window $W$ over a stream of characters from some alphabet of constant size. The user wants to perform deterministic substring matching on the current sliding window content and obtain positions of the matches. We…
We introduce deterministic suffix-reading automata (DSA), a new automaton model over finite words. Transitions in a DSA are labeled with words. From a state, a DSA triggers an outgoing transition on seeing a word ending with the…
The suffix trees are fundamental data structures for various kinds of string processing. The suffix tree of a string $T$ of length $n$ has $O(n)$ nodes and edges, and the string label of each edge is encoded by a pair of positions in $T$.…
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 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…
We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds…
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
Let two static sequences of strings $P$ and $S$, representing prefix and suffix conditions respectively, be given as input for preprocessing. For the query, let two positive integers $k_1$ and $k_2$ be given, as well as a string $T$ given…
We introduce deterministic suffix-reading automata (DSA), a new automaton model over finite words. Transitions in a DSA are labeled with words. From a state, a DSA triggers an outgoing transition on seeing a word ending with the…