Related papers: Wee LCP
Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
For many kinds of prefix-free codes there are efficient and compact alternatives to the traditional tree-based representation. Since these put the codes into canonical form, however, they can only be used when we can choose the order in…
Real-world point sets tend to be clustered, so using a machine word for each point is wasteful. In this paper we first show how a compact representation of quadtrees using $\Oh{1}$ bits per node can break this bound on clustered point sets,…
The size of the \textit{smallest suffixient set} of positions of a string recently emerged as a new measure of string \textit{repetitiveness} -- a measure reflecting how much of repetitive content the string contains. We study how to…
A common complaint about adaptive prefix coding is that it is much slower than static prefix coding. Karpinski and Nekrich recently took an important step towards resolving this: they gave an adaptive Shannon coding algorithm that encodes…
In this paper, we present the first study of the computational complexity of converting an automata-based text index structure, called the Compact Directed Acyclic Word Graph (CDAWG), of size $e$ for a text $T$ of length $n$ into other text…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
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 +…
Computing the LZ factorization (or LZ77 parsing) of a string is a computational bottleneck in many diverse applications, including data compression, text indexing, and pattern discovery. We describe new linear time LZ factorization…
The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively…
LZ77-based compression schemes compress the input text by replacing factors in the text with an encoded reference to a previous occurrence formed by the couple (length, offset). For a given factor, the smallest is the offset, the smallest…
Let a text $T[1..n]$ be the only string generated by a context-free grammar with $g$ (terminal and nonterminal) symbols, and of size $G$ (measured as the sum of the lengths of the right-hand sides of the rules). Such a grammar, called a…
Let $P$ be a simple polygon of $n$ vertices. We consider two-point $L_1$ shortest path queries in $P$. We build a data structure of $O(n)$ size in $O(n)$ time such that given any two query points $s$ and $t$, the length of an $L_1$ shortest…
We revisit the classic border tree data structure [Gu, Farach, Beigel, SODA 1994] that answers the following prefix-suffix queries on a string $T$ of length $n$ over an integer alphabet $\Sigma=[0,\sigma)$: for any $i,j \in [0,n)$ return…
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…
The Fenwick tree is a classical implicit data structure that stores an array in such a way that modifying an element, accessing an element, computing a prefix sum and performing a predecessor search on prefix sums all take logarithmic time.…
Given a string $S$, the \emph{compressed indexing problem} is to preprocess $S$ into a compressed representation that supports fast \emph{substring queries}. The goal is to use little space relative to the compressed size of $S$ while…
We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…