Related papers: Relative Suffix Trees
A grammar-compressed ranked tree is represented with a linear space overhead so that a single traversal step, i.e., the move to the parent or the i-th child, can be carried out in constant time. Moreover, we extend our data structure such…
Suffix Array (SA) is a cardinal data structure in many pattern matching applications, including data compression, plagiarism detection and sequence alignment. However, as the volumes of data increase abruptly, the construction of SA is not…
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.…
Much research has been devoted to optimizing algorithms of the Lempel-Ziv (LZ) 77 family, both in terms of speed and memory requirements. Binary search trees and suffix trees (ST) are data structures that have been often used for this…
Motivation: As a fundamental task in bioinformatics, searching for massive short patterns over a long text is widely accelerated by various compressed full-text indexes. These indexes are able to provide similar searching functionalities to…
We address the problem of efficiently gathering correlated data from a wired or a wireless sensor network, with the aim of designing algorithms with provable optimality guarantees, and understanding how close we can get to the known…
Data compression has been widely applied in many data processing areas. Compression methods use variable-size codes with the shorter codes assigned to symbols or groups of symbols that appear in the data frequently. Fibonacci coding, as a…
We study the compressed representation of a ranked tree by a (string) straight-line program (SLP) for its preorder traversal, and compare it with the well-studied representation by straight-line context free tree grammars (which are also…
Suffix trees are key and efficient data structure for solving string problems. A suffix tree is a compressed trie containing all the suffixes of a given text of length $n$ with a linear construction cost. In this work, we introduce an…
Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…
Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a common leafset. Storing and sharing such large collection of…
Sequence representations supporting not only direct access to their symbols, but also rank/select operations, are a fundamental building block in many compressed data structures. Several recent applications need to represent highly…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits…
Rank and select queries on bitmaps are essential building bricks of many compressed data structures, including text indexes, membership and range supporting spatial data structures, compressed graphs, and more. Theoretically considered yet…
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 +…
The weighted ancestor problem is a well-known generalization of the predecessor problem to trees. It is known to require $\Omega(\log\log n)$ time for queries provided $O(n\mathop{\mathrm{polylog}} n)$ space is available and weights are…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…