Related papers: Parallel Query in the Suffix Tree
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…
We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer…
The Cartesian-tree pattern matching is a recently introduced scheme of pattern matching that detects fragments in a sequential data stream which have a similar structure as a query pattern. Formally, Cartesian-tree pattern matching seeks…
A trie $\mathcal{T}$ is a rooted tree such that each edge is labeled by a single character from the alphabet, and the labels of out-going edges from the same node are mutually distinct. Given a trie $\mathcal{T}$ with $n$ edges, we show how…
Given a text $T$ of length $n$, we propose a deterministic online algorithm computing the sparse suffix array and the sparse longest common prefix array of $T$ in $O(c \sqrt{\lg n} + m \lg m \lg n \lg^* n)$ time with $O(m)$ words of space…
The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint…
We give a parallel $O(\log(n))$-time algorithm on a CRCW PRAM to assign vertical and horizontal segments to the vertices of any planar bipartite graph $G$ in the following manner: i) Two segments cannot share an interior point ii) Two…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
This paper presents a batch-parallel 2-3 tree T in an asynchronous dynamic multithreading model that supports searches, insertions and deletions in sorted batches and has essentially optimal parallelism, even under the restrictive QRMW…
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…
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,…
There is a large body of recent work applying machine learning (ML) techniques to query optimization and query performance prediction in relational database management systems (RDBMSs). However, these works typically ignore the effect of…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
We consider the problem of encoding a string of length $n$ from an integer alphabet of size $\sigma$ so that access and substring equality queries (that is, determining the equality of any two substrings) can be answered efficiently. Any…
We present an algorithm for parallelising the TreePM code. We use both functional and domain decompositions. Functional decomposition is used to separate the computation of long range and short range forces, as well as the task of…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
Balanced search trees are widely used in computer science to efficiently maintain dynamic ordered data. To support efficient set operations (e.g., union, intersection, difference) using trees, the join-based framework is widely studied.…
Arrival of multicore systems has enforced a new scenario in computing, the parallel and distributed algorithms are fast replacing the older sequential algorithms, with many challenges of these techniques. The distributed algorithms provide…
The generalized method to have a parallel solution to a computational problem, is to find a way to use Divide & Conquer paradigm in order to have processors acting on its own data and therefore all can be scheduled in parallel. MapReduce is…
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…