Related papers: EERTREE: An Efficient Data Structure for Processin…

We present several results about position heaps, a relatively new alternative to suffix trees and suffix arrays. First, we show that, if we limit the maximum length of patterns to be sought, then we can also limit the height of the heap and…

Index is an important component in database systems. Learned indexes have been shown to outperform traditional tree-based index structures for fixed-sized integer or floating point keys. However, the application of the learned solution to…

The Suffix Array $SA_S[1\ldots n]$ of an $n$-length string $S$ is a lexicographically sorted array of the suffixes of $S$. The suffix array is one of the most well known and widely used data structures in string algorithms. We present a…

In recent years, stream data have become an immensely growing area of research for the database, computer science and data mining communities. Stream data is an ordered sequence of instances. In many applications of data stream mining data…

Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…

Palindromes are non-empty strings that read the same forward and backward. The problem of recognizing strings that can be represented as the concatenation of even-length palindromes, the concatenation of palindromes of length at least two,…

The suffix trees are fundamental data structures for various kinds of string processing. The suffix tree of a text 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…

The string-matching field has grown at a such complicated stage that various issues come into play when studying it: data structure and algorithmic design, database principles, compression techniques, architectural features, cache and…

We consider how to index strings, trees and graphs for jumbled pattern matching when we are asked to return a match if one exists. For example, we show how, given a tree containing two colours, we can build a quadratic-space index with…

We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…

Given a text, rank and select queries return the number of occurrences of a character up to a position (rank) or the position of a character with a given rank (select). These queries have applications in, e.g., compression, computational…

For a string $S$, a palindromic substring $S[i..j]$ is said to be a \emph{shortest unique palindromic substring} ($\mathit{SUPS}$) for an interval $[s, t]$ in $S$, if $S[i..j]$ occurs exactly once in $S$, the interval $[i, j]$ contains $[s,…

We propose an extension of tree-based space-partitioning indexing structures for data with low intrinsic dimensionality embedded in a high dimensional space. We call this extension an Angle Tree. Our extension can be applied to both…

This dissertation focuses on two fundamental sorting problems: string sorting and suffix sorting. The first part considers parallel string sorting on shared-memory multi-core machines, the second part external memory suffix sorting using…

Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…

We present a new efficient method for approximate search in electronic lexica. Given an input string (the pattern) and a similarity threshold, the algorithm retrieves all entries of the lexicon that are sufficiently similar to the pattern.…

We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…

In this paper we will describe a new approach on the well-known suffix-array algorithm using Big Table Data Technology. We will demonstrate how it is possible to refactor a well-known algorithm coupled by taking advantage of an…

Collective entity disambiguation aims to jointly resolve multiple mentions by linking them to their associated entities in a knowledge base. Previous works are primarily based on the underlying assumption that entities within the same…

In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…