Related papers: Suffix sorting via matching statistics
Fast matching of regular expressions with bounded repetition, aka counting, such as (ab){50,100}, i.e., matching linear in the length of the text and independent of the repetition bounds, has been an open problem for at least two decades.…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
We show how to modify the linear-time construction algorithm for suffix arrays based on induced sorting (Nong et al., DCC'09) such that it computes the array of longest common prefixes (LCP-array) as well. Practical tests show that this…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…
Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
Tasks that model the relation between pairs of tokens in a string are a vital part of understanding natural language. Such tasks, in general, require exhaustive pair-wise comparisons of tokens, thus having a quadratic runtime complexity in…
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…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…
We propose and study a novel supervised approach to learning statistical semantic relatedness models from subjectively annotated training examples. The proposed semantic model consists of parameterized co-occurrence statistics associated…
When writing a summary, humans tend to choose content from one or two sentences and merge them into a single summary sentence. However, the mechanisms behind the selection of one or multiple source sentences remain poorly understood.…
We give the first concise description of the fastest known suffix sorting algorithm in main memory, the DivSufSort by Yuta Mori. We then present an extension that also computes the LCP-array, which is competitive with the fastest known…
A similarity join aims to find all similar pairs between two collections of records. Established approaches usually deal with synthetic differences like typos and abbreviations, but neglect the semantic relations between words. Such…
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 GCIS, a grammar compression algorithm based on the induced suffix sorting algorithm SAIS, introduced by Nong et al. in 2009. Our solution builds on the factorization performed by SAIS during suffix sorting. We construct a…
We present a technique for clustering categorical data by generating many dissimilarity matrices and averaging over them. We begin by demonstrating our technique on low dimensional categorical data and comparing it to several other…
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
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…
Suffix trees and suffix arrays are two of the most widely used data structures for text indexing. Each uses linear space and can be constructed in linear time for polynomially sized alphabets. However, when it comes to answering queries…