Related papers: Faster Approximate Pattern Matching in Compressed …
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
Many database columns contain string or numerical data that conforms to a pattern, such as phone numbers, dates, addresses, product identifiers, and employee ids. These patterns are useful in a number of data processing applications,…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
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…
We consider the approximate pattern matching problem under edit distance. In this problem we are given a pattern $P$ of length $w$ and a text $T$ of length $n$ over some alphabet $\Sigma$, and a positive integer $k$. The goal is to find all…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
This paper explores the notion of approximate data structures, which return approximately correct answers to queries, but run faster than their exact counterparts. The paper describes approximate variants of the van Emde Boas data…
Shannon's entropy is a definitive lower bound for statistical compression. Unfortunately, no such clear measure exists for the compressibility of repetitive strings. Thus, ad hoc measures are employed to estimate the repetitiveness of…
The compact directed acyclic word graph (CDAWG) of a string $T$ of length $n$ takes space proportional just to the number $e$ of right extensions of the maximal repeats of $T$, and it is thus an appealing index for highly repetitive…
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…
Regular expressions constitute a fundamental notion in formal language theory and are frequently used in computer science to define search patterns. A classic algorithm for these problems constructs and simulates a non-deterministic finite…
We present OnPair, a dictionary-based compression algorithm designed to meet the needs of in-memory database systems that require both high compression and fast random access. Existing methods either achieve strong compression ratios at…
Detecting and counting copies of permutation patterns are fundamental algorithmic problems, with applications in the analysis of rankings, nonparametric statistics, and property testing tasks such as independence and quasirandomness…