Related papers: Hidden Words Statistics for Large Patterns
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
We introduce a data structure for counting pattern occurrences in texts compressed with any run-length context-free grammar. Our structure uses space proportional to the grammar size and counts the occurrences of a pattern of length $m$ in…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
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…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
It is well-known that checking whether a given string $w$ matches a given regular expression $r$ can be done in quadratic time $O(|w|\cdot |r|)$ and that this cannot be improved to a truly subquadratic running time of $O((|w|\cdot…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
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…
The problem of finding \emph{distance} between \emph{pattern} of length $m$ and \emph{text} of length $n$ is a typical way of generalizing pattern matching to incorporate dissimilarity score. For both Hamming and $L_1$ distances only a…
The task of the binary classification problem is to determine which of two distributions has generated a length-$n$ test sequence. The two distributions are unknown; two training sequences of length $N$, one from each distribution, are…
Given two sequences over a finite alphabet $\mathcal{L}$, the $D_2$ statistic is the number of $m$-letter word matches between the two sequences. This statistic is used in bioinformatics for expressed sequence tag database searches. Here we…
We study (asymmetric) $U$-statistics based on a stationary sequence of $m$-dependent variables; moreover, we consider constrained $U$-statistics, where the defining multiple sum only includes terms satisfying some restrictions on the gaps…
From the output produced by a memoryless deletion channel from a uniformly random input of known length $n$, one obtains a posterior distribution on the channel input. The difference between the Shannon entropy of this distribution and that…
We study relationships between permutation statistics and pattern-functions, counting the number of times particular patterns occur in a permutation. This allows us to write several familiar statistics as linear combinations of pattern…
The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
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"…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…