Related papers: Optimal Computation of Avoided Words
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…
An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their…
The edit distance of two strings is the minimum number of insertions, deletions, and substitutions of characters needed to transform one string into the other. The textbook dynamic-programming algorithm computes the edit distance of two…
A {\em subsequence} of a word $w$ is a word $u$ that can be obtained by deleting some letters from $w$ while maintaining the relative order of the remaining letters, e.g., $\mathtt{lala}$ is a subsequence of $\mathtt{alfalfa}$. A word, over…
Given two strings of length $n$ over alphabet $\Sigma$, and an upper bound $k$ on their edit distance, the algorithm of Myers (Algorithmica'86) and Landau and Vishkin (JCSS'88) computes the unweighted string edit distance in…
A string $w$ is called a minimal absent word (MAW) for a string $S$ if $w$ does not occur as a substring in $S$ and all proper substrings of $w$ occur in $S$. MAWs are well-studied combinatorial string objects that have potential…
We say that a word $w$ on a totally ordered alphabet avoids the word $v$ if there are no subsequences in $w$ order-equivalent to $v$. In this paper we suggest a new approach to the enumeration of words on at most $k$ letters avoiding a…
A subsequence of a word $w$ is a word $u$ such that $u = w[i_1] w[i_2] , \dots w[i_{|u|}]$, for some set of indices $1 \leq i_1 < i_2 < \dots < i_k \leq |w|$. A word $w$ is $k$-subsequence universal over an alphabet $\Sigma$ if every word…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. In this paper we…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
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 this paper, we consider pattern avoidance in a subset of words on $\{1,1,2,2,\dots,n,n\}$ called reverse double lists. In particular a reverse double list is a word formed by concatenating a permutation with its reversal. We enumerate…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
We give an $\tilde O(n^2)$ time algorithm for computing the exact Dynamic Time Warping distance between two strings whose run-length encoding is of size at most $n$. This matches (up to log factors) the known (conditional) lower bound, and…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
The edit distance is a metric of dissimilarity between strings, widely applied in computational biology, speech recognition, and machine learning. Let $e_k(n)$ denote the average edit distance between random, independent strings of $n$…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
Dynamic time warping distance (DTW) is a widely used distance measure between time series. The best known algorithms for computing DTW run in near quadratic time, and conditional lower bounds prohibit the existence of significantly faster…
This paper revisits the ordered statistics decoding (OSD). It provides a comprehensive analysis of the OSD algorithm by characterizing the statistical properties, evolution and the distribution of the Hamming distance and weighted Hamming…