Related papers: A Generalized Hamming Distance of Sequence Pattern…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
This paper introduces the sequence covering similarity, that we formally define for evaluating the similarity between a symbolic sequence (string) and a set of symbolic sequences (strings). From this covering similarity we derive a…
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…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
A Langford sequence of order $m$ and defect $d$ can be identified with a labeling of the vertices of a path of order $2m$ in which each labeled from $d$ up to $d+m-1$ appears twice and in which the vertices that have been label with $k$ are…
We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several…
Text-to-pattern distance is a fundamental problem in string matching, where given a pattern of length $m$ and a text of length $n$, over an integer alphabet, we are asked to compute the distance between pattern and the text at every…
The paper considers various formalisms based on Automata, Temporal Logic and Regular Expressions for specifying queries over sequences. Unlike traditional binary semantics, the paper presents a similarity based semantics for thse…
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 two random finite sequences from $[k]^n$ such that a prefix of the first sequence is a suffix of the second, we examine the length of their longest common subsequence. If $\ell$ is the length of the overlap, we prove that the expected…
Let $T=t_0 ... t_{n-1}$ be a text and $P = p_0 ... p_{m-1}$ a pattern taken from some finite alphabet set $\Sigma$, and let $\dist$ be a metric on $\Sigma$. We consider the problem of calculating the sum of distances between the symbols of…
In this paper, we present and study the \emph{Hamming distance oracle problem}. In this problem, the task is to preprocess two strings $S$ and $T$ of lengths $n$ and $m$, respectively, to obtain a data-structure that is able to answer…
A pattern of a sequence is a sequence of integer indices with each index describing the order of first occurrence of the respective symbol in the original sequence. In a recent paper, tight general bounds on the block entropy of patterns of…
Let x, y be strings of equal length. The Hamming distance h(x,y) between x and y is the number of positions in which x and y differ. If x is a cyclic shift of y, we say x and y are conjugates. We consider f(x,y), the Hamming distance…
We characterize the orderings of pairs of sets induced by several distances: Hamming, Jaccard, S\o rensen-Dice and Overlap. We also characterize these distances.
A permutation array(or code) of length $n$ and distance $d$, denoted by $(n,d)$ PA, is a set of permutations $C$ from some fixed set of $n$ elements such that the Hamming distance between distinct members $\mathbf{x},\mathbf{y}\in C$ is at…
This paper proposes a general framework for matching similar subsequences in both time series and string databases. The matching results are pairs of query subsequences and database subsequences. The framework finds all possible pairs of…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
Alternative novel measures of the distance between any two partitions of a n-set are proposed and compared, together with a main existing one, namely 'partition-distance' D(.,.). The comparison achieves by checking their restriction to…
Let $\mathbb{F}_q$ be the finite field of order $q$ and $E\subset \mathbb{F}_q^d$, where $4|d$. Using Fourier analytic techniques, we prove that if $|E|>\frac{q^{d-1}}{d}\binom{d}{d/2}\binom{d/2}{d/4}$, then the points of $E$ determine a…