Related papers: A Generalized Hamming Distance of Sequence Pattern…
We propose a general framework for converting global and local similarities between biological sequences to quasi-metrics. In contrast to previous works, our formulation allows asymmetric distances, originating from uneven weighting of…
We study distributed protocols for finding all pairs of similar vectors in a large dataset. Our results pertain to a variety of discrete metrics, and we give concrete instantiations for Hamming distance. In particular, we give improved…
The column Hamming distance of a convolutional code determines the error correction capability when streaming over a class of packet erasure channels. We introduce a metric known as the column sum rank, that parallels column Hamming…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Let $n>1$ and $k>0$ be fixed integers. A matrix is said to be level if all its column sums are equal. A level matrix with $m$ rows is called reducible if we can delete $j$ rows, $0<j<m$, so that the remaining matrix is level. We ask if…
We consider the problem of computing distance between a pattern of length $n$ and all $n$-length subwords of a text in the streaming model. In the streaming setting, only the Hamming distance ($L_0$) has been studied. It is known that…
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…
V. Levenshtein first proposed the sequence reconstruction problem in 2001. This problem studies the model where the same sequence from some set is transmitted over multiple channels, and the decoder receives the different outputs. Assume…
We consider a class of pattern matching problems where a normalising transformation is applied at every alignment. Normalised pattern matching plays a key role in fields as diverse as image processing and musical information processing…
Bounds on the entropy of patterns of sequences generated by independently identically distributed (i.i.d.) sources are derived. A pattern is a sequence of indices that contains all consecutive integer indices in increasing order of first…
The concepts of similarity and distance are crucial in data mining. We consider the problem of defining the distance between two data sets by comparing summary statistics computed from the data sets. The initial definition of our distance…
The classical way of extending an $[n, k, d]$ linear code $\C$ is to add an overall parity-check coordinate to each codeword of the linear code $\C$. This extended code, denoted by $\overline{\C}(-\bone)$ and called the standardly extended…
Ascent sequences are sequences of nonnegative integers with restrictions on the size of each letter, depending on the number of ascents preceding it in the sequence. Ascent sequences have recently been related to (2+2)-free posets and…
This paper presents methods to compare high order networks, defined as weighted complete hypergraphs collecting relationship functions between elements of tuples. They can be considered as generalizations of conventional networks where only…
An inversion sequence of length $n$ is an integer sequence $e=e_{1}e_{2}\dots e_{n}$ such that $0\leq e_{i}<i$ for each $i$. Corteel--Martinez--Savage--Weselcouch and Mansour--Shattuck began the study of patterns in inversion sequences,…
A well-defined distance on the parameter space is key to evaluating estimators, ensuring consistency, and building confidence sets. While there are typically standard distances to adopt in a continuous space, this is not the case for…
We study codes with parameters of the ternary Hamming $(n=(3^m-1)/2,3^{n-m},3)$ code, i.e., ternary $1$-perfect codes. The rank of the code is defined to be the dimension of its affine span. We characterize ternary $1$-perfect codes of rank…
We focus on strongly connected, strong for short, digraphs since in this setting distance is defined for every pair of vertices. Distance ideals generalize the spectrum and Smith normal form of several distance matrices associated with…
The \emph{distance-number} of a graph $G$ is the minimum number of distinct edge-lengths over all straight-line drawings of $G$ in the plane. This definition generalises many well-known concepts in combinatorial geometry. We consider the…
The Ulam sequence is given by $a_1 =1, a_2 = 2$, and then, for $n \geq 3$, the element $a_n$ is defined as the smallest integer that can be written as the sum of two distinct earlier elements in a unique way. This gives the sequence $1, 2,…