Related papers: A Generalized Hamming Distance of Sequence Pattern…
Correlation measure of order $k$ is an important measure of randomness in binary sequences. This measure tries to look for dependence between several shifted version of a sequence. We study the relation between the correlation measure of…
Measuring the distance between data points is fundamental to many statistical techniques, such as dimension reduction or clustering algorithms. However, improvements in data collection technologies has led to a growing versatility of…
High order networks are weighted hypergraphs col- lecting relationships between elements of tuples, not necessarily pairs. Valid metric distances between high order networks have been defined but they are difficult to compute when the…
We develop a new class of distances for objects including lines, hyperplanes, and trajectories, based on the distance to a set of landmarks. These distances easily and interpretably map objects to a Euclidean space, are simple to compute,…
Suppose that $[n]=\left\{0,1,2,...,n\right\}$ is a set of non-negative integers and $h,k \in [n]$. The $L(h,k)$-labeling of graph $G$ is the function $l:V(G)\rightarrow[n]$ such that $\left|l(u)-l(v)\right|\geq h$ if the distance $d(u,v)$…
Let $n$ and $k$ be positive integers, and let $F$ be an alphabet of size $n$. A sequence over $F$ of length $m$ is a \emph{$k$-radius sequence} if any two distinct elements of $F$ occur within distance $k$ of each other somewhere in the…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
Given an abelian category, we characterize the long exact sequences of length six which can be obtained from the snake lemma. Equivalently, these are the long exact sequences which arise as the homology of a triangle in the corresponding…
Sequence memory is an essential attribute of natural and artificial intelligence that enables agents to encode, store, and retrieve complex sequences of stimuli and actions. Computational models of sequence memory have been proposed where…
Sum-rank Hamming codes are introduced in this work. They are essentially defined as the longest codes (thus of highest information rate) with minimum sum-rank distance at least $ 3 $ (thus one-error-correcting) for a fixed redundancy $ r $,…
Nanopore sequencing is a promising technology for DNA sequencing. In this paper, we investigate a specific model of the nanopore sequencer, which takes a $q$-ary sequence of length $n$ as input and outputs a vector of length $n+\ell-1$…
The pattern $(k_1, k_2, \dots, k_\ell)$ is defined to have at least $k_1$ consecutive $1$'s followed by at least $k_2$ consecutive $2$'s, $\dots$, followed by at least $k_\ell$ consecutive $\ell$'s. By iteratively applying the method that…
A new class of distances appropriate for measuring similarity relations between sequences, say one type of similarity per distance, is studied. We propose a new ``normalized information distance'', based on the noncomputable notion of…
Two Delone sets are bounded distance equivalent to each other if there is a bijection between them such that the distance of corresponding points is uniformly bounded. Bounded distance equivalence is an equivalence relation. We show that…
We consider the problem of computing a $(1+\epsilon)$-approximation of the Hamming distance between a pattern of length $n$ and successive substrings of a stream. We first look at the one-way randomised communication complexity of this…
Generalization is a central aspect of learning theory. Here, we propose a framework that explores an auxiliary task-dependent notion of generalization, and attempts to quantitatively answer the following question: given two sets of patterns…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the approximate pattern matching problem asks for computation of a particular \emph{distance} function between $P$ and every $m$-substring of $T$. We consider a…
Sequence classification has numerous applications in various fields. Despite extensive studies in the last decades, many challenges still exist, particularly in pattern-based methods. Existing pattern-based methods measure the…
We model long range correlations of nucleotides in the human DNA sequence using the long range one dimensional Ising model. We show that for distances between $10^3$ and $10^6$ bp the correlations show an universal behaviour and may be…
Sequences of numbers (either natural integers, or integers or rational) of level $k \in \mathbb{N}$ have been defined in \cite{Fra05,Fra-Sen06} as the sequences which can be computed by deterministic pushdown automata of level $k$. This…