Related papers: The Sequence Reconstruction of Permutations under …
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
The sequence reconstruction problem involves a model where a sequence is transmitted over several identical channels. This model investigates the minimum number of channels required for the unique reconstruction of the transmitted sequence.…
Let $M(n,d)$ be the maximum size of a permutation array on $n$ symbols with pairwise Hamming distance at least $d$. Some permutation arrays can be constructed using blocks of certain type [2] called product blocks in this paper. We study…
The trace reconstruction problem studies the number of noisy samples needed to recover an unknown string $\boldsymbol{x}\in\{0,1\}^n$ with high probability, where the samples are independently obtained by passing $\boldsymbol{x}$ through a…
A superpermutation is a sequence that contains every permutation of $n$ distinct symbols as a contiguous substring. For instance, a valid example for three symbols is a sequence that contains all six permutations. This paper introduces a…
We study the diametric problem (i.e., optimal anticodes) in the space of permutations under the Ulam distance. That is, let $S_n$ denote the set of permutations on $n$ symbols, and for each $\sigma, \tau \in S_n$, define their Ulam distance…
An $(n,R)$-covering sequence is a cyclic sequence whose consecutive $n$-tuples form a code of length $n$ and covering radius $R$. Using several construction methods improvements of the upper bounds on the length of such sequences for $n…
In the $k$-mismatch problem, given a pattern and a text of length $n$ and $m$ respectively, we have to find if the text has a sub-string with a Hamming distance of at most $k$ from the pattern. This has been studied in the classical setting…
For positive integers $n,r,s$ with $r > s$, the set-coloring Ramsey number $R(n;r,s)$ is the minimum $N$ such that if every edge of the complete graph $K_N$ receives a set of $s$ colors from a palette of $r$ colors, then there is a subset…
In this paper, we investigate the problem of designing $(n, N; \mathcal{B})$-reconstruction codes for $N\in \{14,11,9,5\}$, where $\mathcal{B}$ is the single-deletion single-substitution ball function that maps a sequence to the set of all…
We give new lower bounds for $M(n,d)$, for various positive integers $n$ and $d$ with $n>d$, where $M(n,d)$ is the largest number of permutations on $n$ symbols with pairwise Hamming distance at least $d$. Large sets of permutations on $n$…
We consider the problem of finding the set of permutations $r_j$ of $\{1,\cdots , n\}$ such that $\sum_{i=1}^n \prod_{j=1}^k r_j(i)$ is maximized or minimized. While the set of permutations maximizing this value are easily determined,…
Recursive decoding techniques are considered for Reed-Muller (RM) codes of growing length $n$ and fixed order $r.$ An algorithm is designed that has complexity of order $n\log n$ and corrects most error patterns of weight up to…
We show that for a fixed $q$, the number of $q$-ary $t$-error correcting codes of length $n$ is at most $2^{(1 + o(1)) H_q(n,t)}$ for all $t \leq (1 - q^{-1})n - C_q\sqrt{n \log n}$ (for sufficiently large constant $C_q$), where $H_q(n, t)…
Let $S_n$ and $S_{n,k}$ be, respectively, the number of subsets and $k$-subsets of $\mathbb{N}_n=\{1,\ldots,n\}$ such that no two subset elements differ by an element of the set $\mathcal{Q}$, the largest element of which is $q$. We prove a…
We investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…
A permutation array(permutation code, PA) 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…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication setting in which a sender transmits a codeword and the receiver observes K independent noisy versions of this codeword. In this work, we study…
Recently, Babson and Steingrimsson (see \cite{BS}) introduced generalized permutations patterns that allow the requirement that two adjacent letters in a pattern must be adjacent in the permutation. In this paper we study the generating…
Let $K_q(n,r)$ denote the minimum size of a $q$-ary covering code of word length $n$ and covering radius $r$. In other words, $K_q(n,r)$ is the minimum size of a set of $q$-ary codewords of length $n$ such that the Hamming balls of radius…