Related papers: The Sequence Reconstruction of Permutations under …
The circular peak set of a permutation $\sigma$ is the set $\{\sigma(i)\mid \sigma(i-1)<\sigma(i)>\sigma(i+1)\}$. In this paper, we focus on the enumeration problems for permutations by circular peak sets. Let $cp_n(S)$ denote the number of…
We consider two related problems arising from a question of R. Graham on quasirandom phenomena in permutation patterns. A ``pattern'' in a permutation $\sigma$ is the order type of the restriction of $\sigma : [n] \to [n]$ to a subset $S…
A $\lambda$-fold $r$-packing (multiple radius-$r$ covering) in a Hamming metric space is a code $C$ such that the radius-$r$ balls centered in $C$ cover each vertex of the space by not more (not less, respectively) than $\lambda$ times. The…
Higher-dimensional rewriting is founded on a duality of rewrite systems and cell complexes, connecting computational mathematics to higher categories and homotopy theory: the two sides of a rewrite rule are two halves of the boundary of an…
Limited magnitude asymmetric error model is well suited for flash memory. In this paper, we consider the construction of asymmetric codes correcting single error over $\mathbb{Z}_{2^{k}r}$ and which are based on so called $B_{1}[4](2^{k}r)$…
We study approximation algorithms for variants of the \emph{median string} problem, which asks for a string that minimizes the sum of edit distances from a given set of $m$ strings of length $n$. Only the straightforward $2$-approximation…
The ''trace reconstruction'' problem asks, given an unknown binary string $x$ and a channel that repeatedly returns ''traces'' of $x$ with each bit randomly deleted with some probability $p$, how many traces are needed to recover $x$? There…
The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence, is considered. First, in the regime in which the…
Given a threshold $L$ and a set $\mathcal{R} = \{R_1, \ldots, R_m\}$ of $m$ haplotype sequences, each having length $n$, the minimum segmentation problem for founder reconstruction is to partition the sequences into disjoint segments…
The permutation language $P_n$ consists of all words that are permutations of a fixed alphabet of size $n$. Using divide-and-conquer, we construct a regular expression $R_n$ that specifies $P_n$. We then give explicit bounds for the length…
Let $S_{n}$ denote the set of permutations of $[n]=\{1,2,\dots, n\}$. For each integer $k\geq 1$, let $S_{n,k}$ be the set of all permutations of $[n]$ with exactly $k$ disjoint cycles. A subset $H\subseteq S_{n,k}$ is to be a matching if…
We consider the problem of reconstructing graphs or labeled graphs from neighborhoods of a given radius r. Special instances of this problem include the well known: DNA shotgun assembly; the lesser-known: neural network reconstruction; and…
Detecting and counting copies of permutation patterns are fundamental algorithmic problems, with applications in the analysis of rankings, nonparametric statistics, and property testing tasks such as independence and quasirandomness…
The rank modulation scheme has been proposed for efficient writing and storing data in non-volatile memory storage. Error-correction in the rank modulation scheme is done by considering permutation codes. In this paper we consider codes in…
This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes.…
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…
Nishimoto and Tabei [CPM, 2021] proposed r-enum, an algorithm to enumerate various characteristic substrings, including maximal repeats, in a string $T$ of length $n$ in $O(r)$ words of compressed working space, where $r \le n$ is the…
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
An $(n,k)$-perfect sequence covering array with multiplicity $\lambda$, denoted PSCA$(n,k,\lambda)$, is a multiset whose elements are permutations of the sequence $(1,2, \dots, n)$ and which collectively contain each ordered length $k$…
We consider a certain variation of the 'isoperimetric problem' adopted for subsets of nonnegative integers. More specifically, we explore the sequence P(n) as described in OEIS A186053. We provide the first exact formulas for P(n) including…