Related papers: Improvements on Permutation Reconstruction from Mi…
We show that for every sufficiently large $n$, the number of monotone subsequences of length four in a permutation on $n$ points is at least $\binom{\lfloor n/3 \rfloor}{4} + \binom{\lfloor(n+1)/3\rfloor}{4} + \binom{\lfloor…
For a set of positive integers $D$, a $k$-term $D$-diffsequence is a sequence of positive integers $a_1<a_2<\cdots<a_k$ such that $a_i-a_{i-1}\in D$ for $i=2,3,\cdots,k$. For $k\in\mathbb{Z}^+$ and $D\subset \mathbb{Z}^+$, we define…
We improve the lower bound on worst case trace reconstruction from $\Omega\left(\frac{n^{5/4}}{\sqrt{\log n}}\right)$ to $\Omega\left(\frac{n^{3/2}}{\log^{7} n}\right)$. As a consequence, we improve the lower bound on average case trace…
Let us say that an element of a given family $\A$ of subsets of $\R^d$ can be reconstructed using $n$ test sets if there exist $T_1,...,T_n \subset \R^d$ such that whenever $A,B\in \A$ and the Lebesgue measures of $A \cap T_i$ and $B \cap…
A $k$-universal permutation, or $k$-superpermutation, is a permutation that contains all permutations of length $k$ as patterns. The problem of finding the minimum length of a $k$-superpermutation has recently received significant attention…
Permutation arrays under the Kendall-$\tau$ metric have been considered for error-correcting codes. Given $n$ and $d\in [1..\binom{n}{2}]$, the task is to find a large permutation array of permutations on $n$ symbols with pairwise…
We study $P(n,3)$, the size of the largest subset of the set of all permutations $S_n$ with minimum Kendall $\tau$-distance $3$. Using a combination of group theory and integer programming, we reduced the upper bound of $P(p,3)$ from…
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…
A superpermutation on $n$ symbols is a string that contains each of the $n!$ permutations of the $n$ symbols as a contiguous substring. The shortest superpermutation on $n$ symbols was conjectured to have length $\sum_{i=1}^n i!$. The…
Let M(n, d) be the maximum size of a permutation array on n symbols with pairwise Hamming distance at least d. We use various combinatorial, algebraic, and computational methods to improve lower bounds for M(n, d). We compute the Hamming…
In this paper we prove new lower bounds for the maximal size of permutation codes by connecting the theory of permutation codes with the theory of linear block codes. More specifically, using the columns of a parity check matrix of an…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
In the beautifully simple-to-state problem of trace reconstruction, the goal is to reconstruct an unknown binary string $x$ given random "traces" of $x$ where each trace is generated by deleting each coordinate of $x$ independently with…
A permutation $\sigma \in S_n$ is a $k$-superpattern (or $k$-universal) if it contains each $\tau \in S_k$ as a pattern. This notion of "superpatterns" can be generalized to words on smaller alphabets, and several questions about…
A permutation $\sigma\in S_n$ is said to be $k$-universal or a $k$-superpattern if for every $\pi\in S_k$, there is a subsequence of $\sigma$ that is order-isomorphic to $\pi$. A simple counting argument shows that $\sigma$ can be a…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…
An $(n, k, d, \alpha)$-MSR (minimum storage regeneration) code is a set of $n$ nodes used to store a file. For a file of total size $k\alpha$, each node stores $\alpha$ symbols, any $k$ nodes recover the file, and any $d$ nodes can repair…
This paper presents an explicit construction of a class of optimal-access, minimum storage regenerating (MSR) codes, for small values of the number $d$ of helper nodes. The construction is valid for any parameter set $(n,k,d)$ with $d \in…
Say that a permutation of $1,2,\ldots,n$ is \textit{$k$-bounded} if every pair of consecutive entries in the permutation differs by no more than $k$. Such a permutation is \textit{anchored} if the first entry is $1$ and the last entry is…
In this paper we prove that the shape optimization problem $$\min\left\{\lambda_k(\Omega):\ \Omega\subset\R^d,\ \Omega\ \hbox{open},\ P(\Omega)=1,\ |\Omega|<+\infty\right\},$$ has a solution for any $k\in\N$ and dimension $d$. Moreover,…