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A hypothesis testing algorithm is replicable if, when run on two different samples from the same distribution, it produces the same output with high probability. This notion, defined by by Impagliazzo, Lei, Pitassi, and Sorell [STOC'22],…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
This paper defines a linear representation for nonlinear maps $F:\mathbb{F}^n\rightarrow\mathbb{F}^n$ where $\mathbb{F}$ is a finite field, in terms of matrices over $\mathbb{F}$. This linear representation of the map $F$ associates a…
Recently, linear codes constructed from defining sets have been studied extensively. They may have nice parameters if the defining set is chosen properly. Let $ m >2$ be a positive integer. For an odd prime $ p $, let $ r=p^m $ and…
We determine a condition on the minimum Hamming weight of some special abelian group codes and, as a consequence of this result, we establish that any such code is, up to permutational equivalence, a subspace of the direct sum of $s$ copies…
Replicability requires that algorithmic conclusions remain consistent when rerun on independently drawn data. A central structural question is composition: given $k$ problems each admitting a $\rho$-replicable algorithm with sample…
We show that the sequence of dimensions of the linear spaces, generated by a given rank-metric code together with itself under several applications of a field automorphism, is an invariant for the whole equivalence class of the code. The…
The minimum distance graph of a code has the codewords as vertices and edges exactly when the Hamming distance between two codewords equals the minimum distance of the code. A constructive proof for reconstructibility of an extended perfect…
An (n,d)-permutation code is a subset C of Sym(n) such that the Hamming distance d_H between any two distinct elements of C is at least equal to d. In this paper, we use the characterisation of the isometry group of the metric space…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
In this article, we investigate properties of cyclic codes over a finite non-chain ring $\mathbb{F}_q+v\mathbb{F}_q+v^2\mathbb{F}_q+v^3\mathbb{F}_q+v^4\mathbb{F}_q,$ where $q=p^r,$ $r$ is a positive integer, $p$ is an odd prime, $4 \mid…
Binary self-dual codes with large minimum distances, such as the extended Hamming code and the Golay code, are fascinating objects in the coding theory. They are closely related to sporadic simple groups, lattices and invariant theory. A…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
We study constacyclic codes, of length $np^s$ and $2np^s$, that are generated by the polynomials $(x^n + \gamma)^{\ell}$ and $(x^n - \xi)^i(x^n + \xi)^j$\ respectively, where $x^n + \gamma$, $x^n - \xi$ and $x^n + \xi$ are irreducible over…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
A \emph{trace} of a sequence is generated by deleting each bit of the sequence independently with a fixed probability. The well-studied \emph{trace reconstruction} problem asks how many traces are required to reconstruct an unknown binary…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…
Let $\mathbb{F}_{p^m}$ be a finite field of cardinality $p^m$ and $R=\mathbb{F}_{p^m}[u]/\langle u^2\rangle=\mathbb{F}_{p^m}+u\mathbb{F}_{p^m}$ $(u^2=0)$, where $p$ is a prime and $m$ is a positive integer. For any $\lambda\in…
A set of linearly constrained permutation matrices are proposed for constructing a class of permutation codes. Making use of linear constraints imposed on the permutation matrices, we can formulate a minimum Euclidian distance decoding…
Let $ \mathbb F_2[u]/ \langle u^k \rangle= \mathbb F_2+u\mathbb F_2+u^2\mathbb F_2+\cdots+u^{k-1}\mathbb F_2 ,$ where $u^k=0$ for a positive integer $k$, and $\mathcal{R}=M_4 (\mathbb F_2( u)/ \langle u^k \rangle)$ be the finite…