Related papers: Coding methods for string reconstruction from erro…
In the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is sent through a probabilistic \emph{deletion channel} which independently deletes each bit with probability $\delta$ and concatenates the surviving…
Let $P = \{p(i)\}$ be a measure of strictly positive probabilities on the set of nonnegative integers. Although the countable number of inputs prevents usage of the Huffman algorithm, there are nontrivial $P$ for which known methods find a…
We consider the complexities of substitutive sequences over a binary alphabet. By studying various types of special words, we show that, knowing some initial values, its complexity can be completely formulated via a recurrence formula…
We consider the problem of constructing a code capable of correcting a single long tandem duplication error of variable length. As the main contribution of this paper, we present a $q$-ary efficiently encodable code of length $n+1$ and…
In this work we investigate codes in $\mathbb{Z}_{2^m}^n$ that can correct errors that occur in just one coordinate of the codeword, with a magnitude of up to a given parameter $t$. We will show upper bounds on these cross codes, derive…
Each positive increasing integer sequence $\{a_n\}_{n\geq 0}$ can serve as a numeration system to represent each non-negative integer by means of suitable coefficient strings. We analyse the case of $k$-generalized Fibonacci sequences…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Prefix parsing asks whether an input prefix can be extended to a complete string generated by a given grammar. In the weighted setting, it also provides prefix probabilities, which are central to context-free language modeling,…
In the trace reconstruction problem, the goal is to reconstruct an unknown string $x$ of length $n$ from multiple traces obtained by passing $x$ through the deletion channel. In the relaxed problem of $approximate$ trace reconstruction, the…
An error correcting code using a tree-like multilayer perceptron is proposed. An original message $\mbi{s}^0$ is encoded into a codeword $\boldmath{y}_0$ using a tree-like committee machine (committee tree) or a tree-like parity machine…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a scenario where the sender transmits a codeword from some codebook, and the receiver obtains $N$ noisy outputs of the codeword. We study the problem of…
Multi-class classification is mandatory for real world problems and one of promising techniques for multi-class classification is Error Correcting Output Code. We propose a method for constructing the Error Correcting Output Code to obtain…
This paper investigates the problem of correcting multiple criss-cross insertions and deletions in arrays. More precisely, we study the unique recovery of $n \times n$ arrays affected by $t$-criss-cross deletions defined as any combination…
In this paper, we study the problem of designing prefix-free encoding schemes having minimum average code length that can be decoded efficiently under a decode cost model that captures memory hierarchy induced cost functions. We also study…
We present efficient algorithms to generate a bit string in which each bit is set with arbitrary probability. By adopting a hybrid algorithm, i.e., a finite-bit density approximation with correction techniques, we achieve 3.8 times faster…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
From the perspective of tree, we design a length-flexible coding scheme. For an arbitrary code length, we first construct a balanced binary tree (BBT) where the root node represents a transmitted codeword, the leaf nodes represent either…
A binary vector of length $N$ has elements that are either 0 or 1. We investigate the question of whether and how a binary vector of known length can be reconstructed from a limited set of its discrete Fourier transform (DFT) coefficients.…
In this paper we study the adaptive prefix coding problem in cases where the size of the input alphabet is large. We present an online prefix coding algorithm that uses $O(\sigma^{1 / \lambda + \epsilon}) $ bits of space for any constants…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…