Related papers: Optimal Reconstruction Codes for Deletion Channels
Recent work by Smagloy et al. (ISIT 2020) shows that the redundancy of a single-deletion $s$-substitution correcting code is asymptotically at least $(s+1)\log n+o(\log n)$, where $n$ is the length of the codes. They also provide a…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
The deletion distance between two binary words $u,v \in \{0,1\}^n$ is the smallest $k$ such that $u$ and $v$ share a common subsequence of length $n-k$. A set $C$ of binary words of length $n$ is called a $k$-deletion code if every pair of…
We study optimal reconstruction codes over the multiple-burst substitution channel. Our main contribution is establishing a trade-off between the error-correction capability of the code, the number of reads used in the reconstruction…
The sequence reconstruction problem for insertion/deletion channels has attracted significant attention owing to their applications recently in some emerging data storage systems, such as racetrack memories, DNA-based data storage. Our goal…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
We study segmented burst-deletion channels motivated by the observation that synchronization errors commonly occur in a bursty manner in real-world settings. In this channel model, transmitted sequences are implicitly divided into…
In the trace reconstruction problem, one observes the output of passing a binary string $s \in \{0,1\}^n$ through a deletion channel $T$ times and wishes to recover $s$ from the resulting $T$ "traces." Most of the literature has focused on…
When digital data are transmitted over a noisy channel, it is important to have a mechanism allowing recovery against a limited number of errors. Normally, a user string of 0's and 1's, called bits, is encoded by adding a number of…
Locally decodable channel codes form a special class of error-correcting codes with the property that the decoder is able to reconstruct any bit of the input message from querying only a few bits of a noisy codeword. It is well known that…
In this paper, we investigate codes designed to correct two bursts of deletions, where each burst has a length of exactly $b$, where $b>1$. The previous best construction, achieved through the syndrome compression technique, had a…
Consider a binary word being transmitted through a communication channel that introduces deletable errors where each bit of the word is either retained, flipped, erased or deleted. The simplest code for correcting \emph{all} possible…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
This paper studies codes that correct bursts of deletions. Namely, a code will be called a $b$-burst-deletion-correcting code if it can correct a deletion of any $b$ consecutive bits. While the lower bound on the redundancy of such codes…
We give an explicit construction of length-$n$ binary codes capable of correcting the deletion of two bits that have size $2^n/n^{4+o(1)}$. This matches up to lower order terms the existential result, based on an inefficient greedy choice…
Recent advances in DNA sequencing technology and DNA storage systems have rekindled the interest in deletion channels. Multiple recent works have looked at variants of sequence reconstruction over a single and over multiple deletion…
In this paper, we investigate binary reconstruction codes capable of correcting one deletion and one substitution. We define the \emph{single-deletion single-substitution ball} function $ \mathcal{B} $ as a mapping from a sequence to the…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
In this work, we present a new version of non-binary VT codes that are capable of correcting a single deletion or single insertion. Moreover, we provide the first known linear time algorithms that encode user messages into these codes of…
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…