Related papers: Correcting Contextual Deletions in DNA Nanopore Re…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
We study two basic problems regarding edit error, i.e. document exchange and error correcting codes for edit errors (insdel codes). For message length $n$ and edit error upper bound $k$, it is known that in both problems the optimal sketch…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
The deletion channel is the simplest point-to-point communication channel that models lack of synchronization. Input bits are deleted independently with probability d, and when they are not deleted, they are not affected by the channel.…
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,…
In this work, we investigate the problem of constructing codes capable of correcting two deletions. In particular, we construct a code that requires redundancy approximately 8 log n + O(log log n) bits of redundancy, where n is the length…
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…
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…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
We study codes that can detect the exact number of deletions and insertions in concatenated binary strings. We construct optimal codes for the case of detecting up to $\del$ deletions. We prove the optimality of these codes by deriving a…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
We study error-correcting codes in the space $\mathcal{S}_{n,q}$ of length-$n$ multisets over a $q$-ary alphabet, motivated by permutation channels in which ordering is completely lost and errors act solely by deletions of symbols, i.e., by…
The noise model of deletions poses significant challenges in coding theory, with basic questions like the capacity of the binary deletion channel still being open. In this paper, we study the harder model of worst-case deletions, with a…
Erasure coding is widely used for massive storage in data centers to achieve high fault tolerance and low storage redundancy. Since the cross-rack communication cost is often high, it is critical to design erasure codes that minimize the…
We consider the problem of constructing binary codes to recover from $k$-bit deletions with efficient encoding/decoding, for a fixed $k$. The single deletion case is well understood, with the Varshamov-Tenengolts-Levenshtein code from 1965…
We study near optimal error correction codes for real-time communication. In our setup the encoder must operate on an incoming source stream in a sequential manner, and the decoder must reconstruct each source packet within a fixed playback…
Burst errors involving simultaneous insertions, deletions, and substitutions occur in practical scenarios, including DNA data storage and document synchronization, motivating developments of channel codes that can correct such errors. In…