Related papers: Correcting Multiple Substitutions in Nanopore-Sequ…
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…
The persistent storage of big data requires advanced error correction schemes. The classical approach is to use error correcting codes (ECCs). This work studies an alternative approach, which uses the redundancy inherent in data itself for…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
An error-erasure channel is a simple noise model that introduces both errors and erasures. While the two types of errors can be corrected simultaneously with error-correcting codes, it is also known that any linear code allows for first…
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…
Permutation codes and multi-permutation codes have been widely considered due to their various applications, especially in flash memory. In this paper, we consider permutation codes and multi-permutation codes against a burst of stable…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
Although prone to fabrication error, the nanowire crossbar is a promising candidate component for next generation nanometer-scale circuits. In the nanowire crossbar architecture, nanowires are addressed by controlling voltages on the…
Grammatical error correction can be viewed as a low-resource sequence-to-sequence task, because publicly available parallel corpora are limited. To tackle this challenge, we first generate erroneous versions of large unannotated corpora…
Nanopore protein sequencing produces long, noisy ionic current traces in which key molecular phases, such as protein capture and translocation, are embedded. Capture phases mark the successful entry of a protein into the pore and serve as…
This paper considers the problem of channel coding with a given (possibly suboptimal) maximum-metric decoding rule. A cost-constrained random-coding ensemble with multiple auxiliary costs is introduced, and is shown to achieve error…
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…
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…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
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…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
The noise in physical qubits is fundamentally asymmetric: in most devices, phase errors are much more probable than bit flips. We propose a quantum error correcting code which takes advantage of this asymmetry and shows good performance at…
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 sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common…
In this paper, we propose a novel method based on character sequence-to-sequence models to correct documents already processed with Optical Character Recognition (OCR) systems. The main contribution of this paper is a set of strategies to…