Related papers: Coding for Strand Breaks in Composite DNA
Regenerating codes are a class of codes proposed for providing reliability of data and efficient repair of failed nodes in distributed storage systems. In this paper, we address the fundamental problem of handling errors and erasures during…
Distributed storage systems need to store data redundantly in order to provide some fault-tolerance and guarantee system reliability. Different coding techniques have been proposed to provide the required redundancy more efficiently than…
Encoding digital information into DNA sequences offers an attractive potential solution for storing rapidly growing data under the information age and the rise of artificial intelligence. However, practical implementations of DNA storage…
Emerging DNA storage technologies use composite DNA letters, where information is represented by a probability vector, leading to higher information density and lower synthesis costs. However, it faces the problem of information leakage in…
This paper investigates the use of redundancy and self repairing against node failures in distributed storage systems, using various strategies. In replication method, access to one replication node is sufficient to reconstruct a lost node,…
Erasure codes provide a storage efficient alternative to replication based redundancy in (networked) storage systems. They however entail high communication overhead for maintenance, when some of the encoded fragments are lost and need to…
In recent years, the emergence of DNA storage systems has led to a widespread focus on the research of codes correcting insertions, deletions, and classic substitutions. During the initial investigation, Levenshtein discovered the VT codes…
In this paper, we present a novel design strategy of DNA codes with length $3n$ over the non-chain ring $R=\mathbb{Z}_4+u\mathbb{Z}_4+u^2\mathbb{Z}_4$ with $64$ elements and $u^3=1$, where $n$ denotes the length of a code over $R$. We first…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
We consider the problem of designing low-redundancy codes in settings where one must correct deletions in conjunction with substitutions or adjacent transpositions; a combination of errors that is usually observed in DNA-based data storage.…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
Scientific computing workflows generate enormous distributed data that is short-lived, yet critical for job completion time. This class of data is called intermediate data. A common way to achieve high data availability is to replicate…
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…
Motivated by the sequence reconstruction problem initiated by Levenshtein, reconstruction codes were introduced by Cai \emph{et al}. to combat errors when a fixed number of noisy channels are available. The central problem on this topic is…
We investigate the problem of encoding data into an $(n, t)$-break-resilient code ($(n, t)$-BRC), i.e., a collections of sequences of length~$n$ from which the original data can be reconstructed even if they are adversarially broken at up…
We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…
In this paper, we present Reed-Solomon coded single-stranded representation learning (RSRL), a novel end-to-end model for learning representations for multi-modal lossless DNA storage. In contrast to existing learning-based methods, the…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…