Related papers: Improved Coding over Sets for DNA-Based Data Stora…

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…

DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…

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…

DNA-based storage has emerged as a promising alternative to traditional data storage methods, offering unmatched advantages in data density, longevity, and sustainability. Two main approaches have developed: in-vitro storage, where…

Motivated by DNA-based storage, we study the noisy shuffling channel, which can be seen as the concatenation of a standard noisy channel (such as the BSC) and a shuffling channel, which breaks the data block into small pieces and shuffles…

This work presents a theoretical analysis of the probability of successfully retrieving data encoded with MDS codes (e.g., Reed-Solomon codes) in DNA storage systems. We study this probability under independent and identically distributed…

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…

This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…

In this paper we define the overflow problem of a network coding storage system in which the encoding parameter and the storage parameter are mismatched. Through analyses and experiments, we first show the impacts of the overflow problem in…

DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…

We demonstrate that error correcting codes (ECCs) can be used to construct a labeled data set for finetuning of "trainable" communication systems without sacrificing resources for the transmission of known symbols. This enables adaptive…

In this paper, we investigate the problem of recovering source information from an incomplete set of network coded data. We first study the theoretical performance of such systems under maximum a posteriori (MAP) decoding and derive the…

A number of methods have been proposed over the last decade for encoding information using deoxyribonucleic acid (DNA), giving rise to the emerging area of DNA data embedding. Since a DNA sequence is conceptually equivalent to a sequence of…

In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…

The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…

As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…

We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…

We consider the problem of joint source and channel coding of structured data such as natural language over a noisy channel. The typical approach to this problem in both theory and practice involves performing source coding to first…

Error-correction codes are central for fault-tolerant information processing. Here we develop a rigorous framework to describe various coding models based on quantum resource theory of superchannels. We find, by treating codings as…

Exponential increase of data has motivated advances of data storage technologies. As a promising storage media, DeoxyriboNucleic Acid (DNA) storage provides a much higher data density and superior durability, compared with state-of-the-art…