Related papers: Coding for Ordered Composite DNA Sequences
This paper is motivated by the problem of error control in network coding when errors are introduced in a random fashion (rather than chosen by an adversary). An additive-multiplicative matrix channel is considered as a model for random…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
Capacity formulas and random-coding exponents are derived for a generalized family of Gel'fand-Pinsker coding problems. These exponents yield asymptotic upper bounds on the achievable log probability of error. In our model, information is…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme…
We consider the zero-error capacity of deletion channels. Specifically, we consider the setting where we choose a codebook ${\cal C}$ consisting of strings of $n$ bits, and our model of the channel corresponds to an adversary who may delete…
This paper focuses on error-correcting codes that can handle a predefined set of specific error patterns. The need for such codes arises in many settings of practical interest, including wireless communication and flash memory systems. In…
The continuously increasing amount of digital data generated by today's society asks for better storage solutions. This survey looks at a new generation of coding techniques designed specifically for the needs of distributed networked…
Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an…
In traditional software programs, it is easy to trace program logic from variables back to input, apply assertion statements to block erroneous behavior, and compose programs together. Although deep learning programs have demonstrated…
Non-binary codes correcting multiple deletions have recently attracted a lot of attention. In this work, we focus on multiplicity-free codes, a family of non-binary codes where all symbols are distinct. Our main contribution is a new…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
Error correction code is a major part of the communication physical layer, ensuring the reliable transfer of data over noisy channels. Recently, neural decoders were shown to outperform classical decoding techniques. However, the existing…
Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…