相关论文: Codes in the Damerau Distance for DNA Storage
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
The problem of error control in random linear network coding is addressed from a matrix perspective that is closely related to the subspace perspective of K\"otter and Kschischang. A large class of constant-dimension subspace codes is…
The construction of deletion codes for the Levenshtein metric is reduced to the construction of codes over the integers for the Manhattan metric by run length coding. The latter codes are constructed by expurgation of translates of…
In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
Storing digital data in synthetic DNA faces challenges in ensuring data reliability in the presence of edit errors--deletions, insertions, and substitutions--that occur randomly during various stages of the storage process. Current…
Levenshtein distance is a commonly used edit distance metric, typically applied in language processing, and to a lesser extent, in molecular biology analysis. Biological nucleic acid sequences are often embedded in longer sequences and are…
This paper studies the cardinality of codes correcting insertions and deletions. We give improved upper and lower bounds on code size. Our upper bound is obtained by utilizing the asymmetric property of list decoding for insertions and…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
We improve Levenshtein's upper bound for the cardinality of a code of length four that is capable of correcting single deletions over an alphabet of even size. We also illustrate that the new upper bound is sharp. Furthermore we construct…
Permutation codes have recently garnered substantial research interest due to their potential in various applications including cloud storage systems, genome resequencing and flash memories. In this paper, we study the theoretical bounds…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
DNA is an attractive candidate for data storage. Its millennial durability and nanometer scale offer exceptional data density and longevity. Its relevance to medical applications also drives advances in DNA-related biotechnology. To protect…
We consider the problem of correcting insertion and deletion errors in the $d$-dimensional space. This problem is well understood for vectors (one-dimensional space) and was recently studied for arrays (two-dimensional space). For vectors…
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…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
Rank modulation is a way of encoding information to correct errors in flash memory devices as well as impulse noise in transmission lines. Modeling rank modulation involves construction of packings of the space of permutations equipped with…