Related papers: Single-Deletion Single-Substitution Correcting Cod…
The performance of Reed--Solomon codes (RS codes, for short) in the presence of insertion and deletion errors has attracted growing attention in recent literature. In this work, we further study this intriguing mathematical problem,…
For variable-length coding with an almost-sure distortion constraint, Zhang et al. show that for discrete sources the redundancy is upper bounded by $\log n/n$ and lower bounded (in most cases) by $\log n/(2n)$, ignoring lower order terms.…
Motivated by distributed storage applications, we investigate the degree to which capacity achieving encodings can be efficiently updated when a single information bit changes, and the degree to which such encodings can be efficiently…
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…
Recently, codes for correcting a burst of errors have attracted significant attention. One of the most important reasons is that bursts of errors occur in certain emerging techniques, such as DNA storage. In this paper, we investigate a…
A covering code is a set of codewords with the property that the union of balls, suitably defined, around these codewords covers an entire space. Generally, the goal is to find the covering code with the minimum size codebook. While most…
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…
Explicit non-asymptotic upper bounds on the sizes of multiple-deletion correcting codes are presented. In particular, the largest single-deletion correcting code for $q$-ary alphabet and string length $n$ is shown to be of size at most…
We consider the problem of constructing codes that can correct $\delta$ deletions occurring in an arbitrary binary string of length $n$ bits. Varshamov-Tenengolts (VT) codes, dating back to 1965, are zero-error single deletion $(\delta=1)$…
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…
We study error-correcting codes in the space $\mathcal{S}_{n,q}$ of length-$n$ multisets over a $q$-ary alphabet, motivated by permutation channels in which ordering is completely lost and errors act solely by deletions of symbols, i.e., by…
In this paper, we investigate the optimum way to allocate redundancy of finite-length nested codes for modern nonvolatile memories suffering from both permanent defects and transient errors (erasures or random errors). A nested coding…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
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…
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…
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…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
Motivated by DNA-based data storage, we investigate a system where digital information is stored in an unordered set of several vectors over a finite alphabet. Each vector begins with a unique index that represents its position in the whole…
Owing to its several merits over other DNA sequencing technologies, nanopore sequencers hold an immense potential to revolutionize the efficiency of DNA storage systems. However, their higher error rates necessitate further research to…
In a {\em locally recoverable} or {\em repairable} code, any symbol of a codeword can be recovered by reading only a small (constant) number of other symbols. The notion of local recoverability is important in the area of distributed…