相关论文: Codes in the Damerau Distance for DNA Storage
Motivated by the sequence reconstruction problem from traces in DNA-based storage, we consider the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder. We propose simple…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
In coding theory, handling errors that occur when symbols are inserted or deleted from a transmitted message is a long-standing challenge. Optimising redundancy for insertion and deletion channels remains a key open problem with significant…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…
We consider rank modulation codes for flash memories that allow for handling arbitrary charge-drop errors. Unlike classical rank modulation codes used for correcting errors that manifest themselves as swaps of two adjacently ranked…
Reliability is an important requirement for both communication and storage systems. Due to continuous scale down of technology multiple adjacent bits error probability increases. The data may be corrupted due soft errors. Error correction…
In this paper, we study the problem of storing an archive of versioned data in a reliable and efficient manner in distributed storage systems. We propose a new storage technique called differential erasure coding (DEC) where the differences…
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…
Several measures exist for string similarity, including notable ones like the edit distance and the indel distance. The former measures the count of insertions, deletions, and substitutions required to transform one string into another,…
Edit distance, also known as Levenshtein distance, is an essential way to compare two strings that proved to be particularly useful in the analysis of genetic sequences and natural language processing. However, edit distance is a discrete…
The problem of finding code distance has been long studied for the generic ensembles of linear codes and led to several algorithms that substantially reduce exponential complexity of this task. However, no asymptotic complexity bounds are…
For many optimization problems it is possible to define a distance metric between problem variables that correlates with the likelihood and strength of interactions between the variables. For example, one may define a metric so that the…
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…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
Three-dimensional (3D) printing's accessibility enables rapid manufacturing but also poses security risks, such as the unauthorized production of untraceable firearms and prohibited items. To ensure traceability and accountability,…
The rapid development of DNA storage has brought the deletion and insertion channel to the front line of research. When the number of deletions is equal to the number of insertions, the Fixed Length Levenshtein (FLL) metric is the right…
Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…
The problem of designing codes for deletion-correction and synchronization has received renewed interest due to applications in DNA-based data storage systems that use nanopore sequencers as readout platforms. In almost all instances,…