Related papers: Sequence-Subset Distance and Coding for Error Cont…
We initiate the study of DNA-based distributed storage systems, where information is encoded across multiple DNA data storage containers to achieve robustness against container failures. In this setting, data are distributed over $M$…
This paper presents a novel coding scheme for distributed storage systems containing nodes with adversarial errors. The key challenge in such systems is the propagation of erroneous data from a single corrupted node to the rest of the…
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…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
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…
Efficient computation or approximation of Levenshtein distance, a widely-used metric for evaluating sequence similarity, has attracted significant attention with the emergence of DNA storage and other biological applications. Sequence…
Ternary channels can be used to model the behavior of some memory devices, where information is stored in three different levels. In this paper, error correcting coding for a ternary channel where some of the error transitions are not…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…
It is well known that the minimum distance for linear network codes plays the same role as the minimum distance for classical error control codes. However, Yang and Yeung (2008) discovered that for nonlinear network codes, the minimum…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…
We investigate the problem of maintaining an encoded distributed storage system when some nodes contain adversarial errors. Using the error-correction capabilities that are built into the existing redundancy of the system, we propose a…
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
With the emergence of new storage and communication methods, the insertion, deletion, and substitution (IDS) channel has attracted considerable attention. However, many topics on the IDS channel and the associated Levenshtein distance…
In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…
For a bounded metric space X, we define a metric on the set of all finite subsets of X. This generalizes the sequence-subset distance introduced by Wentu Song, Kui Cai and Kees A. Schouhamer Immink to study error correcting codes for DNA…
Storing information in DNA molecules is of great interest because of its advantages in longevity, high storage density, and low maintenance cost. A key step in the DNA storage pipeline is to efficiently cluster the retrieved DNA sequences…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
We ask what is the general framework for a quantum error correcting code that is defined by a sequence of measurements. Recently, there has been much interest in Floquet codes and space-time codes. In this work, we define and study the…
We propose to use the concept of the Hamming bound to derive the optimal criteria for learning hash codes with a deep network. In particular, when the number of binary hash codes (typically the number of image categories) and code length…