Related papers: On Codes for the Noisy Substring Channel
Deep neural networks have incredible capacity and expressibility, and can seemingly memorize any training set. This introduces a problem when training in the presence of noisy labels, as the noisy examples cannot be distinguished from clean…
Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
To make DNA a suitable medium for archival data storage, it is essential to consider the decay process of the strands observed in DNA storage systems. This paper studies the decay process as a probabilistic noisy torn paper channel (TPC),…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
We study the following semi-deterministic setting of the joint source-channel coding problem: a deterministic source sequence (a.k.a. individual sequence) is transmitted via a memoryless channel, using delay-limited encoder and decoder,…
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…
Stochastic encoders for channel coding and lossy source coding are introduced with a rate close to the fundamental limits, where the only restriction is that the channel input alphabet and the reproduction alphabet of the lossy source code…
This paper proves the separation between source-network coding and channel coding in networks of noisy, discrete, memoryless channels. We show that the set of achievable distortion matrices in delivering a family of dependent sources across…
Nanopore sequencing is an emerging DNA sequencing technology that has been proposed for use in DNA storage systems. We propose the noisy nanopore channel model for nanopore sequencing. This model captures duplications, inter-symbol…
We consider a molecular channel, in which messages are encoded to the frequency of objects (or concentration of molecules) in a pool, and whose output during reading time is a noisy version of the input frequencies, as obtained by sampling…
The design of codes for communicating reliably over a statistically well defined channel is an important endeavor involving deep mathematical research and wide-ranging practical applications. In this work, we present the first family of…
We consider the situation in which a transmitter attempts to communicate reliably over a discrete memoryless channel while simultaneously ensuring covertness (low probability of detection) with respect to a warden, who observes the signals…
We study the channel coding problem when errors and uncertainty occur in the encoding process. For simplicity we assume the channel between the encoder and the decoder is perfect. Focusing on linear block codes, we model the encoding…
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…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of…
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…