相关论文: The Capacity of the Weighted Read Channel
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
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…
Due to the redundant nature of DNA synthesis and sequencing technologies, a basic model for a DNA storage system is a multi-draw "shuffling-sampling" channel. In this model, a random number of noisy copies of each sequence is observed at…
Motivated by DNA-based storage, we study the noisy shuffling channel, which can be seen as the concatenation of a standard noisy channel (such as the BSC) and a shuffling channel, which breaks the data block into small pieces and shuffles…
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…
In diffusion-based molecular communications, messages can be conveyed via the variation in the concentration of molecules in the medium. In this paper, we intend to analyze the achievable capacity in transmission of information from one…
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…
This paper investigates the capacity of a wireless two way relay channel in which two end nodes exchange information via a relay node. The capacity is defined in the information-theoretic sense as the maximum information exchange rate…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
In this paper, we propose a strategy for making DNA-based data storage information-theoretically secure through the use of wiretap channel coding. This motivates us to extend the shuffling-sampling channel model of Shomorony and Heckel…
We consider the problem of estimating an upper bound on the capacity of a memoryless channel with unknown channel law and continuous output alphabet. A novel data-driven algorithm is proposed that exploits the dual representation of…
The readout of a classical memory can be modelled as a problem of quantum channel discrimination, where a decoder retrieves information by distinguishing the different quantum channels encoded in each cell of the memory [S. Pirandola, Phys.…
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…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
The shotgun sequencing process involves fragmenting a long DNA sequence (input string) into numerous shorter, unordered, and overlapping segments (referred to as \emph{reads}). The reads are sequenced, and later aligned to reconstruct the…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
Two novel views are presented on the trapdoor channel. First, by deriving the underlying iterated function system (IFS), it is shown that the trapdoor channel with input blocks of length $n$ can be regarded as the $n$th element of a…