相关论文: The Geometry of Codes for Random Access in DNA Sto…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
MDS (maximum distance separable) array codes are widely used in storage systems due to their computationally efficient encoding and decoding procedures. An MDS code with r redundancy nodes can correct any r erasures by accessing (reading)…
The paper presents techniques for analyzing the expected download time in distributed storage systems that employ systematic availability codes. These codes provide access to hot data through the systematic server containing the object and…
Random embeddings project high-dimensional spaces to low-dimensional ones; they are careful constructions which allow the approximate preservation of key properties, such as the pair-wise distances between points. Often in the field of…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
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…
Maximum distance separable (MDS) array codes are widely employed in modern distributed storage systems to provide high data reliability with small storage overhead. Compared with the data access latency of the entire file, the data access…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
The rise of machine-to-machine communications has rekindled the interest in random access protocols as a support for a massive number of uncoordinatedly transmitting devices. The legacy ALOHA approach is developed under a collision model,…
Graph reconstruction can efficiently detect the underlying topology of massive networks such as the Internet. Given a query oracle and a set of nodes, the goal is to obtain the edge set by performing as few queries as possible. An algorithm…
A random access code (RAC) is a communication task in which the sender encodes a random message into a shorter one to be decoded by the receiver so that a randomly chosen character of the original message is recovered with some probability.…
Consider an algorithm performing a computation on a huge random object. Is it necessary to generate the entire object up front, or is it possible to provide query access to the object and sample it incrementally "on-the-fly"? Such an…
We study medium access control layer random access under the assumption that the receiver can perform successive interference cancellation, without feedback. During recent years, a number of protocols with impressive error performance have…
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…