Related papers: Managing Reliability Skew in DNA Storage
Emerging DNA storage technologies use composite DNA letters, where information is represented by a probability vector, leading to higher information density and lower synthesis costs. However, it faces the problem of information leakage in…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
With the widespread deployment of deep neural networks (DNNs), ensuring the reliability of DNN-based systems is of great importance. Serious reliability issues such as system failures can be caused by numerical defects, one of the most…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
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…
The reliability of erasure-coded distributed storage systems, as measured by the mean time to data loss (MTTDL), depends on the repair bandwidth of the code. Repair-efficient codes provide reliability values several orders of magnitude…
The persistent storage of big data requires advanced error correction schemes. The classical approach is to use error correcting codes (ECCs). This work studies an alternative approach, which uses the redundancy inherent in data itself for…
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…
Several technological limitations of traditional silicon based computing are leading towards the paradigm shift, from silicon to carbon, in computational world. Among the unconventional modes of computing evolved in past several decades,…
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…
A distributed storage system (DSS) needs to be efficiently accessible and repairable. Recently, considerable effort has been made towards the latter, while the former is usually not considered, since a trivial solution exists in the form of…
When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
Since security is one of the most important issues, the evolve of cryptography and cryptographic analysis are considered as the fields of on-going research. The latest development on this field is DNA cryptography. It has emerged after the…
We consider the probability of data loss, or equivalently, the reliability function for an erasure coded distributed data storage system under worst case conditions. Data loss in an erasure coded system depends on probability distributions…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…