Related papers: Random Access in DNA Storage: Algorithms, Construc…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
The Matrix-based Renyi's entropy enables us to directly measure information quantities from given data without the costly probability density estimation of underlying distributions, thus has been widely adopted in numerous statistical…
Random access codes are a type of communication task that is widely used in quantum information science. The optimal average success probability that can be achieved through classical strategies is known for any random access code. However,…
Hinging on ideas from physical-layer network coding, some promising proposals of coded random access systems seek to improve system performance (while preserving low complexity) by means of packet repetitions and decoding of linear…
In a {\em locally recoverable} or {\em repairable} code, any symbol of a codeword can be recovered by reading only a small (constant) number of other symbols. The notion of local recoverability is important in the area of distributed…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
We propose a protocol to encode classical bits in the measurement statistics of many-body Pauli observables, leveraging quantum correlations for a random access code. Measurement contexts built with these observables yield outcomes with…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
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…
We show an essentially tight bound on the number of adaptively chosen statistical queries that a computationally efficient algorithm can answer accurately given $n$ samples from an unknown distribution. A statistical query asks for the…
We consider the setting of data storage across n nodes in a distributed manner. A data collector (DC) should be able to reconstruct the entire data by connecting to any k out of the n nodes and downloading all the data stored in them. When…
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…
We consider the problem of efficient recovery of the data stored in any individual node of a distributed storage system, from the rest of the nodes. Applications include handling failures and degraded reads. We measure efficiency in terms…
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…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
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…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…