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In this paper we study the problem of storing reliably an archive of versioned data. Specifically, we focus on systems where the differences (deltas) between subsequent versions rather than the whole objects are stored - a typical model for…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
This paper mainly focuses on the problem of lossy compression storage from the perspective of message importance when the reconstructed data pursues the least distortion within limited total storage size. For this purpose, we transform this…
Training a deep neural network heavily relies on a large amount of training data with accurate annotations. To alleviate this problem, various methods have been proposed to annotate the data automatically. However, automatically generating…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
This paper investigates the use of redundancy and self repairing against node failures in distributed storage systems, using various strategies. In replication method, access to one replication node is sufficient to reconstruct a lost node,…
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…
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…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…
The population recovery problem asks one to recover an unknown distribution over $n$-bit strings given access to independent noisy samples of strings drawn from the distribution. Recently, Ban et al. [BCF+19] studied the problem where the…
Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…
Regenerating codes provide an efficient way to recover data at failed nodes in distributed storage systems. It has been shown that regenerating codes can be designed to minimize the per-node storage (called MSR) or minimize the…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
DNA-based storage has emerged as a promising alternative to traditional data storage methods, offering unmatched advantages in data density, longevity, and sustainability. Two main approaches have developed: in-vitro storage, where…
Label noise in datasets could significantly damage the performance and robustness of deep neural networks (DNNs) trained on these datasets. As the size of modern DNNs grows, there is a growing demand for automated tools for detecting such…
Deoxyribonucleic acid (DNA) has emerged as a promising building block for next-generation ultra-high density storage devices. Although DNA has high durability and extremely high density in nature, its potential as the basis of storage…
Distributed storage systems provide large-scale reliable data storage services by spreading redundancy across a large group of storage nodes. In such a large system, node failures take place on a regular basis. When a storage node breaks…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
One of the basic tasks in bioinformatics is localizing a short subsequence $S$, read while sequencing, in a long reference sequence $R$, like the human geneome. A natural rapid approach would be finding a hash value for $S$ and compare it…
Data availability is critical in distributed storage systems, especially when node failures are prevalent in real life. A key requirement is to minimize the amount of data transferred among nodes when recovering the lost or unavailable data…