Related papers: VL-DNA: Enhance DNA Storage Capacity with Variable…
The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…
Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
Existing caching strategies, in the storage domain, though well suited to exploit short range spatio-temporal patterns, are unable to leverage long-range motifs for improving hitrates. Motivated by this, we investigate novel Bayesian…
Solid-State Drives (SSDs) have significant performance advantages over traditional Hard Disk Drives (HDDs) such as lower latency and higher throughput. Significantly higher price per capacity and limited lifetime, however, prevents…
The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is widely used for gene delivery. It is considered here in terms of discrete charges of DNA. We concentrate on the worst scenario case when in the…
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…
Transformer-based large language models (LLMs) have already achieved remarkable results on long-text tasks, but the limited GPU memory (VRAM) resources struggle to accommodate the linearly growing demand for key-value (KV) cache as the…
Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of…
High density Solid State Drives, such as QLC drives, offer increased storage capacity, but a magnitude lower Program and Erase (P/E) cycles, limiting their endurance and hence usability. We present the design and implementation of…
Hashing has emerged as a popular technique for large-scale similarity search. Most learning-based hashing methods generate compact yet correlated hash codes. However, this redundancy is storage-inefficient. Hence we propose a lossless…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
A number of methods have been proposed over the last decade for encoding information using deoxyribonucleic acid (DNA), giving rise to the emerging area of DNA data embedding. Since a DNA sequence is conceptually equivalent to a sequence of…
Persistent memory (PM) is an emerging class of storage technology that combines the benefits of DRAM and SSD. This characteristic inspires research on persistent objects in PM with fine-grained concurrency control. Among such objects,…
Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA…