Related papers: Efficient Constraining of Transcoding in DNA-Based…

We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…

In this paper we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where a data set is represented by an unordered set of $M$ sequences, each of length $L$. Errors…

We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…

Recent advancements in deep learning-based image compression are notable. However, prevalent schemes that employ a serial context-adaptive entropy model to enhance rate-distortion (R-D) performance are markedly slow. Furthermore, the…

Exponential increase of data has motivated advances of data storage technologies. As a promising storage media, DeoxyriboNucleic Acid (DNA) storage provides a much higher data density and superior durability, compared with state-of-the-art…

Image compression has been a frequent topic of presentations at ADASS. Compression is often viewed as just a technique to fit more data into a smaller space. Rather, the packing of data - its "density" - affects every facet of local data…

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…

Deep Convolutional Neural Networks (CNN) have been successfully applied to many real-life problems. However, the huge memory cost of deep CNN models poses a great challenge of deploying them on memory-constrained devices (e.g., mobile…

Motivation: Storage of genomic data is a major cost for the Life Sciences, effectively addressed mostly via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technologies is seen…

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…

Compression aims to reduce the size of an input, while maintaining its relevant properties. For multi-parameter persistent homology, compression is a necessary step in any computational pipeline, since standard constructions lead to large…

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…

This article introduces a new DNA sequence compression algorithm which is based on LUT and LZ77 algorithm. Combined a LUT-based pre-coding routine and LZ77 compression routine,this algorithm can approach a compression ratio of 1.9bits…

DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…

DNA-based storage has emerged as a promising approach to the global data crisis, offering molecular-scale density and millennial-scale stability at low maintenance cost. Over the past decade, substantial progress has been made in storing…

Can we analyze data without decompressing it? As our data keeps growing, understanding the time complexity of problems on compressed inputs, rather than in convenient uncompressed forms, becomes more and more relevant. Suppose we are given…

We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…

The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…

Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…

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…