Related papers: A Fixed-Length Coding Algorithm for DNA Sequence C…
Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are either unable to…
Natural language processing (NLP) models often require a massive number of parameters for word embeddings, resulting in a large storage or memory footprint. Deploying neural NLP models to mobile devices requires compressing the word…
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
Many applications require data processing to be performed on individual pieces of data which are of finite sizes, e.g., files in cloud storage units and packets in data networks. However, traditional universal compression solutions would…
In this paper, we investigate lossy compression of deep neural networks (DNNs) by weight quantization and lossless source coding for memory-efficient deployment. Whereas the previous work addressed non-universal scalar quantization and…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…
The paper introduces a new lossless, highly robust compression algorithm that similar with LZW algorithm, yet the algorithm discards dictionary processing and uses irregular sequences with massive, random information instead. Then the paper…
In this paper, we consider the decoding of fountain codes where the received symbols may have errors. It is motivated by the application of fountain codes in DNA-based data storage systems where the inner code decoding, which generally has…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
Universal source coding at short blocklengths is considered for an exponential family of distributions. The \emph{Type Size} code has previously been shown to be optimal up to the third-order rate for universal compression of all memoryless…
Most of the world's digital data is currently encoded in a sequential form, and compression methods for sequences have been studied extensively. However, there are many types of non-sequential data for which good compression techniques are…
Recently, DNA storage has surfaced as a promising alternative for data storage, presenting notable benefits in terms of storage capacity, cost-effectiveness in maintenance, and the capability for parallel replication. Mathematically, the…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…
Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of…
Constrained sequence (CS) codes, including fixed-length CS codes and variable-length CS codes, have been widely used in modern wireless communication and data storage systems. Sequences encoded with constrained sequence codes satisfy…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…