Related papers: Disk-based genome sequencing data compression
Hybrid non-orthogonal multiple access (H-NOMA) is inherently an enabler of massive machine type communications, a key use case for sixth-generation (6G) systems. Together with backscatter communication (BackCom), it seamlessly integrates…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
We tackle the problem of unsupervised visual descriptors compression, which is a key ingredient of large-scale image retrieval systems. While the deep learning machinery has benefited literally all computer vision pipelines, the existing…
Studying the solar system and especially the Sun relies on the data gathered daily from space missions. These missions are data-intensive and compressing this data to make them efficiently transferable to the ground station is a twofold…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
Data on the number of Open Reading Frames (ORFs) coded by genomes from the 3 domains of Life show some notable general features including essential differences between the Prokaryotes and Eukaryotes, with the number of ORFs growing linearly…
In the field of biological research, it is essential to comprehend the characteristics and functions of molecular sequences. The classification of molecular sequences has seen widespread use of neural network-based techniques. Despite their…
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme…
The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…
Parser-based log compressors have been widely explored in recent years because the explosive growth of log volumes makes the compression performance of general-purpose compressors unsatisfactory. These parser-based compressors preprocess…
Efficient lossless compression is essential for minimizing storage costs and transmission overhead while preserving data integrity. Traditional compression techniques, such as dictionary-based and statistical methods, often struggle to…
The accelerating growth of global data generation demands data storage platforms that offer high capacity, long lifespan, and low energy consumption beyond the limits of electronic memory technologies. Optical storage provides an attractive…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
Quantization is commonly used in Deep Neural Networks (DNNs) to reduce the storage and computational complexity by decreasing the arithmetical precision of activations and weights, a.k.a. tensors. Efficient hardware architectures employ…
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]…
We consider lossy compression of an information source when the decoder has lossless access to a correlated one. This setup, also known as the Wyner-Ziv problem, is a special case of distributed source coding. To this day, practical…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…