Related papers: Engineering Relative Compression of Genomes
In this paper we propose an index key compression scheme based on the notion of distinction bits by proving that the distinction bits of index keys are sufficient information to determine the sorted order of the index keys correctly. While…
We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel-Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
The rapid growth of high-resolution scientific simulations and observation systems is generating massive spatiotemporal datasets, making efficient, error-bounded compression increasingly important. Meanwhile, decoder-only large language…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
Model compression has gained significant popularity as a means to alleviate the computational and memory demands of machine learning models. Each compression technique leverages unique features to reduce the size of neural networks.…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…
In this report, we investigate the potential use of large language models (LLM's) in the task of data compression. Previous works have demonstrated promising results in applying LLM's towards compressing not only text, but also a wide range…
The paper proposes an improved error-resilient Lempel-Ziv'77 (LZ'77) algorithm employing an adaptive amount of parity bits for error protection. It is a modified version of error resilient algorithm LZRS'77, proposed recently, which uses a…
The scalability of statistical estimators is of increasing importance in modern applications. One approach to implementing scalable algorithms is to compress data into a low dimensional latent space using dimension reduction methods. In…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
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…
Prompt engineering enables Large Language Models (LLMs) to perform a variety of tasks. However, lengthy prompts significantly increase computational complexity and economic costs. To address this issue, we study six prompt compression…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Machine-generated data is rapidly growing and poses challenges for data-intensive systems, especially as the growth of data outpaces the growth of storage space. To cope with the storage issue, compression plays a critical role in storage…
Storage systems often rely on multiple copies of the same compressed data, enabling recovery in case of binary data errors, of course, at the expense of a higher storage cost. In this paper we show that a wiser method of duplication entails…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Large language models (LLMs) exhibit excellent performance in various tasks. However, the memory requirements of LLMs present a great challenge when deploying on memory-limited devices, even for quantized LLMs. This paper introduces a…