25 papers · ranked by Valyu relevance
Jin Sima, Netanel Raviv, Jehoshua Bruck
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In this paper, we address this problem and present an order-wise optimal…
Daniella Bar-Lev, Adir Kobovich, Orian Leitersdorf, Eitan Yaakobi
—This paper presents a novel approach to address the constrained coding challenge of generating almost-balanced sequences. While strictly balanced sequences have been well studied in the past, the problem of designing efficient algorithms with small redundancy, preferably constant or even a single bit, for almost…
Amir Said
Entropy coding, compression, complexity This introduction to arithmetic coding is divided in two parts. The first explains how and why arithmetic coding works. We start presenting it in very general terms, so that its simplicity is not lost under layers of implementation details. Next, we show some of its basic…
Robert Bamler
Entropy coding is the backbone data compression. Novel machine-learning based compression methods often use a new entropy coder called Asymmetric Numeral Systems (ANS) [Duda et al., 2015], which provides very close to optimal bitrates and simplifies [Townsend et al., 2019] advanced compression techniques such as…
Tomasz Krokosz, Jarogniew Rykowski, Małgorzata Zajęcka, Robert Brzoza-Woch + 2 more
'Robert Brzoza-Woch' 'Leszek Rutkowski' 'Amitabh Mishra'] Modern, commonly used cryptosystems based on encryption keys require that the length of the stream of encrypted data is approximately the length of the key or longer. In practice, this approach unnecessarily complicates strong encryption of very short messages…
Jia Lu, Ryan Tsoi, Nan Luo, Yuanchi Ha + 8 more
Dynamical systems often generate distinct outputs according to different initial conditions, and one can infer the corresponding input configuration given an output. This property captures the essence of information encoding and decoding. Here, we demonstrate the use of self-organized patterns, combined with machine…
M. Gao, Kenneth W. Shum
single-deletion-correcting permutation codes Authors: ['M. Gao' 'Kenneth W. Shum'] A permutation code is a nonlinear code whose codewords are permutation of a set of symbols. We consider the use of permutation code in the deletion channel, and consider the symbol-invariant error model, meaning that the values of the…
Anas Al-okaily, Abdelghani Tbakhi
Data compression is a challenging and increasingly important problem. As the amount of data generated daily continues to increase, efficient transmission and storage have never been more critical. In this study, a novel encoding algorithm is proposed, motivated by the compression of DNA data and associated…
Mohammad Hosseini
—Today, with the growing demands of information storage and data transfer, data compression is becoming increasingly important. Data Compression is a technique which is used to decrease the size of data. This is very useful when some huge files have to be transferred over networks or being stored on a data storage…
Kevin D. Volkel, Paul W. Hook, Albert Keung, Winston Timp + 1 more
As nanopore technology reaches ever higher throughput and accuracy, it becomes an increasingly viable candidate for reading out DNA data storage. Nanopore sequencing offers considerable flexibility by allowing long reads, real-time signal analysis, and the ability to read both DNA and RNA. We need flexible and…
Roland Wittler
To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σ^k^ k-mers and the interval [0, σ^k^ −1], where σ is the alphabet size. In many…
Nanming Li, Shucui Xie, Jianzhong Zhang, Shu-Chuan Chu
A color image encryption algorithm based on double fractional order chaotic neural network (CNN), interlaced dynamic deoxyribonucleic acid (DNA) encoding and decoding, zigzag confusion, bidirectional bit-level diffusion and convolution operation is proposed. Firstly, two fractional order chaotic neural networks (CNNs)…
Xuyang Zhao, Junyao Li, Qingyuan Fan, Jing Dai + 5 more
DNA, as the origin for the genetic information flow, has also been a compelling alternative to non-volatile information storage medium. Reading digital information from this highly dense but lightweighted medium nowadays relied on conventional next-generation sequencing (NGS), which involves ‘wash and read’ cycles for…
M Baritha Begum, N. Deepa, Mueen Uddin, Rajesh Kaluri + 2 more
'Maha Abdelhaq' 'Raed Alsaqour'] Data stored on physical storage devices and transmitted over communication channels often have a lot of redundant information, which can be reduced through compression techniques to conserve space and reduce the time it takes to transmit the data. The need for adequate security…
Erick Lamilla, Christian Sacarelo, Manuel S. Alvarez-Alvarado, Arturo Pazmino + 4 more
'Arturo Pazmino' 'Peter Iza' 'Yichuang Sun' 'Haeyoung Lee' 'Oluyomi Simpson'] Based on orbital angular momentum (OAM) properties of Laguerre-Gaussian beams LG( $p,ℓ$), a robust optical encoding model for efficient data transmission applications is designed. This paper presents an optical encoding model based on an…
Heping Wen, Linchao Ma, Linhao Liu, Yiming Huang + 7 more
'Rui Li' 'Zhen Liu' 'Wenxing Lin' 'Jiahao Wu' 'Yunqi Li' 'Chongfu Zhang'] With the arrival of the age of big data, the amount and types of data in the process of information transmission have increased significantly, and the full-disk encryption mode used by traditional encryption algorithms has certain limitations of…
Melih Şahin, Beyza E. Ortlek, Özgür B. Akan
(IoBNT) Authors: ['Melih Şahin' 'Beyza E. Ortlek' 'Özgür B. Akan'] Abstract—Molecular Communication (MC) has emerged as a promising paradigm employing molecules to transfer information at the nano-scale. Unlike MC channel coding, MC source coding has remained mostly an unexplored area of research. In a recent paper…
Da Qiu, Tingting Zhang, Jingyi Liu, Song Liu + 2 more
'Amelia Carolina Sparavigna'] This study proposes an innovative image encryption algorithm based on the DNAS_box and hyperchaos. The algorithm dynamically constructs a DNAS_box using 2-bit deoxyribonucleic acid (DNA) coding and 4-bit DNA-like coding, enabling seamless conversion between these two coding schemes. The…
Franklin Leong, Babak Rahmani, Demetri Psaltis, Christophe Moser + 1 more
A fundamental challenge in neuroengineering is determining a proper input to a sensory system that yields the desired functional output. In neuroprosthetics, this process is known as sensory encoding, and it holds a crucial role in prosthetic devices restoring sensory perception in individuals with disabilities. For…
Ibrahim Nawaz, Parv Agarwal, Thomas Heinis
DNA storage is a developing field that uses DNA to archive digital data owing to its superior information density and stability. Although DNA storage has been performed on a significant scale, challenges arise from the synthesis and sequencing of data-encoded oligonucleotides. Synthesis of DNA introduces significant…
Rıza Özçelik, Laura van Weesep, Sarah de Ruiter, Francesca Grisoni
In this work, we introduce peptidy -- a lightweight Python library that facilitates converting peptides (expressed as aminoacid sequences) to numerical representations suited to machine learning. peptidy is free from external dependencies, integrates seamlessly into modern Python environments, and supports a range of…
Hajime Tamaki, Yoh Matsuki
Fast magic-angle spinning (MAS) solid-state NMR spectroscopy is a powerful tool for gaining structural and dynamics in-formation on solid proteins. To access such information site-specifically, the signal assignment process is unavoidable. In the assignment process, Cα and Cβ chemical shifts are of paramount importance…
Authors not listed
Experimental design plays an important role in efficiently acquiring informative data for system characterization and deriving robust conclusions under resource limitations. Recent advancements in high-throughput experimentation coupled with machine learning have notably improved experimental procedures. While Bayesian…
Jürgen Köfinger, Gerhard Hummer
The proper balancing of information from experiment and theory is a long-standing problem in the analysis of noisy and incomplete data. Viewed as a Pareto optimization problem, improved agreement with the experimental data comes at the expense of growing inconsistencies with the theoretical reference model. Here, we…
Jürgen Köfinger, Gerhard Hummer
The proper balancing of information from experiment and theory is a long-standing problem in the analysis of noisy and incomplete data. Viewed as a Pareto optimization problem, improved agreement with the experimental data comes at the expense of growing inconsistencies with the theoretical reference model. Here, we…