21 papers · ranked by Valyu relevance
Krai Cheamsawat, Thiparat Chotibut, Xiao Yuan, Xiaoming Zhang + 1 more
'Bálint Koczor'] Quantum reservoir computing (QRC) has emerged as a promising paradigm for harnessing near-term quantum devices to tackle temporal machine learning tasks. Yet, identifying the mechanisms that underlie enhanced performance remains challenging, particularly in many-body open systems where nonlinear…
Lekang Yuan, Zhen Xie, Ye Wang, Xiaowo Wang
Background Using DNA as a storage medium is appealing due to the information density and longevity of DNA, especially in the era of data explosion. A significant challenge in the DNA data storage area is to deal with the noises introduced in the channel and control the trade-off between the redundancy of error…
Tuan Thanh Nguyen, Kui Cai, Han Mao Kiah, Kees A. Schouhamer Immink + 1 more
'Yeow Meng Chee'] Such constraints are crucial in several data storage systems, those regard the information data as two-dimensional (2D) instead of one-dimensional (1D), such as the crossbar resistive memory arrays and the holographic data storage. In this work, efficient encoding/decoding algorithms are presented for…
Zhi Ping, Shihong Chen, Guangyu Zhou, Xiaoluo Huang + 11 more
'Haoling Zhang' 'Henry H. Lee' 'Zhaojun Lan' 'Jie Cui' 'Tai Chen' 'Wenwei Zhang' 'Huanming Yang' 'Xun Xu' 'George M. Church' 'Yue Shen'] DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density…
Jin Sima, Chao Pan, S. Kasra Tabatabaei, Alvaro G. Hernandez + 2 more
'Charles M. Schroeder' 'Olgica Milenkovic'] DNA-based data storage systems face practical challenges due to the high cost of DNA synthesis. A strategy to address the problem entails encoding data via topological modifications of the DNA sugar-phosphate backbone. The DNA Punchcards system, which introduces nicks (cuts)…
Jingcheng Zhang, Lei Chen, Jinlin Sun, Shumin Li + 5 more
DNA has emerged as a compelling archival storage medium, offering unprecedented information density and millennia-scale durability. Despite its promise, DNA-based data storage faces critical challenges due to error-prone processes during DNA synthesis, storage, and sequencing. In this study, we introduce Gungnir, a…
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…
Xiaoluo Huang, Junting Cui, Wei Qiang, Jianwen Ye + 4 more
'Xinying Xie' 'Yuanzhen Li' 'Junbiao Dai'] Title: Abstract Deoxyribonucleic acid (DNA) has been suggested as a very promising medium for data storage in recent years. Although numerous studies have advocated for DNA data storage, its practical application remains obscure and there is a lack of a user-oriented platform.…
Parth K Raval, Wing Yui Ngan, Jenna Gallie, Deepa Agashe
The rate and accuracy of translation hinges upon multiple components – including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules – many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on…
Thomas Heinis, Roman Sokolovskii, Jamie J. Alnasir
Key to DNA storage is encoding the information to a sequence of nucleotides before it can be synthesised for storage. Definition of such an encoding or mapping must adhere to multiple design restrictions. First, not all possible sequences of nucleotides can be synthesised. Homopolymers, e.g., sequences of the same…
Xiangzhen Zan, Ranze Xie, Xiangyu Yao, Peng Xu + 1 more
Thanks to its high density and long durability, synthetic DNA has been widely considered as a promising solution to the data explosion problem. However, due to the large amount of random base insertion-deletion-substitution (IDSs) errors from sequencing, reliable data recovery remains a critical challenge, which…
Johan Chrisnata, Han Mao Kiah, Van Long Phuoc Pham
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common type of synthesis process where multiple DNA strands are synthesized in parallel…
Sean Ericson, Hailin Wang, S. J. van Enk
We extend the classical ideas of the Partial Information Decomposition (PID) to the quantum domain and quantify unique, redundant, and synergistic quantum information. We show that unique information plays the central role in quantum error correction codes: any erasure-correctable subset of encoding qubits must contain…
Licheng Mao, Shenghao Yang, Xuan Huang, Yanyan Dong + 1 more
Systematic codes are of important practical interest for communications. Network coding, however, seems to conflict with systematic codes: although the source node can transmit message packets, network coding at the intermediate network nodes may significantly reduce the number of message packets received by the…
Fajia Sun, Yiming Dong, Ming Ni, Zhi Ping + 3 more
DNA has been pursued as a novel biomaterial for digital data storage. While large-scale data storage and random access have been achieved in DNA oligonucleotide pools, repeated data accessing requires constant data replenishment, and these implementations are confined in professional facilities. Here, a mobile data…
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…
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…
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…
Pawel M. Mordaka, Kitty Clouston, Jing Cui, Andre Holzer + 3 more
Genome scale engineering has enabled codon compression of the universal genetic code of up to three codons in E. coli, providing the means for genetic code expansion. To go much beyond this number, smaller and simpler genetic systems are needed to avoid significant technical challenges. Chloroplast genomes offer…
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…
Oskar Weser, Björn Hein Hanke, Ricardo Mata
In this work, we present a fully automated method for the construction of chemically meaningful sets of non-redundant internal coordinates (also commonly denoted as Z-matrices) from the cartesian coordinates of a molecular system. Particular focus is placed on avoiding ill-definitions of angles and dihedrals due to…