Minimum Free Energy Coding for DNA Storage
Minimum Free Energy Coding for DNA Storage
复制标题
DNA 存储的最小自由能编码
DOI：
10.1109/tnb.2021.3056351
复制
发表时间：
2021-04-01
影响因子：
3.9
通讯作者：
Wei, Xiaopeng
中科院分区：
文献类型：
--
作者：
Cao, Ben;Zhang, Xiaokang;Wei, Xiaopeng
随着信息技术的发展，海量的数据同时产生。如何高效、低成本地存储数据已成为迫切需要解决的问题。 DNA 是一种高密度且持久的介质，使 DNA 存储成为可行的解决方案。在DNA数据存储系统中，首先考虑的是如何将数据有效地编码成码字。但DNA链在杂交反应过程中容易发生非特异性杂交，在合成和测序过程中容易出现错误。为了降低错误率，提出了热力学最小自由能（MFE）约束并将其应用于DNA存储编码集的构建。布朗多节优化器（BMVO）算法在多节优化器（MVO）算法的基础上，融合了布朗运动和Nelder-Mead方法的思想，用于设计更好的DNA存储编码集。此外，与之前的工作相比，编码集的大小增加了4%~50%，并且具有更好的热力学性质。随着DNA编码集质量的提高，读写的准确性和DNA存储系统的鲁棒性也随之增强。
With the development of information technology, huge amounts of data are produced at the same time. How to store data efficiently and at low cost has become an urgent problem. DNA is a high-density and persistent medium, making DNA storage a viable solution. In a DNA data storage system, the first consideration is how to encode the data effectively into code words. However, DNA strands are prone to non-specific hybridization during the hybridization reaction process and are prone to errors during synthesis and sequencing. In order to reduce the error rate, a thermodynamic minimum free energy (MFE) constraint is proposed and applied to the construction of coding sets for DNA storage. The Brownian multi-verse optimizer (BMVO) algorithm, based on the Multi-verse optimizer (MVO) algorithm, incorporates the idea of Brownian motion and Nelder–Mead method, and it is used to design a better DNA storage coding set. In addition, compared with previous works, the coding set has been increasing by 4%–50% in size and has better thermodynamic properties. With the improvement of the quality of the DNA coding set, the accuracy of reading and writing and the robustness of the DNA storage system are also enhanced.