An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO

The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium that is especially suitable for the long-term storage of large datasets. The DNA sequences used in storage need to consider relevant constraints to avoid nonspecific hybridization reaction...

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Vydáno v:International journal of molecular sciences Ročník 21; číslo 6; s. 2191
Hlavní autoři: Yin, Qiang, Cao, Ben, Li, Xue, Wang, Bin, Zhang, Qiang, Wei, Xiaopeng
Médium: Journal Article
Jazyk:angličtina
Vydáno: Switzerland MDPI AG 22.03.2020
MDPI
Témata:
Algorithms
Artificial Intelligence
Base Composition
Codes
Databases, Nucleic Acid
Deoxyribonucleic acid
DNA
DNA - chemistry
Experiments
Information storage
OBL
DNA coding design
DNA storage
HHO algorithm
ISSN:1422-0067, 1661-6596, 1422-0067
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Shrnutí:The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium that is especially suitable for the long-term storage of large datasets. The DNA sequences used in storage need to consider relevant constraints to avoid nonspecific hybridization reactions, such as the No-runlength constraint, GC-content, and the Hamming distance. In this work, a new nonlinear control parameter strategy and a random opposition-based learning strategy were used to improve the Harris hawks optimization algorithm (for the improved algorithm NOL-HHO) in order to prevent it from falling into local optima. Experimental testing was performed on 23 widely used benchmark functions, and the proposed algorithm was used to obtain better coding lower bounds for DNA storage. The results show that our algorithm can better maintain a smooth transition between exploration and exploitation and has stronger global exploration capabilities as compared with other algorithms. At the same time, the improvement of the lower bound directly affects the storage capacity and code rate, which promotes the further development of DNA storage technology.
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ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms21062191