DNA storage coding optimization method based on improved Harris Hawk algorithm

An optimization method, Harris Eagle technology, applied in computing, computing models, instruments, etc., can solve the problem that binary models are not widely used, and achieve the effect of speeding up the convergence rate

Active Publication Date: 2020-06-16
DALIAN UNIVERSITY
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  • DNA storage coding optimization method based on improved Harris Hawk algorithm
  • DNA storage coding optimization method based on improved Harris Hawk algorithm
  • DNA storage coding optimization method based on improved Harris Hawk algorithm

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Embodiment 1

[0068] The embodiments of the present invention are carried out under the premise of the technical solution of the present invention, and detailed implementation and specific operation process are provided, but the protection scope of the present invention is not limited to the following embodiments. In the example, the DNA coding length n is 8, the Hamming distance constraint is d≥5, and the full discontinuity constraint and GC content constraint are as described above.

[0069] Step 1: Randomly initialize the population to generate 1000 DNA coding sequences with a length of 8. Relevant parameters required by the initialization algorithm, such as the initial energy E 0 , jumping strength J, and the maximum number of iterations T.

[0070] Step 2: Use MATLAB to carry out simulation experiments to screen the initial population for GC content and full discontinuity constraints to obtain 37 sequences, and then perform pairwise discrimination on the screened 37 sequences whether ...

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Abstract

The invention discloses a DNA storage coding optimization method based on an improved Harris Hawk algorithm. The method specifically comprises the following steps: in order to construct DNA coding sequences meeting a combination constraint condition as many as possible, firstly, initializing a certain number of random DNA sequences as an initial population, and calculating and sequencing fitness values (the sum of Hamming distances) of the population; secondly, updating the initial group by using different strategies of the improved Harris Hawk algorithm, wherein the added nonlinear convergence factor can maintain the smooth transition of the algorithm exploration and development process, a random reverse learning strategy is helpful to prevent the population from falling into the local optimum, and the updated DNA coding sequence with high fitness is selected by an elite selection mechanism; screening the sequence updated each time through a combined constraint condition to judge whether to add an alternative solution set or not; and finally, outputting an optimal DNA coding sequence set. According to the method, the lower bound of the DNA constraint coding sequence set is obviously improved.

Description

technical field [0001] The present invention relates to metaheuristic algorithms and combined constraints used in DNA storage, specifically the use of nonlinear control parameter strategies and stochastic back-learning strategies to improve the Harris Eagle algorithm, which is then applied to encoding in DNA storage In the field of design, construct an optimal constrained coding set. Background technique [0002] The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium, especially suitable for long-term storage of large data sets. Baum first proposed to build a DNA storage model, which laid the foundation for the research of DNA storage technology. Since then, DNA storage technology has been continuously developed and matured. In terms of encoding, DNA encoding is based on the ATCG four-base molecule, and the binary code elements of the original file on the computer will be mapped to a specific encoding model through t...

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Application Information

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IPC IPC(8): G16B40/00G06N3/00
CPCG16B40/00G06N3/006Y02D10/00
Inventor 王宾阴强周士华张强魏小鹏
Owner DALIAN UNIVERSITY
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