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. 2024 Mar 9;25(1):266.
doi: 10.1186/s12864-024-10178-5.

DNA-QLC: an efficient and reliable image encoding scheme for DNA storage

Yanfen Zheng  1 , Ben Cao  1 , Xiaokang Zhang  1 , Shuang Cui  1 , Bin Wang  2 , Qiang Zhang  3
Affiliations

DNA-QLC: an efficient and reliable image encoding scheme for DNA storage

Yanfen Zheng et al. BMC Genomics. .

Abstract

Background: DNA storage has the advantages of large capacity, long-term stability, and low power consumption relative to other storage mediums, making it a promising new storage medium for multimedia information such as images. However, DNA storage has a low coding density and weak error correction ability.

Results: To achieve more efficient DNA storage image reconstruction, we propose DNA-QLC (QRes-VAE and Levenshtein code (LC)), which uses the quantized ResNet VAE (QRes-VAE) model and LC for image compression and DNA sequence error correction, thus improving both the coding density and error correction ability. Experimental results show that the DNA-QLC encoding method can not only obtain DNA sequences that meet the combinatorial constraints, but also have a net information density that is 2.4 times higher than DNA Fountain. Furthermore, at a higher error rate (2%), DNA-QLC achieved image reconstruction with an SSIM value of 0.917.

Conclusions: The results indicate that the DNA-QLC encoding scheme guarantees the efficiency and reliability of the DNA storage system and improves the application potential of DNA storage for multimedia information such as images.

Keywords: Combinatorial constraint; Image reconstruction; Levenshtein code; Net information density.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The case of undesired motifs in each encoding scheme
Fig. 2
Fig. 2
Graphic view before and after different image encoding. a, c, e and g are original image examples. b, d, f and h are based on the DNA-QLC with the results of SSIM (S) and Net information density (N, bits/nt)
Fig. 3
Fig. 3
Comparison of the error correction performance of different encoding schemes under different error rates
Fig. 4
Fig. 4
Graphic view of one example. a, b and c are the reconstruction of the image when the error rate of the three coding schemes is 0.5%. e, f and g are the reconstruction of the image when the error rate of the three coding schemes is 1.5%
Fig. 5
Fig. 5
Cost evaluation of different encoding schemes
Fig. 6
Fig. 6
Flowchart of the DNA-QLC encoding scheme
None
Algorithm 1. The pseudocode of DNA-QLC
See this image and copyright information in PMC

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