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通过奇偶编码和局部均值迭代实现稳健的 DNA 图像在一般错误下的存储。

PELMI: Realize robust DNA image storage under general errors via parity encoding and local mean iteration.

机构信息

School of Computer Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian, Liaoning 116024, China.

The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, No. 10 Xuefu Street, Dalian Economic-Technological Development Zone, Dalian, Liaoning 116622, China.

出版信息

Brief Bioinform. 2024 Jul 25;25(5). doi: 10.1093/bib/bbae463.

Abstract

DNA molecules as storage media are characterized by high encoding density and low energy consumption, making DNA storage a highly promising storage method. However, DNA storage has shortcomings, especially when storing multimedia data, wherein image reconstruction fails when address errors occur, resulting in complete data loss. Therefore, we propose a parity encoding and local mean iteration (PELMI) scheme to achieve robust DNA storage of images. The proposed parity encoding scheme satisfies the common biochemical constraints of DNA sequences and the undesired motif content. It addresses varying pixel weights at different positions for binary data, thus optimizing the utilization of Reed-Solomon error correction. Then, through lost and erroneous sequences, data supplementation and local mean iteration are employed to enhance the robustness. The encoding results show that the undesired motif content is reduced by 23%-50% compared with the representative schemes, which improves the sequence stability. PELMI achieves image reconstruction under general errors (insertion, deletion, substitution) and enhances the DNA sequences quality. Especially under 1% error, compared with other advanced encoding schemes, the peak signal-to-noise ratio and the multiscale structure similarity address metric were increased by 10%-13% and 46.8%-122%, respectively, and the mean squared error decreased by 113%-127%. This demonstrates that the reconstructed images had better clarity, fidelity, and similarity in structure, texture, and detail. In summary, PELMI ensures robustness and stability of image storage in DNA and achieves relatively high-quality image reconstruction under general errors.

摘要

DNA 分子作为存储介质具有编码密度高、能耗低的特点,使得 DNA 存储成为一种极具前景的存储方式。然而,DNA 存储也存在一些缺点,尤其是在存储多媒体数据时,一旦发生地址错误,图像重构就会失败,导致数据完全丢失。因此,我们提出了一种奇偶校验编码和局部均值迭代(PELMI)方案,以实现图像的稳健 DNA 存储。所提出的奇偶校验编码方案满足 DNA 序列的常见生化约束和不需要的模体内容。它解决了二进制数据中不同位置的像素权重不同的问题,从而优化了 Reed-Solomon 纠错的利用。然后,通过丢失和错误序列,采用数据补充和局部均值迭代来增强稳健性。编码结果表明,与代表性方案相比,不需要的模体内容减少了 23%-50%,从而提高了序列稳定性。PELMI 在一般错误(插入、删除、替换)下实现了图像重构,并提高了 DNA 序列的质量。特别是在 1%的错误率下,与其他先进的编码方案相比,峰值信噪比和多尺度结构相似性度量分别提高了 10%-13%和 46.8%-122%,而均方误差降低了 113%-127%。这表明重构图像的清晰度、保真度和结构、纹理以及细节的相似性都更好。总之,PELMI 确保了 DNA 中图像存储的稳健性和稳定性,并在一般错误下实现了相对高质量的图像重构。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/64ef/11407442/d6dea0073309/bbae463f1.jpg

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