GCNSA: DNA storage encoding with a graph convolutional network and self-attention
Summary: DNA Encoding, as a key step in DNA storage, plays an important role in reading and writing accuracy and the storage error rate. However, currently, the encoding efficiency is not high enough and the encoding speed is not fast enough, which limits the performance of DNA storage systems. In t...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223003085 |
| _version_ | 1811161677909983232 |
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| author | Ben Cao Bin Wang Qiang Zhang |
| author_facet | Ben Cao Bin Wang Qiang Zhang |
| author_sort | Ben Cao |
| collection | DOAJ |
| description | Summary: DNA Encoding, as a key step in DNA storage, plays an important role in reading and writing accuracy and the storage error rate. However, currently, the encoding efficiency is not high enough and the encoding speed is not fast enough, which limits the performance of DNA storage systems. In this work, a DNA storage encoding system with a graph convolutional network and self-attention (GCNSA) is proposed. The experimental results show that DNA storage code constructed by GCNSA increases by 14.4% on average under the basic constraints, and by 5%-40% under other constraints. The increase of DNA storage codes effectively improves the storage density of 0.7-2.2% in the DNA storage system. The GCNSA predicted more DNA storage codes in less time while ensuring the quality of codes, which lays a foundation for higher read and write efficiency in DNA storage. |
| first_indexed | 2024-04-10T06:18:13Z |
| format | Article |
| id | doaj.art-2cc31a2d760f4a0883bb53403e2fbfdd |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-10T06:18:13Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-2cc31a2d760f4a0883bb53403e2fbfdd2023-03-02T05:02:57ZengElsevieriScience2589-00422023-03-01263106231GCNSA: DNA storage encoding with a graph convolutional network and self-attentionBen Cao0Bin Wang1Qiang Zhang2School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, ChinaKey Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, ChinaSchool of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China; Corresponding authorSummary: DNA Encoding, as a key step in DNA storage, plays an important role in reading and writing accuracy and the storage error rate. However, currently, the encoding efficiency is not high enough and the encoding speed is not fast enough, which limits the performance of DNA storage systems. In this work, a DNA storage encoding system with a graph convolutional network and self-attention (GCNSA) is proposed. The experimental results show that DNA storage code constructed by GCNSA increases by 14.4% on average under the basic constraints, and by 5%-40% under other constraints. The increase of DNA storage codes effectively improves the storage density of 0.7-2.2% in the DNA storage system. The GCNSA predicted more DNA storage codes in less time while ensuring the quality of codes, which lays a foundation for higher read and write efficiency in DNA storage.http://www.sciencedirect.com/science/article/pii/S2589004223003085Computational chemistryBiological sciencesBiochemistry |
| spellingShingle | Ben Cao Bin Wang Qiang Zhang GCNSA: DNA storage encoding with a graph convolutional network and self-attention iScience Computational chemistry Biological sciences Biochemistry |
| title | GCNSA: DNA storage encoding with a graph convolutional network and self-attention |
| title_full | GCNSA: DNA storage encoding with a graph convolutional network and self-attention |
| title_fullStr | GCNSA: DNA storage encoding with a graph convolutional network and self-attention |
| title_full_unstemmed | GCNSA: DNA storage encoding with a graph convolutional network and self-attention |
| title_short | GCNSA: DNA storage encoding with a graph convolutional network and self-attention |
| title_sort | gcnsa dna storage encoding with a graph convolutional network and self attention |
| topic | Computational chemistry Biological sciences Biochemistry |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223003085 |
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