An Asymmetric-Error-Aware LDPC Decoding Algorithm for DNA Storage

With the rapid growth of data, DNA is attracting attention as a promising storage medium due to its durability, large storage capacity, and high bulk density. However, errors occur in DNA synthesis and sequencing processes, with substitutions being the most common errors in DNA storage process. To a...

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Vydané v:	IEEE communications letters Ročník 27; číslo 1; s. 1
Hlavní autori:	Sun, Yi, Han, Guojun, Liu, Chang, Wang, Yixin, Fang, Yi
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	New York IEEE 01.01.2023 The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Predmet:	Algorithms asymmetric substitutions Asymmetry belief-propagation (BP) decoding Bit error rate bit error rate reduction Bulk density Codes Data storage Decoding DNA DNA data storage Error correcting codes Error correction Error reduction Gene sequencing Iterative decoding Likelihood ratio low-density parity-check (LDPC) codes Memory Nucleotides Sequential analysis Storage capacity Symbols
ISSN:	1089-7798, 1558-2558
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Abstract	With the rapid growth of data, DNA is attracting attention as a promising storage medium due to its durability, large storage capacity, and high bulk density. However, errors occur in DNA synthesis and sequencing processes, with substitutions being the most common errors in DNA storage process. To address this issue, we select low-density parity-check (LDPC) codes as the error correction method to guarantee data reliability. However, unlike traditional data storage channels, errors occurring between nucleotides in the DNA channel are asymmetric. Therefore, traditional belief propagation (BP) decoding algorithm is not sufficient for effective error correction under DNA channel. In this letter, we propose to use two LDPC codes and take error types as additional information for calibrating log-likelihood ratio (LLR) value. In addition, compared with previous works, simulation results show that our proposed decoding algorithm can reduce bit error rate (BER) by 33% ~ 94%.
AbstractList	With the rapid growth of data, DNA is attracting attention as a promising storage medium due to its durability, large storage capacity, and high bulk density. However, errors occur in DNA synthesis and sequencing processes, with substitutions being the most common errors in DNA storage process. To address this issue, we select low-density parity-check (LDPC) codes as the error correction method to guarantee data reliability. However, unlike traditional data storage channels, errors occurring between nucleotides in the DNA channel are asymmetric. Therefore, traditional belief propagation (BP) decoding algorithm is not sufficient for effective error correction under DNA channel. In this letter, we propose to use two LDPC codes and take error types as additional information for calibrating log-likelihood ratio (LLR) value. In addition, compared with previous works, simulation results show that our proposed decoding algorithm can reduce bit error rate (BER) by [Formula Omitted]. With the rapid growth of data, DNA is attracting attention as a promising storage medium due to its durability, large storage capacity, and high bulk density. However, errors occur in DNA synthesis and sequencing processes, with substitutions being the most common errors in DNA storage process. To address this issue, we select low-density parity-check (LDPC) codes as the error correction method to guarantee data reliability. However, unlike traditional data storage channels, errors occurring between nucleotides in the DNA channel are asymmetric. Therefore, traditional belief propagation (BP) decoding algorithm is not sufficient for effective error correction under DNA channel. In this letter, we propose to use two LDPC codes and take error types as additional information for calibrating log-likelihood ratio (LLR) value. In addition, compared with previous works, simulation results show that our proposed decoding algorithm can reduce bit error rate (BER) by 33% ~ 94%.
Author	Fang, Yi Wang, Yixin Sun, Yi Han, Guojun Liu, Chang
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SubjectTerms	Algorithms asymmetric substitutions Asymmetry belief-propagation (BP) decoding Bit error rate bit error rate reduction Bulk density Codes Data storage Decoding DNA DNA data storage Error correcting codes Error correction Error reduction Gene sequencing Iterative decoding Likelihood ratio low-density parity-check (LDPC) codes Memory Nucleotides Sequential analysis Storage capacity Symbols
Title	An Asymmetric-Error-Aware LDPC Decoding Algorithm for DNA Storage
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