Concatenated Codes for Recovery From Multiple Reads of DNA Sequences
Concatenated Codes for Recovery From Multiple Reads of DNA Sequences
复制标题
用于从 DNA 序列多次读取中恢复的串联代码
DOI：
10.1109/itw46852.2021.9457675
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
A. G. Amat
中科院分区：
文献类型：
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作者：
A. Lenz;I. Maarouf;L. Welter;A. Wachter;E. Rosnes;A. G. Amat
译码序列源于码字在插入、删除和替换通道上的多次传输，是高效脱氧核糖核酸(DNA)数据存储系统的关键组件。在本文中，我们考虑了一种由外部低密度奇偶校验码和内部卷积码或分组码组成的级联编码方案。我们提出了两种新的用于从多个接收序列中推断的译码算法，它们都将内码和信道结合到一个联合隐马尔可夫模型中来推断符号形式的后验概率(APP)。第一解码器通过联合解码接收的序列来计算准确的APP，而第二解码器通过组合单独解码的接收序列的结果来近似APP。通过可实现的信息速率和蒙特卡罗仿真，对所提出的算法进行了译码性能评估。与单个接收序列相比，我们显示出显著的性能提升。
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a concatenated coding scheme with an outer low-density parity-check code and either an inner convolutional code or a block code. We propose two new decoding algorithms for inference from multiple received sequences, both combining the inner code and channel to a joint hidden Markov model to infer symbolwise a posteriori probabilities (APPs). The first decoder computes the exact APPs by jointly decoding the received sequences, whereas the second decoder approximates the APPs by combining the results of separately decoded received sequences. Using the proposed algorithms, we evaluate the performance of decoding multiple received sequences by means of achievable information rates and Monte-Carlo simulations. We show significant performance gains compared to a single received sequence.