论文标题
DNA纳米孔测序通道的可实现信息率和串联代码
Achievable Information Rates and Concatenated Codes for the DNA Nanopore Sequencing Channel
论文作者
论文摘要
基于DNA的存储中发生的误差在本质上是相关的，这是合成和测序过程的直接结果。在本文中，我们考虑了Hamoum等人最近引入的内存 - $ K $纳米通道模型，该模型建模了通道的固有内存。我们为此通道模型得出了最大后验（MAP）解码器。派生的地图解码器允许我们计算真实DNA存储通道可实现的信息速率，假设与内存不匹配的解码器与内存 - $ K $ nanopore通道模型相匹配，并量化了假设记忆长度较小的性能损失，从而限制解码复杂性。此外，派生的地图解码器可用于设计针对DNA存储通道的错误校正代码。我们表明，具有外部低密度平价检查代码和内部卷积代码的串联编码方案可产生出色的性能。
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et al., which models the inherent memory of the channel. We derive the maximum a posteriori (MAP) decoder for this channel model. The derived MAP decoder allows us to compute achievable information rates for the true DNA storage channel assuming a mismatched decoder matched to the memory-$k$ nanopore channel model, and quantify the loss in performance assuming a small memory length--and hence limited decoding complexity. Furthermore, the derived MAP decoder can be used to design error-correcting codes tailored to the DNA storage channel. We show that a concatenated coding scheme with an outer low-density parity-check code and an inner convolutional code yields excellent performance.
