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arXiv 2102.01412cs.ITmath.IT
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论噪声子串信道的编码

On Codes for the Noisy Substring Channel

Yonatan Yehezkeally, Nikita Polyanskii

AI总结:

研究噪声子串信道的编码问题,针对替换和删除噪声提出纠错码族及组合界,证明次线性冗余且无渐近速率损失,并开发高效编码器以避免DNA链二级结构形成。

摘要:

我们考虑子串信道的编码问题,其中信息串仅通过其子串(多重集)被观测。由于现有DNA测序技术和基于DNA的存储系统中的应用,近年来对该信道的兴趣重新燃起。与现有文献不同,我们考虑了一种噪声信道模型,其中信息在被子串采样之前会受到噪声影响,其动机源于体内存储。我们研究了两种独立的噪声模型:替换或删除。在这两种情况下,我们检查了可用于纠错的码族,并给出了其大小的组合界。通过对无重复串概念的推广,我们证明了由于这种不完美观测假设而增加的所需冗余是次线性的,这在观测子串长度中的错误比例足够小或该长度足够长时均成立。这表明在这些情况下,该信道模型不会产生渐近的速率损失。此外,我们在某些情况下为这种受约束串开发了一种高效的编码器。最后,我们展示了如何使用类似的编码器来避免编码DNA链中二级结构的形成,即使在考虑不完美结构时也是如此。

英文摘要:

We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems, interest in this channel has renewed in recent years. In contrast to existing literature, we consider a noisy channel model where information is subject to noise before its substrings are sampled, motivated by in-vivo storage. We study two separate noise models, substitutions or deletions. In both cases, we examine families of codes which may be utilized for error-correction and present combinatorial bounds on their sizes. Through a generalization of the concept of repeat-free strings, we show that the added required redundancy due to this imperfect observation assumption is sublinear, either when the fraction of errors in the observed substring length is sufficiently small, or when that length is sufficiently long. This suggests that no asymptotic cost in rate is incurred by this channel model in these cases. Moreover, we develop an efficient encoder for such constrained strings in some cases. Finally, we show how a similar encoder can be used to avoid formation of secondary-structures in coded DNA strands, even when accounting for imperfect structures.

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