论文标题
纳米孔测序的有限状态半摩托夫通道
Finite-State Semi-Markov Channels for Nanopore Sequencing
论文作者
论文摘要
纳米孔测序是一种新兴的DNA测序技术，已提出用于DNA存储系统。我们提出了用于纳米孔测序的嘈杂的纳米孔通道模型。该模型通过连接I.I.D.捕获重复，符号间干扰和嘈杂的测量。具有有限状态半马尔科夫频道的重复渠道。与以前的模型相比，该通道模拟了纳米孔的主要扭曲，同时保持可拖动。预期未来的编码方案，我们得出了地图检测算法并估算可实现的速率。鉴于有限状态的半马尔科夫通道是带有内存的通道的子类，我们猜想可以使用广义的blahut-arimoto算法的变体来优化嘈杂的纳米孔通道的可实现速率。
Nanopore sequencing is an emerging DNA sequencing technology that has been proposed for use in DNA storage systems. We propose the noisy nanopore channel model for nanopore sequencing. This model captures duplications, inter-symbol interference, and noisy measurements by concatenating an i.i.d. duplication channel with a finite-state semi-Markov channel. Compared to previous models, this channel models the dominant distortions of the nanopore while remaining tractable. Anticipating future coding schemes, we derive MAP detection algorithms and estimate achievable rates. Given that finite-state semi-Markov channels are a subclass of channels with memory, we conjecture that the achievable rate of the noisy nanopore channel can be optimised using a variation of the generalised Blahut-Arimoto algorithm.
