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The k-mappability problem revisited
arXiv - CS - Data Structures and Algorithms Pub Date : 2021-06-13 , DOI: arxiv-2106.07017
Amihood Amir, Itai Boneh, Eitan Kondratovsky

The $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately tackled by Alzamel et al. For a text with constant alphabet $\Sigma$ and $k \in O(1)$, they present an algorithm with linear space and $O(n\log^{k+1}n)$ time. For the case in which $k = 1$ and a constant size alphabet, a faster algorithm with linear space and $O(n\log(n)\log\log(n))$ time was presented in a 2020 paper by Alzamel et al. In this work, we enhance the techniques of Alzamel et al.'s 2020 paper to obtain an algorithm with linear space and $O(n \log(n))$ time for $k = 1$. Our algorithm removes the constraint of the alphabet being of constant size. We also present linear algorithms for the case of $k=1$, $|\Sigma|\in O(1)$ and $m=\Omega(\sqrt{n})$.

中文翻译:

重新审视 k-可映射性问题

$k$-mappability 问题有两个整数参数 $m$ 和 $k$。对于文本 $S$ 中每个大小为 $m$ 的子词,我们希望报告 $S$ 中该词出现最多 $k$ 不匹配的索引数量。Alzamel 等人最近解决了这个问题。对于具有常量字母 $\Sigma$ 和 $k \in O(1)$ 的文本,他们提出了一个具有线性空间和 $O(n\log^{k+1}n)$ 时间的算法。对于 $k = 1$ 和固定大小字母表的情况,Alzamel 在 2020 年的一篇论文中提出了一种具有线性空间和 $O(n\log(n)\log\log(n))$ 时间的更快算法等。在这项工作中,我们增强了 Alzamel 等人 2020 年论文的技术,以获得具有线性空间和 $O(n\log(n))$ 时间的算法,$k = 1$。我们的算法消除了字母表大小不变的约束。
更新日期:2021-06-15
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