过剩词的优化计算
Optimal Computation of Overabundant Words
摘要：
在给定序列$x$中观察到的单词$w$的最长正确前缀、最长正确后缀和最长中缀的频率可用于将$w$分类为避免的或过度丰富的。Brendel等人（J Biomol Struct Dyn 1986）描述了该统计模型中用于$w$预期和偏差的定义，并进行了生物学论证。我们最近引入了一种时间最优算法，用于计算整数字母表上给定序列的所有避免单词（Algorithms Mol Biol 2017）。在这篇文章中，我们提出了一个$\mathcal{O}(n)$-时间和$\mathcal{O}(n)$-空间算法计算所有过剩的话在一个序列$x$的长度$n$在一个整数字母表。我们的主要结果是基于一个新的非平凡的组合性质的后缀树$\mathcal{T}$的$x$：$x$的最长中缀是标签的显式节点的$\mathcal{T}$的不同的因素的数目不超过$3n-4$。我们进一步表明，所提出的算法是时间最优的证明，$\mathcal{O}(n)$是一个紧上限的数量过剩的话。最后，我们提出的实验结果，使用合成和真实的数据，证明我们的方法在实践中的有效性和效率。
英文摘要：
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation and deviation of $w$ in this statistical model were described and biologically justified by Brendel et al. (J Biomol Struct Dyn 1986). We have very recently introduced a time-optimal algorithm for computing all avoided words of a given sequence over an integer alphabet (Algorithms Mol Biol 2017). In this article, we extend this study by presenting an $\mathcal{O}(n)$-time and $\mathcal{O}(n)$-space algorithm for computing all overabundant words in a sequence $x$ of length $n$ over an integer alphabet. Our main result is based on a new non-trivial combinatorial property of the suffix tree $\mathcal{T}$ of $x$: the number of distinct factors of $x$ whose longest infix is the label of an explicit node of $\mathcal{T}$ is no more than $3n-4$. We further show that the presented algorithm is time-optimal by proving that $\mathcal{O}(n)$ is a tight upper bound for the number of overabundant words. Finally, we present experimental results, using both synthetic and real data, which justify the effectiveness and efficiency of our approach in practical terms.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
