用CDAWG表示后缀树

D. Belazzougui, F. Cunial
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引用次数: 29

摘要

给定一个字符串$T$,我们知道它的后缀树可以使用具有$e_T$弧的紧凑有向无环词图(CDAWG)来表示,占用了整个$O(e_T+e_{{\overline{T}}})$个词的空间,其中${\overline{T}}$是$T$的反转,并且在最坏的情况下支持$O(1)$和$O(\log{\log{n}})$之间的一些关键操作。这种表示对高度重复的字符串特别有吸引力,比如相似基因组的集合或版本控制文档,在这些字符串中,$e_T$实际上在$T$的长度中呈次线性增长。在本文中,我们增强了这种表示,在RAM模型中支持在$O(1)$和$O(\log{n})$之间的最坏情况下的一些额外查询,而不会逐渐增加空间复杂性。我们的技术基于后缀树的重路径分解,还支持后缀数组、反向后缀数组和$T$本身的表示,它们占用$O(e_T)$个空间单词,并支持在$O(\log{n})$时间内的随机访问。此外,我们在$T$的反向CDAWG和生成$T$且仅产生$T$的上下文无关语法之间建立了连接,这两个语法可能具有独立的兴趣。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Representing the suffix tree with the CDAWG
Given a string $T$, it is known that its suffix tree can be represented using the compact directed acyclic word graph (CDAWG) with $e_T$ arcs, taking overall $O(e_T+e_{{\overline{T}}})$ words of space, where ${\overline{T}}$ is the reverse of $T$, and supporting some key operations in time between $O(1)$ and $O(\log{\log{n}})$ in the worst case. This representation is especially appealing for highly repetitive strings, like collections of similar genomes or of version-controlled documents, in which $e_T$ grows sublinearly in the length of $T$ in practice. In this paper we augment such representation, supporting a number of additional queries in worst-case time between $O(1)$ and $O(\log{n})$ in the RAM model, without increasing space complexity asymptotically. Our technique, based on a heavy path decomposition of the suffix tree, enables also a representation of the suffix array, of the inverse suffix array, and of $T$ itself, that takes $O(e_T)$ words of space, and that supports random access in $O(\log{n})$ time. Furthermore, we establish a connection between the reversed CDAWG of $T$ and a context-free grammar that produces $T$ and only $T$, which might have independent interest.
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