On Extensions of Maximal Repeats in Compressed Strings

利用惰性 LCP 评估实现更快的极大精确匹配

Faster Maximal Exact Matches with Lazy LCP Evaluation

针对 MONI 索引中 LCE 查询耗时问题，提出惰性评估 LCP 的变体，使处理时间由 MEM 数量界定并保持对数延迟。

A Searchable Compressed Edit-Sensitive Parsing

Practical data structures for the edit-sensitive parsing (ESP) are proposed. Given a string S, its ESP tree is equivalent to a context-free grammar G generating just S, which is represented by a DAG. Using the succinct data structures for trees and permutations, G is decomposed to two LOUDS bit strings and single array in (1+ε)n\log n+4n+o(n) bits for any 0<ε<1 and the number n of variables in G. The time to count occurrences of P in S is in O(\frac{1}ε(m\log n+occ_c(\log m\log u)), whereas m = |P|, u = |S|, and occ_c is the number of occurrences of a maximal common subtree in ESPs of P and S.…

游程长度压缩BWT中长匹配查询的高效数据结构与算法

An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT

本文提出局部极大精确匹配（LEMs）概念及长LEMs查询算法，依托改进的BWT游程压缩字符串索引，实现$O(m+occ)$期望时间的长匹配查询，可补充MEMs忽略的相似性信息，适用于泛基因组等场景。

对高度压缩字符串的不一致敏感访问

Incongruity-sensitive access to highly compressed strings

本文提出了一种基于不一致性的高效访问高度压缩字符串中不可压缩子字符串的方法，通过构建特定数据结构实现快速访问。

The Compressed Overlap Index

For analysing text algorithms, for computing superstrings, or for testing random number generators, one needs to compute all overlaps between any pairs of words in a given set. The positions of overlaps of a word onto itself, or of two words, are needed to compute the absence probability of a word in a random text, or the numbers of common words shared by two random texts. In all these contexts, one needs to compute or to query overlaps between pairs of words in a given set. For this sake, we designed COvI, a compressed overlap index that supports multiple queries on overlaps: like computing t…

CDAWG索引与语法压缩字符串上的模式匹配

The CDAWG Index and Pattern Matching on Grammar-Compressed Strings

本研究提出将CDAWG用作语法压缩字符串的索引，实现了高效模式匹配，实验验证其运行时性能达当前最优，且空间复杂度符合已知最优渐近界。

r-enum重访：上下文敏感重复和净频率的速度提升与扩展

R-enum Revisited: Speedup and Extension for Context-Sensitive Repeats and Net Frequencies

本文改进了r-enum算法，使其在O(n)时间内处理上下文敏感重复和净频率，同时扩展了算法以计算NSMRs和超级最大重复，并展示了如何在O(r)空间内高效计算净频率。

Compressed Communication Complexity of Longest Common Prefixes

We consider the communication complexity of fundamental longest common prefix (Lcp) problems. In the simplest version, two parties, Alice and Bob, each hold a string, $A$ and $B$, and we want to determine the length of their longest common prefix $l=\text{Lcp}(A,B)$ using as few rounds and bits of communication as possible. We show that if the longest common prefix of $A$ and $B$ is compressible, then we can significantly reduce the number of rounds compared to the optimal uncompressed protocol, while achieving the same (or fewer) bits of communication. Namely, if the longest common prefix has…

更快的游程长度压缩后缀数组

Faster run-length compressed suffix arrays

该研究针对游程长度压缩后缀数组（RLCSA），通过修改其结构并应用新结果，将查找aP的SA区间的时间复杂度从O(log r_a + log log n)降至O(log r_a)，同时不增加空间复杂度，还探讨了其对两级索引及最大精确匹配启发式方法的优化作用。

游程编码字符串中最大封闭子串的紧凑枚举

Compact Enumeration of Maximal Closed Substrings in Run-Length Encoded Strings

研究从字符串游程编码直接枚举最大封闭子串，引入紧凑族表示，证明\(O(m^2)\)个族有时必要且总是充分，借助后缀树等处理不同情况，能在特定时间和空间内列出所有最大封闭子串的紧凑表示。

Approximating Dynamic Time Warping Distance Between Run-Length Encoded Strings

Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard dynamic-programming algorithm for DTW takes $O(n^2)$ time, and there are conditional lower bounds showing that no algorithm can do substantially better. In many applications, however, the strings $x$ and $y$ may contain long runs of repeated letters, meaning that they can be compressed using run-length encoding. A natural question is whether the DTW-distance between th…

极大闭子串（Maximal Closed Substrings）

Maximal Closed Substrings

该研究提出极大闭子串（MCS）的定义，明确其与游程、极大带间隙重复的关联，并给出一种能在O(n log n)时间内定位长度为n的字符串中所有MCS的算法。