相关论文: Fast Longest Common Extensions in Small Space

Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…

We consider a sliding window $W$ over a stream of characters from some alphabet of constant size. The user wants to perform deterministic substring matching on the current sliding window content and obtain positions of the matches. We…

Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…

In this paper we revisit the classical regular expression matching problem, namely, given a regular expression $R$ and a string $Q$, decide if $Q$ matches one of the strings specified by $R$. Let $m$ and $n$ be the length of $R$ and $Q$,…

In this paper, we explore worst-case solutions for the problems of single and multiple matching on strings in the word RAM model with word length w. In the first problem, we have to build a data structure based on a pattern p of length m…

Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…

An extended regular expression $R$ specifies a set of strings formed by characters from an alphabet combined with concatenation, union, intersection, complement, and star operators. Given an extended regular expression $R$ and a string $Q$,…

The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…

Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…

This note provides very simple, efficient algorithms for computing the number of distinct longest common subsequences of two input strings and for computing the number of LCS embeddings.

We consider the problem of decompressing the Lempel--Ziv 77 representation of a string $S$ of length $n$ using a working space as close as possible to the size $z$ of the input. The folklore solution for the problem runs in $O(n)$ time but…

We propose a new approach for calculating the Lempel-Ziv factorization of a string, based on run length encoding (RLE). We present a conceptually simple off-line algorithm based on a variant of suffix arrays, as well as an on-line algorithm…

Let $\mathcal{D}$ be a collection of $D$ documents, which are strings over an alphabet of size $\sigma$, of total length $n$. We describe a data structure that uses linear space and and reports $k$ most relevant documents that contain a…

Extending large language models (LLMs) to process longer inputs is crucial for a wide range of applications. However, the substantial computational cost of transformers and limited generalization of positional encoding restrict the size of…

We introduce the first grammar-compressed representation of a sequence that supports searches in time that depends only logarithmically on the size of the grammar. Given a text $T[1..u]$ that is represented by a (context-free) grammar of…

We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…

We study the problem of computing a longest increasing subsequence in a sequence $S$ of $n$ distinct elements in the presence of persistent comparison errors. In this model, every comparison between two elements can return the wrong result…

Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…

Given an array of size $n$ from a total order, we consider the problem of constructing a data structure that supports various queries (range minimum/maximum queries with their variants and next/previous larger/smaller queries) efficiently.…

The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…