Related papers: Minimal Absent Words on Run-Length Encoded Strings

Given an LZW/LZ78 compressed text, we want to find an approximate occurrence of a given pattern of length m. The goal is to achieve time complexity depending on the size n of the compressed representation of the text instead of its length.…

Enumerating characteristic substrings (e.g., maximal repeats, minimal unique substrings, and minimal absent words) in a given string has been an important research topic because there are a wide variety of applications in various areas such…

Repetitiveness measures quantify how much repetitive structure a string contains and serve as parameters for compressed representations and indexing data structures. We study the measure $\chi$, defined as the size of the smallest…

Nishimoto and Tabei [CPM, 2021] proposed r-enum, an algorithm to enumerate various characteristic substrings, including maximal repeats, in a string $T$ of length $n$ in $O(r)$ words of compressed working space, where $r \le n$ is the…

Word Break is a prototypical factorization problem in string processing: Given a word $w$ of length $N$ and a dictionary $\mathcal{D} = \{d_1, d_2, \ldots, d_{K}\}$ of $K$ strings, determine whether we can partition $w$ into words from…

The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…

Minimizers sampling is one of the most widely-used mechanisms for sampling strings. Let $S=S[0]\ldots S[n-1]$ be a string over an alphabet $\Sigma$. In addition, let $w\geq 2$ and $k\geq 1$ be two integers and $\rho=(\Sigma^k,\leq)$ be a…

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…

A palindrome is a string that reads the same forward and backward. A palindromic substring $w$ of a string $T$ is called a minimal unique palindromic substring (MUPS) of $T$ if $w$ occurs only once in $T$ and any proper palindromic…

We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…

Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of…

The compression of highly repetitive strings (i.e., strings with many repetitions) has been a central research topic in string processing, and quite a few compression methods for these strings have been proposed thus far. Among them, an…

We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…

Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…

We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…

We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…

Multi-parameter persistent homology is a recent branch of topological data analysis. In this area, data sets are investigated through the lens of homology with respect to two or more scale parameters. The high computational cost of many…

We consider the problem of computing the Maximal Exact Matches (MEMs) of a given pattern $P[1 .. m]$ on a large repetitive text collection $T[1 .. n]$, which is represented as a (hopefully much smaller) run-length context-free grammar of…

The Run Length Encoding (RLE) compression method is a long standing simple lossless compression scheme which is easy to implement and achieves a good compression on input data which contains repeating consecutive symbols. In its pure form…

We show how to represent sets in a linear space data structure such that expressions involving unions and intersections of sets can be computed in a worst-case efficient way. This problem has applications in e.g. information retrieval and…