Related papers: Fast and Simple Jumbled Indexing for Binary RLE St…
We study a generalized binary search problem on the line and general trees. On the line (e.g., a sorted array), binary search finds a target node in $O(\log n)$ queries in the worst case, where $n$ is the number of nodes. In situations with…
This paper considers the task of performing binary search under noisy decisions, focusing on the application of target area localization. In the presence of noise, the classical partitioning approach of binary search is prone to error…
A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present an…
We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern…
Re-Pair is a grammar compression scheme with favorably good compression rates. The computation of Re-Pair comes with the cost of maintaining large frequency tables, which makes it hard to compute Re-Pair on large scale data sets. As a…
This note makes an observation that significantly simplifies a number of previous parallel, two-way merge algorithms based on binary search and sequential merge in parallel. First, it is shown that the additional merge step of distinguished…
Much research in stringology focuses on structures that can, in a way, ``grasp'' repeats (substrings that occur multiple times) as, for example, the so-called runs, a.k.a. maximal repetitions, compactly describe all tandem repeats. In this…
There is growing interest in representing image data and feature descriptors using compact binary codes for fast near neighbor search. Although binary codes are motivated by their use as direct indices (addresses) into a hash table, codes…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
Given a pattern of length $m$ and a text of length $n$, the goal in $k$-mismatch pattern matching is to compute, for every $m$-substring of the text, the exact Hamming distance to the pattern or report that it exceeds $k$. This can be…
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
We generalize Karp-Rabin string matching to handle multiple patterns in $\mathcal{O}(n \log n + m)$ time and $\mathcal{O}(s)$ space, where $n$ is the length of the text and $m$ is the total length of the $s$ patterns, returning correct…
Given a text $T$ and a pattern $P$, the order-preserving matching problem is to find all substrings in $T$ which have the same relative orders as $P$. Order-preserving matching has been an active research area since it was introduced by…
We present an approach to implement binary search trees in the rule-based graph programming language GP 2. Our implementation uses GP 2's rooted graph transformation rules to be fast and supports insertion, deletion and query operations. We…
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…
We analyze algorithms for computing the $n$th prime $p_n$ and establish asymptotic bounds for several approaches. Using existing results on the complexity of evaluating the prime-counting function $\pi(x)$, we show that the binary search…
Template matching is widely used for many applications in image and signal processing and usually is time-critical. Traditional methods usually focus on how to reduce the search locations by coarse-to-fine strategy or full search combined…
The $r$-index (Gagie et al., JACM 2020) represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude. Its space usage, $\mathcal{O}(r)$ where $r$ is the number of…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…