Related papers: New algorithms for binary jumbled pattern matching

The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high…

Let two static sequences of strings $P$ and $S$, representing prefix and suffix conditions respectively, be given as input for preprocessing. For the query, let two positive integers $k_1$ and $k_2$ be given, as well as a string $T$ given…

In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…

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 $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately…

Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…

We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…

In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…

In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…

The Permutation Pattern Matching problem asks, given two permutations $\sigma$ on $n$ elements and $\pi$, whether $\sigma$ admits a subsequence with the same relative order as $\pi$ (or, in the counting version, how many such subsequences…

A Random Access query to a string $T\in [0..\sigma)^n$ asks for the character $T[i]$ at a given position $i\in [0..n)$. In $O(n\log\sigma)$ bits of space, this fundamental task admits constant-time queries. While this is optimal in the…

Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…

In this paper we are interested in indexing texts for substring matching queries with one edit error. That is, given a text $T$ of $n$ characters over an alphabet of size $\sigma$, we are asked to build a data structure that answers the…

The Permutation Pattern Matching problem, asking whether a pattern permutation $\pi$ is contained in a permutation $\tau$, is known to be NP-complete. In this paper we present two polynomial time algorithms for special cases. The first…

We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…

Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…

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…

We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…

A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…

The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…