相关论文: Fast and linear-time string matching algorithms ba…
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 a seminal paper on finding large matchings in sparse random graphs, Karp and Sipser proposed two algorithms for this task. The second algorithm has been intensely studied, but due to technical difficulties, the first algorithm has…
We consider the problem of computing the q-gram profile of a string \str of size $N$ compressed by a context-free grammar with $n$ production rules. We present an algorithm that runs in $O(N-\alpha)$ expected time and uses $O(n+q+\kq)$…
In this work, we tackle a natural variation of the String Matching Problem on the case of a dynamic pattern, that is, given a static text $T$ and a pattern $P$, we want to support character additions and deletions to the pattern, and after…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
The parameterized matching problem is a variant of string matching, which is to search for all parameterized occurrences of a pattern $P$ in a text $T$. In considering matching algorithms, the combinatorial natures of strings, especially…
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…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
Given an indeterminate string pattern $p$ and an indeterminate string text $t$, the problem of order-preserving pattern matching with character uncertainties ($\mu$OPPM) is to find all substrings of $t$ that satisfy one of the possible…
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…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
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…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…
String matching is a fundamental problem in computer science, with critical applications in text retrieval, bioinformatics, and data analysis. Among the numerous solutions that have emerged for this problem in recent decades,…
We propose smooth $q$-gram, the first variant of $q$-gram that captures $q$-gram pair within a small edit distance. We apply smooth $q$-gram to the problem of detecting overlapping pairs of error-prone reads produced by single molecule real…
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…
Given two sets $S$ and $T$ of points in the plane, of total size $n$, a {many-to-many} matching between $S$ and $T$ is a set of pairs $(p,q)$ such that $p\in S$, $q\in T$ and for each $r\in S\cup T$, $r$ appears in at least one such pair.…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…