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We generalize the monotone local search approach of Fomin, Gaspers, Lokshtanov and Saurabh [J. ACM 2019], by establishing a connection between parameterized approximation and exponential-time approximation algorithms for monotone subset…
The goal of this paper is to understand how exponential-time approximation algorithms can be obtained from existing polynomial-time approximation algorithms, existing parameterized exact algorithms, and existing parameterized approximation…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
The pattern matching problem with swaps is to find all occurrences of a pattern in a text while allowing the pattern to swap adjacent symbols. The goal is to design fast matching algorithm that takes advantage of the bit parallelism of…
In this article, we describe an algorithm to determine whether a permutation class C given by a finite basis B of excluded patterns contains a finite number of simple permutations. This is a continuation of the work initiated in [Brignall,…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
We consider several types of internal queries, that is, questions about fragments of a given text $T$ specified in constant space by their locations in $T$. Our main result is an optimal data structure for Internal Pattern Matching (IPM)…
We study the fundamental problem of selecting optimal features for model construction. This problem is computationally challenging on large datasets, even with the use of greedy algorithm variants. To address this challenge, we extend the…
We consider the problem of sorting $n$ elements subject to persistent random comparison errors. In this problem, each comparison between two elements can be wrong with some fixed (small) probability $p$, and comparing the same pair of…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
Let $k\ge 1$ be an integer, and let $P= (f_1(x), \ldots, f_k(x) )$ be $k$ admissible linear polynomials over the integers, or \textit{the pattern}. We present two algorithms that find all integers $x$ where $\max{ \{f_i(x) \} } \le n$ and…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
Problems on repeated geometric patterns in finite point sets in Euclidean space are extensively studied in the literature of combinatorial and computational geometry. Such problems trace their inspiration to Erd\H{o}s' original work on that…
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…
Let $S_{n}$ denote the set of permutations of $[n]=\{1,2,\dots, n\}$. For each integer $k\geq 1$, let $S_{n,k}$ be the set of all permutations of $[n]$ with exactly $k$ disjoint cycles. A subset $H\subseteq S_{n,k}$ is to be a matching if…
More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
The decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), asks to list all fragments of $T$ that are at edit distance at…