Related papers: Improved Extended Regular Expression Matching
In a typical regular expression (regex) crossword puzzle, you are given two nonempty lists $R_1,\ldots,R_m$ and $C_1,\ldots,C_n$ of regular expressions over some alphabet, and your goal is to fill in an $m\times n$ grid with letters from…
In the Proper Interval Completion problem we are given a graph G and an integer k, and the task is to turn G using at most k edge additions into a proper interval graph, i.e., a graph admitting an intersection model of equal-length…
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…
A fundamental problem in shape matching and geometric similarity is computing the maximum area overlap between two polygons under translation. For general simple polygons, the best-known algorithm runs in $O((nm)^2 \log(nm))$ time [Mount,…
We study the non-overlapping indexing problem: Given a text T, preprocess it so that you can answer queries of the form: given a pattern P, report the maximal set of non-overlapping occurrences of P in T. A generalization of this problem is…
We study the problem of efficiently correcting an erroneous product of two $n\times n$ matrices over a ring. Among other things, we provide a randomized algorithm for correcting a matrix product with at most $k$ erroneous entries running in…
The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of…
Selecting appropriate regularization coefficients is critical to performance with respect to regularized empirical risk minimization problems. Existing theoretical approaches attempt to determine the coefficients in order for regularized…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
Given $d$ strings over the alphabet $\{0,1,\ldots,\sigma{-}1\}$, the classical Aho--Corasick data structure allows us to find all $occ$ occurrences of the strings in any text $T$ in $O(|T| + occ)$ time using $O(m\log m)$ bits of space,…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
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,…
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 a text and a pattern over an alphabet, the pattern matching problem searches for all occurrences of the pattern in the text. An equivalence relation $\approx$ is called a substring consistent equivalence relation (SCER), if for two…
Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem. The input is a text of length $n$ over a fixed alphabet…
In this paper we further investigate the well-studied problem of finding a perfect matching in a regular bipartite graph. The first non-trivial algorithm, with running time $O(mn)$, dates back to K\"{o}nig's work in 1916 (here $m=nd$ is the…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
The problem of parsing has been studied extensively for various formal grammars. Given an input string and a grammar, the parsing problem is to check if the input string belongs to the language generated by the grammar. A closely related…
A gapped repeat is a factor of the form $uvu$ where $u$ and $v$ are nonempty words. The period of the gapped repeat is defined as $|u|+|v|$. The gapped repeat is maximal if it cannot be extended to the left or to the right by at least one…