Related papers: Elastic-Degenerate String Matching with 1 Error
We study the convergence of the Expectation-Maximization (EM) algorithm for mixtures of linear regressions with an arbitrary number $k$ of components. We show that as long as signal-to-noise ratio (SNR) is $\tilde{\Omega}(k)$,…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
In the minimum $k$-edge-connected spanning subgraph ($k$-ECSS) problem the goal is to find the minimum weight subgraph resistant to up to $k-1$ edge failures. This is a central problem in network design, and a natural generalization of the…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
In the Exact Matching Problem (EM), we are given a graph equipped with a fixed coloring of its edges with two colors (red and blue), as well as a positive integer $k$. The task is then to decide whether the given graph contains a perfect…
The palindromic tree (a.k.a. eertree) for a string $S$ of length $n$ is a tree-like data structure that represents the set of all distinct palindromic substrings of $S$, using $O(n)$ space [Rubinchik and Shur, 2018]. It is known that, when…
We consider the problem of computing a shortest solid cover of an indeterminate string. An indeterminate string may contain non-solid symbols, each of which specifies a subset of the alphabet that could be present at the corresponding…
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…
The edit distance (ED) and longest common subsequence (LCS) are two fundamental problems which quantify how similar two strings are to one another. In this paper, we consider these problems in the asymmetric streaming model introduced by…
Pattern matching on graphs has been widely studied lately due to its importance in genomics applications. Unfortunately, even the simplest problem of deciding if a string appears as a subpath of a graph admits a quadratic lower bound under…
Practical data structures for the edit-sensitive parsing (ESP) are proposed. Given a string S, its ESP tree is equivalent to a context-free grammar G generating just S, which is represented by a DAG. Using the succinct data structures for…
We study the internal dictionary matching (IDM) problem where a dictionary $\mathcal{D}$ containing $d$ substrings of a text $T$ is given, and each query concerns the occurrences of patterns in $\mathcal{D}$ in another substring of $T$. We…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
Online string matching is a computational problem involving the search for patterns or substrings in a large text dataset, with the pattern and text being processed sequentially, without prior access to the entire text. Its relevance stems…
In the Palindrome Problem one tries to find all palindromes (palindromic substrings) in a given string. A palindrome is defined as a string which reads forwards the same as backwards, e.g., the string "racecar". A related problem is the…
We consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size $N$ over alphabet $[1,\sigma]$ is composed of $D$ copies…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
An extended regular expression $R$ specifies a set of strings formed by characters from an alphabet combined with concatenation, union, intersection, complement, and star operators. Given an extended regular expression $R$ and a string $Q$,…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. A simple dynamic…
Matching of images and analysis of shape differences is traditionally pursued by energy minimization of paths of deformations acting to match the shape objects. In the Large Deformation Diffeomorphic Metric Mapping (LDDMM) framework,…