Related papers: Elastic-Degenerate String Matching with 1 Error
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…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
We consider the \emph{exact} error correction of a noisy Euclidean distance matrix, EDM, where the elements are the squared distances between $n$ points in $R^d$. For our problem we are given two facts: (i) the embedding dimension, $d$,…
We consider deterministic distributed algorithms for reaching agreement in synchronous networks of arbitrary topologies. Links are bi-directional and prone to failures while nodes stay non-faulty at all times. A faulty link may omit…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
We study the fundamental problem of approximating the edit distance of two strings. After an extensive line of research led to the development of a constant-factor approximation algorithm in almost-linear time, recent years have witnessed a…
Palindromes are non-empty strings that read the same forward and backward. The problem of recognizing strings that can be represented as the concatenation of even-length palindromes, the concatenation of palindromes of length at least two,…
In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the…
The well-known Eulerian path problem can be solved in polynomial time (more exactly, there exists a linear time algorithm for this problem). In this paper, we model the problem using a string matching framework, and then initiate an…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
Cadences are structurally maximal arithmetic progressions of indices corresponding to equal characters in an underlying string. This paper provides a polynomial time detection algorithm for 3-cadences in grammar-compressed binary strings.…
In his 1987 paper entitled "Generalized String Matching", Abrahamson introduced {\em pattern matching with character classes} and provided the first efficient algorithm to solve it. The best known solution to date is due to Linhart and…
We study the convergence rates of the EM algorithm for learning two-component mixed linear regression under all regimes of signal-to-noise ratio (SNR). We resolve a long-standing question that many recent results have attempted to tackle:…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
In the $k$-mismatch problem, given a pattern and a text of length $n$ and $m$ respectively, we have to find if the text has a sub-string with a Hamming distance of at most $k$ from the pattern. This has been studied in the classical setting…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
Given a graph $G$ and a digraph $D$ whose vertices are the edges of $G$, we investigate the problem of finding a spanning tree of $G$ that satisfies the constraints imposed by $D$. The restrictions to add an edge in the tree depend on its…