Related papers: Finding Maximal Exact Matches in Graphs
We show how to chain maximal exact matches (MEMs) between a query string $Q$ and a labeled directed acyclic graph (DAG) $G=(V,E)$ to solve the longest common subsequence (LCS) problem between $Q$ and $G$. We obtain our result via a new…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
Finding maximum-cardinality matchings in undirected graphs is arguably one of the most central graph problems. For general m-edge and n-vertex graphs, it is well-known to be solvable in $O(m \sqrt{n})$ time. We develop a linear-time…
We consider the problem of computing the Maximal Exact Matches (MEMs) of a given pattern $P[1 .. m]$ on a large repetitive text collection $T[1 .. n]$, which is represented as a (hopefully much smaller) run-length context-free grammar of…
We describe a compression-aware method to compute all-vs-all maximal exact matches (MEM) among strings of a repetitive collection $\mathcal{T}$. The key concept in our work is the construction of a fully-balanced grammar $\mathcal{G}$ from…
Temporal graphs are graphs where the topology and/or other properties of the graph change with time. They have been used to model applications with temporal information in various domains. Problems on static graphs become more challenging…
We present efficient parallel algorithms for computing maximal matchings in hypergraphs. Our algorithm finds locally maximal edges in the hypergraph and adds them in parallel to the matching. In the CRCW PRAM models our algorithms achieve…
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…
Finding a maximum-cardinality or maximum-weight matching in (edge-weighted) undirected graphs is among the most prominent problems of algorithmic graph theory. For $n$-vertex and $m$-edge graphs, the best known algorithms run in…
We design quantum algorithms for maximum matching. Working in the query model, in both adjacency matrix and adjacency list settings, we improve on the best known algorithms for general graphs, matching previously obtained results for…
We consider the problem Minimum Error Correction (MEC). A MEC instance is an n x m matrix M with entries from {0,1,-}. Feasible solutions are composed of two binary m-bit strings, together with an assignment of each row of M to one of the…
Understanding the power of space-bounded computation with access to catalytic space has been an important theme in complexity theory over the recent years. One of the key algorithmic results in this area is that bipartite maximum matching…
We study the fully dynamic maximum matching problem. In this problem, the goal is to efficiently maintain an approximate maximum matching of a graph that is subject to edge insertions and deletions. Our focus is on algorithms that maintain…
In this paper we study the problem of fully dynamic maximal matching with lookahead. In a fully dynamic $n$-vertex graph setting, we have to handle updates (insertions and removals of edges), and answer queries regarding the current graph,…
A maximal $\varepsilon$-near perfect matching is a maximal matching which covers at least $(1-\varepsilon)|V(G)|$ vertices. In this paper, we study the number of maximal near perfect matchings in generalized quasirandom and dense graphs. We…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
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…
Given a pair of graphs with the same number of vertices, the inexact graph matching problem consists in finding a correspondence between the vertices of these graphs that minimizes the total number of induced edge disagreements. We study…