Shortest paths with euclidean distances: An explanatory model

Networks ◽  
1978 ◽  
Vol 8 (4) ◽  
pp. 297-314 ◽  
Author(s):  
B. L. Golden ◽  
M. Ball
Author(s):  
Liron Cohen ◽  
Tansel Uras ◽  
Shiva Jahangiri ◽  
Aliyah Arunasalam ◽  
Sven Koenig ◽  
...  

We present a new preprocessing algorithm for embedding the nodes of a given edge-weighted undirected graph into a Euclidean space. The Euclidean distance between any two nodes in this space approximates the length of the shortest path between them in the given graph. Later, at runtime, a shortest path between any two nodes can be computed with an A* search using the Euclidean distances as heuristic. Our preprocessing algorithm, called FastMap, is inspired by the data-mining algorithm of the same name and runs in near-linear time. Hence, FastMap is orders of magnitude faster than competing approaches that produce a Euclidean embedding using Semidefinite Programming. FastMap also produces admissible and consistent heuristics and therefore guarantees the generation of shortest paths. Moreover, FastMap applies to general undirected graphs for which many traditional heuristics, such as the Manhattan Distance heuristic, are not well defined. Empirically, we demonstrate that A* search using the FastMap heuristic is competitive with A* search using other state-of-the-art heuristics, such as the Differential heuristic.


2013 ◽  
Author(s):  
Lisa S. Arduino ◽  
Marialuisa Martelli ◽  
Silvia Primativo ◽  
Maria De Luca ◽  
Andrea Albonico ◽  
...  

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
James R. Gayvert ◽  
Melissa Wei ◽  
Ksenia B. Bravaya

<p>eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or to the user-specified target. The identified pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.</p>


Author(s):  
Mark Newman

This chapter introduces some of the fundamental concepts of numerical network calculations. The chapter starts with a discussion of basic concepts of computational complexity and data structures for storing network data, then progresses to the description and analysis of algorithms for a range of network calculations: breadth-first search and its use for calculating shortest paths, shortest distances, components, closeness, and betweenness; Dijkstra's algorithm for shortest paths and distances on weighted networks; and the augmenting path algorithm for calculating maximum flows, minimum cut sets, and independent paths in networks.


2001 ◽  
Vol 110 (2-3) ◽  
pp. 151-167 ◽  
Author(s):  
Danny Z. Chen ◽  
Gautam Das ◽  
Michiel Smid

2022 ◽  
Vol 184 ◽  
pp. 111165
Author(s):  
Lorena Gutierrez ◽  
Lilian Velasco ◽  
Sheila Blanco ◽  
Patricia Catala ◽  
María Ángeles Pastor-Mira ◽  
...  

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