To compile the C++ code for mex use the following command in Matlab: mex gomezMex.cpp psi.cpp dataSet.cpp metricTests.cpp Use vpTreeTest.m to run distribution tests.
JASSS (2022)
Akopov Andranik
Review of data structures for computationally efficient nearest-neighbour entropy estimators for large systems with periodic boundary conditions
By Brown Josh, Bossomaier Terry, and Barnett Lionel
Journal of Computational Science (2017)
Abstract
×Information theoretic quantities are extremely useful in discovering relationships between two or more data sets. One popular method—particularly for continuous systems—for estimating these quantities is the nearest neighbour estimators. When system sizes are very large or the systems have periodic boundary conditions issues with performance and correctness surface, however solutions are known for each problem. Here we show that these solutions are inappropriate in systems that simultaneously contain both features and discuss a lesser known alternative solution involving Vantage Point trees that is capable of addressing both issues.
Suggested citation
×Brown J., Bossomaier T., and Barnett L. (2017) Review of data structures for computationally efficient nearest-neighbour entropy estimators for large systems with periodic boundary conditions. Journal of Computational Science.