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The distance matrix is widely used in the bioinformatics field, and it is present in several methods, algorithms and programs. Distance matrices are used to represent protein structures in a coordinate-independent manner, as well as the pairwise distances between two sequences in sequence space.
In mathematics, a Euclidean distance matrix is an n×n matrix representing the spacing of a set of n points in Euclidean space. For points x 1 , x 2 , … , x n {\displaystyle x_{1},x_{2},\ldots ,x_{n}} in k -dimensional space ℝ k , the elements of their Euclidean distance matrix A are given by squares of distances between them.
The trace distance is a generalization of the total variation distance, and for two commuting density matrices, has the same value as the total variation distance of the two corresponding probability distributions.
Wasserstein metrics measure the distance between two measures on the same metric space. The Wasserstein distance between two measures is, roughly speaking, the cost of transporting one to the other. The set of all m by n matrices over some field is a metric space with respect to the rank distance (,) = ().
The normalized angle, referred to as angular distance, between any two vectors and is a formal distance metric and can be calculated from the cosine similarity. [5] The complement of the angular distance metric can then be used to define angular similarity function bounded between 0 and 1, inclusive.
One first computes the distance correlation (involving the re-centering of Euclidean distance matrices) between two random vectors, and then compares this value to the distance correlations of many shuffles of the data. Several sets of (x, y) points, with the distance correlation coefficient of x and y for each set.
This result generalises the earlier example of the Wasserstein distance between two point masses (at least in the case =), since a point mass can be regarded as a normal distribution with covariance matrix equal to zero, in which case the trace term disappears and only the term involving the Euclidean distance between the means remains.
The measure gives rise to an (,)-sized similarity matrix for a set of n points, where the entry (,) in the matrix can be simply the (reciprocal of the) Euclidean distance between and , or it can be a more complex measure of distance such as the Gaussian ‖ ‖ /. [5]