neighbor_overlap {rnndescent}

Overlap between the indices of two nearest neighbor graphs

Description

Calculates the mean average number of neighbors in common between the two graphs. The per-item overlap can also be returned. This function can be useful as a measure of accuracy of approximation algorithms, if the exact nearest neighbors are known, or as a measure of diversity of two different approximate graphs.

Usage

neighbor_overlap(idx1, idx2, k = NULL, ret_vec = FALSE)

Arguments

idx1

Indices of a nearest neighbor graph, i.e. a matrix of nearest neighbor indices. Can also be a list containing an idx element.

idx2

Indices of a nearest neighbor graph, i.e. a matrix of nearest neighbor indices. Can also be a list containing an idx element. This is considered to be the ground truth.

k

Number of neighbors to consider. If NULL, then the minimum of the number of neighbors in idx1 and idx2 is used.

ret_vec

If TRUE, also return a vector containing the per-item overlap.

Details

The graph format is the same as that returned by e.g. nnd_knn() and should be of dimensions n by k, where n is the number of points and k is the number of neighbors. If you pass a neighbor graph directly, the index matrix will be extracted if present. If the two graphs have different numbers of neighbors, then the smaller number of neighbors is used.

Value

The mean overlap between idx1 and idx2. If ret_vec = TRUE, then a list containing the mean overlap and the overlap of each item in is returned with names mean and overlaps, respectively.

Examples

set.seed(1337)
# Generate two random neighbor graphs for iris
iris_rnn1 <- random_knn(iris, k = 15)
iris_rnn2 <- random_knn(iris, k = 15)

# Overlap between the two graphs
mean_overlap <- neighbor_overlap(iris_rnn1, iris_rnn2)

# Also get a vector of per-item overlap
overlap_res <- neighbor_overlap(iris_rnn1, iris_rnn2, ret_vec = TRUE)
summary(overlap_res$overlaps)