sparseDistanceMatrix: Create sparse distance, covariance or correlation matrix

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Create sparse distance, covariance or correlation matrix

Description

Exploit k-nearest neighbor algorithms to estimate a sparse similarity matrix. Critical to the validity of this function is the basic mathematical relationships between euclidean distance and correlation and between correlation and covariance. For applications of such matrices, one may see relevant publications by Mauro Maggioni and other authors.

Usage

sparseDistanceMatrix(
  x,
  k = 3,
  r = Inf,
  sigma = NA,
  kmetric = c("euclidean", "correlation", "covariance", "gaussian"),
  eps = 0.000001,
  ncores = NA,
  sinkhorn = FALSE,
  kPackage = "RcppHNSW",
  verbose = FALSE
)

Arguments

x	input matrix, should be n (samples) by p (measurements)
k	number of neighbors
r	radius of epsilon-ball
sigma	parameter for kernel PCA.
kmetric	similarity or distance metric determining k nearest neighbors
eps	epsilon error for rapid knn
ncores	number of cores to use
sinkhorn	boolean
kPackage	name of package to use for knn. FNN is reproducbile but RcppHNSW is much faster (with nthreads controlled by enviornment variable ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS) for larger problems. For large problems, compute the regularization once and save to disk; load for repeatability.
verbose	verbose output

Value

matrix sparse p by p matrix is output with p by k nonzero entries

Author(s)

Avants BB

References

http://www.math.jhu.edu/~mauro/multiscaledatageometry.html

Examples

## Not run: 
set.seed(120)
mat <- matrix(rnorm(60), ncol = 10)
smat <- sparseDistanceMatrix(mat, 2)
r16 <- antsImageRead(getANTsRData("r16"))
mask <- getMask(r16)
mat <- getNeighborhoodInMask(
  image = r16, mask = mask, radius = c(0, 0),
  physical.coordinates = TRUE, spatial.info = TRUE
)
smat <- sparseDistanceMatrix(t(mat$indices), 10) # close points
testthat::expect_is(smat, "Matrix")
testthat::expect_is(smat, "dgCMatrix")
testthat::expect_equal(sum(smat), 18017)

## End(Not run)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.