affinity: Gaussian affinity matrix constructor

In kazumits/ddhodge: Modeling Latent Flow Structure using Hodge Decomposition

Gaussian affinity matrix constructor

Description

equivalent to diffusion maps (Coifman, 2015) with adaptive scaling according to local density.

Usage

affinity(R, k = 7, sigma = NULL, log = FALSE, normalize = FALSE)

Arguments

R	symmetric matrix; distance or any similarity matrix.
k	integer; number of neighbours in adaptive-scaling. (ignored if sigma is specified)
sigma	numeric; fixed sigma for isotropic diffusion
log	logical; if TRUE, log-transformed affinity matrix is returned.
normalize	logical; scale s.t. row summing to 1 (i.e. returns transition matrix)

References

"Self-tuning spectral clustering"

kazumits/ddhodge documentation built on June 12, 2025, 1:48 a.m.