diffusionMap (version 1.2.0)

diffuse: Compute diffusion map coordinates from pair-wise distances.

Description

Uses the pair-wise distance matrix for a data set to compute the diffusion map coefficients. Computes the Markov transition probability matrix, and its eigenvalues and left & right eigenvectors. Returns a 'dmap' object.

Usage

diffuse(D, eps.val = epsilonCompute(D), neigen = NULL, t = 0,
  maxdim = 50, delta = 10^-5)

Arguments

D

n-by-n pairwise distance matrix for a data set with n points, or alternatively output from the dist() function

eps.val

epsilon parameter for the diffusion weight matrix, exp(-D$^2$/(eps.val)). Default is to use the epsilon corresponding to the median distance to the 0.01*n nearest neighbor

neigen

number of dimensions of final diffusion map representation. Default uses number of dimensions corresponding to a 95% drop-off in eigenvalue multiplier.

t

optional time-scale parameter in the diffusion map. The (recommended) default uses multiscale geometry.

maxdim

the maximum number of diffusion map dimensions returned if 95% drop-off is not attained.

delta

sparsity cut-off for the symmetric graph Laplacian. Default of 10^-5 is used. Higher value induces more sparsity in Laplacian (and faster computations)

Value

The returned value is an object of 'class' 'diffuse'.

The function 'plot' is used to plot the diffusion coordinates in 1, 2, or 3 dimensions. The function 'print' displays the computed eigen-multipliers and the value of epsilon used.

An object of class 'dmap' is a list containing the following components:

X

matrix of n diffusion map coordinates, entered column-wise (does not include the trivial coordinate)

phi0

trivial left eigenvector of Markov matrix (stationary distribution of Markov random walk) in diffusion map construction

eigenvals

eigen-values of the svd of the symmetric graph Laplacian

eigenmult

eigen-multipliers of the diffusion map

psi

right eigenvectors of the Markov matrix (first row is the trivial right eigenvector)

phi

left eigenvectors of the Markov matrix (first row is the trivial left eigenvector)

neigen

number of diffusion map dimensions used

epsilon

the value of epsilon used

Details

Diffusion map is a powerful tool for data parametrization that exploits the natural geometry of a data set. Diffusion map uses local interactions between data points, propogated to larger scales, to construct a global representation of the data.

The parameter eps.val controls the degree of localness in the diffusion weight matrix. For most statisitical inference problems using diffusion map, results should be optimized over eps.val. Generally a good starting point is to pick eps.val as $2*$med.knn$^2$, where med.knn is the median distance to the kth nearest neighbor, and k is chosen 1-2% of n. The default uses 1% of n.

Computation of the diffusion map coordinates requires singular value decomposition of the normalized graph Laplacian. This operation is optimized for speed by exploiting the sparseness of the graph Laplacian and by using ARPACK for fast matrix decomposition. Increasing the sparseness parameter, delta, will speed up the algorithm.

References

Coifman, R. R., & Lafon, S., (2006), Appl. Comput. Harmon. Anal., 21, 5

Lafon, S., & Lee, A., (2006), IEEE Trans. Pattern Anal. and Mach. Intel., 28, 1393

Richards, J. W., Freeman, P. E., Lee, A. B., Schafer, C. M., (2009), ApJ, 691, 32

Examples

# NOT RUN {
library(stats)
## example with noisy spiral
n=2000
t=runif(n)^.7*10
al=.15;bet=.5;
x1=bet*exp(al*t)*cos(t)+rnorm(n,0,.1)
y1=bet*exp(al*t)*sin(t)+rnorm(n,0,.1)
plot(x1,y1,pch=20,main="Noisy spiral")
D = dist(cbind(x1,y1))
dmap = diffuse(D,neigen=10) # compute diffusion map
par(mfrow=c(2,1))
plot(t,dmap$X[,1],pch=20,axes=FALSE,xlab="spiral parameter",ylab="1st diffusion coefficient")
box()
plot(1:10,dmap$eigenmult,typ='h',xlab="diffusion map dimension",ylab="eigen-multipliers")

## example with annulus data set
data(annulus)
plot(annulus,main="Annulus Data",pch=20,cex=.7)
D = dist(annulus) # use Euclidean distance
dmap = diffuse(D,eps.val=.1) # compute diffusion map & plot
print(dmap)
plot(dmap)
# }