plkernel {TDAkit} | R Documentation |
Persistence Landscape Kernel
Description
Given multiple persistence landscapes \Lambda_1 (t), \Lambda_2 (t), \ldots, \Lambda_N (t)
, compute
the persistence landscape kernel under the L_2
sense.
Usage
plkernel(landlist)
Arguments
landlist |
a length- |
Value
an (N\times N)
kernel matrix.
References
Jan Reininghaus, Stefan Huber, Ulrich Bauer, and Roland Kwitt (2015). “A stable multi-scale kernel for topological machine learning.” Proc. 2015 IEEE Conf. Comp. Vision & Pat. Rec. (CVPR ’15).
Examples
# ---------------------------------------------------------------------------
# Persistence Landscape Kernel in Dimension 0 and 1
#
# We will compare dim=0,1 with top-20 landscape functions with
# - Class 1 : 'iris' dataset with noise
# - Class 2 : samples from 'gen2holes()'
# - Class 3 : samples from 'gen2circles()'
# ---------------------------------------------------------------------------
## Generate Data and Diagram from VR Filtration
ndata = 10
list_rips = list()
for (i in 1:ndata){
dat1 = as.matrix(iris[,1:4]) + matrix(rnorm(150*4), ncol=4)
dat2 = gen2holes(n=100, sd=1)$data
dat3 = gen2circles(n=100, sd=1)$data
list_rips[[i]] = diagRips(dat1, maxdim=1)
list_rips[[i+ndata]] = diagRips(dat2, maxdim=1)
list_rips[[i+(2*ndata)]] = diagRips(dat3, maxdim=1)
}
## Compute Persistence Landscapes from Each Diagram with k=5 Functions
# We try to get distance in dimensions 0 and 1.
list_land0 = list()
list_land1 = list()
for (i in 1:(3*ndata)){
list_land0[[i]] = diag2landscape(list_rips[[i]], dimension=0, k=5)
list_land1[[i]] = diag2landscape(list_rips[[i]], dimension=1, k=5)
}
## Compute Persistence Landscape Kernel Matrix
plk0 <- plkernel(list_land0)
plk1 <- plkernel(list_land1)
## Visualize
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,2), pty="s")
image(plk0[,(3*(ndata)):1], axes=FALSE, main="Kernel : dim=0")
image(plk1[,(3*(ndata)):1], axes=FALSE, main="Kernel : dim=1")
par(opar)
[Package TDAkit version 0.1.2 Index]