sparseDecom: Convenience wrapper for eigenanatomy decomposition.

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

Convenience wrapper for eigenanatomy decomposition.

Description

Decomposes a matrix into sparse eigenevectors to maximize explained variance. Note: we do not scale the matrices internally. We leave scaling choices to the user.

Usage

sparseDecom(
  inmatrix = NA,
  inmask = NULL,
  sparseness = 0.1,
  nvecs = 10,
  its = 5,
  cthresh = 50,
  statdir = NA,
  z = 0,
  smooth = 0,
  initializationList = list(),
  mycoption = 0,
  robust = 0,
  ell1 = 1,
  getSmall = 0,
  verbose = FALSE,
  powerit = 0,
  priorWeight = 0,
  maxBased = FALSE
)

Arguments

inmatrix	n by p input images , subjects or time points by row , spatial variable lies along columns
inmask	optional antsImage mask
sparseness	lower values equal more sparse
nvecs	number of vectors
its	number of iterations
cthresh	cluster threshold
statdir	place on disk to save results
z	u penalty, experimental
smooth	smoothness eg 0.5
initializationList	see initializeEigenanatomy
mycoption	0, 1 or 2 all produce different output 0 is combination of 1 (spatial orthogonality) and 2 (subject space orthogonality)
robust	rank transform input data - good for data checking
ell1	the ell1 grad descent param
getSmall	try to get smallest evecs (bool)
verbose	activates verbose output
powerit	alternative power iteration implementation, faster
priorWeight	scalar weight typically in range zero to two
maxBased	boolean that chooses max-based thresholding

Value

outputs a decomposition of a population or time series matrix

Author(s)

Avants BB

Examples

mat <- replicate(100, rnorm(20))
mydecom <- sparseDecom(mat)
mat <- scale(mat)
mydecom2 <- sparseDecom(mat)
# params that lead to algorithm similar to NMF
mydecom3 <- sparseDecom(mat, z = 1, sparseness = 1)

## Not run: 
# for prediction
if (usePkg("randomForest") & usePkg("spls") & usePkg("BGLR")) {
  data(lymphoma) # from spls
  training <- sample(rep(c(TRUE, FALSE), 31))
  sp <- 0.02
  myz <- 0
  ldd <- sparseDecom(lymphoma$x[training, ],
    nvecs = 5, sparseness = (sp),
    mycoption = 1, z = myz
  ) # NMF style
  traindf <- data.frame(
    lclass = as.factor(lymphoma$y[training]),
    eig = lymphoma$x[training, ] %*% as.matrix(ldd$eigenanatomyimages)
  )
  testdf <- data.frame(
    lclass = as.factor(lymphoma$y[!training]),
    eig = lymphoma$x[!training, ] %*% as.matrix(ldd$eigenanatomyimages)
  )
  myrf <- randomForest(lclass ~ ., data = traindf)
  predlymp <- predict(myrf, newdata = testdf)
  print(paste(
    "N-errors:", sum(abs(testdf$lclass != predlymp)),
    " non-zero ", sum(abs(ldd$eigenanatomyimages) > 0)
  ))
  # compare to http://arxiv.org/pdf/0707.0701v2.pdf
  # now SNPs
  data(mice)
  snps <- quantifySNPs(mice.X, shiftit = TRUE)
  numericalpheno <- as.matrix(mice.pheno[, c(4, 5, 13, 15)])
  nfolds <- 6
  train <- sample(rep(c(1:nfolds), 1800 / nfolds))
  train <- (train < 4)
  lrmat <- lowrankRowMatrix(as.matrix(snps[train, ]), 50)
  lrmat <- scale(lrmat)
  snpd <- sparseDecom(lrmat - min(lrmat), nvecs = 20, sparseness = (0.001), z = -1)
  projmat <- as.matrix(snpd$eig)
  snpse <- as.matrix(snps[train, ]) %*% projmat
  traindf <- data.frame(bmi = numericalpheno[train, 3], snpse = snpse)
  snpse <- as.matrix(snps[!train, ]) %*% projmat
  testdf <- data.frame(bmi = numericalpheno[!train, 3], snpse = snpse)
  myrf <- randomForest(bmi ~ ., data = traindf)
  preddf <- predict(myrf, newdata = testdf)
  cor.test(preddf, testdf$bmi)
  plot(preddf, testdf$bmi)
} # check for packages
# prior-based example
set.seed(123)
ref <- antsImageRead(getANTsRData("r16"))
ref <- iMath(ref, "Normalize")
mi <- antsImageRead(getANTsRData("r27"))
mi2 <- antsImageRead(getANTsRData("r30"))
mi3 <- antsImageRead(getANTsRData("r62"))
mi4 <- antsImageRead(getANTsRData("r64"))
mi5 <- antsImageRead(getANTsRData("r85"))
refmask <- getMask(ref)
refmask <- iMath(refmask, "ME", 2) # just to speed things up
ilist <- list(mi, mi2, mi3, mi4, mi5)
for (i in 1:length(ilist))
{
  ilist[[i]] <- iMath(ilist[[i]], "Normalize")
  mytx <- antsRegistration(
    fixed = ref, moving = ilist[[i]],
    typeofTransform = c("Affine")
  )
  mywarpedimage <- antsApplyTransforms(
    fixed = ref, moving = ilist[[i]],
    transformlist = mytx$fwdtransforms
  )
  ilist[[i]] <- mywarpedimage
}
mat <- imageListToMatrix(ilist, refmask)
kmseg <- kmeansSegmentation(ref, 3, refmask)
initlist <- list()
for (k in 1:3) {
  initlist[[k]] <-
    thresholdImage(kmseg$probabilityimages[[k]], 0.1, Inf) *
      kmseg$probabilityimages[[k]]
}
eanat <- sparseDecom(mat,
  inmask = refmask, ell1 = 0.1,
  sparseness = 0.0, smooth = 0.5, verbose = 1,
  initializationList = initlist, cthresh = 25,
  nvecs = 3, priorWeight = 0.5
)
ee <- matrixToImages(eanat$eigenanatomyimages, refmask)
eseg <- eigSeg(refmask, ee)
priormat <- imageListToMatrix(initlist, refmask)
cor(t(eanat$eigenanatomyimages), t(priormat))
plot(ref, eseg)

## End(Not run)

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