K-means over sparse data input with constraints on cluster weights

Multithreaded weighted Minkowski and spherical K-means via Lloyd's algorithm over sparse representation of data given cluster size (weight) constraints.

  Xw = rep(1, length(X)),
  clusterWeightUB = rep(length(X) + 1, length(centroid)),
  minkP = 2,
  convergenceTail = 5L,
  tailConvergedRelaErr = 1e-04,
  maxIter = 100L,
  maxCore = 7L,
  paraSortInplaceMerge = FALSE,
  verbose = TRUE

A list of size N, the number of observations. X[[i]] is a 2-column data frame. The 1st column is a sorted integer vector of the indexes of nonzero dimensions. Values in these dimensions are stored in the 2nd column as a numeric vector. Internally the algorithm sets a 32-bit int pointer to the beginning of the 1st column and a 64-bit double pointer to the beginning of the 2nd column, so it is critical that the input has the correct type.


An integer. The dimensionality of X. d MUST be no less than the maximum of all index vectors in X.


A list of size K, the number of clusters. centroid[[i]] can be in dense or sparse representation. If dense, a numeric vector of size d. If sparse, a 2-column data frame in the same sense as X[[i]].


A numeric vector of size N. Xw[i] is the weight on observation X[[i]]. Users should normalize Xw such that the elements sum up to N. Default uniform weights for all observations.


An integer vector of size K. The upper bound of weight for each cluster. If Xw are all 1s, clusterWeightUB upper-bound cluster sizes.


A numeric value or a character string. If numeric, minkP is the power p in the definition of Minkowski distance. If character string, "max" implies Chebyshev distance, "cosine" implies cosine dissimilarity. Default 2.


An integer. The algorithm may end up with "cyclical convergence" due to the size / weight constraints, that is, every few iterations produce the same clustering. If the cost (total in-cluster distance) of each of the last convergenceTail iterations has a relative difference less than tailConvergedRelaErr against the cost from the prior iteration, the program stops.


A numeric value, explained in convergenceTail.


An integer. The maximal number of iterations. Default 100.


An integer. The maximal number of threads to invoke. No more than the total number of logical processors on machine. Default 7.


A boolean value. TRUE let the algorithm call std::inplace_merge() (std refers to C++ STL namespace) instead of std::merge() for parallel-sorting the observation-centroid distances. In-place merge is slower but requires no extra memory.


A boolean value. TRUE prints progress.


See details for KMconstrained() and KM()


A list of size K, the number of clusters. Each element is a list of 3 vectors:


a numeric vector of size d.


an integer vector of indexes of elements grouped to centroid.


a numeric vector of the same size of clusterMember. The ith element is the Minkowski distance or cosine dissimilarity from centroid to the clusterMember[i]th observation in X.

Empty clusterMember implies empty cluster.

  • KMconstrainedSparse
N = 5000L # Number of points.
d = 500L # Dimensionality.
K = 50L # Number of clusters.

# Create a data matrix, about 95% of which are zeros.
dat = matrix(unlist(lapply(1L : N, function(x)
  tmp = numeric(d)
  # Nonzero entries.
  Nnz = as.integer(max(1, d * runif(1, 0, 0.05)))
  tmp[sample(d, Nnz)] = runif(Nnz) + rnorm(Nnz)
})), nrow = d); gc()

# Convert to sparse representation.
# GMKMcharlie::d2s() is equivalent.
sparsedat = apply(dat, 2, function(x)
  nonz = which(x != 0)
  list(nonz, x[nonz])
}); gc()

centroidInd = sample(length(sparsedat), K)

# Test speed using sparse representation.
sparseCentroid = sparsedat[centroidInd]
# Size upper bounds vary in [N / K * 1.5, N / K * 2]
sizeConstraints = as.integer(round(runif(K, N / K * 1.5, N / K * 2)))
system.time({sparseRst = GMKMcharlie::KMconstrainedSparse(
  X = sparsedat, d = d, centroid = sparseCentroid,
  clusterWeightUB = sizeConstraints,
  tailConvergedRelaErr = 1e-6,
  maxIter = 100, minkP = 2, maxCore = 2, verbose = TRUE)})
# }
Documentation reproduced from package GMKMcharlie, version 1.0.3, License: GPL-3

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