Package 'GridOnClusters'

Discretize Multivariate Continuous Data by Cluster-Preserving Grid

Description

Discretize multivariate continuous data using a grid that captures the joint distribution via preserving clusters in original data

Usage

discretize.jointly(
  data,
  k = c(2:10),
  min_level = 1,
  max_level = 100,
  cluster_method = c("Ball+BIC", "kmeans+silhouette", "PAM"),
  grid_method = c("DP approx likelihood 1-way", "DP approx likelihood 2-way",
    "DP exact likelihood", "DP Compressed majority", "DP", "Sort+split",
    "MultiChannel.WUC"),
  eval_method = c("ARI", "purity", "upsllion", "CAIR"),
  cluster_label = NULL,
  cutoff = 0,
  entropy = FALSE,
  noise = FALSE,
  dim_reduction = FALSE,
  scale = FALSE,
  variance = 0.5,
  nthread = 1
)

Arguments

data	a numeric matrix for multivariate data or a numeric vector for univariate data. In case of a matrix, columns are continuous variables; rows are observations.
k	either an integer, a integer vector, or Inf, specifying the number of clusters. The default is a vector of integers from 2 to 10. If k is a single number, data will be grouped into into exactly k clusters. If k is an integer vector, an optimal k is chosen among the integers. If k is set to Inf, an optimal k is chosen from 2 to nrow(data). If cluster_label is specified, k is ignored.
min_level	an integer or an integer vector, to specify the minimum number of levels along each dimension. If a vector of size ncol(data), then each element will be mapped 1:1 to each dimension in order. If an integer, then all dimensions will have the same minimum number of levels.
max_level	an integer or an integer vector, to specify the maximum number of levels along each dimension. It works in the same way as min_level. max_level will be set to the smaller between number of compressed zones and itself, if grid_method is a likelihood approach or "DP Compressed majority".
cluster_method	a character string to specify a clustering method to be used. Ignored if cluster_label is not NULL. We offer three build-in options: "Ball+BIC" (default) uses mclust::Mclust (modelNames = "VII" for 2-D or higher dimensions; "V" for 1-D) to cluster data and BIC score to select number of clusters. "kmeans+silhouette" uses k-means to cluster data and the average Silhouette width to select number of clusters. "PAM" uses the algorithm partition around medoids to perform clustering.
grid_method	a character string to specify a grid discretization method. Default: "DP approx likelihood 1-way". The methods can be roughly separate into three different categories: by cluster likelihood, by density, and by SSE (Sum of Squared Errors). See Details for more information.
eval_method	a character string to specify a method to evaluate quality of discretized data.
cluster_label	a vector of labels for each data point or observation. It can be class labels on the input data for supervised learning; it can also be cluster labels for unsupervised learning. If NULL (default), clustering is performed to obtain labels.
cutoff	a numeric value. A grid line is added only when the quality of the line is not smaller than cutoff. It is applicable only to grid_method "DP" or "DP Compressed majority".
entropy	a logical to chose either entropy (TRUE) or likelihood (FALSE, default).
noise	a logical to apply jitter noise to original data if TRUE. Default: FALSE. It is only applicable to cluster_method "Ball+BIC". When data contain many duplicated values, adding noise can help Mclust clustering.
dim_reduction	a logical to turn on/off dimension reduction. Default: FALSE.
scale	a logical to specify linear scaling of the variable in each dimension if TRUE. Default: FALSE.
variance	a numeric value to specify noise variance to be added to the data
nthread	an integer to specify number of CPU threads to use. Automatically adjusted if invalid or exceeding available cores.

Details

The function implements both published algorithms described in (Wang et al. 2020) and new algorithms for multivariate discretization.

The included grid discretization methods can be summarized into three categories:

• By Density

  • "Sort+split" (Wang et al. 2020) sorts clusters by mean in each dimension. It then splits consecutive pairs only if the sum of error rate of each cluster is less than or equal to 50%. It is possible that no grid line will be added in a certain dimension. The maximum number of lines is the number of clusters minus one.

• By SSE (Sum of Squared Errors)

  • "MultiChannel.WUC" splits each dimension by weighted with-in cluster sum of squared distances by Ckmeans.1d.dp::MultiChannel.WUC(). Applied in each projection on each dimension. The channel of each point is defined by its multivariate cluster label.

  • "DP" orders labels by data in each dimension and then cuts data into a maximum of max_level bins. It evaluates the quality of each cut to find a best number of bins.

  • "DP Compressed majority" orders labels by data in each dimension. It then compresses labels neighbored by the same label to avoid discretization within consecutive points of the same cluster label, so as to greatly reduce runtime of dynamic programming. Then it cuts data into a maximum of max_level bins, and it evaluates the quality of each cut by the majority of data to find a best number of bins.

• By cluster likelihood

  • "DP exact likelihood" orders labels by data in each dimension. It then compresses labels neighbored by the same label to avoid discretization within consecutive points of the same cluster label, so as to greatly reduce runtime of dynamic programming. Then cut the data into a maximum of max_level bins.

  • "DP approx likelihood 1-way" is a sped-up version of the "DP exact likelihood" method, but it is not always optimal.

  • "DP approx likelihood 2-way" is a bidirectional variant of the "DP approx likelihood" method. It performs approximate dynamic programming in both the forward and backward directions and selects the better of the two results. This approach provides additional robustness compared to the one-directional version, but optimality is not always achieved.

Value

A list that contains four items:

D	a matrix of discretized values from original data. Discretized values are one(1)-based.
grid	a list of numeric vectors of decision boundaries for each variable/dimension.
clabels	a vector of cluster labels for each observation in data.
csimilarity	a similarity score between clusters from joint discretization D and cluster labels clabels. The score is the adjusted Rand index.

Note

The default grid_method is changed from "Sort+Split" (Wang et al. 2020) (up to released package version 0.1.0.2) to "DP approx likelihood 1-way" (since version 0.3.2), representing a major improvement.

Author(s)

Jiandong Wang, Sajal Kumar, and Mingzhou Song

References

Wang J, Kumar S, Song M (2020). “Joint Grid Discretization for Biological Pattern Discovery.” In Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. ISBN 9781450379649. doi:10.1145/3388440.3412415.

See Also

See Ckmeans.1d.dp for discretizing univariate continuous data.

Examples

# using a specified k
x = rnorm(100)
y = sin(x)
z = cos(x)
data = cbind(x, y, z)
discretized_data = discretize.jointly(data, k=5)$D

# using a range of k
x = rnorm(100)
y = log1p(abs(x))
z = tan(x)
data = cbind(x, y, z)
discretized_data = discretize.jointly(data, k=c(3:10))$D

# using k = Inf
x = c()
y = c()
mns = seq(0,1200,100)
for(i in 1:12){
  x = c(x,runif(n=20, min=mns[i], max=mns[i]+20))
  y = c(y,runif(n=20, min=mns[i], max=mns[i]+20))
}
data = cbind(x, y)
discretized_data = discretize.jointly(data, k=Inf)$D

# using an alternate clustering method to k-means
library(cluster)
x = rnorm(100)
y = log1p(abs(x))
z = sin(x)
data = cbind(x, y, z)

# pre-cluster the data using partition around medoids (PAM)
cluster_label = pam(x=data, diss = FALSE, metric = "euclidean", k = 5)$clustering
discretized_data = discretize.jointly(data, cluster_label = cluster_label)$D

---

Plotting Grid on Continuous Data

Description

Plots discretized data based on grid that preserves clusters in original data.

Usage

## S3 method for class 'GridOnClusters'
plot(
  x,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  main.table = NULL,
  col,
  line_col = "black",
  cex = 1.125,
  sub = NULL,
  pch = 19,
  plot.table = TRUE,
  ...
)

Arguments

x	the result generated by discretize.jointly
xlab	the horizontal axis label
ylab	the vertical axis label
main	the title of the clustering scatter plots
main.table	the title of the discretized data plots
col	the color of data points
line_col	the color of grid lines
cex	A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default.
sub	the subtitle
pch	the symbol for points on the scatter plots
plot.table	a logical to show the contingency table. Default: TRUE.
...	additional graphical parameters

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