Clustering of unsupervised data using SID (Mantero and Ishwaran, 2020). Also implements the artificial two-class approach of Breiman (2003).

  method = "sid",
  k = NULL,
  reduce = TRUE,
  ntree = 500,
  ntree.reduce = function(p, vtry){100 * p / vtry},
  fast = FALSE, = NULL,
  use.sid.for.x = TRUE,
  x.only = NULL, y.only = NULL,
  dist.sharpen = TRUE, ...)



Data frame containing the unsupervised data.


The method used for unsupervised clustering. Default is "sid" which implements sidClustering using SID (Staggered Interaction Data; see Mantero and Ishwaran, 2020). A second approach transforms the unsupervised learning problem into a two-class supervised problem (Breiman, 2003) using artificial data created using mode 1 or mode 2 of Shi-Horvath (2006). This approach is specified by any one of the following: "sh", "SH", "sh1", "SH1" for mode 1, or "sh2", "SH2" for mode 2. Finally, a third approach is a plain vanilla method where the data are used both as features and response with splitting implemented using the multivariate splitting rule. This is faster than sidClustering but potentially less accurate. This method is specified using "unsupv".


Requested number of clusters. Can be a number or a vector. If a fixed number, returns a vector recording clustering of data. If a vector, returns a matrix of clusters with each column recording the clustering of the data for the specified number of clusters.


Apply dimension reduction? Uses holdout vimp which is computationally intensive and conservative but has good false discovery properties. Only applies to method="sid".


Number of trees used by sidClustering in the main analysis.


Number of trees used by holdout vimp in the reduction step. See holdout.vimp for details.


Use fast random forests, rfsrcFast, in place of rfsrc? Improves speed but is less accurate.

Features not to be "sid-ified": meaning that these features are to be included in the final design matrix without SID processing. Can be either a data frame (should not overlap with data), or a character vector containing the names of features from the original data that the user wishes to protect from sidification. Applies only to method="sid".


If FALSE, reverses features and outcomes in the SID analysis. Thus, staggered interactions are used for the outcomes rather than staggered features. This is much slower and is generally much less effective. This option is only retained for legacy reasons. Applies only to method="sid".


Use only these variables for the features. Applies only to method="unsupv".


Use only these variables for the multivariate outcomes. Applies only to method="unsupv".


By default, distance sharpening is requested, which applies Euclidean distance to the random forest distance matrix to sharpen it. Because of this, the returned distance matrix will not have values between 0 and 1 (as for random forests distance) when this option is in effect. Distance sharpening is a useful, but slow step. Set this option to FALSE to improve computational times, however clustering performance will not be as good. Applies only when method="sid" or method="unsupv".


Further arguments to be passed to the rfsrc function to specify random forest parameters.


Given an unsupervised data set, random forests is used to calculate the distance between all pairs of data points. The distance matrix is used for clustering the unsupervised data where the default is to use hierarchcial clustering. Users can apply other clustering procedures to the distance matrix. See the examples below.

The default method, method="sid", implements sidClustering. The sidClustering algorithm begins by first creating an enhanced SID (Staggered Interaction Data) feature space by sidification of the original variables. Sidification results in: (a) SID main features which are the original features that have been shifted in order to make them strictly positive and staggered so all of their ranges are mutually exclusive; and (b) SID interaction features which are the multiplicative interactions formed between every pair of SID main features. Multivariate random forests are then trained to predict the main SID features using the interaction SID features as predictors. The basic premise is if features are informative for clusters, then they will vary over the space in a systematic manner, and because each SID interaction feature is uniquely determined by the original feature values used to form the interaction, cuts along the SID interaction feature will be able to find the regions where the informative features vary by cluster, thereby not only reducing impurity, but also separating the clusters which are dependent on those features. See Mantero and Ishwaran (2020) for details.

Because SID uses all pairwise interactions, the dimension of the feature space is proportional to the square of the number of original features (or even larger if factors are present). Thus it is helpful to reduce the feature space. The reduction step (applied by default) utilizes holdout VIMP to accomplish this. It is recommended this step be skipped only when the dimension is reasonably small. For very large data sets this step may be slow.

A second approach (Breiman, 2003; Shi-Horvath, 2006) transforms the unsupervised learning problem into a two class supervised problem. The first class consists of the original observations, while the second class is artificially created. The idea is that in detecting the first class out of the second, the model will generate the random forest proximity between observations of which those for the original class can be extracted and used for clustering. Note in this approach the distance matrix is defined to equal one minus the proximity. This is unlike the distance matrix from SID which is not proximity based. Artificial data is created using "mode 1" or "mode 2" of Shi-Horvath (2006). Mode 1 randomly draws from each set of observed features. Mode 2 draws a uniform value from the minimum and maximum values of a feature.

Mantero and Ishwaran (2020) studied both methods and found SID worked well in all settings, whereas Breiman/Shi-Horvath was sensitive to cluster structure. Performance was poor when clusters were hidden in lower dimensional subspaces; for example when interactions were present or in mixed variable settings (factors/continuous variables). See the V-shaped cluster example below. Generally Shi-Horvath mode 1 outperforms mode 2.

Finally, a third method where the data is used for both the features and outcome is implemented using method="unsupv". Tree nodes are split using the multivariate splitting rule. This is much faster than sidClustering but potentially less accurate.

There is an internal function sid.perf.metric for evaluating performance of the procedures using a normalized measure score. Smaller values indicate better performance. See Mantero and Ishwaran (2020) for details.


A list with the following components:


Vector or matrix containing indices mapping data points to their clusters.


Random forest object (either a multivariate forest or RF-C object).


Distance matrix.


The "sid-ified" data. Conveniently broken up into separate values for outcomes and features used by the multivariate forest.


Hemant Ishwaran and Udaya B. Kogalur


Breiman, L. (2003). Manual on setting up, using and understanding random forest, V4.0. University of California Berkeley, Statistics Department, Berkeley.

Mantero A. and Ishwaran H. (2021). Unsupervised random forests. Statistical Analysis and Data Mining, 14(2):144-167.

Shi, T. and Horvath, S. (2006). Unsupervised learning with random forest predictors. Journal of Computational and Graphical Statistics, 15(1):118-138.

See also


# \donttest{
## ------------------------------------------------------------
## mtcars example
## ------------------------------------------------------------

## default SID method 
o1 <- sidClustering(mtcars)
print(split(mtcars, o1$cl[, 10]))

## using artifical class approach <- sidClustering(mtcars, method = "sh")
print(split(mtcars,$cl[, 10]))

## ------------------------------------------------------------
## glass data set
## ------------------------------------------------------------

if (library("mlbench", logical.return = TRUE)) {

  ## this is a supervised problem, so we first strip the class label
  glass <- Glass
  y <- Glass$Type
  glass$Type <- NULL

  ## default SID call 
  o2 <- sidClustering(glass, k = 6)
  print(table(y, o2$cl))
  print(sid.perf.metric(y, o2$cl))

  ## compare with Shi-Horvath mode 1 <- sidClustering(glass, method = "sh1", k = 6)

  ## plain-vanilla unsupervised analysis
  o2.un <- sidClustering(glass, method = "unsupv", k = 6)
  print(table(y, o2.un$cl))
  print(sid.perf.metric(y, o2.un$cl))


## ------------------------------------------------------------
## vowel data set
## ------------------------------------------------------------

if (library("mlbench", logical.return = TRUE) &&
    library("cluster", logical.return = TRUE)) {

  ## strip the class label
  vowel <- Vowel
  y <- Vowel$Class
  vowel$Class <- NULL

  ## SID 
  o3 <- sidClustering(vowel, k = 11)
  print(table(y, o3$cl))
  print(sid.perf.metric(y, o3$cl))

  ## compare to Shi-Horvath which performs poorly in
  ## mixed variable settings <- sidClustering(vowel, method = "sh1", k = 11)

  ## Shi-Horvath improves with PAM clustering
  ## but still not as good as SID <- pam($dist, k = 11)$clustering

  ## plain-vanilla unsupervised analysis
  o3.un <- sidClustering(vowel, method = "unsupv", k = 11)
  print(table(y, o3.un$cl))
  print(sid.perf.metric(y, o3.un$cl))


## ------------------------------------------------------------
##  two-d V-shaped cluster (y=x, y=-x) sitting in 12-dimensions 
##  illustrates superiority of SID to Breiman/Shi-Horvath
## ------------------------------------------------------------

p <- 10
m <- 250
n <- 2 * m
std <- .2

x <- runif(n, 0, 1)
noise <- matrix(runif(n * p, 0, 1), n)
y <- rep(NA, n)
y[1:m] <- x[1:m] + rnorm(m, sd = std)
y[(m+1):n] <- -x[(m+1):n] + rnorm(m, sd = std)
vclus <- data.frame(clus = c(rep(1, m), rep(2,m)), x = x, y = y, noise)

## SID
o4 <- sidClustering(vclus[, -1], k = 2)
print(table(vclus[, 1], o4$cl))
print(sid.perf.metric(vclus[, 1], o4$cl))

## Shi-Horvath <- sidClustering(vclus[, -1], method = "sh1", k = 2)
print(table(vclus[, 1],$cl))
print(sid.perf.metric(vclus[, 1],$cl))

## plain-vanilla unsupervised analysis
o4.un <- sidClustering(vclus[, -1], method = "unsupv", k = 2)
print(table(vclus[, 1], o4.un$cl))
print(sid.perf.metric(vclus[, 1], o4.un$cl))

## ------------------------------------------------------------
##  two-d V-shaped cluster using fast random forests
## ------------------------------------------------------------

o5 <- sidClustering(vclus[, -1], k = 2, fast = TRUE)
print(table(vclus[, 1], o5$cl))
print(sid.perf.metric(vclus[, 1], o5$cl))

# }