kmeans_smote: KMeans-SMOTE Algorithm

In themis: Extra Recipes Steps for Dealing with Unbalanced Data

KMeans-SMOTE Algorithm

Description

KMeans-SMOTE clusters the predictor space, keeps only the clusters that are dominated by the class being over-sampled, and generates new examples with SMOTE inside those clusters, giving sparser clusters more of the new points.

Usage

kmeans_smote(
  df,
  var,
  k = 2,
  over_ratio = 1,
  num_clusters = NULL,
  cluster_balance_threshold = 1,
  density_exponent = NULL,
  distance = "euclidean"
)

Arguments

df	data.frame or tibble. Must have 1 factor variable and remaining numeric variables.
var	Character, name of variable containing factor variable.
k	An integer. Number of nearest neighbor that are used to generate the new examples of the minority class.
over_ratio	A numeric value for the ratio of the minority-to-majority frequencies. The default value (1) means that all other levels are sampled up to have the same frequency as the most occurring level. A value of 0.5 would mean that the minority levels will have (at most) (approximately) half as many rows as the majority level. A named numeric vector can be used instead to give different levels different targets, for example c(a = 1, b = 0.5). The names must be levels of the outcome and the values are ratios of the majority level, exactly as in the single-number case. Levels that are not named are left untouched, as are rows with a missing outcome. Because a vector of targets is not a single value, supplying one means this argument can no longer be tuned. See vignette("ratio", package = "themis") for more details.
num_clusters	An integer, the number of clusters to split the predictor space into, or NULL (the default) to use max(2, floor(sqrt(n / 2))) where n is the number of observations.
cluster_balance_threshold	A number. A cluster is used for over-sampling a class only if it contains at least cluster_balance_threshold times as many observations of that class as of all other classes combined. Defaults to 1, meaning that the class must be at least as common as the rest of the data within the cluster. Smaller values keep more clusters.
density_exponent	A number, the exponent applied to the average pairwise distance when measuring how sparse a cluster is, or NULL (the default) to use the number of predictors.
distance	A character string specifying the distance metric used for nearest neighbor calculations, defaulting to "euclidean". The available metrics fall into three groups. "euclidean", "cosine", and "mahalanobis" use approximate nearest neighbors via the RANN package and scale well to large datasets. "squared_chord", "matusita", "hellinger", and "bhattacharyya" are probability-divergence measures that treat each row as a distribution over the predictors, so they require non-negative values. "hellinger" and "bhattacharyya" further require each row to sum to 1. All four also use the RANN package and scale well to large datasets. "manhattan", "chebyshev", "canberra", "soergel", "lorentzian", "jeffreys", "topsoe", "jensen-shannon", "jensen_difference", "taneja", and "kumar-johnson" compute an exact all-pairs distance matrix. This takes time and memory proportional to the square of the number of observations in a class, so these are best suited to smaller datasets. Everything from "canberra" onwards is a probability divergence requiring non-negative values, is provided by the philentropy package (which must be installed separately), and in the case of "jeffreys", "taneja", and "kumar-johnson" requires strictly positive values, since those divide by individual predictor values. The probability divergences are meaningful for compositional predictors such as proportions or counts normalized per observation, and are generally not appropriate for standardized predictors.

Details

KMeans-SMOTE combines k-means clustering with SMOTE to avoid generating synthetic points in regions where the minority class is not actually present. It works in three stages:

1. The predictor space of the whole data set is clustered with stats::kmeans() into num_clusters clusters.

2. Each cluster is either kept or filtered out. A cluster is kept for a given minority class if the ratio of that class's observations to all other observations in the cluster is at least cluster_balance_threshold, and if the cluster contains more than neighbors observations of that class so that interpolation is possible.

3. The synthetic points are distributed over the kept clusters according to how sparse each cluster is. The sparsity of a cluster is mean_pairwise_distance ^ density_exponent / n, where n is the number of minority observations in the cluster. Sparser clusters receive more points. Within each cluster the points are then generated by ordinary SMOTE interpolation, using only that cluster's observations as neighbors.

Filtering on cluster balance keeps synthetic points away from majority-dominated regions, and the density weighting counteracts within-class imbalance rather than only between-class imbalance.

The clustering is done once on all observations, so in a multi-class problem every minority class shares the same clusters; only the filtering and weighting are done per class. Note also that k-means always uses Euclidean distance. The distance argument affects the nearest-neighbor search used for interpolation and the sparsity calculation, not the clustering itself.

All columns used in this function must be numeric with no missing data.

Value

A data.frame or tibble, depending on type of df.

References

Douzas, G., Bacao, F., and Last, F. (2018). Improving imbalanced learning through a heuristic oversampling method based on k-means and SMOTE. Information Sciences, 465:1-20.

See Also

step_kmeans_smote() for step function of this method

Other Direct Implementations: adasyn(), bsmote(), cluster_centroids(), cnn(), enn(), instance_hardness(), ncl(), nearmiss(), oss(), rose(), smogn(), smote(), smoten(), smotenc(), svmsmote(), tomek()

Examples

circle_numeric <- circle_example[, c("x", "y", "class")]

res <- kmeans_smote(circle_numeric, var = "class")

res <- kmeans_smote(circle_numeric, var = "class", num_clusters = 10)

res <- kmeans_smote(circle_numeric, var = "class", over_ratio = 0.8)

themis documentation built on Aug. 2, 2026, 9:07 a.m.