Author: Jiandong Wang, Sajal Kumar, and Joe Song

# Examples of joint grid discretization

#### Jiandong Wang, Sajal Kumar, and Joe Song

#### Updated: 2025-12-11; 2022-01-27; 2022-01-17; 2020-09-13; 2020-08-01; Created: 2020-03-17

## Example 1. Nonlinear curves using kmeans+silhouette and Ball+BIC clustering with a fixed number of clusters

    require(GridOnClusters)
    #> Loading required package: GridOnClusters
    x = rnorm(500)
    y = sin(x)+rnorm(500, sd = 0)
    z = cos(x)+rnorm(500, sd = 0)
    data = cbind(x, y, z)
    ks = 2:20

    res = discretize.jointly(data, k=ks, cluster_method = "kmeans+silhouette",
                             grid_method = "Sort+split")
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "kmeans+silhouette",
      grid_method = "DP exact likelihood")
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "DP approx likelihood 1-way")
    plot(res)

Example 1. Nonlinear curves using kmeans+silhouette and Ball+BIC clustering with a fixed number of clusters.

## Example 2. Nonlinear curves and patterns using kmeans+silhouette and Ball+BIC clustering with a range for the number of clusters

    x = rnorm(100)
    y = log1p(abs(x))
    z = ifelse(x >= -0.5 & x <= 0.5, 0, 1) + rnorm(100, 0, 0.1)
    data = cbind(x, y, z)
    ks = c(2:5)

    #res = discretize.jointly(data, k=ks, cluster_method = "Ball+BIC",
    #                         grid_method = "Sort+split", min_level = 1)
    #plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "kmeans+silhouette",
      grid_method = "Sort+split", min_level = 1)

    plot(res)

    #res = discretize.jointly(data, k=ks, cluster_method = "kmeans+silhouette",
    #                         grid_method = "DP exact likelihood", min_level = 1)
    #plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "DP exact likelihood", min_level = 1)
    plot(res)

Example 2. Using a range for the number of kmeans+silhouette and Ball+BIC clusters

## Example 3. Using the partition around medoids clustering method

    # using a clustering method other than kmeans+silhouette
    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 = cluster::pam(x=data, diss = FALSE, metric = "euclidean", k = 4)$clustering

    res = discretize.jointly(
      data, cluster_label = cluster_label,
      grid_method = "Sort+split", min_level = 1)
    res = discretize.jointly(
      data, cluster_label = cluster_label,
      grid_method = "DP exact likelihood", min_level = 1)
    plot(res, main="Original data\nPAM clustering",
         main.table="Discretized data\nPAM & Sort+split")

Example 3. Using the partition around medoids clustering method.

## Example 4 Random patterns using kmeans+silhouette and Ball+BIC clustering with a range for the number of clusters.

    ks = 2:20
    n = 40*10
    sd = 60*4

    x=rnorm(2*n, sd=sd)
    y=rnorm(2*n, sd=sd)
    x=c(x,rnorm(2*n, sd=sd/3))
    y=c(y,rnorm(2*n, sd=sd/3)+200)

    data = cbind(x, y)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "Sort+split", min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "kmeans+silhouette",
      grid_method = "Sort+split", min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "kmeans+silhouette",
      grid_method = "DP approx likelihood 1-way", min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "DP approx likelihood 1-way", min_level = 1)
    plot(res)

Example 4. Random patterns using kmeans+silhouette and Ball+BIC clustering with a range.

## Example 5. Multi-cluster random patterns using kmeans+silhouette and Ball+BIC clustering with a range for the number of clusters.

    n <- 50*8
    ks <- 2:20

    X.C1 <- matrix(
       c(rnorm(n, 5, sd=2),
         rnorm(n, 0, sd=40)),
       ncol = 2, byrow = FALSE
    )
    X.C2 <- matrix(
       c(rnorm(n, 70, sd=1),
         rnorm(n, 0, sd=1)),
       ncol = 2, byrow = FALSE
    )

    X.C3 <- matrix(
       c(rnorm(n, 150, sd=30),
         rnorm(n, 0, sd=30)),
       ncol = 2, byrow = FALSE
    )

    data = rbind(X.C1, X.C3)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "Sort+split", min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "kmeans+silhouette",
      grid_method = "Sort+split", min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "kmeans+silhouette",
      grid_method = "DP approx likelihood 1-way",
      min_level = 1, cutoff = 1)
    plot(res)
    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "DP approx likelihood 1-way",
      min_level = 1)
    plot(res)

Example 5. Multi-cluster random patterns using kmeans+silhouette and Ball+BIC clustering with a range.

## Example 6. Exclusive or.

    n <- 100
    ks <- 2:10

    label = c(rep(1, n), rep(2,n), rep(3,n), rep(4,n))

    X1 = c(rnorm(n, 0, sd=2),
         rnorm(n, 0, sd=2),
         rnorm(n, 10, sd=2),
         rnorm(n, 10, sd=2))

    X2 = c(rnorm(n, 10, sd=2),
         rnorm(n, 0, sd=2),
         rnorm(n, 10, sd=2),
         rnorm(n, 0, sd=2))

    X3 = c(rnorm(4*n, 20, sd=10))

    X4 = c(rnorm(4*n, 3, sd=20))

    data = cbind(X1, X2, X3, X4)

    #res = discretize.jointly(data, k=ks, cluster_method = "kmeans+silhouette",
    #                         grid_method = "DP approx likelihood", min_level = 1)
    #plot(res)
    #
    #res = discretize.jointly(data, k=ks, cluster_method = "kmeans+silhouette",
    #                         grid_method = "DP Compressed majority", min_level = 1)
    #plot(res)

    #res = discretize.jointly(data, k=ks, cluster_method = "Ball+BIC",
    #                         grid_method = "DP exact likelihood", min_level = 1)
    #plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "DP approx likelihood 1-way",
      min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_label = label,
      grid_method = "DP approx likelihood 1-way",
      min_level = 1)
    plot(res)

    #res = discretize.jointly(data, k=ks, cluster_label = label,
    #                         grid_method = "Sort+split", min_level = 1)
    #plot(res)
    #
    #res = discretize.jointly(data, k=ks, cluster_method = "kmeans+silhouette",
    #                         grid_method = "Sort+split", min_level = 1)
    #plot(res)

Example 6. Exclusive or. Dim1 ⊕ Dim2, Dim3 and Dim4 are random

##Example 8. The testing dataset provided by Ruby, most of the points overlap with each other in this dataset

##Example 7. Three well separated rounds.

    n <- 20
    ks <- 2:10

    label = c(rep(1, n), rep(2,5*n), rep(3, 5*n))

    X1 = c(rnorm(n, 0, sd=1), rnorm(5*n, 15, sd=3), rnorm(5*n, 35, sd=3))
    X2 = c(rnorm(n, 0, sd=1), rnorm(5*n, 0, sd=3), rnorm(5*n, 0, sd=3))

    data = cbind(X1, X2)

    res = discretize.jointly(
      data, cluster_label = label,
      grid_method = "DP exact likelihood", min_level = 1)
    plot(res)
    res = discretize.jointly(
      data,  cluster_label = label,
      grid_method = "DP approx likelihood 1-way",
      min_level = 1)
    plot(res)

    res.entropy = discretize.jointly(
      data,  cluster_label = label,
      grid_method = "DP exact likelihood", min_level = 1, entropy = TRUE)
    plot(res.entropy)

Example 7. Three rounds well seperated on x axis

##Example 8. Four sphers with different centers and radius

    n <- 200
    ks <- 2:10

    label = c(rep(1, n), rep(2,5*n), rep(3,n), rep(4,3*n))

    X1 = c(rnorm(n, 0, sd=3), rnorm(5*n, 15, sd=3), rnorm(n, 5, sd=2), rnorm(3*n, 15, sd=4))

    X2 = c(rnorm(n, 0, sd=4), rnorm(5*n, 15, sd=3), rnorm(n, 10, sd=2), rnorm(3*n, 0, sd=4))

    data = cbind(X1, X2)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "DP exact likelihood", min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "DP approx likelihood 1-way",
      min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "Ball+BIC",
      grid_method = "DP exact likelihood", min_level = 1, entropy = TRUE)
    plot(res)

Example 8. Four sphers with different centers and radius

##Example 9. A small dense spher overlaped by a big scatter spher, to test whether the method can seperate two sphers or not.

    n <- 200
    ks <- 2:10

    label = c(rep(1, n), rep(2,5*n))

    X1 = c(rnorm(n, 0, sd=1), rnorm(5*n, 6, sd=3))
    X2 = c(rnorm(n, 0, sd=1), rnorm(5*n, 0, sd=3))

    data = cbind(X1, X2)

    res = discretize.jointly(
      data, k=ks, cluster_label = label,
      grid_method = "DP exact likelihood", min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks,  cluster_label = label,
      grid_method = "DP approx likelihood 1-way",
      min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks, cluster_method = "mclust_VII",
      grid_method = "DP approx likelihood 1-way", min_level = 1)
    plot(res)

    res = discretize.jointly(
      data, k=ks,  cluster_method = "Ball+BIC",
      grid_method = "DP approx likelihood 1-way",
      min_level = 1)
    plot(res)

    res.entropy = discretize.jointly(
      data, k=ks,  cluster_label = label,
      grid_method = "DP exact likelihood", min_level = 1, entropy = TRUE)
    plot(res.entropy)

Example 9. A small dense spher overlaped by a big scatter spher, to test whether the method can seperate two sphers or not..