Clustering methods R.W. Oldford Interactive data visualization An - - PowerPoint PPT Presentation

Clustering methods

R.W. Oldford

Interactive data visualization

An important advantage of data visualization is that much structure (e.g. density, groupings, regular patterns, relationships, outliers, connections across dimensions, etc.) can be easily seen visually, even though it might be more difficult to describe mathematically. Moreover, the structure observed need not have been anticipated. Interaction which allows fairly arbitrary changes to the plot via direct manipulation (e.g. mouse gestures) and also via command line (i.e. programmatically), further enables the analyst, providing quick and easy data queries, marking of structure, and when the visualizations are themselves data structures quick setting and extraction of observed information. Direct interaction amplifies the advantage of data visualization and creates a powerful tool for uncovering structure. In contrast, we might choose to have some statistical algorithm search for structure in the data. This would of course require specifying in advance how that structure might be described mathematically.

Interactive data visualization

The two approaches naturally complement one another.

◮ Structure searched for algorithmically must be precisely characterised

mathematically, and so is necesssarily determined prior to the analysis.

◮ Interactive data visualization depends on the human visual system which

has evolved over millions of years to be able to see patterns, both anticipated and not. In the hands of an experienced analyst, one complements and amplifies the

• ther; the two are worked together to give much greater insight than either

approach could alone. We have already seen the value of using both in conjunction with one another in, for example, hypothesis testing, density estimation, and smoothing.

Finding groups in data

Consider the “Old Faithful” geyser data (from the MASS package), centred and scaled as follows. library(MASS) ## ## Attaching package: 'MASS' ## The following object is masked from 'package:dplyr': ## ## select xrange <- diff(range(geyser$duration)) yrange <- diff(range(geyser$waiting)) data <- as.data.frame(scale(geyser[,c("duration", "waiting")], scale = c(xrange, yrange))) data is now centred with the average in each direction and scaled so that the ranges of the two directions are identical. We do this so that when we consider the clustering methods, they will work on data and visual distances observed on any (square) scatterplot will correspond to Euclidean distances in the space of measurememts (which any clustering method would use).

Finding groups in data

Oftentimes we observe that the data have grouped together in patterns. In a scatterplot, for example, we might notice that the observations concentrate more in some areas than they do in others.

A simple scatterplot with larger point sizes with alpha blending shows ◮ 3 regions of concentration, ◮ 3 vertical lines, ◮ and a few outliers. Contours of constant kernel density estimate show ◮ two modes at right, ◮ a higher mode at left, and ◮ a smooth continuous mathematical function Perhaps the points could be automatically grouped by using the contours?

duration waiting

0.5 0.5 1 1 1 . 5 1 . 5 2 2 2.5 2.5 2.5 3 3 3 3 . 5 3 . 5 3.5 4 4 . 5

Finding groups in data - K-means

A great many methods exist (and continue to be developed) to automatically find groups in data. These have historically been called clustering methods by data analysts and more recently sometimes called unsupervised learning methods (in the sense that we do not know the “classes” of the observations as in “supervised learning”) by many artificial intelligence researchers. One of the earliest clustering methods is “K-means”. In its simplest form, it begins with the knowledge that there are exactly K clusters to be determined. The idea is to identify K clusters, C1, . . . , CK , where every multivariate observation xi for i = 1, . . . , n in the data set appears in one and only one cluster Ck. The clusters are to be chosen so that the total within cluster spread is as small as possible. For every cluster, the total spread for that cluster is measured by the sum of squared Euclidean distances from the cluster “centroid”, namely SSEk =

• i∈Ck d2(i, k)

=

• i∈Ck ||xi − ck||2

where ck is the cluster “centroid”. Typically, the cluster average xk =

i∈Ck xi/nk

(where nk denotes the cardinality of cluster Ck) is chosen as the cluster centroid (i.e. choose ck = xk). The K clusters are chosen to minimize K

i=1 SSEk.

Algorithms typically begin with “seed” centroids c1, . . . , cK, possibly randomly chosen, then assign every observation to its nearest centroid. Each centroid is then recalculated based on the values of xi ∀ i ∈ Ck (e.g. ck = xk), and the data are reassigned to the new centroids. Repeat until there is no change in the clustering.

Finding groups in data - K-means

There are several implementations of K-means in R. Many of these are available via the base R function kmeans().

result <- kmeans(data, centers = 3) str(result) ## List of 9 ## $ cluster : Named int [1:299] 2 3 1 2 2 3 1 2 3 1 ... ## ..- attr(*, "names")= chr [1:299] "1" "2" "3" "4" ... ## $ centers : num [1:3, 1:2] 0.21 0.1392 -0.3166 -0.2655 0.0968 ... ## ..- attr(*, "dimnames")=List of 2 ## .. ..$ : chr [1:3] "1" "2" "3" ## .. ..$ : chr [1:2] "duration" "waiting" ## $ totss : num 32 ## $ withinss : num [1:3] 1.33 1.19 1.58 ## $ tot.withinss: num 4.09 ## $ betweenss : num 27.9 ## $ size : int [1:3] 101 91 107 ## $ iter : int 2 ## $ ifault : int 0 ##

• attr(*, "class")= chr "kmeans"

The cluster component identifies which of three clusters the corresponding

• beservation has been assigned.

Finding groups in data - K-means

Plotting this information in loon

library(loon) p <- l_plot(data, linkingGroup = "geyser", showScales = FALSE, showLabels = FALSE, showGuides= # Add the density contours l_layer_contourLines(p, kde2d(data$duration, data$waiting, n=100), color = "grey") ## loon layer "lines" of type lines of plot .l0.plot ## [1] "layer0" # Colour the clusters p['color'] <- result$cluster

Finding groups in data - K-means

Plotting this information in loon plot(p) which looks pretty good.

Finding groups in data - K-means

Had we selected only K = 2: which we might not completely agree with.

Finding groups in data - K-means

How about K = 4?: which, again, we might or might not agree.

Finding groups in data - K-means

How about K = 5?: which, again, we might or might not agree.

Finding groups in data - K-means

How about K = 6?: which, again, we might or might not agree.

Finding groups in data - K-means

Let’s try K = 6 again: which, is different!

Finding groups in data - K-means

Some comments and questions:

◮ K means depends on total squared Euclidean distance to the centroids ◮ K means implicitly presumes that the clusters will be "globular" or "spherical" ◮ different clusters might arise on different calls (random starting position for

centroids)

◮ how do we choose k? ◮ should we enforce a hierarchy on the clusters? ◮ with an interactive visualization, we should be able to readjust the clusters by

changing their colours

Finding groups in data - model based clustering

A related approach to K means, but one that is much more general and which comes from a different reasoning base is that of so-called “model-based clustering”. Here, the main idea is that the data xi are a sample independently and identically distributed (iid) multivariate observations from some multivariate mixture distribution. That is X1, . . . , Xn ∼ fp(x ; Θ) where fp(x ; θ) is a p-variate continuous density parameterized by some collection of parameters ˆ that can be expressed as a finite mixture of individual p-variate densities gp(): fp(x ; Θ) =

K

• k=1

αkgp(x ; θk). Here αk ≥ 0, K

k=1 αk = 1, the individual densities gp(x ; θk) are of known shape and

are identical up to differences given by their individual parameter vectors θk. Neither αk nor θk are known for any k = 1, . . . , K and must be estimated from the observations (i.e. Θ = {α1, . . . , αK, θ1, . . . , θK}). Typically gp(x, θk) are taken to be multivariate Gaussian densities of the form gp(x ; θk) = φp(x ; µk, Σk) with φp(x ; µk, Σk) = (2π)− p

2 |Σk|− p 2 e− 1 2 (x−µk)TΣ−1 k

(x−µk)

and θk = (µk, Σk).

Finding groups in data - model based clustering

We can imagine fitting the mixture model to the data for fixed K and αk > 0 ∀ k via, say, maximum likelihood. This can be accomplished by introducing latent variates zik which are 1 when xi came from the kth mixture component and zero otherwise. Suffice to say that the ziks are treated as “missing” and that an “EM” or “Expectation-Maximization” algorithm is then used to perform maximum likelihood estimation on the finite mixture. The parameters µk and Σ can also be constrained (the eigen decomposition Σk = ODσOT is useful in this) to restrict the problem further. An information criterion like the “Bayesian Information Criterion”, or “BIC”, is used to compare values of K across models. This adds a penalty to the log-likelihood that penalizes larger models. Look for models that have high information (as measured by BIC). (Note that some writers (e.g. Wikipedia) use minus this and hence minimize their

• bjective function.)

Note that by using a Gaussian model that the clusters are inherently taken to be elliptically shaped. An implementation of model-based clustering can be found in the R package mclust

Finding groups in data - model based clustering

For the geyser data

library(mclust) resultmc <- Mclust(data, G = 1:10) # G = number of mixtures to consider plot(resultmc, what = "BIC") # (VVV is the most general)

100 200 300 400 500 600 Number of components BIC 1 2 3 4 5 6 7 8 9 10 EII VII EEI VEI EVI VVI EEE EVE VEE VVE EEV VEV EVV VVV

Finding groups in data - model based clustering

For the geyser data

summary(resultmc) ## ---------------------------------------------------- ## Gaussian finite mixture model fitted by EM algorithm ## ---------------------------------------------------- ## ## Mclust VVI (diagonal, varying volume and shape) model with 4 components: ## ## log-likelihood n df BIC ICL ## 375.3983 299 19 642.4882 612.5996 ## ## Clustering table: ## 1 2 3 4 ## 90 17 98 94

We could check the agreement with K-means

table(result4$cluster, resultmc$classification) ## ## 1 2 3 4 ## 1 0 60 ## 2 0 13 0 94 ## 3 82 4 ## 4 8 0 38

Finding groups in data - model based clustering

And update the loon plot

p['color'] <- resultmc$classification which is interesting . . .

Finding groups in data - model based clustering

Plotting the mixtures

plot(resultmc, what = "classification")

−0.6 −0.4 −0.2 0.0 0.2 0.4 −0.4 −0.2 0.0 0.2 0.4 duration waiting

The model is imposing its structure on the data.

Dissimilarity based methods

There are a number of clustering methods which are based entirely on some measure of the dissimilarity δij = δ(xi, xj) between every pair (i, j) of

• bservations xi and xj (for all i = j).

Usually (but not always) the dissimilarity δij is a distance function in that it

• beys the axioms of a metric. Namely, for all vectors x, y, z, a function d(x, y)

is a metric or distance if it satisfies

• 1. d(x, y) ≥ 0
• 2. d(x, y) = 0 ⇐

⇒ x = y

• 3. d(x, y) = d(y, x)
• 4. d(x, z) ≤ d(x, y) + d(y, z)

Dissimilarity measures δ(x, y) typically obey the first three of these; some do not additionally obey the fourth (the triangle inequality). When all four hold, so that the measure is a distance, we will denote the dissimilarity by dij rather than by δij.

Example distances - some common choices

There are numerous functions that could be used, depending on the application. Some examples for x, y ∈ Rp include:

◮ Euclidean distance:

d(x, y) = (x − y)T(x − y) 1

2

◮ Minkowski distance or k-norm distance (k > 0):

d(x, y) =

• p
• j=1

|xj − yj|k

1

k

◮ City block distance (or Manhattan, or Taxicab):

d(x, y) =

p

• j=1

|xj − yj|

◮ Infinity norm, or supremum, or maximum, distance:

d(x, y) = limk→∞

p

j=1|xj − yj|k 1

k

= maxj=1,...,p|xj − yj| The dist() function in R will calculate these and others.

Example distances - x / ∈ Rp

There are are also numerous other distances/disimilarities that arise even when x, y / ∈ Rp. Some examples are

◮ Cosine similarity. Often used for measuring similarity of text documents

where each element of x contains the count of some word for that document implying x, y ∈ Rp

+. If the vector (i.e. document) length is to be ignored,

then x and y are more similar the larger is cos ∠(x, y). A distance could be d(x, y) = 1 − cos ∠(x, y)

◮ Jaccard distance. Here x and y are finite sets. The Jaccard index

J(x, y) = |x ∩ y| |x ∪ y| is a measure of how similar the two sets x and y are. A corresponding dissimilarity measure would be d(x, y) = 1 − J(x, y).

◮ Hamming distance. Here x and y are strings having the same number of

characters (the jth element of the vector is the jth character in the string). The Hamming distance is the minimum number of substitutions required to turn one string into the other. That is, it is the number of positions at which the two strings are different. (See also Levenshtein distance for strings of unequal length.)

Euclidean squared distances and the Gram matrix

Recall how point configurations x1, . . . , xn, their matrix D⋆ of squared Euclidean distances when d2

ij = ||xi − xj||2, and the Gram matrix G of inner products xi Txj

are related. Namely, D⋆ = 1gT − 2G + g1T G = −1 2 (In − P) D⋆ (In − P) where P = 1(1T1)−11T Or, since the Gram matrix is a matrix of inner products, we could begin with kernel functions K(xi, xj) as the inner-product of some transformation ψ(x) of the original xs. The kernel matrix (row and column centred) then acts as the Gram matrix. Finally, given a Gram matrix, a point configuration (and hence possibly a lower dimensional embedding) can always be determined from an eigen-decomposition of G = XXT = UDλUT (i.e. principal components). Together, these relationships open up a lot of possibilities for clustering based on distances.

Dissimilarity based methods - hierarchical clustering

Perhaps the most popular way in which distance (or dissimilariy) methods are used is to construct a hierarchical clustering of the observations based on the distances between points. Typically, the hierarchy is produced in one of two ways:

• 1. Top-down, or divisive:

Begin with all observations in a single cluster C(0)

1 , then split this into two clusters

C(1)

1

and C(1)

2

such that the distance between clusters, d(C(1)

1 , C(1) 2 ) is maximized.

Repeat this for each cluster, until every cluster consists of a single location x.

• 2. Bottom-up, or agglomerative:

Begin with each observation in its own cluster. Join the two clusters Ci and Ck that are closest to one another in that they have the smallest between cluster distance d(Ci, Cj). Repeat this, joining clusters, until only a single cluster containing all observations is constructed. In either case, the clustering method is hierarchical in that the clusters can be nested in a tree whose nodes are clusters (called a dendrogram). Note that the clustering which results will depend upon the definition of the between cluster distances.

Dissimilarity based methods - hierarchical clustering

Some common choices of distance between clusters A and B are

• 1. Single linkage

d(A, B) = min{d(x, y) : x ∈ A, y ∈ B}

• 2. Complete linkage

d(A, B) = max{d(x, y) : x ∈ A, y ∈ B}

• 3. Average linkage

d(A, B) = 1 |A| × |B|

• x∈A
• y∈B

d(x, y)

• 4. Centroid linkage

d(A, B) = ||cA − cB|| where cA and cB are the centroids of the clusters A and B, respectively. A function hclust() in R implements these and other methods. There is also a package called cluster which implements a variety of agglomerative and divisive hierarchical methods, as well as partitioning methods like K-means.

Hierarchical clustering - example

Suppose we try single-linkage clustering on the geyser data.

d <- dist(data, method = "euclidean") single <- hclust(d, method = "single") str(single) ## List of 7 ## $ merge : int [1:298, 1:2] -3 -64 -4 -5 -207 -6 -266 -23 -24 -297 ... ## $ height : num [1:298] 0 0 0 0 0 0 0 0 0 0 ... ## $ order : int [1:299] 149 61 243 58 12 62 169 265 247 187 ... ## $ labels : chr [1:299] "1" "2" "3" "4" ... ## $ method : chr "single" ## $ call : language hclust(d = d, method = "single") ## $ dist.method: chr "euclidean" ##

• attr(*, "class")= chr "hclust"

class(single) ## [1] "hclust"

Hierarchical clustering - example

The result can be displayed as a tree, or dendrogram

plot(single, cex = 0.25)

0.00 0.05 0.10 0.15 0.20

Cluster Dendrogram

hclust (*, "single") d Height

Hierarchical clustering - example

Clusters can be determined by cutting across the dendrogram at any specified height

plot(single, cex = 0.25) abline(h = c(0.04, 0.05, 0.06), col = c("red", "blue", "forestgreen"), lty = c(2,1,3))

0.00 0.05 0.10 0.15 0.20

Cluster Dendrogram

hclust (*, "single") d Height

Hierarchical clustering - example

Clusters can be determined by cutting across the dendrogram at any specified height

p['color'] <- cutree(single, h = 0.06)

Hierarchical clustering - example

Clusters can be determined by cutting across the dendrogram at any specified height

p['color'] <- cutree(single, h = 0.05)

Hierarchical clustering - example

Clusters can be determined by cutting across the dendrogram at any specified height

p['color'] <- cutree(single, h = 0.04)

Hierarchical clustering - example

Or by specifying the number of clusters

p['color'] <- cutree(single, k = 3)

Hierarchical clustering - example

Or by specifying the number of clusters

p['color'] <- cutree(single, k = 10)

Hierarchical clustering - example

Or by specifying the number of clusters

Hierarchical clustering - example

Or by specifying the number of clusters

Hierarchical clustering - example

Average-linkage:

avelinkage <- hclust(d, method = "average") plot(avelinkage, cex = 0.25) abline(h = c(0.2, 0.3), col = c("red", "blue"), lty = c(2,1))

0.0 0.1 0.2 0.3 0.4 0.5 0.6

Cluster Dendrogram

hclust (*, "average") d Height

Hierarchical clustering - example

Average-linkage:

p['color'] <- cutree(avelinkage, h = 0.3)

Hierarchical clustering - example

Average-linkage:

p['color'] <- cutree(avelinkage, h = 0.2)

Hierarchical clustering - example

Complete-linkage:

completeLinkage <- hclust(d, method = "complete") plot(completeLinkage, cex = 0.25) abline(h = c(0.25, 0.5, 0.8), col = c("red", "blue", "forestgreen"), lty = c(2,1,3))

0.0 0.2 0.4 0.6 0.8 1.0 1.2

Cluster Dendrogram

hclust (*, "complete") d Height

Hierarchical clustering - example

Complete-linkage:

p['color'] <- cutree(completeLinkage, h=0.8)

Hierarchical clustering - example

Complete-linkage:

p['color'] <- cutree(completeLinkage, h=0.5)

Hierarchical clustering - example

Complete-linkage:

p['color'] <- cutree(completeLinkage, h=0.25)

Hierarchical clustering - linkage methods

Note that depending on how clusters are joined/split, different linkage methods may favour different shaped clusters. For example, single linkage corresponds to finding the minimal spanning tree of the (complete) geometric graph of the points. It will therefore track “stringy” structure as clusters. In contrast, complete linkage will prefer compact small diameter clusters over stringy ones.

• Similarly. average linkage will have a tendency to avoid stringy clusters.

An advantage of any of these hierarchical methods over partitional methods like K-means is that they provide a nested sequence of potential clusterings.

Density based clustering - dbscan

Data clusters might also be defined to be points in those regions of the space where there is high density. This naturally leads to a cluster tree where points separate whenever high density regions separate (by a low-density region appearing between them) and, at least in principle, have no reason to favour any shaped cluster over any other. For example, the contours of our original density estimate on the geyser data actually define (by their level curves) a sequence of clusters where each set of clusters have fewer points. The resulting cluster tree would have only three branches (two binary branchings). One way of determining density in higher dimensional space is by the average (or maximum, or some other size measure) of the distances from any location to its k nearest neighbours, the smaller the value the greater the local density. The package dbscan (“Density Based Clustering of Applications with Noise”) contains the functions kNN() and kNNdist() which will calculate the distances of the k nearest neighbours to each point in the data set and return these in a matrix:

library(dbscan) kDists <- kNNdist(data, 5) head(kDists) ## 1 2 3 4 5 6 ## 0.01580251 0.06321004 0.01538462 0.01538462 0.01538462 0.01538462

Density based clustering - dbscan

A plot of these distances is produced by kNNdissplot() (to which we have added three horizontal lines).

kNNdistplot(data, 5) abline(h = c(0.025, 0.05, 0.075), col = c("red", "blue", "forestgreen"), lty = c(2,1,3))

50 100 150 200 250 300 0.00 0.05 0.10 0.15 0.20 Points (sample) sorted by distance 5−NN distance

Note that this is just a quantile plot with the x axis relabelled by the number (rather than the proportion) of distances whose value is less than or equal to the vertical value. The vertical azis records the actual nearest neighbour distances. The horizontal lines were placed after visual inspection of the graph to mark (roughly) the “knee” of the graph beyond which the nearest neighbour differences become relatively huge. This is an important paramater for dbscan(). Small nearest neighbour distances correspond to high density.

Density based clustering - dbscan

Density based clustering uses the horizontal cutoff as a parameter ǫ (argument eps) to determine a local neighbourhood for each point. Density around each point is now determined to be proportional to the number of points within the radius ǫ of each point. In addition to determining the number of clusters, dbscan() also identifies “noise” points which it does not assign to any cluster. A function to update our plot based on the data and ǫ is

updatePlot <- function(plot, data, eps){ results <- dbscan(data, eps = eps) clusters <- results$cluster plot["color"] <- clusters # Noise points plot["glyph"] <- "ccircle" plot["glyph"][clusters == 0] <- "ocircle" # Noise points in cluster 0 }

This can now be used to find density based clusters for different ǫ.

Density based clustering - dbscan

updatePlot(p, data, 0.075)

Density based clustering - dbscan

updatePlot(p, data, 0.05)

Density based clustering - dbscan

updatePlot(p, data, 0.025)

Other clustering methods

There are many other clustering methods and R packages which implement them. For example, the package cluster contains numerous functions and graphical tools for determining variations on traditional partitional, agglomerative, and divisive methods. The package kernlab contains functions clustering methods based on using kernel functions in traditional methods like K-means. kernlab also contains functions to apply “spectral clustering” methods (also in conjunction with kernels) on data. Any clustering method should be used in conjunction with an interactive data visualization system like loon to determine whether the clustering makes sense for the data in hand.