I am running a mixed type data cluster analysis in R and I am trying to interpret the Silhouette Plot. For whatever reason, it is telling me that more clusters is ideal for analysis. Why could this be? I am using a sample of 10k with 6 variables (4 of which are categorical). enter image description here

  • $\begingroup$ Your Silhouette values are very low. Actually, the plot tells that you have no clusters. Range between .17 and .22 is so narrow: your line approaches straight line. Smooth line of any clustering criterion, even if it is not horizontal, should be interpreted as "no clear clusters". $\endgroup$ – ttnphns Dec 30 '17 at 9:51


This answer has been completely revised, largely in reaction to a useful comment by @Anony-Mousse in his answer. He says, "categorical data frequently does not contain clusters". I do not want to put words in his mouth, but I understand this to mean "does not contain meaningful clusters". This is to amplify that comment in the context of the question.

What I think you are doing is using Gower distance on your data and then applying some clustering algorithm. Finding the number of clusters that maximizes the average silhouette is consistent with the advice given on the Wikipedia page Determining the number of clusters in a data set.

Let me go through an example of that using just four binary categorical variables, ignoring your continuous variables. I generate some data, cluster the data using PAM on Gower distance and various values for the number of clusters. I compute the silhouette and plot the results, obtaining a graph not dissimilar from yours. Spoiler alert! The process produces misleading results.


set.seed(2018)              # Happy New Year!
c1 = factor(sample(2, 1000, replace=TRUE))
c2 = factor(sample(2, 1000, replace=TRUE))
c3 = factor(sample(2, 1000, replace=TRUE))
c4 = factor(sample(2, 1000, replace=TRUE))
Cat4 = data.frame(c1,c2,c3,c4)

DM = daisy(Cat4)
SIL = sapply(2:20, function(i) {
    mean(silhouette(pam(DM, i), DM)[,3]) })
plot(c(0,SIL), type="b")

Plot of Silhouette values

I set the random seed to get a fully reproducible result, but I suggest running this a few times without the setting the seed to see that you (almost) always get a graph that peaks at 16 clusters. That must be the right number of clusters, right? No way! Notice that I generated the data at random. This is what uniform random data looks like. So why does the "silhouette method" give a clear answer of 16 clusters?

Let's look at the distance matrix.

as.matrix(DM)[1:6, 1:6]
     1    2    3    4    5    6
1 0.00 0.25 0.75 0.75 0.75 0.25
2 0.25 0.00 0.50 0.50 0.50 0.50
3 0.75 0.50 0.00 0.00 0.00 0.50
4 0.75 0.50 0.00 0.00 0.00 0.50
5 0.75 0.50 0.00 0.00 0.00 0.50
6 0.25 0.50 0.50 0.50 0.50 0.00

     0   0.25    0.5   0.75      1 
 31044 124449 188147 124462  31398 

Given two points, they can disagree in 0,1,2,3 or 4 coordinates. Gower distance normalizes this to distances of 0, ¼, ½, ¾ or 1. These are the only possible distance values. With 4 binary categorical variables, there are 16 possible vector values. If all points with the same vector of four values are in the same cluster, then they all have distance zero from each other and distance at least 0.25 from any other point. This will make the silhouette a "perfect" 1 with 16 clusters. But again, this example is just random data. These clusters are not meaningful. For every point, the points at distance 0.25 are in another cluster even though no smaller distance between unequal points is possible. The discretization of distances encourages every distinct value to be treated as its own cluster.

I think this is what you are seeing in your graph. Of course, I am not looking at your categorical variables and I am ignoring any effect of the continuous ones. I don't even know if your categorical variables are binary or could have multiple values. But here is something worth trying. Compute the number of possible combinations of your categorical variables. If your variables are binary you should get 16. If they are not not binary, use

MaxComb = length(levels(c1)) * length(levels(c2)) *
        length(levels(c3)) * length(levels(c4))

Use whatever clustering method you have been using with MaxComb clusters. Then for each categorical variable, make a table of the cluster number vs the value of the categorical variable. Here is what happens with one variable in my example.

P16 = pam(DM, 16)
table(P16$clustering, c1)
      1  2
  1  53  0
  2  69  0
  3  71  0
  4  59  0
  5   0 64
  6   0 62
  7   0 60
  8  55  0
  9   0 52
  10  0 59
  11  0 68
  12  0 65
  13 58  0
  14 68  0
  15 65  0
  16  0 72

Notice that within each cluster, the categorical variable takes on only one value. This works with all four categorical variables. The clusters are determined by the four variables. Even including your continuous variables, does that happen with your data? If so, the discretized categorical variables are dominating the clustering process and this separation may not mean much. When you include the continuous variables, the distances won't be strictly discretized, but may fall into groups based only on the categorical variables.

Some people seem to get clustering results they are satisfied with using Gower distance. See for example K-Means clustering for mixed numeric and categorical data but I think that this discretization of distances means that interpreting the results requires a lot of caution.

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  • $\begingroup$ 4 of the variables are categorical, but two of them are not. A single continuous variable can encode an arbitrary number of clusters. The number and type of variables available for analysis does not suggest how many clusters may exist in the data. $\endgroup$ – David Marx Dec 30 '17 at 0:48
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    $\begingroup$ I agree that one variable can encode an arbitrary number of clusters. What I am saying is that the categorical variables make it likely that there are at least 16 clusters - explaining the OP's graph. Note that with Gower distance, the other variables will be scaled so that they cannot greatly increase the distance between points and negate the separation given by the categorical variables. $\endgroup$ – G5W Dec 30 '17 at 0:54
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    $\begingroup$ Anony-Mousse is skeptical about clusters in categorical data at all (I wouldn't hurry to agree in that respect with him). See e.g. his 1st comment to this Q: stats.stackexchange.com/q/218604/3277. $\endgroup$ – ttnphns Dec 30 '17 at 20:50
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    $\begingroup$ I haven't had time to further explore this. But I believe the "conventional" notion of clusters, as evaluated by Silhouette, and as assumed by Gower's distance does not often work for categoricial data (there will, for sure, be a few cases and data sets where it makes perfect sense). I believe in many cases, a more meaningful notion is along the lines of frequent itemset mining (I.e., frequent combinations of some attributes values only). But that doesn't satisfy the perceived need of many users to divide their data into k disjoint partitions, so it will be equally unsatisfactory for them. A $\endgroup$ – Has QUIT--Anony-Mousse Dec 30 '17 at 22:40
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    $\begingroup$ "Discretization of distances" may be a key issue with using Gower's for clustering. Adding a numerical attribute may make it less obvious, but it will still exist. Look at it from this point of view: if it is a reliable clustering, it should be stable with respect to tiny "epsilon" changes in the data. But if you have just 5 attributes, the tiniest possible change due to a categoricial attribute is 20% of the maximum dissimilarity. So if we want a "stable" clustering result, we would likely need to base it on thousands of (redundant) attributes. $\endgroup$ – Has QUIT--Anony-Mousse Dec 30 '17 at 22:47

Silhouette values less than 0.4 are bad.

So none of your clusterings worked well. The clusters are not reliable. You probably need to use a different algorithm, metric, or your data might not contain any clusters at all (categoricial data frequently does not contain clusters).

P.S. Silhouette plot commonly refers to a plot showing the Silhouette of each point in just one data set, not parameter k vs. average Silhouette like you used for plotting.

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  • $\begingroup$ Completely agree with the first. As for terminology, it is ok to call the OP's plot (average) Silhouette criterion plot, while what you refer to is called Silhouette Width plot. $\endgroup$ – ttnphns Dec 30 '17 at 9:55

There's no way we can reasonably answer this question, especially without context into the problem you are working on. The number of clusters that naturally occur in your data doesn't have to have any correspondence to the number of variables you're modeling against. Consider the following example:

n_classes <- 10
n_feats <- 2
n_obs <- 100

y <- sample(n_classes, n_obs, replace=TRUE)
X <- sapply(1:n_feats, function(i) y + rnorm(n_obs))/n_classes

plot(X, col=y)

I chose n_feats <- 2 here just to give you something easy to plot, but as long as n_classes < n_obs, you can pick whatever values you want for those three parameters. My point here is that as soon as you introduce a single continuous variable, there is no limit to the number of classes your available features could represent because any continuous interval ([0,1] in the example above) can be divided into infinite segments of arbitrary length.

The number of classes your available features are capable of representing has absolutely no bearing on the number of classes that it might be appropriate to use when modeling your data. Silhouette is just a heuristic: if your subject matter knowledge about the problem suggests the silhouette plot is giving you bad advice, go find a different heuristic to direct your choice of the number of clusters.

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