K-Medoids and K-Means are two popular methods of partitional clustering. The consensus is that K-Medoids is better at clustering data when there are outliers (source). This is because it chooses data points as cluster centers (and uses Manhattan distance), whereas K-Means chooses any center that minimizes the sum of squares, so it is more influenced by outliers.

This makes sense, however when I use these methods to do a simple test on made up data, it does not suggest that using Medoids is better at dealing with outliers, in fact it is sometimes worse. My question is: Where in the following test have I gone wrong? Perhaps I have some fundamental misunderstanding about these methods.


First, some made up data (named 'comp') which makes 3 obvious clusters

x <- c(2, 3, 2.4, 1.9, 1.6, 2.3, 1.8, 5, 6, 5, 5.8, 6.1, 5.5, 7.2, 7.5, 8, 7.2, 7.8, 7.3, 6.4)
y <- c(3, 2, 3.1, 2.6, 2.7, 2.9, 2.5, 7, 7, 6.5, 6.4, 6.9, 6.5, 7.5, 7.25, 7, 7.8, 7.5, 8.1, 7)

data.frame(x,y) -> comp

ggplot(comp, aes(x, y)) + geom_point(alpha=.5, size=3, pch = 16)

enter image description here

It is clustered with the package 'vegclust', which can do both K-Means and K-Medoids.

k <- vegclust(x=comp, mobileCenters=3, method="KM", nstart=100, iter.max=1000) #K-Means
k <- vegclust(x=comp, mobileCenters=3, method="KMdd", nstart=100, iter.max=1000) #K-Medoids

When making a scatterplot, both K-Means and K-Medoids pick up the 3 obvious clusters.

color <- k$memb[,1]+k$memb[,2]*2+k$memb[,3]*3 # Making the different clusters have different colors

# K-Means scatterplot
ggplot(comp, aes(x, y)) + geom_point(alpha=.5, color=color, pch = 16, size=3)

# K-Medoids scatterplot
ggplot(comp, aes(x, y)) + geom_point(alpha=.5, color=color, size=3, pch = 16)

See *figure 2* in the link

Now an outlier is added:

comp[21,1] <- 3
comp[21,2] <- 7.5

This outlier shifts the center of the blue cluster to the left of the graph.

As a result, when using K-Medoids on the new data, the right-most point of the blue cluster is broken off and joins the red cluster.

See *figure 3* in the link

K-Medoids finds the correct clusters 0% of the time. Interestingly, K-means actually generates better (more intuitive) clusters with the new data about 25% of the time depending on the random initial cluster centers (you may have to run several times to get the correct clustering).

See *figure 4* in the link

As you can see from this example, K-Means was actually better at handling outliers than K-Medoids (same data, same package etc.). While K-Means wasn't always correct, K-Medoids was never correct. If a researcher studied this data and ran both K-Means and K-Medoids several times, then chose the best result from each, K-Means would have been better at dealing with the outlier.

Can someone explain these results? Have I done something wrong in my test or misunderstood how these methods work?

  • $\begingroup$ This is a really interesting question, and I appreciate the amount of work you've put into studying it. I know it's been 3 years since you posted this, but have you found a suitable answer? If not, I'd like to open a bounty on this problem with my own reputation. $\endgroup$ – user3002473 Nov 22 '18 at 20:10

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.