An extensive comparative study of cluster validity indices

Olatz Arbelaitz, Ibai Gurrutxagan, Javier Muguerza, Jesu´

sM.Pe´

rez, In˜

igo Perona

Department of Computer Architecture and Technology, University of the Basque Country UPV/EHU, Manuel Lardizabal 1, 20018 Donostia, Spain

article info

Article history:

Received 3 February 2012

Received in revised form

26 July 2012

Accepted 31 July 2012

Available online 9 August 2012

Keywords:

Crisp clustering

Cluster validity index

Comparative analysis

abstract

The validation of the results obtained by clustering algorithms is a fundamental part of the clustering

process. The most used approaches for cluster validation are based on internal cluster validity indices.

Although many indices have been proposed, there is no recent extensive comparative study of their

performance. In this paper we show the results of an experimental work that compares 30 cluster

validity indices in many different environments with different characteristics. These results can serve

as a guideline for selecting the most suitable index for each possible application and provide a deep

insight into the performance differences between the currently available indices.

&2012 Elsevier Ltd. All rights reserved.

1. Introduction

Clustering is an unsupervised pattern classi?cation method

that partitions the input space into clusters. The goal of a

clustering algorithm is to perform a partition where objects

within a cluster are similar and objects in different clusters are

dissimilar. Therefore, the purpose of clustering is to identify

natural structures in a dataset1–4 and it is widely used in

many ?elds such as psychology5, biology4, pattern recogni-

tion3, image processing6and computer security7.

Once a clustering algorithm has processed a dataset and

obtained a partition of the input data, a relevant question arises:

How well does the proposed partition ?t the input data? This

question is relevant for two main reasons. First, an optimal

clustering algorithm does not exist. In other words, different

algorithms—or even different con?gurations of the same algo-

rithm—produce different partitions and none of them have

proved to be the best in all situations8. Thus, in an effective

clustering process we should compute different partitions and

select the one that best ?ts the data. Secondly, many clustering

algorithms are not able to determine the number of natural

clusters in the data, and therefore they must initially be supplied

with this information—frequently known as thekparameter.

Since this information is rarely previously known, the usual

approach is to run the algorithm several times with a different

kvalue for each run. Then, all the partitions are evaluated and the

partition that best ?ts the data is selected. The process ofestimating how well a partition ?ts the structure underlying the

data is known as cluster validation1.

Cluster validation is a dif?cult task and lacks the theoretical

background other areas, such as supervised learning, have. More-

over, a recent work argues the suitability of context-dependent

evaluation methods9. Nevertheless, the authors also state that the

analysis of cluster validation techniques is a valid research question

in some contexts, such as clustering algorithms’ optimization.

Moreover, in our opinion, cluster validation tools analyzed in

context-independent evaluations will greatly contribute to context-

dependent evaluation strategies. Therefore, our work is based on a

general, context-independent cluster evaluation process.

In this context, it is usual to classify the cluster validation

techniques into three groups—internal, external and relative

validation—but the classi?cation criteria are not always clear

10,1,2,11. In any case, there is a clear distinction between valida-

tion techniques if we focus on the information available in the

validation process. Some techniques—related to external validation

—validate a partition by comparing it with the correct partition.

Other techniques—related to internal validation—validate a

partition by examining just the partitioned data. Obviously, the

former can only make sense in a controlled test environment, since

in a real application the underlying structure of the data is unknown

and, therefore, the correct partition is not available.

When the correct partition is available the usual approach is to

compare it with the partition proposed by the clustering algo-

rithm based on one of the many indices that compare data

partitions; e.g. Rand, Adjusted Rand, Jaccard, Fowlkes–Mallows,

Variation of Information12.

On the other hand, when the correct partition is not available

there are several approaches to validating a partition. One of

them is to focus on the partitioned data and to measure the

Contents lists available atSciVerse ScienceDirect

journal homepage:www.elsevier.com/locate/pr

Pattern Recognition

0031-3203/$ – see front matter;2012 Elsevier Ltd. All rights reserved.

http://dx.doi.org/10.1016/j.patcog.2012.07.021

nCorresponding author. Tel.:þ34 943015166; fax:þ34 943015590.

E-mail addresses:[email protected] (O. Arbelaitz),

[email protected] (I. Gurrutxaga), [email protected] (J. Muguerza),

[email protected] (J.M. Pe´

rez), [email protected] (I. Perona).

Pattern Recognition 46 (2013) 243–256

compactness and separation of the clusters. In this case another

type of index is used; e.g. Dunn13, Davies–Bouldin14,

Calinski–Harabasz15. Another more recent approach is the

stability based validation16,17 which is not model dependant

and does not require any assumption of compactness. This

approach does not directly validate a partition, but it relies on

the stability of the clustering algorithm over different samples of

the input dataset.

The differences of the mentioned validation approaches make it

dif?cult to compare all of them in the same framework. This work

focuses on the ?rst approach mentioned, which directly estimates

the quality of a partition by measuring the compactness and

separation of the clusters. Although there is no standard terminol-

ogy, in the remainder of this paper we will callCluster Validity Index

(CVI) to these kind of indices. For the indices that compare two

partitions we will use the termPartition Similarity Measure.

Previous works have shown that there is no single CVI that

outperforms the rest18–20. This is not surprising since the same

occurs in many other areas and this is why we usually deal with

multiple clustering algorithms, partition similarity measures, clas-

si?cation algorithms, validation techniques, etc. This makes it

obvious that researchers and practitioners need some guidelines

on which particular tool they should use in each environment.

Focusing on internal cluster validation, we can ?nd some

works that compare a set of CVIs and, therefore, these could be

used as guidelines for selecting the most suitable CVI in each

environment. However, most of these comparisons are related to

the proposal of a new CVI6,21–24 or variants of known CVIs

25,8,26 and, unfortunately, the experiments are usually per-

formed in restricted environments—few CVIs compared on few

datasets, just one clustering algorithm implied. There are few

works that do not propose a new CVI but compare some of them

in order to draw some general conclusions10,18,27,20. Surpris-

ingly, the 25 year-old paper of Milligan and Cooper20is the

work most cited as a CVI comparison reference. Certainly, to the

best of our knowledge, nobody has since published such an

extensive and systematic comparative study.

In this paper we present the results of an extensive CVI

comparison along the same lines as Milligan and Cooper20,

which is the last work that compares a set of 30 CVIs based on the

results obtained in hundreds of environments. We claim that we

have improved the referenced work in three main areas. First, we

can compare many new indices that did not exist in 1985 and

discard those that have rarely been used since. Second, we can

take advantage of the increases in computational power achieved

in recent decades to carry out a wider experiment. Finally, thanks

to the advances in communication technologies we can easily

store all the detailed results available in electronic format, so that

every reader can access them and focus on the results that are

relevant in his/her particular environment.

Moreover, our work is based on a corrected methodology that

avoids an incorrect assumption made by the usual CVI compar-

ison methodology28. Therefore, we present two main contribu-

tions in this paper. First, we present the main results of the most

extensive CVI comparison ever carried out. Second, this compar-

ison is the ?rst extensive CVI comparison carried out with the

methodological correction proposed by Gurrutxaga et al.

28.

Moreover, although the experiment’s size prevents us from

publishing all the results in this paper, they are all available in

electronic format in the web.

1

The next section discusses other works related to CVI compar-

ison.Section 3describes all the cluster validity indices compared

in this work andSection 4describes the particular details of theexperimental design. InSection 5we show the main results of the

work and, ?nally, we draw some conclusions and suggest some

possible extensions inSection 6

2. Related work

Most of the works that compare CVIs use the same approach:

A set of CVIs is used to estimate the number of clusters in a set of

datasets partitioned by several algorithms. The number of suc-

cesses of each CVI in the experiment can be called its score and is

considered an estimator of its ”quality”. For a more formal

description of this methodology and a possible alternative to it

see28.

Despite this widely used approach, most of the works are not

comparable since they differ in the CVIs compared, datasets used,

results analysis. In this section we overview some of the works

that compare a set of CVIs, focusing on the experiment

characteristics.

The paper published by Milligan and Cooper20in 1985 is

still the work of reference on internal cluster validation. That

work compared 30 CVIs. The authors called them ”Stopping

criteria” because they were used to stop the agglomerative

process of a hierarchical clustering algorithm2,4 and this is

why the experiments were done with hierarchical clustering

algorithms (single-linkage, complete-linkage, average-linkage

and Ward). They used 108 synthetic datasets with a varying

number of non-overlapped clusters (2, 3, 4 or 5), dimensionality

(4, 6 or 8) and cluster sizes. They presented the results in a tabular

format, showing the number of times that each CVI predicted the

correct number of clusters. Moreover, the tables also included the

number of times that the prediction of each CVI overestimated or

underestimated the real number of clusters by 1 or 2.

The same tabular format was used by Dubes27two years

later. The novelty of this work is that the author used some tables

where the score of each CVI was shown according to the values of

each experimental factor—clustering algorithm, dataset dimen-

sionality, number of clusters. Moreover, he used the

w2statistic to

test the effect of each factor on the behaviour of the compared

CVIs. Certainly, the use of statistical tests to validate the experi-

mental results is not common practice in clustering, as opposed to

other areas such as supervised learning. The main drawback of

this work is that it compares just 2 CVIs (Davies–Bouldin and the

modi?ed Hubert statistic). The experiment is performed in

2 parallel works of 32 and 64 synthetic datasets, 3 clustering

algorithms (single-linkage, complete-linkage and CLUSTER) and

100 runs. The datasets’ characteristics were controlled in the

generation process and they used different sizes (50 or 100

objects), dimensionality (2, 3, 4 or 5), number of clusters (2, 4,

6 or 8), sampling window (cubic or spherical) and cluster overlap.

In 1997, Bezdek et al.29published a paper comparing 23 CVIs

based on 3 runs of the EM algorithm and 12 synthetic datasets. The

datasets were formed by 3 or 6 Gaussian clusters and the results

were presented in tables that showed the successes of every CVI on

each dataset. Another work that compared 15 CVIs was performed

by Dimitriadou et al.18based on 100 runs of k-means and hard

competitive learning algorithms. The 162 datasets used in this

work were composed of binary attributes which made the experi-

ment and the results presentation somewhat different to the

previously mentioned ones.

More recently, Brun et al.10compared 8 CVIs using several

clustering algorithms: k-means, fuzzy c-means, SOM, single-

linkage, complete-linkage and EM. They used 600 synthetic

datasets based on 6 models with varying dimensionality

(2 or 10), cluster shape (spherical or Gaussian) and number of

clusters (2 or 4). The novelty in this work can be found in the

1http://www.sc.ehu.es/aldapa/cvi.O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256 244

comparison methodology. The authors compared the partitions

obtained by the clustering algorithms with the correct partitions

and computed an error value for each partition. Then, the

”quality” of the CVI is measured as its correlation with the

measured error values. In this work, not just internal but also

external and relative indices are examined. The results show that

the Rand index is highly correlated with the error measure.

The mentioned correlation between the error measure and the

Rand index makes one think about the adequacy of the error as a

de?nitive measure. In the recent work of Gurrutxaga et al.28the

authors accepted that there is no single way of establishing the

quality of a partition and they proposed using one of the external

indices available—or even better, several of them. This is the ?rst

work that clearly confronted a methodological drawback ignored by

many authors, but noticed by others10,22,23,20. Since the main

goal of this work was to present a modi?cation of the traditional

methodology, they compared just 7 CVIs based on 7 synthetic and

3 real datasets and 10 runs of the k-means algorithm.

Other CVI comparisons can be found where new CVIs are

proposed, but in this case the experiment is usually limited. It is

common to ?nd works comparing 5 or 10 CVIs on a similar

number of datasets6,21,22,25,8,26,24.

3. Cluster validity indices

In this section we describe the 30 CVIs compared in this work.

First, to simplify and reduce the CVI description section we de?ne

the general notation used in this paper and particular notations

used to describe several indices.

3.1. Notation

Let us de?ne a datasetXas a set ofNobjects represented

as vectors in anF-dimensional space:X¼fx

1,x2,…,xNgDRF.

A partition or clustering inXis a set of disjoint clusters that

partitionsXintoKgroups:C¼fc

1,c2,…,cKgwhereSckACck¼

X,c

kcl¼|8kal. The centroid of a clusterckis its mean vector,

ck¼1=9ck9PxiACkxiand, similarly, the centroid of the dataset is

the mean vector of the whole dataset,

X¼1=NPxiAXxi.

We will denote the Euclidean distance between objectsx

iand

x

jas deðxi,xjÞ. We de?ne the Point Symmetry-Distance30

between the objectx

iand the clusterckas

d

npsðxi,ckÞ¼1=2X

minð2ÞxjAckfdeð2ckxi,xjÞg:

The point 2

ckxiis called the symmetric point ofxiwith respect

to the centroid ofc

k. The functionP

min can be seen as a

variation of the min function whereP

minðnÞcomputes the sum

of thenlowest values of its argument. Similarly, we can de?ne the

P

max function as an analogue variation of the max function.

Finally, let us de?nen

wsince it is used by several indices.nwis

the number of object pairs in a partition that are in the same

cluster,n

w¼PckACð9ck9

2Þ.

3.2. Index de?nitions

Next, we describe the 30 CVIs compared in this work. We

focused on CVIs that can be easily evaluated by the usual

methodologies and avoided those that could lead to confusion

due to the need for a subjective decision by the experimenter.

Therefore, we have discarded some indices that needed to deter-

mine a ”knee” in a plot—such as the Modi?ed Hubert index31

—need to tune a parameter or need some kind of normalization—

such as thev

SVindex32or the Jump index33.Wehave

also avoided fuzzy indices, since our goal was to focus oncrisp clustering. In brief, we focused on crisp CVIs that allow

selection of the best partition based on its lowest or highest value.

Most of the indices estimate the cluster cohesion (within or

intra-variance) and the cluster separation (between or inter-

variance) and combine them to compute a quality measure.

The combination is performed by a division (ratio-type indices)

or a sum (summation-type indices)25.

For each index we de?ne an abbreviation that will be helpful

in the results section. Moreover, we accompanied each abbrevia-

tion with an up or down arrow. The down arrow denotes that a

lower value of that index means a ”better” partition. The up arrow

means exactly the opposite.

Dunn index (Dm)13: This index has many variants and

some of them will be described next. It is a ratio-type index

where the cohesion is estimated by the nearest neighbour

distance and the separation by the maximum cluster dia-

meter. The original index is de?ned as

DðCÞ¼

minckACfminclACckfdðck,clÞgg

max

ckACfDðckÞg,

where

dðck,clÞ¼minxiAckminxjAclfdeðxi,xjÞg,

DðckÞ¼maxxi,xjAckfdeðxi,xjÞg:

Calinski–Harabasz (CHm)15: This index obtained the best

results in the work of Milligan and Cooper20. It is a ratio-

type index where the cohesion is estimated based on the

distances from the points in a cluster to its centroid.

The separation is based on the distance from the centroids to

the global centroid, as de?ned inSection 3.1. It can be de?ned as

CHðCÞ¼

NK

K1PckAC9ck9deðck,XÞ

P

ckACPxiAckdeðxi,ckÞ:

Gamma index (Gk)34: The Gamma index is an adaptation

of Goodman and Kruskal’s Gamma index and can be

described as

GðCÞ¼

PckACPxi,xjAckdlðxi,xjÞ

n

wN

2

nw

,

where dlðx

i,xjÞdenotes the number of all object pairs inX,

namelyx

kandxl, that ful?l two conditions: (a)xkandxlare in

different clusters, and (b) d

eðxk,xlÞodeðxi,xjÞ. In this case the

denominator is just a normalization factor.

C-Index (CIk)35: This index is a type of normalized

cohesion estimator and is de?ned as

CIðCÞ¼

SðCÞSminðCÞ

S

maxðCÞSminðCÞ,

where

SðCÞ¼X

ckAC

X

xi,xjAckdeðxi,xjÞ,

S

minðCÞ¼X

minðnwÞxi,xjAXfdeðxi,xjÞg,

S

maxðCÞ¼X

maxðnwÞxi,xjAXfdeðxi,xjÞg:

Davies–Bouldin index (DBk)14: This is probably one of the

most used indices in CVI comparison studies. It estimates the

cohesion based on the distance from the points in a cluster to

O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256245

its centroid and the separation based on the distance between

centroids. It is de?ned as

DBðCÞ¼

1

KX

ckACmaxclACck

SðckÞþSðclÞ

d

eðck,clÞ

,

where

Sðc

kÞ¼1=9ck9XxiAckdeðxi,ckÞ:

Silhouette index (Silm)36: This index is a normalized

summation-type index. The cohesion is measured based on

the distance between all the points in the same cluster and

the separation is based on the nearest neighbour distance.

It is de?ned as

SilðCÞ¼1=NX

ckAC

X

xiAck

bðxi,ckÞaðxi,ckÞ

maxfaðx

i,ckÞ,bðxi,ckÞg,

where

aðx

i,ckÞ¼1=9ck9XxjAckdeðxi,xjÞ,

bðx

i,ckÞ¼minclACck1=9cl9XxjAcldeðxi,xjÞ 8

:

and

aðx

i,ckÞ¼1=9ck9XxjAckdeðxi,xjÞ,bðx

i,ckÞ¼1=9ck9X

minxj= 2ck

ð9ck9Þfdeðxi,xjÞg:

4. Experimental setup

In this section we describe the experiment performed to

compare the CVIs listed in the previous section. As shown in

Section 2, there are many possible experimental designs for such

a comparison. Since we want to compare the CVIs in a wide

variety of con?gurations we designed an experiment with several

factors. Unfortunately, due to combinatorial explosion we had to

limit each factor to just a few levels and this ?nally led us to an

experiment with 6480 con?gurations.

The comparative methodology that we used is a variation of

the traditional problem of estimating the number of clusters of a

dataset. The usual approach is to run a clustering algorithm over a

dataset with a set of different values for thekparameter—the

number of clusters of the computed partition—obtaining a set of

different partitions. Then, the evaluated CVI is computed for all

the partitions. The number of clusters in the partition obtaining

the best results is considered the prediction of the CVI for that

particular dataset. If this prediction matches the true number of

clusters, the prediction is considered successful.

The variation we used modi?es the problem so that the CVIs

are not used to estimate the correct number of clusters. They are

used to predict which is the ”best” partition in the mentioned set

of partitions. The ”best” partition is de?ned as the one that is the

most similar to the correct one—measured by a partition simi-

larity measure—which is not always the one with the correct

number of clusters. For a formal and more detailed description

see28. In order to avoid the possible bias introduced by the

selection of a particular partition similarity measure, we repli-

cated all the experiments using three partition similarity mea-

sures: Adjusted Rand31, Jaccard41and Variation of

Information42.

We used three clustering algorithms to compute partitions

from the datasets: k-means, Ward and average-linkage2. These

are well known and it is easy to obtain different partitions by

modifying the parameter that controls the number of clusters of

the output partition. Each algorithm was used to compute a set of

partitions with the number of clusters ranging from 2 to????

N p

,

whereNis the number of objects in the dataset. In the case of the

real datasets, the number of clusters in a partition was limited to

25 to avoid computational problems with large datasets.

As usual, we used several synthetically generated datasets for

the CVI evaluation. Furthermore, we also compared them using 20

real datasets drawn from the UCI repository43. In any case, it is

important to note that results based on real datasets should be

analyzed with caution since these datasets are usually intended to

be used with supervised learning and, therefore, they are not

always well adapted to the clustering problem9. On the

contrary, the synthetic datasets avoid many problems found with

real datasets. For instance, in synthetic datasets categories exists

independent of human experience and their characteristics can be

easily controlled by the experiment designer.

The synthetic datasets were created to cover all the possible

combinations of ?ve factors: number of clusters (K), dimension-

ality (dim), cluster overlap (ov), cluster density (den) and noise

level (nl). We de?ned two types of overlap:strict, meaning that

the

ovoverlap level must be exactly satis?ed, andbounded,

meaning thatovis the maximum allowed overlap.

A ?xed hypercubic sampling window is de?ned to create all

the synthetic datasets. The window is de?ned by theð0,0,…,0Þ

andð50,50,…,50Þcoordinates. In a similar way, a reduced sampling

O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256247

window is de?ned by theð3,3,…,3Þandð47,47,…,47Þcoordi-

nates. Then, the centre for the ?rst cluster,c

0, is randomly drawn

in the reduced sampling window based on a uniform distribution.

The ?rst cluster is created by randomly drawingn

mindenpoints

following a multivariate normal distribution ofdimdimensions

with meanc

0and the identity as covariance matrix. All points

located outside the sampling window are removed and new

points are drawn to replace them.

The remaining clusters will haven

minpoints and this produces

a density asymmetry whendena1. This occurs because a

different number of points will be located in the same approx-

imate volume.

In particular, we build the remainingK1 clusters as follows:

if the overlap isbounded, the centre of the cluster,c

i, is drawn

uniformly from the reduced sampling window. Otherwise, a

previously created cluster centre,c

k, is randomly selected and

the new cluster centre,c

i, is set to a random point located at a

distance of 2ovfromc

k. In any case, if deðci,clÞo2ov8clacithe cluster centre is discarded and a new one is selected. Once the

cluster centre has been de?ned the cluster is built by drawingn

minpoints in the same way as we did for the ?rst cluster.

Finally, when all the clusters have been built,nlN0points are

randomly created following a uniform distribution in the sam-

pling window, whereN

0is the number of non-noise points in the

dataset,N0¼nminðdenþK1Þ.

The values of the parameters used to create the synthetic

datasets are shown inTable 1, making 72 different con?gurations.

As we created 10 datasets from each con?guration we used 720

synthetic datasets. Multiplying this value by three partition

similarity measures and three clustering algorithms we obtain

the 6480 con?gurations previously mentioned. Notice that the

n

minparameter ensures that every cluster is composed of at least

100 objects.

Fig. 1shows an example of 4 two-dimensional datasets we

have used. In the ?gure we can see how the different values of the

generation parameters affects the point distribution in the data-

sets.Fig. 1a shows a dataset with four clusters, with no cluster

overlap, no noise and no density asymmetry. The other three plots

show dataset with similar characteristics except for overlap,

density and noise parameters.

The 20 real datasets and their main characteristics are shown

inTable 2. In this case the experiment is based on 180

con?gurations—20 datasets, 3 algorithms and 3 partition simi-

larity measures.

Including synthetic and real datasets, and taking into account

the different number of partitions computed for each dataset,

each of the 30 CVIs was computed for 156 069 partitions.

5. Results

One of the goals of this work is to present the results in such a

way that readers can focus on the particular con?gurations they

are interested in. However, the vast amount of results obtainedprohibits all of them being shown in this paper. Therefore, we

focus here on the overall results; drawing some important

conclusions. However, all the detailed results are available in

the web.

In this section we ?rst describe the results obtained for the

synthetic datasets and then the results for the real datasets are

described. Finally, we present a brief discussion on the use of

statistical analysis in clustering and we show the conclusions we

drew by applying some statistical tests to the results.

5.1. Synthetic datasets

The overall results for the synthetic datasets are shown in

Fig. 2. The ?gure shows the percentage of correct guesses

Table 1

Values of the parameters used in the synthetic

dataset generation step.

Param. Value

n

min100

K2, 4, 8

dim2, 4, 8

ov1.5 (strict), 5 (bounded)

den1, 4

nl0, 0.1

Fig. 1.Two-dimensional plots of four synthetic datasets used in the experiment.

(a) Shows a ”neutral” dataset with no cluster overlap, no density asymmetry and

no noise. (b) Shows a similar dataset with high cluster overlap. (c) Shows a dataset

with cluster density asymmetry. (d) Shows a dataset with noise.

Table 2

The characteristics of the real datasets drawn from the UCI repository.

Dataset No. of objects Features Classes

Breast tissue 106 9 6

Breast Wisconsin 569 30 2

Ecoli 336 7 8

Glass 214 9 7

Haberman 306 3 2

Ionosphere 351 34 2

Iris 150 4 3

Movement libras 360 90 15

Musk 476 166 2

Parkinsons 195 22 2

Segmentation 2310 19 7

Sonar all 208 60 2

Spectf 267 44 2

Transfusion 748 4 2

Vehicle 846 18 4

Vertebral column 310 6 3

Vowel context 990 10 11

Wine 178 13 3

Winequality red 1599 11 6

Yeast 1484 8 10 O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256 248

(successes) achieved by each CVI, which are sorted by the number

of successes. Notice that this percentage refers to the 6480

con?gurations. The graph shows that Silhouette achieves the best

overall results and is the only one that exceeds the 50% score. DB

n

and CH also show a good result, with a success rate beyond 45%.

It is also noticeable that in most cases variations of a CVI

behave quite similarly; they appear in contiguous positions in the

?gure. The clearest cases are the generalized Dunn indices that

use

D3as cohesion estimator—gD33, gD43 and gD53—and the

graph theory based Dunn indices—DMST,DRNGand DGG.

Next we will show a similar graph for each experimental

factor. In this case the value of each CVI is shown for each value of

the analyzed factor. We will keep the CVI order shown inFig. 2,so

a decreasing graph will denote that the analyzed factor does not

change the overall ranking.

First of all, let us focus on the graph corresponding to the

partition similarity measure. Remind that this is a parameter of

the validation methodology we have used (seeSection 4). InFig. 3

we can see that the selected partition similarity measure does notaffect the results. This result suggests that the CVI comparison is

not affected by the particular selection of a parameter of the

evaluation methodology and, therefore, we can be con?dent of

the results. Also notice that although Adjusted Rand and Jaccard

show very similar results the use of the VI partition similarity

measure produces slightly higher success rates.

In the following ?gures a similar breakdown can be found with

regard to the characteristics of the datasets. InFig. 4we can see

how the number of clusters of the datasets affects the results. As

expected, all the CVIs obtain better results with fewer

clusters—average result fork¼2 drops from 50.2% to 30.7%

(k¼4) and 24.8% (k¼8). We can also see that for high values of

this parameter the differences between the CVIs are reduced.

Furthermore, some indices, such as COP, show little sensitivity to

this parameter making it the best CVI fork¼8.

With respect to dimensionality (seeFig. 5), the results show

that the dif?culty imposed by an increment in the number of

dimensions does not severely affect the behaviour of the

CVIs—except for NI. Moreover, some indices, such as Sym, show

Success rate (%)

0 1020304050

Sil

DB*

CH

gD33

gD43

gD53

SF

DB

Sym33

COP

DMST

DRNG

DGG

SDbw

Sym

DBMST

DBRNG

gD41

SymDB

gD51

DBGG

gD31

SV

CS

D

SymD

G

CI

OS

NI

Fig. 2.Overall results for the experiment with synthetic datasets.

Adjusted Rand

Jaccard

VI

Success rate (%)

0 1020304050

Sil

DB*

CH

gD33

gD43

gD53

SF

DB

Sym33

COP

DMST

DRNG

DGG

SDbw

Sym

DBMST

DBRNG

gD41

SymDB

gD51

DBGG

gD31

SV

CS

D

SymD

G

CI

OS

NI

Fig. 3.Results for synthetic datasets broken down by partition similarity measure.O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256249

a better behaviour for datasets with higher dimensionality.

Silhouette also achieves the best results for every value analyzed

for this parameter.

Let us now focus on the results shown inFig. 6. This graph

shows that, as expected, datasets with no overlapping clusters

lead to better CVI success rates. The average result decreases from

52.9% to 17.6% when well separated clusters are replaced by

overlapped clusters. The graph also shows that although this

parameter does not severely affect the overall trend, some CVIs

are more hardly affected by cluster overlap, e.g. DB, COP and

SymDB. Some others, such as G, CI and OS, seem not to work at all

when clusters overlap.

With respect to the density of the clusters,Fig. 7shows that

having a cluster four times denser than the others, does not

severely affect the CVIs. It seems that the best behaving indices

are quite insensitive to this parameter while the rest show a

better result when density heterogeneity is present. Silhouette is

again, clearly, the CVI showing best results.Noise level, the last dataset characteristic analyzed in this

work, has a major impact on the scores of the CVIs (Fig. 8). In fact,

the scores in noisy environments are on average three times

lower than they are when no noise is present. Silhouette, and

mostly SDbw, are the main exception to this rule since they show

similar score values for noisy and noiseless environments.

Besides, the overall trend is not always followed and CH is the

CVI that achieves the best results when no noise is present.

Finally,Fig. 9shows how the clustering algorithm used in the

experiment affects the scores of the indices evaluated. Although

we cannot ?nd a clear pattern, it seems that the overall compara-

tive results are not severely affected since the decreasing pattern

of the graph is somehow maintained. Most of the CVIs obtain

their worst results for the k-means algorithm, but there are some

exceptions where the opposite holds—COP, G, CI and OS are the

most remarkable examples. Silhouette is again the one achieving

the best results for hierarchical algorithms, but CH is the best CVI

when k-means is used as clustering algorithm.

2 clusters

4 clusters

8 clusters

Success rate (%)

0 20406080

Sil

DB*

CH

gD33

gD43

gD53

SF

DB

Sym33

COP

DMST

DRNG

DGG

SDbw

Sym

DBMST

DBRNG

gD41

SymDB

gD51

DBGG

gD31

SV

CS

D

SymD

G

CI

OS

NI

Fig. 4.Results for synthetic datasets broken down by number of clusters.

2 dims.

4 dims.

8 dims.

Success rate (%)

0 1020304050

Sil

DB*

CH

gD33

gD43

gD53

SF

DB

Sym33

COP

DMST

DRNG

DGG

SDbw

Sym

DBMST

DBRNG

gD41

SymDB

gD51

DBGG

gD31

SV

CS

D

SymD

G

CI

OS

NI

Fig. 5.Results for synthetic datasets broken down by dimensionality. O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256 250

5.2. Real datasets

In this section we show the results obtained for 20 real

datasets following a similar style to the one we used for synthetic

datasets. Obviously, since we do not have control over the dataset

design the number of experimental factors is reduced to 2:

partition similarity measure and clustering algorithms.

First, inFig. 10we show the overall results for real datasets. A

quick comparison to the overall results for the synthetic datasets

(Fig. 2) shows that the results are qualitatively similar. Most of

CVIs that obtained worst results with synthetic datasets are also

in the tail of the ranking in the ?gure for real datasets. Focusing

on the head of the ranking we can see that the generalized Dunn

indices—gD33, gD43 and gD53—remain in a similar position;

SF, graph theory based Dunn and COP improve their position; and

Silhouette, DB

nand CH go down the ranking. Considering these

results we can say that the mentioned generalizations of the

Dunn index show the steadiest results.

Returning to the two experimental factors involved in the

experiments with real datasets, inFig. 11we show the resultsbroken down by partition similarity measure. We can see that in

this case it seems that the partition similarity measure selected

can affect the results. Although Jaccard and VI follow the overall

pattern the Adjusted Rand index does not. Furthermore, it is clear

that in every case the average scores are much lower when

Adjusted Rand is used, dropping from 39.1% (VI) or 31.1%

(Jaccard) to 10.0%.

With regard to the clustering algorithm used (seeFig. 12) the

results are contradictory. On the one hand, if we focus on k-means

and Ward, it seems that this factor does not severely affect the

results. On the other hand, results for average-linkage reduce the

differences between CVIs and do not follow the overall results. In

this case, Sym shows the best results while SF achieves the

highest success rates for k-means and Ward.

5.3. Statistical tests

Although the assessment of the experimental results using

statistical tests is a widely studied technique in machine learning,

it is rarely used in the clustering area. Among the works cited in

Overlap

No overlap

Success rate (%)

0 10203040506070

Sil

DB*

CH

gD33

gD43

gD53

SF

DB

Sym33

COP

DMST

DRNG

DGG

SDbw

Sym

DBMST

DBRNG

gD41

SymDB

gD51

DBGG

gD31

SV

CS

D

SymD

G

CI

OS

NI

Fig. 6.Results for synthetic datasets broken down by cluster overlap.

1:1

4:1

Success rate (%)

0 1020304050

Sil

DB*

CH

gD33

gD43

gD53

SF

DB

Sym33

COP

DMST

DRNG

DGG

SDbw

Sym

DBMST

DBRNG

gD41

SymDB

gD51

DBGG

gD31

SV

CS

D

SymD

G

CI

OS

NI

Fig. 7.Results for synthetic datasets broken down by density. O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256251

Section 2just Dubes27used a statistical test to assess the

in?uence of each experimental factor on the results obtained.

However, in our case we focused on checking whether the

observed differences between CVIs were statistically signi?cant

or not.

We argue that an effort should be made by the clustering and

statistics communities to adapt these tools to clustering and

effectively introduce them in the area. These types of tests would

be even more important in extensive comparative works such as

the one described in this paper. Therefore, although it is not the

goal of this work, we propose a possible direct adaptation of a

comparison method used in supervised learning. This method has

been chosen due to the proximity of the supervised learning area

to clustering and because the use of statistical tests in this area

has been widely studied44–46.

We next describe the method and the proposed adaptation.

Then, we conclude this section by discussing the results obtainedwhen we applied the proposed tests to the results obtained in the

experiment carried out in our work to compare the performance

of CVIs.

We based our statistical method on a common scenario in

supervised learning where classi?cation algorithms are com-

pared. In this case it is usual to run the algorithms on several

datasets and to compute a ”quality” estimate, such as the

accuracy or the AUC value, for each algorithm and database pair.

A usual approach is to test the quality values achieved by all the

algorithms for each dataset independently45. However, Dems?

ar

44recently argued that a single test based on all the algorithms

and all the datasets is a better choice. One of the advantages of

this method is that the different values compared in the statistical

test are independent, since they come from different datasets.

We have adapted the method proposed by Dems?

ar44and

subsequently extended by Garc?´

a and Herrera46to CVI com-

parisons. In brief, we simply replaced the classi?cation algorithms

No noise

10%

Success rate (%)

0 10203040506070

Sil

DB*

CH

gD33

gD43

gD53

SF

DB

Sym33

COP

DMST

DRNG

DGG

SDbw

Sym

DBMST

DBRNG

gD41

SymDB

gD51

DBGG

gD31

SV

CS

D

SymD

G

CI

OS

NI

Fig. 8.Results for synthetic datasets broken down by noise.

K-means

Ward

Average-linkage

Success rate (%)

0 102030405060

Sil

DB*

CH

gD33

gD43

gD53

SF

DB

Sym33

COP

DMST

DRNG

DGG

SDbw

Sym

DBMST

DBRNG

gD41

SymDB

gD51

DBGG

gD31

SV

CS

D

SymD

G

CI

OS

NI

Fig. 9.Results for synthetic datasets broken down by clustering algorithm.O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256 252

by CVIs. However, this is not enough, since in our experiments we

obtained a Boolean value for each CVI-con?guration pair instead

of a ”quality” estimate. Moreover, the con?gurations we obtained

by varying the clustering algorithm and partition similarity

measure are based on the same dataset, so it can be argued that

they are not suf?ciently independent.

Our solution was to add for each dataset the number of

successes each CVI obtained for each clustering algorithm–parti-

tion similarity measure pair. Moreover, in order to obtain a more

precise estimate, we also added the number of successes obtained

in every run—remember that we created 10 datasets for each

combination of dataset characteristics. We thus obtained 72

values ranging from 0 to 90 for each CVI, that gave us a ”quality”

estimate for independent datasets. Finally, we applied the statis-

tical tests with no further modi?cations.

The tests we used were designed for comparisons of multiple

classi?ers (CVIs) in an all-to-all way. We used the Friedman test

to check if any statistical difference existed and the Nemenyi test

for pairwise CVI comparison44. Furthermore, we performedadditional pairwise CVI comparisons with the Shaffer test as

suggested by Garc?´

a and Herrera46. In both cases we performed

the tests with 5% and 10% con?dence level.

The main conclusion obtained by applying the above tests is

that there are undoubtedly statistically signi?cant differences

between the 30 CVIs, as the Friedman test categorically shows

with ap-value on the order of 10

80. All the performed pair-wise

comparisons show a very similar result, so inFig. 13we only

show the results for the most powerful test that we

performed—Shaffer with a con?dence level of 10%.

Since the used statistical tests are based on average rank values,

the ?gure shows all the CVIs sorted by average rank. The results are

very similar to those based on average scores (Fig. 2), but there are

a couple of differences that should be underlined. First of all, the

CVI order slightly changed, but most of the movements occurred in

the central part of the ranking. Secondly, the CVIs formed quite

well separated groups. In the ?rst group there are 10 indices with

an average rank between 9 and 13. Taking into account variations

of a CVI as a single one, the group contains six indices: Silhouette,

Success rate (%)

0 10203040

SF

DGG

DRNG

DMST

COP

gD33

gD43

gD53

Sil

DB*

gD51

Sym33

gD31

gD41

DBMST

DB

DBRNG

DBGG

CH

D

Sym

SDbw

OS

SymD

SymDB

G

NI

CI

SV

CS

Fig. 10.Overall results for real datasets.

Adjusted Rand

Jaccard

VI

Success rate (%)

0 102030405060

SF

DGG

DRNG

DMST

COP

gD33

gD43

gD53

Sil

DB*

gD51

Sym33

gD31

gD41

DBMST

DB

DBRNG

DBGG

CH

D

Sym

SDbw

OS

SymD

SymDB

G

NI

CI

SV

CS

Fig. 11.Results for real datasets broken down by partition similarity measure.O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256253

Davies–Bouldin, Calinski–Harabasz, generalized Dunn, COP and

SDbw. There is also a crowded central group with 14 CVIs and

average rank between 14 and 17; and ?nally, a group of six indices

with average rank between 19 and 23.

The bars in the ?gure group the indices that do not show

statistically signi?cant differences. The highly overlapped bars

dif?cult the task of drawing categorical conclusions, but on the

following we resume the information in the graph and remark the

most interesting points:

No signi?cant difference exists between CVIs in the same

group.

All the CVIs in the ?rst group perform signi?cantly better than

the CVIs in the third group.

The best behaving CVI, Sil, obtains signi?cantly better results

than all the CVIs in the second group, except Sym.

All the CVIs in the second group, except Sym and SymDB, have

no statistically signi?cant differences with at least one CVI in

the third group.

In conclusion, the data does not show suf?ciently strong

evidence to distinguish a small set of CVIs as being signi?cantly

better than the rest. Nevertheless, there is a group of about 10

indices that seems to be recommendable and Silhouette, Davies–

Bouldin* and Calinski–Harabasz are in the top of this group. We

have also performed statistical test to the experiment subsets

shown in the results section, but no CVI can be considered

signi?cantly better than the others in any case.6. Conclusions and further work

In this paper we presented a comparison of 30 cluster validity

indices on an extensive set of con?gurations. It is, to the best of

our knowledge, the most extensive CVI comparison ever pub-

lished. Moreover, it is the ?rst non-trivial CVI comparison

that uses the methodological correction recently proposed by

Gurrutxaga et al.28.

Due to the huge size of the experiment we have not been able to

show all the results obtained. However, the interested reader can

access them in electronic format in the web. The great advantage of

this is that readers can focus on the results for the con?gurations

they are interested in and we therefore provide a tool to enable

them to select the most suitable CVIs for their particular application.

This procedure is very recommendable since there is not a single CVI

that showed clear advantage over the rest in every context, although

Silhouette index obtained the best results in many of them.

We next summarize the main conclusions we drew from the CVI

comparison. First, we observed that some CVIs appear to be more

suitable for certain con?gurations, although the results were not

conclusive. Furthermore, the overall trend never changed dramatically

when we focused on a particular factor. Another fact worth noting is

that the results for real and synthetic datasets are qualitatively similar,

although they show disagreements for some particular indices.

With regard to the experimental factors, noise and cluster

overlap had the greatest impact on CVI performance. The number

of successes is dramatically reduced when noise is present or

clusters overlap. In particular, the inclusion of 10% random noise

reduces the average score to a third part. A very similar score

reduction was found when the clusters were moved closer so they

highly overlapped. Another remarkable and surprising fact is that

some indices showed better results in (a priori) more complex

con?gurations. For example, some indices improved their results

when the dimensionality of the datasets increased or the homo-

geneity of the cluster densities disappeared.

Finally, we con?rmed that the selection of a partition similar-

ity measure that enables correction of the experimental metho-

dology is not a critical factor. Nevertheless, it is clear that it can

produce some variations in the results, so our suggestion is to use

several of them to obtain more robust results. Our work shows

that CVIs appear to be better adapted to the VI and Jaccard

partition similarity measures than to Adjusted Rand.

K-means

Ward

Average-linkage

Success rate (%)

0 1020304050

SF

DGG

DRNG

DMST

COP

gD33

gD43

gD53

Sil

DB*

gD51

Sym33

gD31

gD41

DBMST

DB

DBRNG

DBGG

CH

D

Sym

SDbw

OS

SymD

SymDB

G

NI

CI

SV

CS

Fig. 12.Results for real datasets broken down by clustering algorithm.

Fig. 13.Results for Shaffer test with a signi?cance level of 10%.O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256 254

An statistical signi?cance analysis of the results showed that

there are three main groups of indices and the indices in the ?rst

group—Silhouette, Davies–Bouldin, Calinski–Harabasz, general-

ized Dunn, COP and SDbw—behave better than indices in the last

group—Dunn and its Point Symmetry-Distance based variation,

Gamma, C-Index, Negentropy increment and OS-Index—being

the differences statistically signi?cant.

This work also raises some questions and, therefore, suggests

some future work. It is obvious that this type of work can always

be improved. Although we consider that we performed an

extensive comparison there is room for extending it to include

more CVIs, datasets, clustering algorithms and so on. In this

context noise and overlap would appear to be the most interest-

ing factors to analyse in greater depth. We also limited this work

to crisp clustering, so a fuzzy CVI comparison would be a natural

continuation. The analysis of some other kind of indices, such as

stability based ones, would also be of great interest.

Finally, we argued that statistical tests are a very valuable tool

in data mining and that an effort should be made to use them

more widely in clustering. We adapted a method widely accepted

in the supervised learning area for our work, but this is just a ?rst

approach to the problem and there is a vast ?eld of theoretical

research to be addressed.

Acknowledgements

This work was funded by the University of the Basque Country,

general funding for research groups (Aldapa, GIU10/02), by the

Science and Education Department of the Spanish Government

(ModelAccess project, TIN2010-15549), by the Basque Govern-

ment’s SAIOTEK program (Datacc project, S-PE11UN097) and by

the Diputacio´

n Foral de Gipuzkoa (Zer4you project, DG10/5).

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Olatz Arbelaitzreceived the M.Sc. and Ph.D. degrees in Computer Science from the University of the Basque Country in 1993 and 2002, respectively. She is an Associate

Professor in the Computer Architecture and Technology Department of the University of the Basque Country. She has worked in autonomous robotics, combinatorial

optimization and supervised and unsupervised machine learning techniques, focusing lately in web mining.O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256255

Ibai Gurrutxagareceived the M.Sc. and Ph.D. degrees in Computer Science from the University of the Basque Country in 2002 and 2010. He is an Associate Professor in the

Computer Architecture and Technology Department of the University of the Basque Country. He is working in data mining and pattern recognition, focusing on supervised

and unsupervised classi?cation (decision trees, clustering, computer security and intrusion detection), and high performance computing.

Javier Muguerzareceived the M.Sc. and Ph.D. degrees in Computer Science from the University of the Basque Country in 1990 and 1996, respectively. He is an Associate

Professor in the Computer Architecture and Technology Department of the University of the Basque Country. His research interests include data mining, pattern

recognition and high performance computing.

Jesu´

s Mar?´

aPe´

rezreceived the M.Sc. and Ph.D. degrees in Computer Science from the University of the Basque Country in 1993 and 2006, respectively. He is an Associate

Professor in the Computer Architecture and Technology Department of the University of the Basque Country. His research interests include data mining and pattern

recognition techniques, focusing on classi?ers with explanation capacities, learning from imbalanced data and statistical analysis.

In˜

igo Peronareceived the M.Sc. degree in Computer Science from the University of the Basque Country in 2008. He is granted to pursue the Ph.D. at the Computer

Architecture and Technology Department of the University of the Basque Country. He is working in data mining and pattern recognition, focusing on supervised and

unsupervised classi?cation (web mining, clustering, computer security and intrusion detection).O. Arbelaitz et al. / Pattern Recognition 46 (2013) 243–256 256

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