electronics

Review
The k-means Algorithm: A Comprehensive Survey
and Performance Evaluation
Mohiuddin Ahmed 1, * , Raihan Seraj 2 and Syed Mohammed Shamsul Islam 1,3
1 School of Science, Edith Cowan University, Joondalup 6027, Australia; [email protected]
2 Department of Electrical and Computer Engineering, McGill University, Montréal, QC H3A 0G4, Canada;
[email protected]
3 School of Computer Science and Software Engineering, The University of Western Australia,
Crawley 6009, Australia
* Correspondence: [email protected]




Received: 29 May 2020; Accepted: 7 August 2020; Published: 12 August 2020


Abstract: The k-means clustering algorithm is considered one of the most powerful and popular
data mining algorithms in the research community. However, despite its popularity, the algorithm
has certain limitations, including problems associated with random initialization of the centroids
which leads to unexpected convergence. Additionally, such a clustering algorithm requires the
number of clusters to be defined beforehand, which is responsible for different cluster shapes and
outlier effects. A fundamental problem of the k-means algorithm is its inability to handle various data
types. This paper provides a structured and synoptic overview of research conducted on the k-means
algorithm to overcome such shortcomings. Variants of the k-means algorithms including their recent
developments are discussed, where their effectiveness is investigated based on the experimental
analysis of a variety of datasets. The detailed experimental analysis along with a thorough comparison
among different k-means clustering algorithms differentiates our work compared to other existing
survey papers. Furthermore, it outlines a clear and thorough understanding of the k-means algorithm
along with its different research directions.

Keywords: clustering; k-means; initialization; categorical attributes; cyber security; healthcare;

unsupervised learning

1. Introduction
The advancements in computing, along with the rapid growth and availability of data repositories,
have often emphasized the task of gaining meaningful insights from the data. This encourages taking
appropriate measures based on knowledge discovery approaches. Machine Learning (ML) can be
broadly classified into two: supervised and unsupervised learning. In the case of supervised learning,
a function is learned that maps a given input to an output based on the available input–output
pairs. These learning algorithms thus require the availability of labeled data with the desired output
value [1]. The availability of labeled data represents an ideal scenario; however, such datasets are
often expensive and challenging to obtain. For instance, in the intrusion detection domain, zero-day
attacks are rare instances and obtaining labels for them is expensive. Hence, when the labels of the
datasets are unavailable, unsupervised learning approaches are typically used [2]. Under such a
learning framework, the algorithm has no prior knowledge of the true labels of the dataset and tries
to draw inferences from the dataset itself. A more recent and popular set of algorithms referred to
as semi-supervised learning consists of algorithms that lie in between supervised and unsupervised
learning. Such a learning framework makes use of labeled and unlabeled data for better inference.
Existing research on semi-supervised learning corroborates that adding a skimpy amount of labeled

Electronics 2020, 9, 1295; doi:10.3390/electronics9081295 www.mdpi.com/journal/electronics

Electronics 2020, 9, 1295 2 of 12

data together with a large amount of unlabeled data produces considerable improvements in the
accuracy of the predictive model. This manuscript primarily deals with different variations of the
k-means algorithm, which falls under the family of unsupervised learning. Therefore, this paper will
focus only on unsupervised learning algorithms.
Clustering algorithms exploit the underlying structure of the data distribution and define rules
for grouping the data with similar characteristics [3]. This process results in the partition of a given
dataset according to the clustering criteria without any prior knowledge about the dataset. In an
ideal clustering scenario, each cluster consists of similar data instances that are quite dissimilar
from the instances in other clusters. Such a dissimilarity measure relies on the underlying data and
objective of the algorithm. Clustering is central to many data-driven applications and is considered an
interesting and important task in machine learning. It is also studied in statistics, pattern recognition,
computational geometry, bioinformatics, optimization, image processing, and in a variety of other
fields [4–7]. A plethora of clustering techniques have been invented in the last decade, which are being
applied in a wide range of application domains [8]. Table 1 shows the recent applications on k-means
clustering [9] in different application domains.

Table 1. Applications of variants of the k-means algorithm in different application domains.

Reference Application Algorithm

[10] Face detection Symmetry-based version of k-means (SBKM).

[11] Mobile storage positioning Potential k-means.
[12] Load pattern Hierarchical k-means (H-Kmeans).
[13] Wireless sensor networks Distributed k-means and fuzzy c-means.
[14] Partial multiview data Weighted k-means.
[15] Mobile health k-means implemented with CORDIC.
[16] Endpoint detection k-means for realtime detection.
[17] Big data Privacy preserving k-means.
[18] Multiview data k-means.
[19] Wind power forecasting k-means with bagging neural network.
[20] Social tags k-means based on latent semantic analysis.
[21] Sensing for IGBT current k-means with neural network.
[22] Image segmentation. Kernel k-means Nystrom approximation.
[23] Image compression k-means cuckoo optimization.
[24] Sound source angle estimation. Neural network based on global k-means.
[25] Shape recognition Fuzzy k-means clustering ensemble (FKMCE).
[26] Signal processing Compressive k-means clustering (CKM).
[27] Text processing Vanilla k-means.
[28] High dimensional data processing Fast adaptive k-means (FAKM).
[29] Computational complexity Multiple kernel k-means with late fusion.
[30] Image processing A hybrid parallelization of k-means algorithm.
[31] Adaptive clustering Fuzzy k-means with S-distance.
[32] DDoS detection Semi-supervised k-means algorithm with hybrid feature.
[33] Optimization Non alternating stochastic k-means.
[34] Data Summarization Modified x-means.
Electronics 2020, 9, 1295 3 of 12

This survey studies the problems of and solutions to partition-based clustering, and more
specifically the widely used k-means algorithm [9], which has been listed among the top 10 clustering
algorithms for data analysis [35]. Due to their popularity and ease of use, k-means clustering methods
are being used in conjunction with deep learning for tasks such as image segmentation and handwriting
recognition [36]. A more recent work in [37] used a fully connected deep convolution neural network
along with k-means and performed pixel matching between a segmented image and a convoluted
image. This overcomes the problem that exists when useful information from images is lost by
repeated convolution of the images [36]. Although the k-means clustering algorithm itself performs
well with compact and hyper-spherical clusters, we are interested in highlighting its limitations and
suggesting solutions. The primary focus is given to two unavoidable problems of the k-means algorithm:
(i) assignment of centroids and number of clusters and (ii) ability to handle different types of data.
Although researchers have proposed variants (Figure 1) of k-means algorithms to overcome these
impediments, they are however domain specific and do not generalize well. For example, a k-means
algorithm which can handle categorical data might perform poorly because of the initialization
process used. Table 2 outlines a comparative analysis of existing surveys on clustering and highlights
the contributions of this paper. The key contributions of this paper are listed below.

• Existing solutions of the k-means algorithm along with a taxonomy are outlined and discussed in
order to augment the understanding of these variants and their relationships.
• This research frames the problems, analyses their solutions and presents a concrete study on
advances in the development of the k-means algorithm.
• Experiments are performed using the improved k-means algorithms to find out their effectiveness
using six benchmark datasets.

Figure 1. A simple taxonomy of variants of k-means algorithm.

Table 2. Comparison with existing surveys.

Survey Initialization Data Types Applications Experiments

Yang [38] X × × ×
Filippone [39] X × × ×
Rai [40] X × × ×
This paper X X X X

Paper Roadmap
Our paper is structured as follows. Sections 2 and 3 address the problems of the k-means algorithm
and review the existing solutions for them. Section 4 showcases an experimental analysis of the
representative algorithms (from Sections 2 and 3) on six benchmark datasets widely used by the
machine learning and data mining research community. Section 5 concludes the paper, summarizing
the key insights regarding the k-means algorithm.
Electronics 2020, 9, 1295 4 of 12

2. k-means Variants for Solving the Problem of Initialization

The k-means algorithm depends on the value of k; which always needs to be specified in order to
perform any clustering analysis. Clustering with different k values will eventually produce different
results. Different initialization problems that were analyzed in recent studies did not consider the
problem where the algorithm only converges to a poor local minima. In [41], an alternative approach
was adopted to prevent the k-means algorithm from being easily affected by noise and outlier values.
The authors presented a modified k-means algorithm based on self-paced learning theory. Self-paced
learning theory is used in order to select competing training subset that helps the k-means algorithm
to build an initial cluster model. The generalization ability of the algorithm is then improved by
subsequently adding training subsets found by self-paced learning until the model reaches an optimal
performance or all the training samples have been used. The authors proposed this algorithm and
demonstrated its performances on several real datasets.
The authors in [42] proposed an improvement to the vanilla k-means algorithm that prevents it
from getting stuck to a local minima. The improved algorithm incorporates cuckoo search along with
the k-means algorithm. The method incorporates a modified cuckoo search algorithm, which helps
to reach a better solution since the search step size factor is being changed. Overall, the proposed
algorithm is robust as well as fast in reaching a near-optimal solution.
In [43], the authors discussed criteria concerning the stability and the performance of the k-means.
Theoretical results of algorithm stability were proven as the number of instances approaches infinity.
The authors in [44] analyzed the stability of the k-means clustering algorithm in a more practical
scenario, the parameter (cluster number) is chosen by stability-based model selection. The primary
focus was towards drawing random sample points to explain the effect on the stability of the algorithm.
An initial estimation method for computing the covariance matrix for the k-means algorithm
using Mahalanobis distance was proposed in [45]. It involves finding a group of points comprised
of neighbors with a high density that represent the centroids of the selected clusters. These
provide an approximate estimate of the covariance matrix, which is updated successively using
the proposed algorithm.
Ball et al. [46] proposed the ISODATA algorithm to estimate k by parameter tweaking. A similar
strategy is also adopted in adaptive resonance theory [47], which generates new clusters [48]. Since
this approach requires a predefined threshold, it is generally avoided.
In x-means clustering [49], the BIC (Bayesian information criterion) or “Schwarz criterion” [50,51]
is utilised to find the number of k clusters. For a given set of data, a family of different models
initialized with different k values is used to compute the posterior probability distribution. These
distributions are then used to find the score of the different models. This algorithm was utilized in
identifying anomalous patterns in [52,53].
Bradley et al. [54] outlined methods for identifying a more fine grained starting condition that
relies on the estimation of the distribution modes. The algorithm initially chooses small samples from
the dataset and applies k-means clustering. These temporary sets are then further clustered using the
k-means to find better initialization. This algorithm’s computational complexity is significantly lower
compared to vanilla k-means and, more importantly, is scalable to large datasets. Figure 2 displays the
methodology for obtaining refined initial points.
In [55], the author empirically compared four initialization methods. These are as follows:
(i) RANDOM, (ii) FA [56], (iii) MA [9], and (iv) KA [57]. The RANDOM method divides the dataset
randomly into k number of clusters and is one of the most popular initialization methods. The FA
approach [56] randomly chooses k instances from the given dataset and assigns the remaining instances
to the nearest cluster centers. The MA approach [9] randomly selects k instances of the dataset, similar
to basic k-means. The KA approach [57] provides a method where the initial clustering is done by
selecting representative instances successively until k instances are found. The first representative
instance is the most centrally located in the dataset. The remaining representative instances are chosen
based on the heuristic that presents rules of choosing instances with higher numbers compared to
Electronics 2020, 9, 1295 5 of 12

others. Based on their experimental analysis, the RANDOM and KA resulted in superior performance
compared to the other two. Recently, in [58], a co-clustering algorithm is proposed for dealing with
sparse and high dimensional data that outperforms the basic k-means.

Subsample

Cluster Multiple subsamples

Initial Points Refined
Initial
Points

Cluster Solutions (Multiple Starts)

Dataset

Select Best Solution

Figure 2. Refined initial instances, adapted from [54].

These solutions can only handle numerical data. Hence such methods would not be suitable for
datasets consisting of mixed attributes, for instance, categorical and binary. In the next section, we
discuss the research progress dealing with mixed types of data for clustering.

3. k-means Variants for Solving the Problem of Data Issue

In many application domains, datasets include attributes that are of mixed data types [59].
Therefore, a distance calculation scheme is necessary that is able to compute distances between
instances having mixed types of data. This section discusses existing research on k-means to find
similarity or distance metrics between categorical attributes. Although the algorithms discussed in
the previous section solve the initialization problem, they still rely on numerical data for distance
calculation. Therefore, it is necessary to explore the distance calculation mechanism for the k-means
clustering algorithm and our investigation as follows.
Wang et al. [60] introduced an extended form of the fuzzy k-means (xFKM) algorithm for datasets
with non-numerical attributes, such as categorical data. The centroids constitute an extended form to
retain as much clustering information as possible. A computational cost comparison was made among
the k-means, fuzzy k-means and xFKM. They showed that the xFKM is most suitable for datasets with
categorical attributes, where the attributes vary in a medium and acceptable range of diverse values.
Amir et al. [61] offered a cost function and distance measure for clustering datasets with mixed
data (datasets with numerical and categorical data) based on co-occurrences of values. In [62],
a kernel function based on “hamming distance” [62] was proposed for embedding categorical data.
The kernel-k-means provides an add-on to the k-means clustering that is designed to find clusters in a
feature space where distances are calculated via kernel functions.
Huang et al. in [63] provided a variant of the k-means algorithm, where a dissimilarity measure is
used as a metric. The algorithm combines the k-means and k-modes clustering for data having mixed
attributes. In [64], the convergence of different versions of the modified k-modes algorithms was
analyzed. The authors proved that the modified algorithms fail to converge to a local minima without
degrading the original k-mode algorithm. To handle this issue, the authors presented two algorithms,
MKM-NOF and MKM-NDM, that apply different methods for representing clusters by weighted
cluster prototypes.
Electronics 2020, 9, 1295 6 of 12

In [65], an “ellipsoidal k-means” algorithm was proposed that extends the “spherical k-means”
algorithm for selecting features in a sparse and high-dimensional dataset. In [66], an entropy
weighting k-means (EWKM) clustering algorithm was presented for clustering sparse datasets with
high dimensions. The algorithm reduces the dispersion within the cluster and increases the negative
weight entropy.
Existing solutions for handling mixed data certainly enhanced the capability of the k-means;
however, as the solutions do not address the initialization problem, several issues with k-means still
remain. Among many proposed measures [67–69], the overlap measure is considered to be the easiest
and most computationally efficient method to find similarity between two categorical attributes [70].
One of the shortcomings of this method is inability to differentiate between the distinct attribute values,
however, focuses on whether two categorical attributes attain equal values or not. However, after a
thorough experimental analysis in [71] on a number of datasets, the authors came to the conclusion that
“No single measure is always superior or inferior. This is to be expected since each dataset has different
characteristics”. Hence, the overlap measure (for categorical attributes) and Euclidean distance (for
numerical attributes) can be combined into a mixed distance measure, as also used in [6,72].

4. Performance Evaluation of k-means Representative Variants

We performed an experimental analysis to investigate different versions of the k-means algorithms
for different datasets, especially for the initialization and mixed-data-type problems (GitHub Link:
shorturl.at/CR245). All datasets are available in te UCI machine learning repository [73]. Table 3
briefly summarizes the datasets. The next subsections discuss the evaluation metrics used, results
analysis and, last but not least, the analysis of computational complexity.

Table 3. Summary of datasets.

Dataset Summary

Widely used by machine learning researchers. The goal is to detect the

Cleveland Heart Disease
presence of heart disease in a patient.

Contains standard network traffic that contains different types of cyber

KDD-Cup 1999 (10%)
attacks simulated in a military network.

Includes features calculated from the images of fine needle aspirate of

Wisconsin Diagnostic Breast Cancer
breast mass.

Epileptic Seizure Recognition Commonly used for feature epileptic seizure prediction.

Contains a mix of attributes, which makes it interesting to be used with

Credit Approval
k-means for mixed attributes.

Contains both categorical and integer values. The missing values are
Postoperative
replaced with an average.

4.1. Metrics Used for Experimental Analysis

To evaluate the performance of different algorithms, the following metrics [1–3] were chosen:
• Accuracy: This measure outlines the extent to which the predicted labels are in agreement with the
true labels. The predicted labels correspond to the class labels where new instances are clustered.
The accuracy is calculated by Equation (1).

Correctly identified class

Accuracy = × 100 (1)
Total number of class

• Adjusted rand index (ARI): Provides a score of similarity between two different clustering results
of the same dataset. For a given set S consisting of α elements and r subsets and two partitions
Y = {Y1 , Y2 , . . . , Yb } and X = { X1 , X2 , . . . , Xc }, the overlap between the two partitions can be
summarized as follows:
Electronics 2020, 9, 1295 7 of 12

Y1 Y2 ... Yb Sums
X1 α11 α12 α1b r1
X2 α21 α22 α2b r2
.. .. .. .. .. ..
. . . . . .
Xc αc1 αc2 ... αcb rc
Sums s1 s2 ... sb

The adjusted rand index (ARI) is then calculated by Equation (2):

α r s
∑ij ( 2ij ) − [∑i ( 2i ) ∑ j ( 2j )]/( 2 )
α
ARI = 1 ri sj ri sj (2)
2 [ ∑i ( 2 ) + ∑ j ( 2 )] − [ ∑i ( 2 ) ∑ j ( 2 )] / ( 2 )
α

The ARI score is adjusted to have values between 0 and 1 to represent scores for random and
perfect clustering, respectively.

4.2. Results
Experimental analysis with k-means [9], x-means [49], constrained k-means [54], k-prototype [63], and
kernel k-means [74] was performed, and a performance comparison in terms of the metrics described
above was made. For each of the experiments, a 10 fold cross validation scheme was used to split
the dataset, and the reported results consist of average and standard deviation of the scores of these
metrics across 10 validation folds. Table 4 addresses the algorithms that deal with initialization issues,
while Table 5 encompasses mixed data type oriented methods.

Table 4. Comparison of different algorithms addressing initialization issue.

Constrained
Metric k-means x-means
k-means
Wisconsin Diagnostic Breast Cancer
Accuracy 0.223 ± 0.310 0.596 ± 0.406 0.086 ± 0.042
ARI 0.690 ± 0.134 0.682 ± 0.13 0.683 ± 0.128
KDD Cup 1999
Accuracy 0.195 ± 0.077 0.118 ± 0.087 0.045 ± 0.034
ARI 0.004 ± 0.007 0.107 ± 0.059 0.085 ± 0.169
Epileptic Seizure
Accuracy 0.101 ± 0.060 0.099 ± 0.012 0.102 ± 0.053
ARI 0.005 ± 0.001 0.002 ± 0.001 0.002 ± 0.002

Table 5. Comparison of k-prototype and Kernel-k-means algorithm datasets with mixed data types.

Metric k-prototype Kernel-k-means

Credit Approval
Accuracy 0.456 ± 0.061 0.437 ± 0.283
ARI 0.004 ± 0.005 0.044 ± 0.092
Cleveland Heart Disease
Accuracy 0.462 ± 0.043 0.590 ± 0.080
ARI 0.003 ± 0.001 0.017 ± 0.041
Post Operative
Accuracy 0.462 ± 0.043 0.590 ± 0.080
ARI 0.003 ± 0.001 0.017 ± 0.041
Electronics 2020, 9, 1295 8 of 12

Table 4 summarizes the mean and the standard deviation across five validation folds and compares
the performance between regular k-means, x-means, and constrained k-means algorithms in terms of
different metrics for the Wisconsin Diagnostic Breast cancer, KDD Cup 1999 (10%) and Epileptic
Seizure datasets. In Figure 3, it is shown that the algorithm performance varied with different
datasets. For example, the k-means performed best with the KDD Cup datasets and x-means had
the worst accuracy. However, the x-means performed better than the other two in the Epileptic
dataset. The constrained-k-means performed best in the Wisconsin dataset. In terms of ARI score,
the constrained-k-means seemed to perform in a consistent manner. The key takeaway from these
results is that there is no algorithm that will provide a consistent solution regardless of the dataset.
60 1
k-means k-means
constrained k-means Constrained k-means
50 x-means x-means

40
Accuracy (%)

30

ARI
0.5

20

10

0
KDD Cup Wisconsin Epileptic 0
Datasets KDD Cup Wisconsin Epileptic

a. Accuracy b. ARI

Figure 3. Performance of k-means variants addressing initialization issue.

Table 5 compares the performance between the k-prototype and kernel-k-means algorithms.
These algorithms are suitable for datasets that consist of mixed attributes. In Figure 4, it is reflected
that the k-prototype performed better using the Credit Approval and Post Operative datasets when
considering the accuracy of clustering. However, kernel-k-means performed best using the Cleveland
Heart Disease dataset. In terms of ARI score comparison, the kernel-k-means algorithm consistently
performed better than k-prototype using all three datasets containing mixed data.

60 0.1
k-prototype k-prototype
kernel k-means kernel k-means
50
0.08
40
Accuracy (%)

0.06
30
ARI

20 0.04

10 0.02

0
Credit Cleveland Post Operative 0
Datasets with Mixed Data Types Credit Cleveland Post Operative

a. Accuracy b. ARI

Figure 4. Performance of k-means variants addressing mixed data problem.

4.3. Computational Complexity Analysis

In addition to the comparison of these variants of k-means algorithms in terms of different metrics
on different datasets, a time and space complexity comparison of these algorithms was also carried
out. Both the time and space complexities of these algorithms depend on the size n of the datasets.
Finding an optimal solution for the k-means algorithm is hard in the Euclidean space for both the
binary and multi-class clustering problems. The regular k-means algorithm have a time complexity
Electronics 2020, 9, 1295 9 of 12

of O(n2 ), where n is the size of the input data. However, it can be optimized to be linear and be in
the order of O(n) using certain heuristics mentioned in [75,76]. By contrast, the time complexity for
constrained-k-means is of the order O(kn), where k represents the amount of clusters. It reflects that the
constrained-k-means has a lower time complexity than the regular k-means when the dataset size grows.
The x-means algorithm, on the other hand, was mainly proposed in order to address the scalability
issue of the regular k-means algorithm for large datasets, since x-means involves a progressive increase
in the number of clusters within a user-supplied range (k min , k max ). The time complexity of the x-means
algorithm is therefore in the order of O(n log k max ). k max is the maximum number clusters possible in
a dataset. The space complexity for all these k-means variants is O((n + k)d), where d is the number of
features in a dataset. Table 6 shows the complexities of the different clustering algorithms.

Table 6. Complexities of different variants of k-means.

Complexity k-means Constrained-k-means x-means

Time O(n2 ) O(kn) O(n log k max )
Space O((n + k)d) O((n + k)d) O((n + k)d)

5. Conclusions
In a wide range of application domains, data analysis tasks heavily rely on clustering. This paper
focused on the popular k-means algorithm and the issues of initialization and inability to handle data
with mixed types of features. Unlike other review or survey papers, this paper contains both a critical
analysis of the existing literature and an experimental analysis on half a dozen benchmark datasets to
demonstrate the performances of different variants of k-means. The experimental analysis divulged
that there is no universal solution for the problems of the k-means algorithm; rather each of the existing
variants of the algorithm is either application-specific or data-specific. Our future research will focus
on developing a robust k-means algorithm that can address both problems simultaneously. This paper
will also help the data mining research community to design and develop newer types of clustering
algorithms that can address the research issues around Big Data [34,72].

Author Contributions: Conceptualization, M.A.; Data curation, R.S. and M.A.; Formal analysis, M.A., R.S., and
S.M.S.I.; Funding acquisition, M.A., R.S.; Investigation, M.A., R.S., and S.M.S.I.; Methodology, M.A; Project
administration, M.A. and S.M.S.I.; Supervision, M.A. and S.M.S.I.; Validation, R.S. and M.A.; Visualization,
M.A. and R.S.; and Writing—original draft, M.A. and R.S.; Writing—review and editing, M.A., R.S. and S.M.S.I.
All authors have read and agreed to the published version of the manuscript. Authorship must be limited to those
who have contributed substantially to the work reported.
Funding: This research received no external funding.
Conflicts of Interest: The authors declare no conflict of interest.

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