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K-Means Clustering

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180 views

K-Means Clustering

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LUCKY
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© © All Rights Reserved
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k-means clustering

k-means clustering is a method of vector quantization, originally from signal processing, that is popular
for cluster analysis in data mining. k-means clustering aims to partition n observations into k clusters in
which each observation belongs to the cluster with the nearest mean, serving as a prototype of the cluster.
This results in a partitioning of the data space into Voronoi cells. k-Means minimizes within-cluster
variances (squared Euclidean distances), but not regular Euclidean distances, which would be the more
difficult Weber problem: the mean optimizes squared errors, whereas only the geometric median
minimizes Euclidean distances. Better Euclidean solutions can for example be found using k-medians
and k-medoids.

The problem is computationally difficult (NP-hard); however, efficient heuristic algorithms converge
quickly to a local optimum. These are usually similar to the expectation-maximization algorithm for
mixtures of Gaussian distributions via an iterative refinement approach employed by both k-means and
Gaussian mixture modeling. They both use cluster centers to model the data; however, k-means clustering
tends to find clusters of comparable spatial extent, while the expectation-maximization mechanism
allows clusters to have different shapes.

The algorithm has a loose relationship to the k-nearest neighbor classifier, a popular machine learning
technique for classification that is often confused with k-means due to the name. Applying the 1-nearest
neighbor classifier to the cluster centers obtained by k-means classifies new data into the existing
clusters. This is known as nearest centroid classifier or Rocchio algorithm.

Contents
Description
History
Algorithms
Standard algorithm (naive k-means)
Initialization methods
Complexity
Variations
Hartigan–Wong method
Global optimization and metaheuristics
Discussion
Applications
Vector quantization
Cluster analysis
Feature learning
Relation to other algorithms
Gaussian mixture model
K-SVD
Principal component analysis
Mean shift clustering
Independent component analysis
Bilateral filtering
Similar problems
Software implementations
Free Software/Open Source
Proprietary
See also
References

Description
Given a set of observations (x1, x2, ..., xn), where each observation is a d-dimensional real vector, k-
means clustering aims to partition the n observations into k (≤ n) sets S = {S1, S2, ..., Sk} so as to
minimize the within-cluster sum of squares (WCSS) (i.e. variance). Formally, the objective is to find:

where μi is the mean of points in Si. This is equivalent to minimizing the pairwise squared deviations of
points in the same cluster:

The equivalence can be deduced from identity . Because

the total variance is constant, this is equivalent to maximizing the sum of squared deviations between
points in different clusters (between-cluster sum of squares, BCSS),[1] which follows from the law of
total variance.

History
The term "k-means" was first used by James MacQueen in 1967,[2] though the idea goes back to Hugo
Steinhaus in 1956.[3] The standard algorithm was first proposed by Stuart Lloyd of Bell Labs in 1957 as a
technique for pulse-code modulation, though it wasn't published as a journal article until 1982.[4] In
1965, Edward W. Forgy published essentially the same method, which is why it is sometimes referred to
as Lloyd-Forgy.[5]

Algorithms

Standard algorithm (naive k-means)


The most common algorithm uses an iterative refinement technique. Due to its ubiquity, it is often called
"the k-means algorithm"; it is also referred to as Lloyd's algorithm, particularly in the computer science
community. It is sometimes also referred to as "naive k-means", because there exist much faster
alternatives.[6]
Given an initial set of k means m1(1),...,mk(1) (see below), the
algorithm proceeds by alternating between two steps:[7]

Assignment step: Assign each observation to the


cluster whose mean has the least squared Euclidean
distance, this is intuitively the "nearest" mean.[8]
(Mathematically, this means partitioning the
observations according to the Voronoi diagram
generated by the means.)

Convergence of k-means

where each is assigned to exactly one , even if it could be assigned to two or


more of them.

Update step: Calculate the new means (centroids) of the observations in the new
clusters.

The algorithm has converged when the assignments no longer change. The algorithm does not guarantee
to find the optimum.[9]

The algorithm is often presented as assigning objects to the nearest cluster by distance. Using a different
distance function other than (squared) Euclidean distance may stop the algorithm from converging.
Various modifications of k-means such as spherical k-means and k-medoids have been proposed to allow
using other distance measures.

Initialization methods
Commonly used initialization methods are Forgy and Random Partition.[10] The Forgy method randomly
chooses k observations from the dataset and uses these as the initial means. The Random Partition
method first randomly assigns a cluster to each observation and then proceeds to the update step, thus
computing the initial mean to be the centroid of the cluster's randomly assigned points. The Forgy
method tends to spread the initial means out, while Random Partition places all of them close to the
center of the data set. According to Hamerly et al.,[10] the Random Partition method is generally
preferable for algorithms such as the k-harmonic means and fuzzy k-means. For expectation
maximization and standard k-means algorithms, the Forgy method of initialization is preferable. A
comprehensive study by Celebi et al.,[11] however, found that popular initialization methods such as
Forgy, Random Partition, and Maximin often perform poorly, whereas Bradley and Fayyad's approach[12]
performs "consistently" in "the best group" and k-means++ performs "generally well".

Demonstration of the standard algorithm


1. k initial "means" (in 2. k clusters are created 3. The centroid of each
this case k=3) are by associating every of the k clusters
randomly generated observation with the becomes the new mean.
within the data domain nearest mean. The
(shown in color). partitions here represent
the Voronoi diagram
generated by the means.

4. Steps 2 and 3 are


repeated until
convergence has been
reached.

The algorithm does not guarantee convergence to the global optimum. The result may depend on the
initial clusters. As the algorithm is usually fast, it is common to run it multiple times with different
starting conditions. However, worst-case performance can be slow: in particular certain point sets, even
in two dimensions, converge in exponential time, that is 2Ω(n).[13] These point sets do not seem to arise
in practice: this is corroborated by the fact that the smoothed running time of k-means is polynomial.[14]

The "assignment" step is referred to as the "expectation step", while the "update step" is a maximization
step, making this algorithm a variant of the generalized expectation-maximization algorithm.

Complexity
Finding the optimal solution to the k-means clustering problem for observations in d dimensions is:

NP-hard in general Euclidean space (of d dimensions) even for two clusters,[15][16][17][18]
NP-hard for a general number of clusters k even in the plane,[19]
if k and d (the dimension) are fixed, the problem can be exactly solved in time ,
where n is the number of entities to be clustered.[20]
Thus, a variety of heuristic algorithms such as Lloyd's algorithm given above are generally used.
The running time of Lloyd's algorithm (and most variants) is ,[9][21] where:

n is the number of d-dimensional vectors (to be clustered)


k the number of clusters
i the number of iterations needed until convergence.
On data that does have a clustering structure, the number of iterations until convergence is often small,
and results only improve slightly after the first dozen iterations. Lloyd's algorithm is therefore often
considered to be of "linear" complexity in practice, although it is in the worst case superpolynomial when
performed until convergence.[22]

In the worst-case, Lloyd's algorithm needs iterations, so that the worst-case


complexity of Lloyd's algorithm is superpolynomial.[22]
Lloyd's k-means algorithm has polynomial smoothed running time. It is shown that[14] for
arbitrary set of n points in , if each point is independently perturbed by a normal
distribution with mean 0 and variance , then the expected running time of k-means
algorithm is bounded by , which is a polynomial in n, k, d and .
Better bounds are proven for simple cases. For example, in [23] it is shown that the running
time of k-means algorithm is bounded by for n points in an integer lattice
.
Lloyd's algorithm is the standard approach for this problem. However, it spends a lot of processing time
computing the distances between each of the k cluster centers and the n data points. Since points usually
stay in the same clusters after a few iterations, much of this work is unnecessary, making the naive
implementation very inefficient. Some implementations use caching and the triangle inequality in order
to create bounds and accelerate Lloyd's algorithm.[9][24][25][26][27]

Variations
Jenks natural breaks optimization: k-means applied to univariate data
k-medians clustering uses the median in each dimension instead of the mean, and this way
minimizes norm (Taxicab geometry).
k-medoids (also: Partitioning Around Medoids, PAM) uses the medoid instead of the mean,
and this way minimizes the sum of distances for arbitrary distance functions.
Fuzzy C-Means Clustering is a soft version of k-means, where each data point has a fuzzy
degree of belonging to each cluster.
Gaussian mixture models trained with expectation-maximization algorithm (EM algorithm)
maintains probabilistic assignments to clusters, instead of deterministic assignments, and
multivariate Gaussian distributions instead of means.
k-means++ chooses initial centers in a way that gives a provable upper bound on the
WCSS objective.
The filtering algorithm uses kd-trees to speed up each k-means step.[28]
Some methods attempt to speed up each k-means step using the triangle
inequality.[24][25][26][29][27]
Escape local optima by swapping points between clusters.[9]
The Spherical k-means clustering algorithm is suitable for textual data.[30]
Hierarchical variants such as Bisecting k-means,[31] X-means clustering[32] and G-means
clustering[33] repeatedly split clusters to build a hierarchy, and can also try to automatically
determine the optimal number of clusters in a dataset.
Internal cluster evaluation measures such as cluster silhouette can be helpful at determining
the number of clusters.
Minkowski weighted k-means automatically calculates cluster specific feature weights,
supporting the intuitive idea that a feature may have different degrees of relevance at
different features.[34] These weights can also be used to re-scale a given data set,
increasing the likelihood of a cluster validity index to be optimized at the expected number
of clusters.[35]
Mini-batch k-means: k-means variation using "mini batch" samples for data sets that do not
fit into memory.[36]

Hartigan–Wong method
Hartigan and Wong's method[9] provides a variation of k-means algorithm which progresses towards a
local minimum of the minimum sum-of-squares problem with different solution updates. The method is a
local search that iteratively attempts to relocate a sample into a different cluster as long as this process
improves the objective function. When no sample can be relocated into a different cluster with an
improvement of the objective, the method stops (in a local minimum). In a similar way as the classical k-
means, the approach remains a heuristic since it does not necessarily guarantee that the final solution is
globally optimum.

Let be the individual cost of defined by , with the center of the cluster.

Assignment step: Hartigan and Wong's method starts by partitioning the points into random clusters
.

Update step: Next it determines the and for which the following function
reaches a minimum

For the that reach this minimum, moves from the cluster to the cluster .

Termination: The algorithm terminates once is larger than zero for all .

Different move acceptance strategies can be used. In a first-improvement strategy, any improving
relocation can be applied, whereas in a best-improvement strategy, all possible relocations are iteratively
tested and only the best is applied at each iteration. The former approach favors speed, whether the latter
approach generally favors solution quality at the expense of additional computational time. The function
used to calculate the result of a relocation can also be efficiently evaluated by using equality[37]

Global optimization and metaheuristics


The classical k-means algorithm and its variations are known to only converge to local minima of the
minimum-sum-of-squares clustering problem defined as
Many studies have attempted to improve the convergence behavior of the algorithm and maximize the
chances of attaining the global optimum (or at least, local minima of better quality). Initialization and
restart techniques discussed in the previous sections are one alternative to find better solutions. More
recently, mathematical programming algorithms based on branch-and-bound and column generation have
produced ‘’provenly optimal’’ solutions for datasets with up to 2,300 entities[38]. As expected, due to the
NP-hardness of the subjacent optimization problem, the computational time of optimal algorithms for K-
means quickly increases beyond this size. Optimal solutions for small- and medium-scale still remain
valuable as a benchmark tool, to evaluate the quality of other heuristics. To find high-quality local
minima within a controlled computational time but without optimality guarantees, other works have
explored metaheuristics and other global optimization techniques, e.g., based on incremental approaches
and convex optimization[39], random swaps[40] (i.e., iterated local search), variable neighborhood
search[41]and genetic algorithms[42][43]. It is indeed known that finding better local minima of the
minimum sum-of-squares clustering problem can make the difference between failure and success to
recover cluster structures in feature spaces of high dimension[43].

Discussion

A typical example of the k-means convergence to a local minimum. In this example, the result of k-means
clustering (the right figure) contradicts the obvious cluster structure of the data set. The small circles are the
data points, the four ray stars are the centroids (means). The initial configuration is on the left figure. The
algorithm converges after five iterations presented on the figures, from the left to the right. The illustration was
prepared with the Mirkes Java applet.[44]

Three key features of k-


means that make it efficient
are often regarded as its
biggest drawbacks:

Euclidean distance is
used as a metric and
variance is used as a
measure of cluster
scatter.
The number of clusters
k is an input
parameter: an k-means clustering result for the Iris flower data set and actual species
inappropriate choice of visualized using ELKI. Cluster means are marked using larger, semi-
k may yield poor transparent symbols.
results. That is why,
when performing k-
means, it is important to run diagnostic checks for determining the number of clusters in the
data set.
Convergence to a local
minimum may produce
counterintuitive
("wrong") results (see
example in Fig.).
A key limitation of k-means
is its cluster model. The
concept is based on spherical
clusters that are separable so
that the mean converges
k-means clustering vs. EM clustering on an artificial dataset ("mouse"). The
towards the cluster center.
tendency of k-means to produce equal-sized clusters leads to bad results
The clusters are expected to here, while EM benefits from the Gaussian distributions with different radius
be of similar size, so that the present in the data set.
assignment to the nearest
cluster center is the correct
assignment. When for example applying k-means with a value of onto the well-known Iris flower
data set, the result often fails to separate the three Iris species contained in the data set. With , the
two visible clusters (one containing two species) will be discovered, whereas with one of the two
clusters will be split into two even parts. In fact, is more appropriate for this data set, despite the
data set's containing 3 classes. As with any other clustering algorithm, the k-means result makes
assumptions that the data satisfy certain criteria. It works well on some data sets, and fails on others.

The result of k-means can be seen as the Voronoi cells of the cluster means. Since data is split halfway
between cluster means, this can lead to suboptimal splits as can be seen in the "mouse" example. The
Gaussian models used by the expectation-maximization algorithm (arguably a generalization of k-means)
are more flexible by having both variances and covariances. The EM result is thus able to accommodate
clusters of variable size much better than k-means as well as correlated clusters (not in this example). In
counterpart, EM requires the optimization of a larger number of free parameters and poses some
methodological issues due to vanishing clusters or badly-conditioned covariance matrices. K-means is
closely related to nonparametric Bayesian modeling.[45]

Applications
k-means clustering is rather easy to apply to even large data sets, particularly when using heuristics such
as Lloyd's algorithm. It has been successfully used in market segmentation, computer vision, and
astronomy among many other domains. It often is used as a preprocessing step for other algorithms, for
example to find a starting configuration.

Vector quantization
k-means originates from signal processing, and still finds use in this domain. For example, in computer
graphics, color quantization is the task of reducing the color palette of an image to a fixed number of
colors k. The k-means algorithm can easily be used for this task and produces competitive results. A use
case for this approach is image segmentation. Other uses of vector quantization include non-random
sampling, as k-means can easily be used to choose k different but prototypical objects from a large data
set for further analysis.
Cluster analysis
In cluster analysis, the k-means algorithm can be used to partition
the input data set into k partitions (clusters).

However, the pure k-means algorithm is not very flexible, and as


such is of limited use (except for when vector quantization as above
is actually the desired use case). In particular, the parameter k is
known to be hard to choose (as discussed above) when not given by
external constraints. Another limitation is that it cannot be used with
arbitrary distance functions or on non-numerical data. For these use
cases, many other algorithms are superior. Two-channel (for illustration
purposes -- red and green only)
color image.
Feature learning
k-means clustering has been used as a feature learning (or
dictionary learning) step, in either (semi-)supervised learning
or unsupervised learning.[46] The basic approach is first to
train a k-means clustering representation, using the input
training data (which need not be labelled). Then, to project
any input datum into the new feature space, an "encoding"
function, such as the thresholded matrix-product of the
datum with the centroid locations, computes the distance
from the datum to each centroid, or simply an indicator
function for the nearest centroid,[46][47] or some smooth
transformation of the distance.[48] Alternatively,
transforming the sample-cluster distance through a Gaussian
RBF, obtains the hidden layer of a radial basis function Vector quantization of colors present in the
network.[49] image above into Voronoi cells using k-
means.
This use of k-means has been successfully combined with
simple, linear classifiers for semi-supervised learning in
NLP (specifically for named entity recognition)[50] and in computer vision. On an object recognition
task, it was found to exhibit comparable performance with more sophisticated feature learning
approaches such as autoencoders and restricted Boltzmann machines.[48] However, it generally requires
more data, for equivalent performance, because each data point only contributes to one "feature".[46]

Relation to other algorithms

Gaussian mixture model


The slow "standard algorithm" for k-means clustering, and its associated expectation-maximization
algorithm, is a special case of a Gaussian mixture model, specifically, the limiting case when fixing all
covariances to be diagonal, equal and have infinitesimal small variance.[51]:850 Instead of small
variances, a hard cluster assignment can also be used to show another equivalence of k-means clustering
to a special case of "hard" Gaussian mixture modelling.[52](11.4.2.5) This does not mean that it is efficient
to use Gaussian mixture modelling to compute k-means, but just that there is a theoretical relationship,
and that Gaussian mixture modelling can be interpreted as a generalization of k-means; on the contrary, it
has been suggested to use k-means clustering to find starting points for Gaussian mixture modelling on
difficult data.[51]:849

K-SVD
Another generalization of the k-means algorithm is the K-SVD algorithm, which estimates data points as
a sparse linear combination of "codebook vectors". k-means corresponds to the special case of using a
single codebook vector, with a weight of 1.[53]

Principal component analysis


The relaxed solution of k-means clustering, specified by the cluster indicators, is given by principal
component analysis (PCA).[54][55] The PCA subspace spanned by the principal directions is identical to
the cluster centroid subspace. The intuition is that k-means describe spherically shaped (ball-like)
clusters. If the data has 2 clusters, the line connecting the two centroids is the best 1-dimensional
projection direction, which is also the first PCA direction. Cutting the line at the center of mass separates
the clusters (this is the continuous relaxation of the discrete cluster indicator). If the data have three
clusters, the 2-dimensional plane spanned by three cluster centroids is the best 2-D projection. This plane
is also defined by the first two PCA dimensions. Well-separated clusters are effectively modelled by ball-
shaped clusters and thus discovered by k-means. Non-ball-shaped clusters are hard to separate when they
are close. For example, two half-moon shaped clusters intertwined in space do not separate well when
projected onto PCA subspace. k-means should not be expected to do well on this data.[56] It is
straightforward to produce counterexamples to the statement that the cluster centroid subspace is spanned
by the principal directions.[57]

Mean shift clustering


Basic mean shift clustering algorithms maintain a set of data points the same size as the input data set.
Initially, this set is copied from the input set. Then this set is iteratively replaced by the mean of those
points in the set that are within a given distance of that point. By contrast, k-means restricts this updated
set to k points usually much less than the number of points in the input data set, and replaces each point
in this set by the mean of all points in the input set that are closer to that point than any other (e.g. within
the Voronoi partition of each updating point). A mean shift algorithm that is similar then to k-means,
called likelihood mean shift, replaces the set of points undergoing replacement by the mean of all points
in the input set that are within a given distance of the changing set.[58] One of the advantages of mean
shift over k-means is that the number of clusters is not pre-specified, because mean shift is likely to find
only a few clusters if only a small number exist. However, mean shift can be much slower than k-means,
and still requires selection of a bandwidth parameter. Mean shift has soft variants.

Independent component analysis


Under sparsity assumptions and when input data is pre-processed with the whitening transformation, k-
means produces the solution to the linear independent component analysis (ICA) task. This aids in
explaining the successful application of k-means to feature learning.[59]

Bilateral filtering
k-means implicitly assumes that the ordering of the input data set does not matter. The bilateral filter is
similar to k-means and mean shift in that it maintains a set of data points that are iteratively replaced by
means. However, the bilateral filter restricts the calculation of the (kernel weighted) mean to include only
points that are close in the ordering of the input data.[58] This makes it applicable to problems such as
image denoising, where the spatial arrangement of pixels in an image is of critical importance.

Similar problems
The set of squared error minimizing cluster functions also includes the k-medoids algorithm, an approach
which forces the center point of each cluster to be one of the actual points, i.e. it uses medoids in place of
centroids.

Software implementations
Different implementations of the algorithm exhibit performance differences, with the fastest on a test data
set finishing in 10 seconds, the slowest taking 25,988 seconds (~7 hours).[1] The differences can be
attributed to implementation quality, language and compiler differences, different termination criteria and
precision levels, and the use of indexes for acceleration.

Free Software/Open Source


The following implementations are available under Free/Open Source Software licenses, with publicly
available source code.

Accord.NET contains C# implementations for k-means, k-means++ and k-modes.


ALGLIB contains parallelized C++ and C# implementations for k-means and k-means++.
AOSP contains a Java implementation for k-means.
CrimeStat implements two spatial k-means algorithms, one of which allows the user to
define the starting locations.
ELKI contains k-means (with Lloyd and MacQueen iteration, along with different
initializations such as k-means++ initialization) and various more advanced clustering
algorithms.
Julia contains a k-means implementation in the JuliaStats Clustering package.
KNIME contains nodes for k-means and k-medoids.
Mahout contains a MapReduce based k-means.
mlpack contains a C++ implementation of k-means.
Octave contains k-means.
OpenCV contains a k-means implementation.
Orange includes a component for k-means clustering with automatic selection of k and
cluster silhouette scoring.
PSPP contains k-means, The QUICK CLUSTER command performs k-means clustering on
the dataset.
R contains three k-means variations.
SciPy and scikit-learn contain multiple k-means implementations.
Spark MLlib implements a distributed k-means algorithm.
Torch contains an unsup package that provides k-means clustering.
Weka contains k-means and x-means.
Proprietary
The following implementations are available under proprietary license terms, and may not have publicly
available source code.

Ayasdi OriginPro SAS


Mathematica RapidMiner SPSS
MATLAB SAP HANA Stata

See also
BFR algorithm
Centroidal Voronoi tessellation
Head/tail Breaks
k q-flats
K-means++
Linde–Buzo–Gray algorithm
Self-organizing map

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