K-Means Algorithm Implementation

Muhammad Waqas Moin Sheikh (15129145, BJTU)

Practice Course: Machine Learning and Cognitive Computing

I.

Abstract

In this work the K-mean clustering algorithm is applied to Fishers Iris Plant Dataset. The data
set known to include 3 classes of Iris plant data. Setosa, Verginica and Versicolor. One of
which is linearly separable from other two, to assesses the capabilities of clustering algorithm,
it is applied to the data set with varied number of initials centers and stopping thresholds, it
will be shown that the K-means Clustering algorithm is capable of perfectly separating the
Setosa data set from others two, as expected, and able to achieve the acceptable recognition of
the other two plants species.

II.

Introduction

K-Means Clustering is an unsupervised learning algorithm that tries to cluster data based on
their similarity. Unsupervised learning means that there is no outcome to be predicted, and the
algorithm just tries to find patterns in the data. In k means clustering, we have to specify the
number of clusters that we want the data to be grouped into. The algorithm randomly assigns
each observation to a cluster, and finds the centroid of each cluster. Then, the algorithm repeats
through two steps. The first one is to reassign the data points to the cluster whose centroid is
closest and the second one is to calculate new centroids of each clusters.

Figure 1: k-means clustering result for the Iris flower data set and actual species visualized.

III.

Methodology

The K-means algorithm is an unsupervised algorithm that attempts to cluster data into groups
based on a chosen similarity measure. In this work, the similarity measure of choice is
Euclidean distance. To create the clusters, the K-Means algorithm iteratively implements the
following steps:
I. Initialize - Initialize the centre of each cluster.
II. Distribute data points - Assign each data point to the cluster whose centre is the smallest
distance from the data point.
III. Compute new cluster centres Set the position of the cluster centre to the mean of all
data points belonging to that cluster.
IV. Compare new centres to old center, If the new centres are the same as the old centres,
then the algorithm converges. The clusters and centres computed in step 3 are the final
clusters and centres. If they are not the same, return to step 2.
In reality, it may not always be possible to find centers that do not change from iteration to
iteration. In other words, this algorithm may not always lead to a perfect solution. Some
datasets may lead to centers that oscillate between two values, for example. So, to avoid an
infinite loop when iterating through the algorithm, the threshold is used as another stopping
condition. When the new cluster centers are identified at the end of each iteration, the amount
of change in the clusters is also taken into consideration. This is done by measuring the distance
between the new centers and old centers. If this distance is less than the threshold distance, the
algorithm converges.

IV.

Experimental Setup

This project was broken up into two tasks. First, the K-means algorithm was coded into a
general function so that the number of centers and threshold value could be easily varied. Next,
a shell to call the function iteratively for each of the three k values and two threshold values
was created. The results of each run was saved to a cell array. The function can be reviewed in
Appendix A. In addition to making the function more general, the convergence test step was
modified to include the threshold as a stopping condition for the algorithm. So, the function
takes in the following inputs: data, number of centers, and threshold value. Given these
parameters, the K-meansm function will return the following two cells: centers per iteration,
assigned classes per iteration. More in-depth consideration of pertinent steps are presented
below.

Initializing the centers

An important consideration in the K-means algorithm is the choice in initial centers.
Since this is an unsupervised algorithm, I chose to use sample values as the initial
centers. However, instead of using the first k sample values, I decided to choose the
centers at random for each iteration. This was achieved using the code snippet below.
Z = x(randi([1,numSamples],centers,1),:); %k initial centers

Implementing the threshold as a stopping condition

To avoid an infinite loop when the K-means function is called, step 4 of the algorithm
was modified to include the threshold as a stopping condition. First, the new centers are
compared to the old centers. If the new centers do not match the old centers, then the
distance between them is computed using the norm function as shown in the code
snippet below. This difference is compared to the threshold value. If the distance is less
than the threshold, the algorithm converges. This is summarized in the code snippet
below.
case 4 %Step 4: compare new centers to old centers
if Z_iter{m+1} == Z_iter{m} %if new center = current center
NotEq = 0; %algorithm converges
break;
else if m == 1 %if 1st iter, no prev distance, just proceed
m = m+1;
step = 2;
else %if not 1st iter and Z \= Znew
%check stopping conditions
if abs(Dist_iter{m} - Dist_iter{m-1}) < threshold
NotEq = 0;
break;
else
m = m+1; %new iteration
step = 2; %go back to step 2
end
end

Confusion Matrix
After calling the Kmeans function, the confusion matrix was generated for each
simulation using the Matlab confusionmat function. The results can be seen in the
subsequent section.

Result
As previously stated, K-means clustering was applied six times to the dataset. The
results are broken up into two groups and presented based on the chosen threshold
value.

Threshold = 0.01
Below, the confusion matrix for the three different choices of number of initial centers
is shown. In each simulation, the stopping threshold was set to 0.01.
1
Setosa

50 0

Setosa

50

Setosa

50 0

Versicolor 3

47

Versicolor

48

Versicolor 0

Virginica

50

Virginica

36

14

Virginica

21 26 1

Table 1. K = 2 Confusion Matrix

Table 2. K = 3 Confusion Matrix

21 29

Table 3.

It can be seen that in each case, the Setosa plant species was easily separated from the
others. However, the Versicolor and Virginica datasets were not as easily distinguished
from each other as they were from the Setosa. However, it is interesting to see that when
there were just 2 centers, the Virginica dataset was able to be perfectly separated from
the others. The Versicolor. However, is still straddling between the two clusters. It is
mostly clustered with the Virginica dataset, but there are several pieces that were
clustered with the Setosa plants.

Threshold = 0.1
Below, the confusion matrix for the three different choices of number of initial centers
is shown. In each simulation, the stopping threshold was set to 0.1.
1

50

Setosa

50

Setosa

Versicolor 47 3

Versicolor

47

Versicolor 0

25 25 0

Virginica

Virginica

14

36

Virginica

17 1

Setosa

50 0

Table 4. K = 2 Confusion Matrix

Table 5. K = 3 Confusion Matrix

50 0

32

Table 6

Increasing the threshold did not have much of an impact on the final confusion matrices.
Although there is some shifting of the data points, as is evidenced by the values shown
in the tables, the overall clustering results are quite similar. In all three runs, the Setosa
species was perfectly separated from the other two species. The other two species, on
average could not be perfectly separated. However, when there are two centers, the

Setosa and Virginica sets are again easily separated from one another while the
Versicolor is split (unevenly) between the two clusters.
V.

Conclusions

Using Matlab and a personal computer, the K-means algorithm was applied to the Iris plant
dataset. It was shown that the Setosa dataset was able to be perfectly classified in each case.
The other two species Versicolor and Virginica were not as easily separated from each other
as they were from the Setosa plant. After randomly selecting the initial centers, varying the
number of centers, and manipulating the stopping threshold, these results remained true. Since
these results are typical of the Iris plant dataset and the recognition using the K-means
clustering algorithm was able to reach these results, the K-means algorithm was shown to be a
reliable method of clustering.

VI.

Appendix A - Kmeans.m

%This function takes in a dataset and number of clusters and returns

%the clustered data after applying the K-means algorithm
%inputs: data, number of clusters, threshold
%output: clustered data
function [clusCenters,clusData] = Kmeans (x,cen,t)
centers=cen; %number of centers
threshold = t;
numSamples = size(x,1); %number of samples
sampleLength = size(x,2); %dimension of samples
Dist = zeros(numSamples,centers); %array to hold distances
Class = zeros(numSamples,1); %array to hold classes
Znew = zeros(centers,sampleLength); %array to hold new centers
%step 1
Z = x(randi([1,numSamples],centers,1),:); %k initial centers
m=1;
Z_iter{m} = Z; %save Z values
step = 2;
NotEq = true;
while NotEq
switch step
case 2 %distribute samples to clusters
Z = Z_iter{m}; %grab current centers
for k = 1:centers %for each center
for N = 1:numSamples %for each sample
%compute distance between sample and center
Dist(N,k) = norm(x(N,:)-Z(k,:));
end

end
Dist_iter{m} = norm(Dist);
for N = 1:numSamples %for each sample
minDist = min(Dist(N,:)); %get min dist for sample
[i,j] = find(Dist(N,:) == minDist); %index of min
Class(N) = j(1); %index=class, save index/class
end
Class_Iter{m} = Class; %save class assignments for m
step = 3;
case 3 %compute new centers
for k = 1:centers%for each center
C = find(Class == k); %find all samples in class
zt = [0,0];
for i = 1:size(C,1) %for every sample in class
zt = zt + x(C(i),:); %add sample to sum
end
Znew(k,:) = zt/size(C,1); %center = sample mean
end
Z_iter{m+1} = Znew; %save next centers
step = 4;
case 4 %compare new centers to old centers
if Z_iter{m+1} == Z_iter{m} %if new = current
NotEq = 0; %algorithm converges
break;
elseif m == 1 %if 1st iter, no prev distance, proceed
m = m+1;
step = 2;
else %if not 1st iter and Z \= Znew
%check stopping conditions
if abs(Dist_iter{m} - Dist_iter{m-1}) < threshold
NotEq = 0;
break;
else
m = m+1; %new iteration
step = 2; %go back to step 2
end
end
end
end
clusCenters = Z_iter; %return cluster centers per iteration
clusData = Class_Iter; %return clusters per iteration
end

VII. Appendix B project1.m

%This program loads the iris data set, then iteratively calls the k-means
%function to implement the k-means clustering algorithm for k values of 2,
%3, and 4 cluster center using different threshold values.
clear;
iris = csvread('iris.csv'); %load dataset
x = iris(:,1:end-1);
%get all but the class value
y = iris(:,end);
%set simulation parameters
k = [2 3 4];
%number of centers
t = [0.01 0.1];
%stopping threshold
for i = 1:size(k,2)
for j = 1:size(t,2)
[centers, clusters] = Kmeans(x,k(i),t(j));
CONF{i,j} = confusionmat(y,clusters{end});
End
end

VIII. References
[1]http://www.r-bloggers.com/k-means-clustering-in-r/
[2]Monique Kirkman-Bey, K-MEANS CLUSTERING & THE IRIS PLANT DATASET
[3]http://www.cs.colostate.edu/~anderson/cs545/index.html/lib/exe/fetch.php?media=assign
ments:solutions1:two.pdf
[4]https://www.youtube.com/watch?v=Qy2vEecfucY
[5]https://www.google.com/search?q=KMeans+Clustering&biw=1366&bih=667&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjj
k72igbnMAhWMcT4KHWSlAn0Q_AUICCgD#imgrc=o7bZUFEHo72JXM%3A
[6]http://www.mathworks.com/help/stats/kmeans.html?s_tid=gn_loc_drop