The K -Means algorithm implementation from scratch in Python

Mohammed Kharma[0000−0001−8280−3285]

Department of Computer Science, Birzeit University, Birzeit, Palestine

mkharmah@birzeit.edu

1 Introduction

Clustering is an unsupervised machine learning approach that groups together comparable data elements based on their feature values [2]. Several clustering methods are available, each with its own set of advantages and disadvantages based on the nature of the data and the use case. The fundamental structure of the data distribution is exploited by clustering algorithms, which also provide criteria for categorizing data that have matching features [2]. K-Means, also known as c-Means, is a popular clustering algorithm and the first version was suggested in 1957 by Stuart Lloyd as a method for pulse-code modulation, his method was kept inside Bell Labs until he published it in 1982 [3]. K-Means is an unsupervised learning algorithm that works on grouping similar data points together based on their feature values. The k-mean process works by constructing different partitions/ clusters for the targeted dataset based on the clustering rules and with no previous knowledge of the dataset. Each cluster is made up of comparable data points that are very different from the points in the other clusters [1]. Such a dissimilarity metric depends on the underlying data and the algorithm’s goal. Clustering is a fundamental problem in machine learning since it is crucial to many data-driven applications.

The rest of this report is organized as follows, section 2 presents a descrip- tion of each dataset. Section 3 presents algorithm description, pseudo-code, and mathematical formulation. Section 4 presents the experiments and its results. Finally, section 5 provides some takeaways from this work.

2 Dataset

In this report, we report the results of using the following datasets:

• Iris dataset:

- classes : 3
- data points : 150

RangeIndex : 150 entries , 0 to 149 Data columns ( total 5 columns ):

- Column Non − Null Count Dtype

−−− −−−−−− −−−−−−−−−−−−−− −−−−−

The K -Means Project 

0  0 150 non− null float64
0  1 150 non− null float64
0  2 150 non− null float64
0  3 150 non− null float64
0  4 150 non− null object

Dataset description :

0 1 2 3 count 150.000000 150.000000 150.000000 150.000000 mean 5.843333 3.054000 3.758667 1.198667 std 0.828066 0.433594 1.764420 0.763161 min 4.300000 2.000000 1.000000 0.100000 25% 5.100000 2.800000 1.600000 0.300000 50% 5.800000 3.000000 4.350000 1.300000 75% 6.400000 3.300000 5.100000 1.800000 max 7.900000 4.400000 6.900000 2.500000

The K -Means Project 

Dataset sample :

0  1 2 3
0  5.1 3.5 1.4 0.2
0  4.9 3.0 1.4 0.2
0  4.7 3.2 1.3 0.2
0  4.6 3.1 1.5 0.2
0  5.0 3.6 1.4 0.2

• Three separable gaussians:

�4

Iris − setosa Iris − setosa Iris − setosa Iris − setosa Iris − setosa

The K -Means Project 

- classes : 3
- data points : 300

Dataset information :

RangeIndex : 300 entries , 0 to 299 Data columns ( total 3 columns ):

- Column Non − Null Count Dtype

−−− −−−−−− −−−−−−−−−−−−−− −−−−−

0  0 300 non− null float64
0  1 300 non− null float64
0  2 300 non− null float64

The K -Means Project 

Dataset description :

0 1 count 300.000000 300.000000 mean 0.433244 2.688586 std 1.618409 1.566672 min − 2.948656 − 0.765892 25% − 1.091289 1.162992 50% 0.826162 2.909197 75% 1.697028 4.030363

�2 300.000000

1.000000 0.817861

0.000000 0.000000 1.000000 2.000000



max 3.437618 5.474253 2.000000 Dataset sample :

0 1 2

0  0.428577 4.973997 0.0
0  1.619909 0.067645 1.0
0  1.432893 4.376792 0.0

3 − 1.578462 3.034458 2.0

4 − 1.658629 2.267460 2.0

• Slightly overlapping three gaussians:

- classes : 3
- data points : 300

Dataset information :

RangeIndex : 300 entries , 0 to 299 Data columns ( total 3 columns ):

- Column Non − Null Count Dtype

−−− −−−−−− −−−−−−−−−−−−−− −−−−−

0  0 300 non− null float64
0  1 300 non− null float64
0  2 300 non− null float64

The K -Means Project 

Dataset description :

0 1 count 300.000000 300.000000 mean 0.399093 2.679656 std 1.752898 1.721521 min − 3.659532 − 1.597670 25% − 1.006490 1.227617 50% 0.629149 2.856643 75% 1.759564 4.086663 max 4.128793 6.059485 Dataset sample :

0 1 2

0  0.154730 5.309102 0.0
0  1.402230 − 0.347364 1.0
0  1.661204 4.413295 0.0

3 − 1.604242 3.092746 2.0

4 − 1.724491 1.942249 2.0

�2

300.000000 1.000000 0.817861

0.000000 0.000000 1.000000 2.000000 2.000000

The K -Means Project 

• Moons

- classes : 2
- data points : 1000

Dataset information :

RangeIndex : 1000 entries , 0 to 999 Data columns ( total 3 columns ):

- Column Non − Null Count Dtype

−−− −−−−−− −−−−−−−−−−−−−− −−−−−

0  0 1000 non− null float64
0  1 1000 non− null float64
0  2 1000 non− null float64

The K -Means Project 

Dataset description :

0 count 1000.000000 mean 0.499690 std 0.871547 min − 1.120606 25% − 0.043376 50% 0.507788 75% 1.035700 max 2.079038

�1 1000.000000

0.248688 0.496743

- 0.604452
- 0.202149 0.242695 0.710452 1.101272

�2 1000.00000

0.50000 0.50025

0.00000 0.00000 0.50000 1.00000

1.00000

The K -Means Project 

Dataset sample :

0 1 2 0 − 1.036507 0.392617 0.0 1 1.014714 0.177547 0.0 2 − 0.661602 0.705367 0.0 3 − 0.286087 0.967387 0.0 4 − 0.790062 0.615586 0.0

• Circles

- classes : 2
- data points : 1000

Dataset information :

RangeIndex : 1000 entries , 0 to 999 Data columns ( total 3 columns ):

- Column Non − Null Count Dtype

−−− −−−−−− −−−−−−−−−−−−−− −−−−−

0  0 1000 non− null float64
0  1 1000 non− null float64
0  2 1000 non− null float64

The K -Means Project 

Dataset description :

0 count 1000.000000 mean − 0.000930 std 0.560831 min − 1.140872 25% − 0.439114 50% − 0.008458 75% 0.434248 max 1.105457

�1 1000.000000

- 0.001957 0.561995
- 1.111948
- 0.444116 0.000451 0.436093 1.110823

�2 1000.00000

0.50000 0.50025

0.00000 0.00000 0.50000 1.00000 1.00000

The K -Means Project 7

Dataset sample :

0 1 2

0  1.047437 − 0.245648 0.0
0  0.420065 0.168314 1.0
0  0.223487 − 0.337189 1.0 3 − 0.254356 0.497842 1.0
0  0.055423 − 1.014569 0.0

3 Design and Implementation

1. Algorithm illustration

The following illustrates the basic flow of the K-means algorithm:

1. Initialize the center of each cluster K by selecting point P (one instance from the dataset) from the dataset randomly as a center for each cluster C
2. Loop over the whole dataset instances (points) and assign each data point to the closest cluster center based on calculating the Euclidean distance between each data point and each cluster center. Then assign each instance to the closest cluster center.
3. Update the cluster centers K by calculating the mean of all instances assigned in each cluster and update the cluster center of each cluster to be the mean of its data points.
4. Repeat steps 2 and 3 until the cluster centers K has reached the maximum number of iterations or algorithm convergence.
5. Finally, return the cluster centers and their assigned data points

In the following, the algorithm pseudo-code:

# Initialize the cluster centers randomly
clusterCenters <- select c instances randomly from the dataset
maxIteration <- some number like 100 iteration
errorLimit <- some small value to control the algorithm convergence
currentLoopIteration <- 0

While maxIteration < currentLoopIteration || error rate > errorLimit:
    # Assign each data instance to the closest cluster center.
    
    for each data point:
       
        Calculate the similarity measure between the data point and each 
        cluster center using for example Euclidean distance function.
        
        Assign the data instances to the nearest cluster center's cluster.
        
    # Update the cluster center
    
    for all points per each cluster:
        Calculate the mean of all data points assigned to the cluster.
        
        Update the cluster center of the cluster to the calculated mean.
        
    # Calculate the error rate/algorithm convergence based on the change 
    in distance between each cluster point and its current center 
    for 
    all points per each cluster:
        Calculate the Euclidean distance of all data points 
        assigned to the cluster.    
    Get the sum of all Euclidean distances for all points (currentErrorRate)
    and divide it by the number of instances in the dataset.
    
    if currentErrorRate<=errorLimit:
        break
    else
        currentLoopIteration++

Return each cluster center and its assigned data points.

2. Mathematical equations

To calculate the Euclidian distance between the two instances, assume points, P1(X1, Y1) and P2 (X2, Y2). The Euclidian distance equation is shown in equation 1:

D(P 1,P 2) = (P 2−P 1)2 (1)

To calculate the new center in each iteration after the assignment step, cal- culate the mean of each feature using equation 2 where C is the cluster center of a particular cluster J and X is the assigned data points into cluster J. Cj (2)

To calculate the cost function on each iteration, assume we have cluster centers K and datapoints X. So we need to calculate the distance using equation 1 between each data point in X between i and n with the related cluster center j. See equation 2

1/n ∗ D(xi,cj ) (3)

1<j<k Xi∈Cj

4 Experiments and results

1. Experiments using Iris dataset

The experiment setup and execution results are as follows:

• Dataset: Iris dataset.
• Maximum number of iterations: 200 (0-199) iterations.
• Initialize features scaling in order to normalize the data input to values between zero and one.
• Applying dimensionality reduction to 2 classes before running k-means in order to help in reducing the computational cost and improve the perfor- mance of the algorithm, as well as to identify patterns or relationships in the data that may not be easily visible in higher dimensions.
• Using the number of clusters equal two, the classification results with the demonstration of clusters center shown in figure 1. The algorithm conver- gence is shown in figure 2
• Using the number of clusters equal to three, the classification results with the demonstration of clusters center shown in figure 3. The algorithm con- vergence is shown in figure 4

Fig.1. Iris dataset over 2 clusters .

Fig.2. Iris dataset - Algorithm iteration convergence - 2 clusters.

Fig.3. Iris dataset over 3 clusters .

The K -Means Project 9

Fig.4. Iris dataset - Algorithm iteration convergence - 3 clusters.

2. Experiments using three separable gaussians dataset The experiment setup and execution results are as follows:

• Dataset: Three separable gaussians dataset.
• Maximum number of iterations: 200 (0-199) iterations.
• Initialize features scaling in order to normalize the data input to values between zero and one.
• Using the number of clusters equal two, the classification results with the demonstration of clusters center shown in figure 5. The algorithm conver- gence is shown in figure 6
• Using the number of clusters equal to three, the classification results with the demonstration of clusters center shown in figure 7. The algorithm con- vergence is shown in figure 8

Fig.5. Three separable gaussians dataset over 2 clusters .

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Fig.6. Three separable gaussians - Algorithm iteration convergence - 2 clusters.

Fig.7. Three separable gaussians dataset over 3 clusters.

Fig.8. Three separable gaussians - Algorithm iteration convergence - 3 clusters.

The K -Means Project 13

3. Experiments using slightly overlapping three separable gaussians dataset

The experiment setup and execution results are as follows:

• Dataset: Slightly overlapping three separable gaussians dataset.
• Maximum number of iterations: 200 (0-199) iterations.
• Initialize features scaling in order to normalize the data input to values between zero and one.
• Using the number of clusters equal two, the classification results with the demonstration of clusters center shown in figure 9. The algorithm conver- gence is shown in figure 10
• Using the number of clusters equal to three, the classification results with the demonstration of clusters center shown in figure 11. The algorithm con- vergence is shown in figure 12

Fig.9. Slightly overlapping three separable gaussians dataset over 2 clusters.

Fig.10. Slightly overlapping three separable gaussians - Algorithm iteration conver- gence - 2 clusters.

Fig.11. Slightly overlapping three separable gaussians dataset over 3 clusters.

The K -Means Project 15

Fig.12. Slightly overlapping three separable gaussians - Algorithm iteration conver- gence - 3 clusters.

4. Experiments using Moons dataset

The experiment setup and execution results are as follows:

• Dataset: Moons dataset.
• Maximum number of iterations: 200 (0-199) iterations.
• Initialize features scaling in order to normalize the data input to values between zero and one.
• Using the number of clusters equal two, the classification results with the demonstration of clusters center shown in figure 13. The algorithm conver- gence is shown in figure 14
• Using the number of clusters equal to three, the classification results with the demonstration of clusters center shown in figure 15. The algorithm con- vergence is shown in figure 16

Fig.13. Moons dataset over 2 clusters .

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Fig.14. Moons dataset - Algorithm iteration convergence - 2 clusters.

Fig.15. Moons dataset over 3 clusters .

Fig.16. Moons dataset - Algorithm iteration convergence - 3 clusters.

The K -Means Project 19

5. Experiments using Circles dataset

The experiment setup and execution results are as follows:

• Dataset: Circles dataset.
• Maximum number of iterations: 200 (0-199) iterations.
• Initialize features scaling in order to normalize the data input to values between zero and one.
• Using the number of clusters equal two, the classification results with the demonstration of clusters center shown in figure 17. The algorithm conver- gence is shown in figure 18
• Using the number of clusters equal to three, the classification results with the demonstration of clusters center shown in figure 19. The algorithm con- vergence is shown in figure 20

Fig.17. Circles dataset over 2 clusters .

5 Discussion

Based on the conducted experiments, the following takeaway from this project about K-means:

• Clusters centers based algorithm: Where each cluster center represents the mean of all data points belonging to that cluster.

Fig.18. Circles dataset - Algorithm iteration convergence - 2 clusters.

Fig.19. Circles dataset over 3 clusters .

The K -Means Project

Fig.20. Circles dataset - Algorithm iteration convergence - 3 clusters.

• Sensitivity for outlier data points: Where the data point distribution is con-

trolling the cluster center calculation over each round of iterations.

• The impact of the selected starting cluster centers: The selected Centers of the initial clusters have a substantial influence on the final clusters generated by the K-Means method, it is critical to carefully select at the initialization time the initial centers of the cluster that really reflect the nature of data.
• Produce same results under the same conduction: K-means implementation is deterministic where when giving the same number of clusters, the same dataset, the same number of maximum iterations, and the same Algorithm iteration convergence limit (error rate). The produced clusters will be the same.
• The implementation considers that any particular data point is hard clus- tered and it is assigned to one and only one single cluster and is exclusively associated with that cluster.
• The number of clusters must be determined before running the classification iterations: One of the K-Means algorithm’s disadvantages is that the number of clusters must be set in advance, which can be challenging in many real-

world situations where the nature of data is not well understood.

References

1. Ahmed, M., Seraj, R., Islam, S.M.S.: The k-means algorithm: A comprehensive survey and performance evaluation. Electronics 9(8), 1295 (2020)
2. Jain, A.K., Murty, M.N., Flynn, P.J.: Data clustering: A review. ACM Comput. Surv. 31(3), 264–323 (1999). https://doi.org/10.1145/331499.331504, https://doi.org/10.1145/331499.331504
3. Lloyd, S.P.: Least squares quantization in PCM. IEEE Trans. Inf. The- ory 28(2), 129–136 (1982). https://doi.org/10.1109/TIT.1982.1056489, https://doi.org/10.1109/TIT.1982.1056489