K means Clustering – Introduction

27 Jun, 2022
We are given a data set of items, with certain features, and values for these features (like a vector). The task is to categorize those items into groups. To achieve this, we will use the kMeans algorithm; an unsupervised learning algorithm. ‘K’ in the name of the algorithm represents the number of groups/clusters we want to classify our items into.
Overview
(It will help if you think of items as points in an n-dimensional space).  The algorithm will categorize the items into k groups or clusters of similarity. To calculate that similarity, we will use the euclidean distance as measurement.
The algorithm works as follows:  
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First, we initialize k points, called means or cluster centroids, randomly.We categorize each item to its closest mean and we update the mean’s coordinates, which are the averages of the items categorized in that cluster so far.We repeat the process for a given number of iterations and at the end, we have our clusters.
First, we initialize k points, called means or cluster centroids, randomly.
We categorize each item to its closest mean and we update the mean’s coordinates, which are the averages of the items categorized in that cluster so far.
We repeat the process for a given number of iterations and at the end, we have our clusters.
The “points” mentioned above are called means because they are the mean values of the items categorized in them. To initialize these means, we have a lot of options. An intuitive method is to initialize the means at random items in the data set. Another method is to initialize the means at random values between the boundaries of the data set (if for a feature x the items have values in [0,3], we will initialize the means with values for x at [0,3]).
The above algorithm in pseudocode is as follows:  
Initialize k means with random values

--> For a given number of iterations:
    
    --> Iterate through items:
    
        --> Find the mean closest to the item by calculating 
        the euclidean distance of the item with each of the means
        
        --> Assign item to mean
        
        --> Update mean by shifiting it to the average of the items in that cluster
We receive input as a text file (‘data.txt’). Each line represents an item, and it contains numerical values (one for each feature) split by commas. You can find a sample data set here.
We will read the data from the file, saving it into a list. Each element of the list is another list containing the item values for the features. We do this with the following function: 
Python3
def ReadData(fileName):     # Read the file, splitting by lines    f = open(fileName, 'r');    lines = f.read().splitlines();    f.close();     items = [];     for i in range(1, len(lines)):        line = lines[i].split(',');        itemFeatures = [];         for j in range(len(line)-1):                         # Convert feature value to float            v = float(line[j]);                         # Add feature value to dict            itemFeatures.append(v);         items.append(itemFeatures);     shuffle(items);     return items;
Initialize Means
We want to initialize each mean’s values in the range of the feature values of the items. For that, we need to find the min and max for each feature. We accomplish that with the following function: 
Python
def FindColMinMax(items):    n = len(items[0]);    minima = [sys.maxint for i in range(n)];    maxima = [-sys.maxint -1 for i in range(n)];         for item in items:        for f in range(len(item)):            if (item[f] < minima[f]):                minima[f] = item[f];                         if (item[f] > maxima[f]):                maxima[f] = item[f]; return minima,maxima;
The variables minima, maxima are lists containing the min and max values of the items respectively. We initialize each mean’s feature values randomly between the corresponding minimum and maximum in those above two lists: 
Python
def InitializeMeans(items, k, cMin, cMax):     # Initialize means to random numbers between    # the min and max of each column/feature       f = len(items[0]); # number of features    means = [[0 for i in range(f)] for j in range(k)];         for mean in means:        for i in range(len(mean)):             # Set value to a random float            # (adding +-1 to avoid a wide placement of a mean)            mean[i] = uniform(cMin[i]+1, cMax[i]-1);     return means;
Euclidean Distance
We will be using the euclidean distance as a metric of similarity for our data set (note: depending on your items, you can use another similarity metric). 
Python3
def EuclideanDistance(x, y):    S = 0; # The sum of the squared differences of the elements    for i in range(len(x)):        S += math.pow(x[i]-y[i], 2)     #The square root of the sum    return math.sqrt(S)
Update Means
To update a mean, we need to find the average value for its feature, for all the items in the mean/cluster. We can do this by adding all the values and then dividing by the number of items, or we can use a more elegant solution. We will calculate the new average without having to re-add all the values, by doing the following:  
m = (m*(n-1)+x)/n
where m is the mean value for a feature, n is the number of items in the cluster, and x is the feature value for the added item. We do the above for each feature to get the new mean. 
Python
def UpdateMean(n,mean,item):    for i in range(len(mean)):        m = mean[i];        m = (m*(n-1)+item[i])/float(n);        mean[i] = round(m, 3);         return mean;
Classify Items
Now we need to write a function to classify an item into a group/cluster. For the given item, we will find its similarity to each mean, and we will classify the item to the closest one. 
Python
def Classify(means,item):     # Classify item to the mean with minimum distance       minimum = sys.maxint;    index = -1;     for i in range(len(means)):         # Find distance from item to mean        dis = EuclideanDistance(item, means[i]);         if (dis < minimum):            minimum = dis;            index = i;         return index;
Find Means
To actually find the means, we will loop through all the items, classify them to their nearest cluster and update the cluster’s mean. We will repeat the process for a fixed number of iterations. If between two iterations no item changes classification, we stop the process as the algorithm has found the optimal solution.The below function takes as input k (the number of desired clusters), the items and the number of maximum iterations, and returns the means and the clusters. The classification of an item is stored in the array belongsTo and the number of items in a cluster is stored in clusterSizes. 
Python
def CalculateMeans(k,items,maxIterations=100000):     # Find the minima and maxima for columns    cMin, cMax = FindColMinMax(items);         # Initialize means at random points    means = InitializeMeans(items,k,cMin,cMax);         # Initialize clusters, the array to hold    # the number of items in a class    clusterSizes= [0 for i in range(len(means))];     # An array to hold the cluster an item is in    belongsTo = [0 for i in range(len(items))];     # Calculate means    for e in range(maxIterations):         # If no change of cluster occurs, halt        noChange = True;        for i in range(len(items)):             item = items[i];             # Classify item into a cluster and update the            # corresponding means.                   index = Classify(means,item);             clusterSizes[index] += 1;            cSize = clusterSizes[index];            means[index] = UpdateMean(cSize,means[index],item);             # Item changed cluster            if(index != belongsTo[i]):                noChange = False;             belongsTo[i] = index;         # Nothing changed, return        if (noChange):            break;     return means;
Find Clusters
Finally, we want to find the clusters, given the means. We will iterate through all the items and we will classify each item to its closest cluster. 
Python
def FindClusters(means,items):    clusters = [[] for i in range(len(means))]; # Init clusters         for item in items:         # Classify item into a cluster        index = Classify(means,item);         # Add item to cluster        clusters[index].append(item);     return clusters;
The other popularly used similarity measures are:-1. Cosine distance: It determines the cosine of the angle between the point vectors of the two points in the n-dimensional space2. Manhattan distance: It computes the sum of the absolute differences between the coordinates of the two data points.3. Minkowski distance: It is also known as the generalized distance metric. It can be used for both ordinal and quantitative variablesYou can find the entire code on my GitHub, along with a sample data set and a plotting function. Thanks for reading.This article is contributed by Antonis Maronikolakis. If you like GeeksforGeeks and would like to contribute, you can also write an article using write.geeksforgeeks.org or mail your article to review-team@geeksforgeeks.org. See your article appearing on the GeeksforGeeks main page and help other Geeks.Please write comments if you find anything incorrect, or you want to share more information about the topic discussed above. 
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