Python Math: Calculate clusters using Hierarchical Clustering method

Last update on April 24 2025 12:44:11 (UTC/GMT +8 hours)

75. Hierarchical Clustering Simulation

Write a Python program to calculate clusters using the Hierarchical Clustering method.

Sample Solution:

Python Code:

#https://gist.github.com/vineetrok/1391954

import math

def distance(a,b):
    x=float(a[0])-float(b[0])
    x=x*x
    y=float(a[1])-float(b[1])
    y=y*y
    dist=round(math.sqrt(x+y),2)
    return dist

def minimum(matrix):
    p=[0,0]
    mn=1000
    for i in range(0,len(matrix)):        
        for j in range(0,len(matrix[i])):            
            if (matrix[i][j]>0 and matrix[i][j]<mn):
                mn=matrix[i][j]
                p[0]=i
                p[1]=j
    return p 
            
def newpoint(pt):
    x=float(pt[0][0])+float(pt[1][0])
    x=x/2
    y=float(pt[0][1])+float(pt[1][1])
    y=y/2
    midpoint=[x,y]
    return midpoint

if __name__ == '__main__':    
    n=int(input("Input number of points.> "))
    points=list()
    outline='['
    i=0

    while(i<n):
        s=input("Input point (eg. 1,1)"+chr(65+i)+"> ")
        c=s.split(",")
        points.append(c)
        i=i+1

    names={}

    for i in range(0,len(points)):
        names[str(points[i])]=chr(65+i)
    l=0
    while(len(points)>1):
        l=l+1
        matrix=list()
        print('Distance matrix no. '+str(l)+': ')
        for i in range(0,len(points)):
            m=[]
            for j in range(0,len(points)):
                m.append(0)
            for j in range(0,len(points)):
                m[j]=distance(points[i],points[j])
            print(str(m))
            matrix.append(m)
        
        m=minimum(matrix)
        pts=list()
        p1=points[m[0]]
        pts.append(p1)
        points.remove(p1)
        p2=points[m[1]-1]
        pts.append(p2)
        points.remove(p2)   
        midpoint=newpoint(pts)
        points.append(midpoint)    
        c1=names.pop(str(p1))
        c2=names.pop(str(p2))
        names[str(midpoint)]="["+str(c1)+str(c2)+"]"    
        outline=names[str(midpoint)]
        
    print("Cluster is :",names[str(midpoint)])

Sample Output:

Input number of points.> 2                                          
Input point (eg. 1,1)A> 1,2                                         
Input point (eg. 1,1)B> 3,4                                         
Distance matrix no.1:                                               
[0.0, 2.83]                                                         
[2.83, 0.0]                                                         
Cluster is : [AB]

Flowchart:

$Flowchart: Calculate clusters using Hierarchical Clustering method$

For more Practice: Solve these Related Problems:

Write a Python program to perform hierarchical clustering on a small set of 2D points and print the resulting cluster assignments.
Write a Python function that accepts a list of 2D coordinates, computes the Euclidean distance matrix, and applies hierarchical clustering.
Write a Python script to prompt the user for multiple 2D points, perform clustering, and then display the clusters along with the distance matrix.
Write a Python program to simulate hierarchical clustering on randomly generated points and print both the clusters and the dendrogram using matplotlib.

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Python Code Editor:

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