Python Scripts

Numerical One Dimensional Example
In the previous code Bio-Inspired Optimization for Text Mining-1 Motivation we implemented source code for optimization some function using bio-inspired algorithm. Now we need to put actual function for clustering. In clustering we want to group our clusters in such way that the distance from each data to its centroid was minimal.
Here is what Wikipedia is saying about clustering as optimization problem:

In centroid-based clustering, clusters are represented by a central vector, which may not necessarily be a member of the data set. When the number of clusters is fixed to k, k-means clustering gives a formal definition as an optimization problem: find the k cluster centers and assign the objects to the nearest cluster center, such that the squared distances from the cluster are minimized.

The optimization problem itself is known to be NP-hard, and thus the common approach is to search only for approximate solutions. A particularly well known approximative method is Lloyd’s algorithm,[8] often actually referred to as “k-means algorithm”. It does however only find a local optimum, and is commonly run multiple times with different random initializations. Variations of k-means often include such optimizations as choosing the best of multiple runs, but also restricting the centroids to members of the data set (k-medoids), choosing medians (k-medians clustering), choosing the initial centers less randomly (K-means++) or allowing a fuzzy cluster assignment (Fuzzy c-means). [1]

Based on the above our function will calculate total sum of distances from each data to its centroid. For centroid we select the nearest centroid. We do this inside of function evaluate. The script iterates though each centroid (for loop: for c in cand) and keeps track of minimal distance. After loop is done it updates total fitness (fit variable)

Below is the code for clustering one dimensional data. Data is specified in array data.
Function generate defines how many clusters we want to get. The example is using 2 through the number nr_inputs
The Bounder has 0, 10 which is based on the data, the max number in the data is 8.

# -*- coding: utf-8 -*-

# Clustering for one dimensional data
## http://pythonhosted.org/inspyred/examples.html#ant-colony-optimization
## https://aarongarrett.github.io/inspyred/reference.html#benchmarks-benchmark-optimization-functions

from time import time
from random import Random
import inspyred



data = [4,5,5,8,8,8]

def my_observer(population, num_generations, num_evaluations, args):
    best = max(population)
    print('{0:6} -- {1} : {2}'.format(num_generations, 
                                      best.fitness, 
                                      str(best.candidate)))

def generate(random, args):
      nr_inputs = 2
      return [random.uniform(0, 2) for _ in range(nr_inputs)]
    

    
def evaluate(candidates, args):
    
   fitness = []
    
   for cand in candidates:  
     fit=0  
     for d in range(len(data)):
         distance=10000
         for c in cand:
             temp=(data[d]-c)**2
             if temp < distance :
                  distance=temp
         fit=fit + distance
     fitness.append(fit)          
   return fitness  


def main(prng=None, display=False):
    if prng is None:
        prng = Random()
        prng.seed(time()) 
    
   
    
    
   
    ea = inspyred.swarm.PSO(prng)
    ea.observer = my_observer
    ea.terminator = inspyred.ec.terminators.evaluation_termination
    ea.topology = inspyred.swarm.topologies.ring_topology
    final_pop = ea.evolve(generator=generate,
                          evaluator=evaluate, 
                          pop_size=8,
                          bounder=inspyred.ec.Bounder(0, 10),
                          maximize=False,
                          max_evaluations=2000,
                          neighborhood_size=3)
                         

   

if __name__ == '__main__':
    main(display=True)

Output result

 0.6666666666666666 : [8.000000006943864, 4.666666665568784]

Thus we applied bio-inspired optimisation algorithm for clustering problem. In the next post we will extend the source code to several dimensional data.

References
1. Centroid-based clustering
2. Bio-Inspired Optimization for Text Mining-1 Motivation

Motivation
Optimization problem studies maximizing or minimizing some function
y=f(x) with some range of choices available for x. Biologically inspired (bio-inspired) algorithms for optimization problems are now widely used. A few examples of such optimization are:
particle swarm optimization (PSO) that is based on the swarming behavior of fish and birds,
firefly algorithm (FA) that is based on the flashing behavior of swarming fireflies,
ant colony optimization (ACO) that is based on the interaction of social insects (e.g., ants)
bee algorithms are all based on the foraging behavior of honey bees. [1]

Recently on different forums there were questions how this optimization technique can be applied to text mining tasks such as classification or clustering. Those problems usually use algorithms that come from data mining or machine learning fields such as k-means clustering, SVM (support vector machine), naive Bayes.

How can we apply bio-inspired algorithms for clustering?

Let’s take a python package inspyred which has many bio-inspired algorithms including evolutionary computation, swarm intelligence, and immunocomputing [2]. This package has examples for specific predetermined functions that are used as benchmarks.

However the code also can be customized to run for user defined functions.

Below is the example of customized code for finding minimum of function f(x)=(x-1)**2, in this code function evaluate was added to specify how we calculate fitness. In this example we use PSO algorithm.

We run this code and we get what we expected to get. Below you can find also the final output of the program.

So now we understand what we need to change to fit optimization to different problems. Specifically we need to modify fitness function. Additionally we need to modify range and observer.
In the next post Bio-Inspired Optimization for Text Mining-2 Numerical One Dimensional Example we will continue to modify source code for solving clustering problem.

# f(x)=(x-1)**2 minimize  on 0...2
## http://pythonhosted.org/inspyred/examples.html#ant-colony-optimization
## https://aarongarrett.github.io/inspyred/reference.html#benchmarks-benchmark-optimization-functions

from time import time
from random import Random
import inspyred

def my_observer(population, num_generations, num_evaluations, args):
    best = max(population)
    print('{0:6} -- {1} : {2}'.format(num_generations, 
                                      best.fitness, 
                                      str(best.candidate)))


def generate(random, args):
     return [random.uniform(0, 2)]
    
def evaluate(candidates, args):
     fitness = []
     for cand in candidates:
          fit = [(c-1)**2 for c in cand]
          fitness.append(fit)
     return fitness


def main(prng=None, display=False):
    if prng is None:
        prng = Random()
        prng.seed(time()) 
    
   
    
    
    ea = inspyred.swarm.PSO(prng)
    ea.observer = my_observer
    ea.terminator = inspyred.ec.terminators.evaluation_termination
    ea.topology = inspyred.swarm.topologies.ring_topology
    final_pop = ea.evolve(generator=generate,
                          evaluator=evaluate, 
                          pop_size=100,
                          bounder=inspyred.ec.Bounder(0, 2),
                          maximize=False,
                          max_evaluations=30000, 
                          neighborhood_size=2)

    if display:
        best = max(final_pop) 
        print('Best Solution: \n{0}'.format(str(best)))
    return ea

if __name__ == '__main__':
    main(display=True)

The output of program:

Best Solution: 
[1.0] : [0.0]

References
1. A Brief Review of Nature-Inspired Algorithms for Optimization
2. inspyred: Bio-inspired Algorithms in Python
3. Bio-Inspired Optimization for Text Mining-2 Numerical One Dimensional Example