k means clust Algorithm
It is a main undertaking of exploratory data mining, and a common technique for statistical data analysis, used in many fields, including shape recognition, picture analysis, information retrieval, bioinformatics, data compression, computer graphics and machine learning. The appropriate clustering algorithm and parameter settings (including parameters such as the distance function to use, a density threshold or the number of expected clusters) depend on the individual data put and intended purpose of the outcomes.
"""README, Author - Anurag Kumar(mailto:[email protected])
Requirements:
- sklearn
- numpy
- matplotlib
Python:
- 3.5
Inputs:
- X , a 2D numpy array of features.
- k , number of clusters to create.
- initial_centroids , initial centroid values generated by utility function(mentioned
in usage).
- maxiter , maximum number of iterations to process.
- heterogeneity , empty list that will be filled with hetrogeneity values if passed
to kmeans func.
Usage:
1. define 'k' value, 'X' features array and 'hetrogeneity' empty list
2. create initial_centroids,
initial_centroids = get_initial_centroids(
X,
k,
seed=0 # seed value for initial centroid generation,
# None for randomness(default=None)
)
3. find centroids and clusters using kmeans function.
centroids, cluster_assignment = kmeans(
X,
k,
initial_centroids,
maxiter=400,
record_heterogeneity=heterogeneity,
verbose=True # whether to print logs in console or not.(default=False)
)
4. Plot the loss function, hetrogeneity values for every iteration saved in
hetrogeneity list.
plot_heterogeneity(
heterogeneity,
k
)
5. Have fun..
"""
import numpy as np
from matplotlib import pyplot as plt
from sklearn.metrics import pairwise_distances
TAG = "K-MEANS-CLUST/ "
def get_initial_centroids(data, k, seed=None):
"""Randomly choose k data points as initial centroids"""
if seed is not None: # useful for obtaining consistent results
np.random.seed(seed)
n = data.shape[0] # number of data points
# Pick K indices from range [0, N).
rand_indices = np.random.randint(0, n, k)
# Keep centroids as dense format, as many entries will be nonzero due to averaging.
# As long as at least one document in a cluster contains a word,
# it will carry a nonzero weight in the TF-IDF vector of the centroid.
centroids = data[rand_indices, :]
return centroids
def centroid_pairwise_dist(X, centroids):
return pairwise_distances(X, centroids, metric="euclidean")
def assign_clusters(data, centroids):
# Compute distances between each data point and the set of centroids:
# Fill in the blank (RHS only)
distances_from_centroids = centroid_pairwise_dist(data, centroids)
# Compute cluster assignments for each data point:
# Fill in the blank (RHS only)
cluster_assignment = np.argmin(distances_from_centroids, axis=1)
return cluster_assignment
def revise_centroids(data, k, cluster_assignment):
new_centroids = []
for i in range(k):
# Select all data points that belong to cluster i. Fill in the blank (RHS only)
member_data_points = data[cluster_assignment == i]
# Compute the mean of the data points. Fill in the blank (RHS only)
centroid = member_data_points.mean(axis=0)
new_centroids.append(centroid)
new_centroids = np.array(new_centroids)
return new_centroids
def compute_heterogeneity(data, k, centroids, cluster_assignment):
heterogeneity = 0.0
for i in range(k):
# Select all data points that belong to cluster i. Fill in the blank (RHS only)
member_data_points = data[cluster_assignment == i, :]
if member_data_points.shape[0] > 0: # check if i-th cluster is non-empty
# Compute distances from centroid to data points (RHS only)
distances = pairwise_distances(
member_data_points, [centroids[i]], metric="euclidean"
)
squared_distances = distances ** 2
heterogeneity += np.sum(squared_distances)
return heterogeneity
def plot_heterogeneity(heterogeneity, k):
plt.figure(figsize=(7, 4))
plt.plot(heterogeneity, linewidth=4)
plt.xlabel("# Iterations")
plt.ylabel("Heterogeneity")
plt.title(f"Heterogeneity of clustering over time, K={k:d}")
plt.rcParams.update({"font.size": 16})
plt.show()
def kmeans(
data, k, initial_centroids, maxiter=500, record_heterogeneity=None, verbose=False
):
"""This function runs k-means on given data and initial set of centroids.
maxiter: maximum number of iterations to run.(default=500)
record_heterogeneity: (optional) a list, to store the history of heterogeneity
as function of iterations
if None, do not store the history.
verbose: if True, print how many data points changed their cluster labels in
each iteration"""
centroids = initial_centroids[:]
prev_cluster_assignment = None
for itr in range(maxiter):
if verbose:
print(itr, end="")
# 1. Make cluster assignments using nearest centroids
cluster_assignment = assign_clusters(data, centroids)
# 2. Compute a new centroid for each of the k clusters, averaging all data
# points assigned to that cluster.
centroids = revise_centroids(data, k, cluster_assignment)
# Check for convergence: if none of the assignments changed, stop
if (
prev_cluster_assignment is not None
and (prev_cluster_assignment == cluster_assignment).all()
):
break
# Print number of new assignments
if prev_cluster_assignment is not None:
num_changed = np.sum(prev_cluster_assignment != cluster_assignment)
if verbose:
print(
" {:5d} elements changed their cluster assignment.".format(
num_changed
)
)
# Record heterogeneity convergence metric
if record_heterogeneity is not None:
# YOUR CODE HERE
score = compute_heterogeneity(data, k, centroids, cluster_assignment)
record_heterogeneity.append(score)
prev_cluster_assignment = cluster_assignment[:]
return centroids, cluster_assignment
# Mock test below
if False: # change to true to run this test case.
import sklearn.datasets as ds
dataset = ds.load_iris()
k = 3
heterogeneity = []
initial_centroids = get_initial_centroids(dataset["data"], k, seed=0)
centroids, cluster_assignment = kmeans(
dataset["data"],
k,
initial_centroids,
maxiter=400,
record_heterogeneity=heterogeneity,
verbose=True,
)
plot_heterogeneity(heterogeneity, k)
