In [1]:
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import random
from sklearn import datasets
import warnings
warnings.filterwarnings('ignore')
In [2]:
iris, _ = datasets.load_iris(return_X_y=True, as_frame=True)
iris.rename(columns={"sepal length (cm)": "sepal_length", "sepal width (cm)": "sepal_width",
"petal length (cm)": "petal_length", "petal width (cm)": "petal_width"}, inplace=True)
iris.sample(10)
Out[2]:
| sepal_length | sepal_width | petal_length | petal_width | |
|---|---|---|---|---|
| 88 | 5.6 | 3.0 | 4.1 | 1.3 |
| 89 | 5.5 | 2.5 | 4.0 | 1.3 |
| 4 | 5.0 | 3.6 | 1.4 | 0.2 |
| 139 | 6.9 | 3.1 | 5.4 | 2.1 |
| 11 | 4.8 | 3.4 | 1.6 | 0.2 |
| 57 | 4.9 | 2.4 | 3.3 | 1.0 |
| 41 | 4.5 | 2.3 | 1.3 | 0.3 |
| 84 | 5.4 | 3.0 | 4.5 | 1.5 |
| 17 | 5.1 | 3.5 | 1.4 | 0.3 |
| 109 | 7.2 | 3.6 | 6.1 | 2.5 |
K-Means Clustering¶
In today's lecture, we will use the data from the iris dataset from sklearn to perform clustering using two features, petal_length and petal_width. Summary of the algorithm:
- Repeat until convergence:
- Color points according to the closest center.
- Move the center for each color to the center of points with that color.
In [3]:
sns.scatterplot(data=iris, x="petal_length", y="petal_width", color="black")
plt.xlabel('x')
plt.ylabel('y');
In [4]:
class Center():
def __init__(self, data):
"""generates a random center inside the region bounded by the data"""
num_dimensions = data.shape[1]
self.coordinates = np.array([0.0] * num_dimensions)
for i in range(num_dimensions):
min_value = np.min(data[:, i])
max_value = np.max(data[:, i])
random_value = random.uniform(min_value, max_value)
self.coordinates[i] = random_value
def __str__(self):
return str(self.coordinates)
def __repr__(self):
return repr(self.coordinates)
def dist(self, data_point):
return np.sqrt(np.sum((self.coordinates - data_point)**2, axis = 1))
def dist_sq(self, data_point):
return np.sum((self.coordinates - data_point)**2, axis = 1)
In [5]:
c1 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c2 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
In [6]:
# Force coordinates from the lecture demo
c1.coordinates = np.array([2.52364007, 2.31040024])
c2.coordinates = np.array([6.53276402, 1.211463])
In [7]:
def plot_centers_and_black_data(iris, centers):
for center in centers:
plt.plot(center.coordinates[0], center.coordinates[1], '*', markersize=10)
sns.scatterplot(data=iris, x="petal_length", y="petal_width", color="black")
plt.xlabel('petal_length')
plt.ylabel('petal_width')
legend_text = ['c' + str(i) for i in range(1, len(centers) + 1)]
legend_text.append('data')
plt.legend(legend_text)
In [8]:
plot_centers_and_black_data(iris, (c1, c2))
In [9]:
def get_cluster_number(dists):
return np.where(dists == np.min(dists))[0][0]
In [10]:
iris["dist1"] = c1.dist(iris[["petal_length", "petal_width"]])
iris["dist2"] = c2.dist(iris[["petal_length", "petal_width"]])
iris["cluster"] = iris[["dist1", "dist2"]].apply(get_cluster_number, axis = 1)
iris.head(5)
Out[10]:
| sepal_length | sepal_width | petal_length | petal_width | dist1 | dist2 | cluster | |
|---|---|---|---|---|---|---|---|
| 0 | 5.1 | 3.5 | 1.4 | 0.2 | 2.390890 | 5.231474 | 0 |
| 1 | 4.9 | 3.0 | 1.4 | 0.2 | 2.390890 | 5.231474 | 0 |
| 2 | 4.7 | 3.2 | 1.3 | 0.2 | 2.439484 | 5.329623 | 0 |
| 3 | 4.6 | 3.1 | 1.5 | 0.2 | 2.345555 | 5.133398 | 0 |
| 4 | 5.0 | 3.6 | 1.4 | 0.2 | 2.390890 | 5.231474 | 0 |
In [11]:
iris["cluster"].value_counts()
Out[11]:
cluster 0 79 1 71 Name: count, dtype: int64
In [12]:
def plot_centers_and_colorized_data(iris, centers):
plt.figure()
for center in centers:
plt.plot(center.coordinates[0], center.coordinates[1],
marker='*', markersize=10, linestyle="None")
current_palette = sns.color_palette()[0:len(centers)]
sns.scatterplot(data=iris, x="petal_length", y="petal_width", hue="cluster", palette=current_palette)
plt.xlabel('petal_length')
plt.ylabel('petal_width')
legend_text = ['c' + str(i) for i in range(1, len(centers) + 1)]
legend_text.append('data')
plt.legend(legend_text)
In [13]:
plot_centers_and_colorized_data(iris, (c1, c2))
In [14]:
average_c1_length = np.mean(iris[iris["cluster"] == 0]["petal_length"])
average_c1_width = np.mean(iris[iris["cluster"] == 0]["petal_width"])
c1.coordinates = (average_c1_length, average_c1_width)
average_c2_length = np.mean(iris[iris["cluster"] == 1]["petal_length"])
average_c2_width = np.mean(iris[iris["cluster"] == 1]["petal_width"])
c2.coordinates = (average_c2_length, average_c2_width)
In [15]:
plot_centers_and_black_data(iris, (c1, c2))
In [16]:
iris["dist1"] = c1.dist(iris[["petal_length", "petal_width"]])
iris["dist2"] = c2.dist(iris[["petal_length", "petal_width"]])
iris["cluster"] = iris[["dist1", "dist2"]].apply(get_cluster_number, axis = 1)
In [17]:
plot_centers_and_colorized_data(iris, (c1, c2))
In [18]:
average_c1_length = np.mean(iris[iris["cluster"] == 0]["petal_length"])
average_c1_width = np.mean(iris[iris["cluster"] == 0]["petal_width"])
c1.coordinates = (average_c1_length, average_c1_width)
average_c2_length = np.mean(iris[iris["cluster"] == 1]["petal_length"])
average_c2_width = np.mean(iris[iris["cluster"] == 1]["petal_width"])
c2.coordinates = (average_c2_length, average_c2_width)
In [19]:
plot_centers_and_black_data(iris, (c1, c2))
In [20]:
iris["dist1"] = c1.dist(iris[["petal_length", "petal_width"]])
iris["dist2"] = c2.dist(iris[["petal_length", "petal_width"]])
iris["cluster"] = iris[["dist1", "dist2"]].apply(get_cluster_number, axis = 1)
In [21]:
plot_centers_and_colorized_data(iris, (c1, c2))
In [22]:
average_c1_length = np.mean(iris[iris["cluster"] == 0]["petal_length"])
average_c1_width = np.mean(iris[iris["cluster"] == 0]["petal_width"])
c1.coordinates = (average_c1_length, average_c1_width)
average_c2_length = np.mean(iris[iris["cluster"] == 1]["petal_length"])
average_c2_width = np.mean(iris[iris["cluster"] == 1]["petal_width"])
c2.coordinates = (average_c2_length, average_c2_width)
In [23]:
plot_centers_and_black_data(iris, (c1, c2))
In [24]:
iris["dist1"] = c1.dist(iris[["petal_length", "petal_width"]])
iris["dist2"] = c2.dist(iris[["petal_length", "petal_width"]])
iris["cluster"] = iris[["dist1", "dist2"]].apply(get_cluster_number, axis = 1)
In [25]:
plot_centers_and_colorized_data(iris, (c1, c2))
In [26]:
average_c1_length = np.mean(iris[iris["cluster"] == 0]["petal_length"])
average_c1_width = np.mean(iris[iris["cluster"] == 0]["petal_width"])
c1.coordinates = (average_c1_length, average_c1_width)
average_c2_length = np.mean(iris[iris["cluster"] == 1]["petal_length"])
average_c2_width = np.mean(iris[iris["cluster"] == 1]["petal_width"])
c2.coordinates = (average_c2_length, average_c2_width)
In [27]:
plot_centers_and_black_data(iris, (c1, c2))
In [28]:
iris["dist1"] = c1.dist(iris[["petal_length", "petal_width"]])
iris["dist2"] = c2.dist(iris[["petal_length", "petal_width"]])
iris["cluster"] = iris[["dist1", "dist2"]].apply(get_cluster_number, axis = 1)
In [29]:
plot_centers_and_colorized_data(iris, (c1, c2))
In [30]:
average_c1_length = np.mean(iris[iris["cluster"] == 0]["petal_length"])
average_c1_width = np.mean(iris[iris["cluster"] == 0]["petal_width"])
c1.coordinates = (average_c1_length, average_c1_width)
average_c2_length = np.mean(iris[iris["cluster"] == 1]["petal_length"])
average_c2_width = np.mean(iris[iris["cluster"] == 1]["petal_width"])
c2.coordinates = (average_c2_length, average_c2_width)
In [31]:
plot_centers_and_black_data(iris, (c1, c2))
In [32]:
average_c1_length = np.mean(iris[iris["cluster"] == 0]["petal_length"])
average_c1_width = np.mean(iris[iris["cluster"] == 0]["petal_width"])
c1.coordinates = (average_c1_length, average_c1_width)
average_c2_length = np.mean(iris[iris["cluster"] == 1]["petal_length"])
average_c2_width = np.mean(iris[iris["cluster"] == 1]["petal_width"])
c2.coordinates = (average_c2_length, average_c2_width)
In [33]:
plot_centers_and_colorized_data(iris, (c1, c2))
Example for K > 2¶
In [34]:
import copy
def compute_centers_after_N_iterations(data, column_names, centers, N):
centers = copy.deepcopy(centers)
for i in range(N):
# Recompute clusters
dist_names = []
for center_num in range(len(centers)):
data["dist" + str(center_num)] = centers[center_num].dist(data[column_names])
dist_names.append("dist" + str(center_num))
data["cluster"] = data[dist_names].apply(get_cluster_number, axis = 1)
# Update centers
for center_num in range(len(centers)):
for col_num in range(len(column_names)):
col_name = column_names[col_num]
centers[center_num].coordinates[col_num] = np.mean(data[data["cluster"] == center_num][col_name])
return centers
In [35]:
c1 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c2 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c1.coordinates = np.array([2.52364007, 2.31040024])
c2.coordinates = np.array([6.53276402, 1.211463])
In [36]:
def inertia(data, centers):
total_inertia = 0
for center_num in range(len(centers)):
data_in_this_cluster = data[data["cluster"] == center_num]
total_inertia += np.sum(centers[center_num].dist(data_in_this_cluster[["petal_length", "petal_width"]]))
return total_inertia
In [37]:
def distortion(data, centers):
total_distortion = 0
for center_num in range(len(centers)):
data_in_this_cluster = data[data["cluster"] == center_num]
total_distortion += np.sum(centers[center_num].dist(data_in_this_cluster[["petal_length", "petal_width"]]))/len(data_in_this_cluster)
return total_distortion
In [38]:
random.seed(25)
c1 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c2 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c3 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c4 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
new_centers = compute_centers_after_N_iterations(iris, ['petal_length', 'petal_width'], [c1, c2, c3, c4], 12)
print(f"inertia: {inertia(iris, new_centers)}, distortion: {distortion(iris, new_centers)})")
plot_centers_and_colorized_data(iris, new_centers)
inertia: 44.88363871576328, distortion: 1.2530251953116613)
In [39]:
random.seed(29)
c1 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c2 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c3 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c4 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
new_centers = compute_centers_after_N_iterations(iris, ['petal_length', 'petal_width'], [c1, c2, c3, c4], 12)
print(f"inertia: {inertia(iris, new_centers)}, distortion: {distortion(iris, new_centers)})")
plot_centers_and_colorized_data(iris, new_centers)
inertia: 45.87509130916156, distortion: 1.3068391699161572)
In [40]:
random.seed(40)
c1 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c2 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c3 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c4 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
new_centers = compute_centers_after_N_iterations(iris, ['petal_length', 'petal_width'], [c1, c2, c3, c4], 12)
print(f"inertia: {inertia(iris, new_centers)}, distortion: {distortion(iris, new_centers)})")
plot_centers_and_colorized_data(iris, new_centers)
inertia: 54.272527867765156, distortion: 1.4992328098338596)
In [41]:
random.seed(75)
c1 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c2 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c3 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
c4 = Center(iris.loc[:, ['petal_length', 'petal_width']].values)
new_centers = compute_centers_after_N_iterations(iris, ['petal_length', 'petal_width'], [c1, c2, c3, c4], 12)
print(f"inertia: {inertia(iris, new_centers)}, distortion: {distortion(iris, new_centers)})")
plot_centers_and_colorized_data(iris, new_centers)
inertia: 44.88363871576328, distortion: 1.2530251953116613)
Example of Inertia Failing to Match Intuition¶
In [42]:
c1.coordinates = [1.2, 0.15]
c2.coordinates = [4.906000000000001, 1.6760000000000006]
iris["dist1"] = c1.dist(iris[["petal_length", "petal_width"]])
iris["dist2"] = c2.dist(iris[["petal_length", "petal_width"]])
iris["cluster"] = iris[["dist1", "dist2"]].apply(get_cluster_number, axis = 1)
In [43]:
plot_centers_and_colorized_data(iris, (c1, c2))
In [44]:
print(f"inertia: {inertia(iris, [c1, c2])}, distortion: {distortion(iris, [c1, c2])})")
inertia: 94.3164648130483, distortion: 1.0959547804008838)
In [45]:
average_c1_length = np.mean(iris[iris["cluster"] == 0]["petal_length"])
average_c1_width = np.mean(iris[iris["cluster"] == 0]["petal_width"])
c1.coordinates = (average_c1_length, average_c1_width)
average_c2_length = np.mean(iris[iris["cluster"] == 1]["petal_length"])
average_c2_width = np.mean(iris[iris["cluster"] == 1]["petal_width"])
c2.coordinates = (average_c2_length, average_c2_width)
In [46]:
plot_centers_and_black_data(iris, (c1, c2))
In [47]:
iris["dist1"] = c1.dist(iris[["petal_length", "petal_width"]])
iris["dist2"] = c2.dist(iris[["petal_length", "petal_width"]])
iris["cluster"] = iris[["dist1", "dist2"]].apply(get_cluster_number, axis = 1)
In [48]:
plot_centers_and_colorized_data(iris, (c1, c2))
In [49]:
print(f"inertia: {inertia(iris, [c1, c2])}, distortion: {distortion(iris, [c1, c2])})")
inertia: 87.2103463131798, distortion: 0.9775403068856574)
Hierarchical Agglomerative Clustering¶
In [50]:
np.random.seed(42)
iris_small = iris.sample(13).loc[:, 'sepal_length':'petal_width'].reset_index(drop=True)
iris_small = iris_small.drop(8).reset_index(drop=True)
In [51]:
sns.scatterplot(data=iris_small, x="petal_length", y="petal_width", color="black");
In [52]:
iris_small["cluster"] = np.array(range(0, len(iris_small)))
In [53]:
iris_small
Out[53]:
| sepal_length | sepal_width | petal_length | petal_width | cluster | |
|---|---|---|---|---|---|
| 0 | 6.1 | 2.8 | 4.7 | 1.2 | 0 |
| 1 | 5.7 | 3.8 | 1.7 | 0.3 | 1 |
| 2 | 7.7 | 2.6 | 6.9 | 2.3 | 2 |
| 3 | 6.0 | 2.9 | 4.5 | 1.5 | 3 |
| 4 | 6.8 | 2.8 | 4.8 | 1.4 | 4 |
| 5 | 5.4 | 3.4 | 1.5 | 0.4 | 5 |
| 6 | 5.6 | 2.9 | 3.6 | 1.3 | 6 |
| 7 | 6.9 | 3.1 | 5.1 | 2.3 | 7 |
| 8 | 5.8 | 2.7 | 3.9 | 1.2 | 8 |
| 9 | 6.5 | 3.2 | 5.1 | 2.0 | 9 |
| 10 | 4.8 | 3.0 | 1.4 | 0.1 | 10 |
| 11 | 5.5 | 3.5 | 1.3 | 0.2 | 11 |
In [54]:
def plot_clusters(data):
fig = plt.figure()
p1 = sns.scatterplot(data=data, x="petal_length", y="petal_width")
plt.axis('equal')
for line in range(0,data.shape[0]):
p1.text(data["petal_length"][line]+0.05, data["petal_width"][line] - 0.03,
data["cluster"][line], horizontalalignment='left',
size='medium', color='black', weight='semibold')
return fig
fig = plot_clusters(iris_small)
In [55]:
from scipy.spatial.distance import cdist
def closest_clusters(data):
cluster_values = data["cluster"].unique()
closest_pairs = []
processed_pairs = set()
while len(closest_pairs) < 3:
smallest_distance = float("inf")
best_pair = None
for i, cnum1 in enumerate(cluster_values):
for cnum2 in cluster_values[i+1:]:
if (cnum1, cnum2) in processed_pairs or (cnum2, cnum1) in processed_pairs:
continue
# Calculate the maximum distance between any two points in the clusters
cluster1_points = data[data["cluster"] == cnum1][["petal_length", "petal_width"]]
cluster2_points = data[data["cluster"] == cnum2][["petal_length", "petal_width"]]
max_dist = cdist(cluster1_points, cluster2_points).max()
if max_dist < smallest_distance:
smallest_distance = max_dist
best_pair = (cnum1, cnum2)
if best_pair:
closest_pairs.append((best_pair[0], best_pair[1], smallest_distance))
processed_pairs.add(best_pair)
return closest_pairs
In [56]:
def merge_clusters(data, cnum1, cnum2):
# Merge the second cluster into the first
data.loc[data["cluster"] == cnum2, "cluster"] = cnum1
In [57]:
import matplotlib.cm as cm
from scipy.spatial import distance
def plot_clusters(iteration, data, top_pairs):
fig = plt.figure(figsize=(16, 14))
p1 = sns.scatterplot(
data=data,
x="petal_length",
y="petal_width",
hue="cluster",
palette="viridis",
legend=False,
s=200
)
plt.axis('equal')
for line in range(0, data.shape[0]):
p1.text(
data["petal_length"][line] + 0.05,
data["petal_width"][line] - 0.03,
data["cluster"][line],
horizontalalignment='left',
size=18,
color='black',
weight='semibold'
)
# Use a consistent colormap for the top 3 pairs in this iteration
cmap = cm.get_cmap('tab10', len(top_pairs))
legend_lines = []
for i, (cnum1, cnum2, dist) in enumerate(top_pairs):
cluster1_points = data[data["cluster"] == cnum1]
cluster2_points = data[data["cluster"] == cnum2]
if cluster1_points.empty or cluster2_points.empty:
continue
# Find the two points contributing to the maximum distance
dists = distance.cdist(
cluster1_points[["petal_length", "petal_width"]],
cluster2_points[["petal_length", "petal_width"]]
)
max_dist_idx = np.unravel_index(np.argmax(dists), dists.shape)
point1 = cluster1_points.iloc[max_dist_idx[0]]
point2 = cluster2_points.iloc[max_dist_idx[1]]
# Draw the line between these points with a unique color
line_color = cmap(i)
plt.plot(
[point1["petal_length"], point2["petal_length"]],
[point1["petal_width"], point2["petal_width"]],
linestyle='--',
color=line_color,
linewidth=3,
label=f"{dist:.2f}"
)
legend_lines.append((f"{dist:.2f}", line_color))
legend_labels = [f"Distance: {dist}" for dist, _ in legend_lines]
legend_colors = [color for _, color in legend_lines]
handles = [
plt.Line2D([0], [0], color=color, linestyle='--', lw=3)
for color in legend_colors
]
plt.legend(handles, legend_labels, title="Line Distances", loc='upper right', fontsize=18, title_fontsize=20)
plt.title(f'Hierarchical Clustering Progression (Iteration {iteration})', fontsize=24, weight='bold')
plt.xlabel('Petal Length', fontsize=20)
plt.ylabel('Petal Width', fontsize=20)
plt.grid()
plt.xticks(fontsize=18)
plt.yticks(fontsize=18)
# plt.savefig(f"img_output/Clustering_Iteration_{iteration}.png", bbox_inches='tight')
plt.show()
return fig
# Perform clustering with proper annotations
i = 0
while len(iris_small["cluster"].unique()) != 2:
i += 1
top_pairs = closest_clusters(iris_small) # Get top 3 closest pairs
plot_clusters(i, iris_small, top_pairs=top_pairs) # Plot distances first
cnum1, cnum2, _ = top_pairs[0] # Take the closest pair to merge
merge_clusters(iris_small, cnum1, cnum2) # Merge after plotting distances
Run on full dataset¶
In [58]:
def plot_clusters(data):
fig = plt.figure()
p1 = sns.scatterplot(data=data, x="petal_length", y="petal_width")
plt.axis('equal')
for line in range(0,data.shape[0]):
p1.text(data["petal_length"][line]+0.05, data["petal_width"][line] - 0.03,
data["cluster"][line], horizontalalignment='left',
size='medium', color='black', weight='semibold')
return fig
iris_small = iris.copy()
iris_small["cluster"] = np.array(range(0, len(iris_small)))
fig = plot_clusters(iris_small)
In [59]:
from sklearn.cluster import AgglomerativeClustering
clustering = AgglomerativeClustering().fit(iris[["petal_length", "petal_width"]])
In [60]:
clustering.labels_
Out[60]:
array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
In [61]:
iris["cluster"] = clustering.labels_
In [62]:
sns.scatterplot(data=iris, x="petal_length", y="petal_width",
hue ="cluster", legend=None);
plt.axis('equal');
In [63]:
fig = plot_clusters(iris)
In [64]:
# From https://github.com/scikit-learn/scikit-learn/blob/70cf4a676caa2d2dad2e3f6e4478d64bcb0506f7/examples/cluster/plot_hierarchical_clustering_dendrogram.py
from scipy.cluster.hierarchy import dendrogram
def plot_dendrogram(model, **kwargs):
# Children of hierarchical clustering
children = model.children_
# Distances between each pair of children
# Since we don't have this information, we can use a uniform one for plotting
distance = np.arange(children.shape[0])
# The number of observations contained in each cluster level
no_of_observations = np.arange(2, children.shape[0]+2)
# Create linkage matrix and then plot the dendrogram
linkage_matrix = np.column_stack([children, distance, no_of_observations]).astype(float)
# Plot the corresponding dendrogram
dendrogram(linkage_matrix, **kwargs)
plt.title('Hierarchical Clustering Dendrogram')
plot_dendrogram(clustering, labels=clustering.labels_)
In [65]:
from sklearn.preprocessing import StandardScaler
from scipy.cluster.hierarchy import dendrogram, linkage
scaler = StandardScaler()
iris_small_scaled = scaler.fit_transform(iris[["petal_length", "petal_width"]])
# Perform hierarchical clustering
linkage_matrix_small = linkage(iris_small_scaled, method='ward')
# Plot the dendrogram
plt.figure(figsize=(10, 6))
dendrogram(
linkage_matrix_small,
truncate_mode='lastp',
p=10,
leaf_rotation=90.,
leaf_font_size=12.,
show_contracted=True
)
plt.title('Dendrogram for Hierarchical Clustering')
plt.xlabel('Sample Index or Cluster Size')
plt.ylabel('Distance')
plt.axhline(y=5, color='r', linestyle='--', label='Cut at Large Gap')
plt.legend()
plt.show()
Elbow Method¶
In [66]:
from sklearn.cluster import KMeans
distortions = []
inertias = []
mapping1 = {}
mapping2 = {}
K = range(1,10)
X = iris[["petal_length", "petal_width"]]
for k in K:
# Building and fitting the model
kmeanModel = KMeans(n_clusters=k).fit(X)
distortions.append(sum(np.min(distance.cdist(X, kmeanModel.cluster_centers_,
'euclidean'),axis=1)) / X.shape[0])
inertias.append(kmeanModel.inertia_)
mapping1[k] = sum(np.min(distance.cdist(X, kmeanModel.cluster_centers_,
'euclidean'),axis=1)) / X.shape[0]
mapping2[k] = kmeanModel.inertia_
In [67]:
plt.plot(K, inertias, 'bx-')
plt.xlabel('Values of K')
plt.ylabel('Inertia')
plt.title('The Elbow Method using Inertia');
In [68]:
# Analyze clustering results for k=3 (optimal) and k=6 (suboptimal)
k_values_to_analyze = [3, 6]
results = {}
for k in k_values_to_analyze:
kmeans = KMeans(n_clusters=k, random_state=42)
clusters = kmeans.fit_predict(iris[['petal_length', 'petal_width']])
results[k] = {
"model": kmeans,
"clusters": clusters
}
# Plot the clustering results
for k, result in results.items():
plt.figure(figsize=(8, 5))
plt.scatter(
iris['petal_length'],
iris['petal_width'],
c=result['clusters'],
cmap='viridis',
s=50,
alpha=0.7
)
plt.scatter(
result['model'].cluster_centers_[:, 0],
result['model'].cluster_centers_[:, 1],
c='red',
marker='X',
s=200,
label='Centroids'
)
plt.title(f'Clustering Results for k = {k}')
plt.xlabel('Petal Length')
plt.ylabel('Petal Width')
plt.legend()
plt.grid()
plt.show()
Silhouette Scores¶
In [69]:
X.loc[(X["petal_length"] < 3.2) & (X["petal_length"] > 2)]
Out[69]:
| petal_length | petal_width | |
|---|---|---|
| 98 | 3.0 | 1.1 |
In [70]:
from sklearn.metrics import silhouette_samples, silhouette_score
import matplotlib.cm as cm
fig, ax1 = plt.subplots(1, 1)
n_clusters = 2
# The 1st subplot is the silhouette plot.
# The silhouette coefficient can range from -1, 1 but in this example all
# lie within [-0.1, 1]
ax1.set_xlim([-0.1, 1])
# The (n_clusters+1)*10 is for inserting blank space between silhouette
# plots of individual clusters, to demarcate them clearly.
ax1.set_ylim([0, len(X) + (n_clusters + 1) * 10])
cluster_labels = clustering.fit_predict(X)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed clusters
silhouette_avg = silhouette_score(X, cluster_labels)
print("For n_clusters =", n_clusters,
"The average silhouette_score is :", silhouette_avg)
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(X, cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.nipy_spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0, ith_cluster_silhouette_values,
facecolor=color, edgecolor=color, alpha=0.7)
# Label the silhouette plots with their cluster numbers at the middle
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
# Compute the new y_lower for next plot
y_lower = y_upper + 10 # 10 for the 0 samples
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
# The vertical line for average silhouette score of all the values
ax1.axvline(x=silhouette_avg, color="red", linestyle="--");
For n_clusters = 2 The average silhouette_score is : 0.7669465622770762
In [71]:
min(sample_silhouette_values)
Out[71]:
-0.13132990547983361
In [72]:
from sklearn.cluster import AgglomerativeClustering
clustering = AgglomerativeClustering(n_clusters = 3).fit(iris[["petal_length", "petal_width"]])
fig, ax1 = plt.subplots(1, 1)
n_clusters = 3
# The 1st subplot is the silhouette plot
# The silhouette coefficient can range from -1, 1 but in this example all
# lie within [-0.1, 1]
ax1.set_xlim([-0.1, 1])
# The (n_clusters+1)*10 is for inserting blank space between silhouette
# plots of individual clusters, to demarcate them clearly.
ax1.set_ylim([0, len(X) + (n_clusters + 1) * 10])
cluster_labels = clustering.fit_predict(X)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed clusters
silhouette_avg = silhouette_score(X, cluster_labels)
print("For n_clusters =", n_clusters,
"The average silhouette_score is :", silhouette_avg)
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(X, cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.nipy_spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0, ith_cluster_silhouette_values,
facecolor=color, edgecolor=color, alpha=0.7)
# Label the silhouette plots with their cluster numbers at the middle
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
# Compute the new y_lower for next plot
y_lower = y_upper + 10 # 10 for the 0 samples
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
# The vertical line for the average silhouette score of all the values
ax1.axvline(x=silhouette_avg, color="red", linestyle="--");
For n_clusters = 3 The average silhouette_score is : 0.6573949269287823
In [73]:
min(sample_silhouette_values)
Out[73]:
-0.14062817006789843
In [74]:
iris["cluster"] = cluster_labels
current_palette = sns.color_palette()[0:3]
sns.scatterplot(data = iris, x = "petal_length", y= "petal_width", hue="cluster", palette = current_palette);
plt.axis('equal');
