Introduction
This lab demonstrates the characteristics of different clustering algorithms on datasets that are "interesting" but still in 2D. The parameters of each of these dataset-algorithm pairs have been tuned to produce good clustering results. While these examples give some intuition about the algorithms, this intuition might not apply to very high dimensional data.
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Sometimes, you may need to wait a few seconds for Jupyter Notebook to finish loading. The validation of operations cannot be automated because of limitations in Jupyter Notebook.
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Import Libraries
The necessary libraries are imported into the notebook.
import time
import warnings
import numpy as np
import matplotlib.pyplot as plt
from sklearn import cluster, datasets, mixture
from sklearn.neighbors import kneighbors_graph
from sklearn.preprocessing import StandardScaler
from itertools import cycle, islice
Generate Datasets
The datasets are generated to test and compare different clustering algorithms. The following datasets are generated:
- Noisy circles
- Noisy moons
- Blobs
- No structure
- Anisotropicly distributed data
- Blobs with varied variances
n_samples = 500
noisy_circles = datasets.make_circles(n_samples=n_samples, factor=0.5, noise=0.05)
noisy_moons = datasets.make_moons(n_samples=n_samples, noise=0.05)
blobs = datasets.make_blobs(n_samples=n_samples, random_state=8)
no_structure = np.random.rand(n_samples, 2), None
random_state = 170
X, y = datasets.make_blobs(n_samples=n_samples, random_state=random_state)
transformation = [[0.6, -0.6], [-0.4, 0.8]]
X_aniso = np.dot(X, transformation)
aniso = (X_aniso, y)
varied = datasets.make_blobs(
n_samples=n_samples, cluster_std=[1.0, 2.5, 0.5], random_state=random_state
)
Set up Cluster Parameters
The parameters for each clustering algorithm are defined.
default_base = {
"quantile": 0.3,
"eps": 0.3,
"damping": 0.9,
"preference": -200,
"n_neighbors": 3,
"n_clusters": 3,
"min_samples": 7,
"xi": 0.05,
"min_cluster_size": 0.1,
"allow_single_cluster": True,
"hdbscan_min_cluster_size": 15,
"hdbscan_min_samples": 3,
}
datasets = [
(
noisy_circles,
{
"damping": 0.77,
"preference": -240,
"quantile": 0.2,
"n_clusters": 2,
"min_samples": 7,
"xi": 0.08,
},
),
(
noisy_moons,
{
"damping": 0.75,
"preference": -220,
"n_clusters": 2,
"min_samples": 7,
"xi": 0.1,
},
),
(
varied,
{
"eps": 0.18,
"n_neighbors": 2,
"min_samples": 7,
"xi": 0.01,
"min_cluster_size": 0.2,
},
),
(
aniso,
{
"eps": 0.15,
"n_neighbors": 2,
"min_samples": 7,
"xi": 0.1,
"min_cluster_size": 0.2,
},
),
(blobs, {"min_samples": 7, "xi": 0.1, "min_cluster_size": 0.2}),
(no_structure, {}),
]
Create Cluster Objects
Cluster objects are created for each clustering algorithm.
ms = cluster.MeanShift(bandwidth=bandwidth, bin_seeding=True)
two_means = cluster.MiniBatchKMeans(n_clusters=params["n_clusters"], n_init="auto")
ward = cluster.AgglomerativeClustering(
n_clusters=params["n_clusters"], linkage="ward", connectivity=connectivity
)
spectral = cluster.SpectralClustering(
n_clusters=params["n_clusters"],
eigen_solver="arpack",
affinity="nearest_neighbors",
)
dbscan = cluster.DBSCAN(eps=params["eps"])
hdbscan = cluster.HDBSCAN(
min_samples=params["hdbscan_min_samples"],
min_cluster_size=params["hdbscan_min_cluster_size"],
allow_single_cluster=params["allow_single_cluster"],
)
optics = cluster.OPTICS(
min_samples=params["min_samples"],
xi=params["xi"],
min_cluster_size=params["min_cluster_size"],
)
affinity_propagation = cluster.AffinityPropagation(
damping=params["damping"], preference=params["preference"], random_state=0
)
average_linkage = cluster.AgglomerativeClustering(
linkage="average",
metric="cityblock",
n_clusters=params["n_clusters"],
connectivity=connectivity,
)
birch = cluster.Birch(n_clusters=params["n_clusters"])
gmm = mixture.GaussianMixture(
n_components=params["n_clusters"], covariance_type="full"
)
Plot Clusters
A plot is created to show the different clustering algorithms performance on the datasets.
for i_dataset, (dataset, algo_params) in enumerate(datasets):
## update parameters with dataset-specific values
params = default_base.copy()
params.update(algo_params)
X, y = dataset
## normalize dataset for easier parameter selection
X = StandardScaler().fit_transform(X)
## estimate bandwidth for mean shift
bandwidth = cluster.estimate_bandwidth(X, quantile=params["quantile"])
## connectivity matrix for structured Ward
connectivity = kneighbors_graph(
X, n_neighbors=params["n_neighbors"], include_self=False
)
## make connectivity symmetric
connectivity = 0.5 * (connectivity + connectivity.T)
clustering_algorithms = (
("MiniBatch\nKMeans", two_means),
("Affinity\nPropagation", affinity_propagation),
("MeanShift", ms),
("Spectral\nClustering", spectral),
("Ward", ward),
("Agglomerative\nClustering", average_linkage),
("DBSCAN", dbscan),
("HDBSCAN", hdbscan),
("OPTICS", optics),
("BIRCH", birch),
("Gaussian\nMixture", gmm),
)
for name, algorithm in clustering_algorithms:
t0 = time.time()
## catch warnings related to kneighbors_graph
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
message="the number of connected components of the "
+ "connectivity matrix is [0-9]{1,2}"
+ " > 1. Completing it to avoid stopping the tree early.",
category=UserWarning,
)
warnings.filterwarnings(
"ignore",
message="Graph is not fully connected, spectral embedding"
+ " may not work as expected.",
category=UserWarning,
)
algorithm.fit(X)
t1 = time.time()
if hasattr(algorithm, "labels_"):
y_pred = algorithm.labels_.astype(int)
else:
y_pred = algorithm.predict(X)
plt.subplot(len(datasets), len(clustering_algorithms), plot_num)
if i_dataset == 0:
plt.title(name, size=18)
colors = np.array(
list(
islice(
cycle(
[
"#377eb8",
"#ff7f00",
"#4daf4a",
"#f781bf",
"#a65628",
"#984ea3",
"#999999",
"#e41a1c",
"#dede00",
]
),
int(max(y_pred) + 1),
)
)
)
## add black color for outliers (if any)
colors = np.append(colors, ["#000000"])
plt.scatter(X[:, 0], X[:, 1], s=10, color=colors[y_pred])
plt.xlim(-2.5, 2.5)
plt.ylim(-2.5, 2.5)
plt.xticks(())
plt.yticks(())
plt.text(
0.99,
0.01,
("%.2fs" % (t1 - t0)).lstrip("0"),
transform=plt.gca().transAxes,
size=15,
horizontalalignment="right",
)
plot_num += 1
plt.show()
Summary
This lab demonstrates the characteristics of different clustering algorithms on datasets that are "interesting" but still in 2D. The performance of each algorithm was compared and plotted to compare results.