Comparing Algorithms on Toy Datasets

The scikit-learn website compares different clustering algorithms on toy 2D datasets. Below we re-run this illustration on a larger data sample and with the Lumbermark algorithm included.

TL;DR — See the bottom of the page for the resulting figure.

import time
import warnings
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from sklearn import cluster, datasets, mixture
from sklearn.neighbors import kneighbors_graph
from sklearn.preprocessing import StandardScaler
from itertools import cycle, islice
import lumbermark
import genieclust

np.random.seed(1234)

First, we generate the datasets. Note that in the original script, n_samples was set to 500.

n_samples = 10000

seed = 30
noisy_circles = datasets.make_circles(
    n_samples=n_samples, factor=0.5, noise=0.05, random_state=seed
)
noisy_moons = datasets.make_moons(n_samples=n_samples, noise=0.05, random_state=seed)
blobs = datasets.make_blobs(n_samples=n_samples, random_state=seed)
rng = np.random.RandomState(seed)
no_structure = rng.rand(n_samples, 2), None

# Anisotropicly distributed data
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)

# blobs with varied variances
varied = datasets.make_blobs(
    n_samples=n_samples, cluster_std=[1.0, 2.5, 0.5], random_state=random_state
)

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, {}),
]

Then, we run a subset of the clustering procedures and plot the results.

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,
    "random_state": 42,
}

plt.figure(figsize=(6*2+4, 14.5))
plt.subplots_adjust(
    left=0.02, right=0.98, bottom=0.001, top=0.96, wspace=0.05, hspace=0.01
)
plot_num = 1

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)

    # ============
    # Create cluster objects
    # ============
    lmark = lumbermark.Lumbermark(n_clusters=params["n_clusters"])
    ms = cluster.MeanShift(bandwidth=bandwidth, bin_seeding=True)
    two_means = cluster.MiniBatchKMeans(
        n_clusters=params["n_clusters"],
        random_state=params["random_state"],
    )
    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",
        random_state=params["random_state"],
    )
    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"],
        copy=True,
    )
    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=params["random_state"],
    )
    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",
        random_state=params["random_state"],
    )

    clustering_algorithms = (
        # don't run all the algorithms or the plot will not be readable
        ("Lumbermark", lmark),
        ("MiniBatch\nKMeans", two_means),
        #("Affinity\nPropagation", affinity_propagation),
        #("MeanShift", ms),
        ("Spectral\nClustering", spectral),
        #("Ward", ward),
        #("Average\nLinkage", 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.axis("equal")
        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()

Figure 3 Outputs of clustering algorithms

The out-of-the-box Lumbermark algorithm generates quite meaningful partitions. It is also very fast. Even though no algorithm is perfect in all the possible scenarios, give Lumbermark a go in your next data mining challenge.

As with all distance-based methods (this includes k-means and DBSCAN), applying data preprocessing and feature engineering techniques (e.g., feature scaling, feature selection, dimensionality reduction) might lead to more meaningful results.