• In the following code of the DBSCAN algorithm, as a beginner I need an explanation for what happens to the data in the bottom for loop and why ?

Generate sample data

import numpy as np

from sklearn.cluster import DBSCAN
from sklearn import metrics
from sklearn.datasets import make_blobs
from sklearn.preprocessing import StandardScaler
centers = [[1, 1], [-1, -1], [1, -1]]
X, labels_true = make_blobs(n_samples=750, centers=centers, cluster_std=0.4,

X = StandardScaler().fit_transform(X)

Compute DBSCAN

db = DBSCAN(eps=0.3, min_samples=10).fit(X)
core_samples_mask = np.zeros_like(db.labels_, dtype=bool)
core_samples_mask[db.core_sample_indices_] = True
labels = db.labels_

Number of clusters in labels, ignoring noise if present.

n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
n_noise_ = list(labels).count(-1)

Plot result

import matplotlib.pyplot as plt

Black removed and is used for noise instead.

unique_labels = set(labels)
colors = [plt.cm.Spectral(each)
          for each in np.linspace(0, 1, len(unique_labels))]
for k, col in zip(unique_labels, colors):
    if k == -1:
        # Black used for noise.
        col = [0, 0, 0, 1]

    class_member_mask = (labels == k)

    xy = X[class_member_mask & core_samples_mask]
    plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col),
             markeredgecolor='k', markersize=14)

    xy = X[class_member_mask & ~core_samples_mask]
    plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col),
             markeredgecolor='k', markersize=6)

plt.title('Estimated number of clusters: %d' % n_clusters_)

1 Answer 1


First I'm going to use a simplier way (gives the same plot just without changing dots size according to its distance to core samples) of visualizing the cluster results:

plt.scatter(X[:,0], X[:,1], c = db.labels_, cmap = "RdGy", alpha = .5)
plt.title(f"DBSCAN for {len(np.unique(db.labels_)) - 1} clusters")


enter image description here

In this case in my drawing, the red dots are marked as anomalies since those are not in dense areas.

Those points are marked as anomalies since there are no 10 points (min_samples) in a radius of .3 (eps / euclidian distance) from them

Those are without question the most important parameter for this algorithm and must be chosen carefully.

From Scikit-learn docs:

While the parameter min_samples primarily controls how tolerant the algorithm is towards noise (on noisy and large data sets it may be desirable to increase this parameter), the parameter eps is crucial to choose appropriately for the data set and distance function and usually cannot be left at the default value. It controls the local neighborhood of the points. When chosen too small, most data will not be clustered at all (and labeled as -1 for “noise”). When chosen too large, it causes close clusters to be merged into one cluster, and eventually the entire data set to be returned as a single cluster. Some heuristics for choosing this parameter have been discussed in the literature, for example based on a knee in the nearest neighbor distances plot (as discussed in the references below).

  • $\begingroup$ thx for sharing , i fully understand your concept but what still stucks in mind these 2 lines: xy = X [class_member_mask & core_samples_mask] whats the aim of this new xy ? how it sorted from the original X ...thx in advance $\endgroup$
    – soufi-43
    Aug 12, 2021 at 10:50
  • $\begingroup$ xy = X[class_member_mask & core_samples_mask] and xy = X[class_member_mask & ~core_samples_mask] are simply separating for each of the 3 different clusters, the core samples on each cluster for the points that are no core samples in the same cluster (plots of each xy are give different size). For example, for cluster k = 0 [class_member_mask & core_samples_mask] will give True only when both, the cluster db.labels_ = 0 and the point is a core_sample, those points will be plotted with size 14, and you repeat this for each cluster for both core and no core samples $\endgroup$
    – Multivac
    Aug 12, 2021 at 13:17
  • $\begingroup$ understood , thank you very much for the effort $\endgroup$
    – soufi-43
    Aug 12, 2021 at 13:56

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