DBSCAN#

class sklearn.cluster.DBSCAN(eps=0.5, *, min_samples=5, metric='euclidean', metric_params=None, algorithm='auto', leaf_size=30, p=None, n_jobs=None)[source]#

Perform DBSCAN clustering from vector array or distance matrix.

DBSCAN - Density-Based Spatial Clustering of Applications with Noise. Finds core samples of high density and expands clusters from them. Good for data which contains clusters of similar density.

This implementation has a worst case memory complexity of $O({n}^2)$, which can occur when the eps param is large and min_samples is low, while the original DBSCAN only uses linear memory. For further details, see the Notes below.

See also

OPTICS: A similar clustering at multiple values of eps. Our implementation is optimized for memory usage.

Notes

For an example, see demo of DBSCAN clustering algorithm.

This implementation bulk-computes all neighborhood queries, which increases the memory complexity to O(n.d) where d is the average number of neighbors, while original DBSCAN had memory complexity O(n). It may attract a higher memory complexity when querying these nearest neighborhoods, depending on the algorithm.

One way to avoid the query complexity is to pre-compute sparse neighborhoods in chunks using NearestNeighbors.radius_neighbors_graph with mode='distance', then using metric='precomputed' here.

Another way to reduce memory and computation time is to remove (near-)duplicate points and use sample_weight instead.

OPTICS provides a similar clustering with lower memory usage.

References

Ester, M., H. P. Kriegel, J. Sander, and X. Xu, “A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise”. In: Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining, Portland, OR, AAAI Press, pp. 226-231. 1996

Schubert, E., Sander, J., Ester, M., Kriegel, H. P., & Xu, X. (2017). “DBSCAN revisited, revisited: why and how you should (still) use DBSCAN.” ACM Transactions on Database Systems (TODS), 42(3), 19.

Examples

>>> from sklearn.cluster import DBSCAN
>>> import numpy as np
>>> X = np.array([[1, 2], [2, 2], [2, 3],
...               [8, 7], [8, 8], [25, 80]])
>>> clustering = DBSCAN(eps=3, min_samples=2).fit(X)
>>> clustering.labels_
array([ 0,  0,  0,  1,  1, -1])
>>> clustering
DBSCAN(eps=3, min_samples=2)

fit(X, y=None, sample_weight=None)[source]#

Perform DBSCAN clustering from features, or distance matrix.

Parameters:

X{array-like, sparse matrix} of shape (n_samples, n_features), or (n_samples, n_samples): Training instances to cluster, or distances between instances if metric='precomputed'. If a sparse matrix is provided, it will be converted into a sparse csr_matrix.
yIgnored: Not used, present here for API consistency by convention.
sample_weightarray-like of shape (n_samples,), default=None: Weight of each sample, such that a sample with a weight of at least min_samples is by itself a core sample; a sample with a negative weight may inhibit its eps-neighbor from being core. Note that weights are absolute, and default to 1.

Returns:

selfobject: Returns a fitted instance of self.

fit_predict(X, y=None, sample_weight=None)[source]#

Compute clusters from a data or distance matrix and predict labels.

Parameters:

X{array-like, sparse matrix} of shape (n_samples, n_features), or (n_samples, n_samples): Training instances to cluster, or distances between instances if metric='precomputed'. If a sparse matrix is provided, it will be converted into a sparse csr_matrix.
yIgnored: Not used, present here for API consistency by convention.
sample_weightarray-like of shape (n_samples,), default=None: Weight of each sample, such that a sample with a weight of at least min_samples is by itself a core sample; a sample with a negative weight may inhibit its eps-neighbor from being core. Note that weights are absolute, and default to 1.

Returns:

labelsndarray of shape (n_samples,): Cluster labels. Noisy samples are given the label -1.

get_metadata_routing()[source]#

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns:

routingMetadataRequest: A MetadataRequest encapsulating routing information.

get_params(deep=True)[source]#

Get parameters for this estimator.

Parameters:

deepbool, default=True: If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns:

paramsdict: Parameter names mapped to their values.

set_fit_request(*, sample_weight: bool | None | str = '$UNCHANGED$') → DBSCAN[source]#

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.
False: metadata is not requested and the meta-estimator will not pass it to fit.
None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.
str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

Added in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a Pipeline. Otherwise it has no effect.

Parameters:

sample_weightstr, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED: Metadata routing for sample_weight parameter in fit.

Returns:

selfobject: The updated object.

set_params(**params)[source]#

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters:

**paramsdict: Estimator parameters.

Returns:

selfestimator instance: Estimator instance.

Gallery examples#

Comparing different clustering algorithms on toy datasets

demo of DBSCAN clustering algorithm

demo of HDBSCAN clustering algorithm