sklearn.cluster
.FeatureAgglomeration¶
- class sklearn.cluster.FeatureAgglomeration(n_clusters=2, *, affinity='deprecated', metric=None, memory=None, connectivity=None, compute_full_tree='auto', linkage='ward', pooling_func=<function mean>, distance_threshold=None, compute_distances=False)[source]¶
Agglomerate features.
Recursively merges pair of clusters of features.
Read more in the User Guide.
- Parameters:
- n_clustersint or None, default=2
The number of clusters to find. It must be
None
ifdistance_threshold
is notNone
.- affinitystr or callable, default=’euclidean’
The metric to use when calculating distance between instances in a feature array. If metric is a string or callable, it must be one of the options allowed by
sklearn.metrics.pairwise_distances
for its metric parameter. If linkage is “ward”, only “euclidean” is accepted. If “precomputed”, a distance matrix (instead of a similarity matrix) is needed as input for the fit method.Deprecated since version 1.2:
affinity
was deprecated in version 1.2 and will be renamed tometric
in 1.4.- metricstr or callable, default=None
Metric used to compute the linkage. Can be “euclidean”, “l1”, “l2”, “manhattan”, “cosine”, or “precomputed”. If set to
None
then “euclidean” is used. If linkage is “ward”, only “euclidean” is accepted. If “precomputed”, a distance matrix is needed as input for the fit method.New in version 1.2.
- memorystr or object with the joblib.Memory interface, default=None
Used to cache the output of the computation of the tree. By default, no caching is done. If a string is given, it is the path to the caching directory.
- connectivityarray-like or callable, default=None
Connectivity matrix. Defines for each feature the neighboring features following a given structure of the data. This can be a connectivity matrix itself or a callable that transforms the data into a connectivity matrix, such as derived from
kneighbors_graph
. Default isNone
, i.e, the hierarchical clustering algorithm is unstructured.- compute_full_tree‘auto’ or bool, default=’auto’
Stop early the construction of the tree at
n_clusters
. This is useful to decrease computation time if the number of clusters is not small compared to the number of features. This option is useful only when specifying a connectivity matrix. Note also that when varying the number of clusters and using caching, it may be advantageous to compute the full tree. It must beTrue
ifdistance_threshold
is notNone
. By defaultcompute_full_tree
is “auto”, which is equivalent toTrue
whendistance_threshold
is notNone
or thatn_clusters
is inferior to the maximum between 100 or0.02 * n_samples
. Otherwise, “auto” is equivalent toFalse
.- linkage{“ward”, “complete”, “average”, “single”}, default=”ward”
Which linkage criterion to use. The linkage criterion determines which distance to use between sets of features. The algorithm will merge the pairs of cluster that minimize this criterion.
“ward” minimizes the variance of the clusters being merged.
“complete” or maximum linkage uses the maximum distances between all features of the two sets.
“average” uses the average of the distances of each feature of the two sets.
“single” uses the minimum of the distances between all features of the two sets.
- pooling_funccallable, default=np.mean
This combines the values of agglomerated features into a single value, and should accept an array of shape [M, N] and the keyword argument
axis=1
, and reduce it to an array of size [M].- distance_thresholdfloat, default=None
The linkage distance threshold at or above which clusters will not be merged. If not
None
,n_clusters
must beNone
andcompute_full_tree
must beTrue
.New in version 0.21.
- compute_distancesbool, default=False
Computes distances between clusters even if
distance_threshold
is not used. This can be used to make dendrogram visualization, but introduces a computational and memory overhead.New in version 0.24.
- Attributes:
- n_clusters_int
The number of clusters found by the algorithm. If
distance_threshold=None
, it will be equal to the givenn_clusters
.- labels_array-like of (n_features,)
Cluster labels for each feature.
- n_leaves_int
Number of leaves in the hierarchical tree.
- n_connected_components_int
The estimated number of connected components in the graph.
New in version 0.21:
n_connected_components_
was added to replacen_components_
.- n_features_in_int
Number of features seen during fit.
New in version 0.24.
- feature_names_in_ndarray of shape (
n_features_in_
,) Names of features seen during fit. Defined only when
X
has feature names that are all strings.New in version 1.0.
- children_array-like of shape (n_nodes-1, 2)
The children of each non-leaf node. Values less than
n_features
correspond to leaves of the tree which are the original samples. A nodei
greater than or equal ton_features
is a non-leaf node and has childrenchildren_[i - n_features]
. Alternatively at the i-th iteration, children[i][0] and children[i][1] are merged to form noden_features + i
.- distances_array-like of shape (n_nodes-1,)
Distances between nodes in the corresponding place in
children_
. Only computed ifdistance_threshold
is used orcompute_distances
is set toTrue
.
See also
AgglomerativeClustering
Agglomerative clustering samples instead of features.
ward_tree
Hierarchical clustering with ward linkage.
Examples
>>> import numpy as np >>> from sklearn import datasets, cluster >>> digits = datasets.load_digits() >>> images = digits.images >>> X = np.reshape(images, (len(images), -1)) >>> agglo = cluster.FeatureAgglomeration(n_clusters=32) >>> agglo.fit(X) FeatureAgglomeration(n_clusters=32) >>> X_reduced = agglo.transform(X) >>> X_reduced.shape (1797, 32)
Methods
fit
(X[, y])Fit the hierarchical clustering on the data.
fit_transform
(X[, y])Fit to data, then transform it.
get_feature_names_out
([input_features])Get output feature names for transformation.
Get metadata routing of this object.
get_params
([deep])Get parameters for this estimator.
inverse_transform
([Xt, Xred])Inverse the transformation and return a vector of size
n_features
.set_output
(*[, transform])Set output container.
set_params
(**params)Set the parameters of this estimator.
transform
(X)Transform a new matrix using the built clustering.
- fit(X, y=None)[source]¶
Fit the hierarchical clustering on the data.
- Parameters:
- Xarray-like of shape (n_samples, n_features)
The data.
- yIgnored
Not used, present here for API consistency by convention.
- Returns:
- selfobject
Returns the transformer.
- property fit_predict¶
Fit and return the result of each sample’s clustering assignment.
- fit_transform(X, y=None, **fit_params)[source]¶
Fit to data, then transform it.
Fits transformer to
X
andy
with optional parametersfit_params
and returns a transformed version ofX
.- Parameters:
- Xarray-like of shape (n_samples, n_features)
Input samples.
- yarray-like of shape (n_samples,) or (n_samples, n_outputs), default=None
Target values (None for unsupervised transformations).
- **fit_paramsdict
Additional fit parameters.
- Returns:
- X_newndarray array of shape (n_samples, n_features_new)
Transformed array.
- get_feature_names_out(input_features=None)[source]¶
Get output feature names for transformation.
The feature names out will prefixed by the lowercased class name. For example, if the transformer outputs 3 features, then the feature names out are:
["class_name0", "class_name1", "class_name2"]
.- Parameters:
- input_featuresarray-like of str or None, default=None
Only used to validate feature names with the names seen in
fit
.
- Returns:
- feature_names_outndarray of str objects
Transformed feature names.
- 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.
- inverse_transform(Xt=None, Xred=None)[source]¶
Inverse the transformation and return a vector of size
n_features
.- Parameters:
- Xtarray-like of shape (n_samples, n_clusters) or (n_clusters,)
The values to be assigned to each cluster of samples.
- Xreddeprecated
Use
Xt
instead.Deprecated since version 1.3.
- Returns:
- Xndarray of shape (n_samples, n_features) or (n_features,)
A vector of size
n_samples
with the values ofXred
assigned to each of the cluster of samples.
- set_output(*, transform=None)[source]¶
Set output container.
See Introducing the set_output API for an example on how to use the API.
- Parameters:
- transform{“default”, “pandas”}, default=None
Configure output of
transform
andfit_transform
."default"
: Default output format of a transformer"pandas"
: DataFrame outputNone
: Transform configuration is unchanged
- Returns:
- selfestimator instance
Estimator instance.
- 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.
- transform(X)[source]¶
Transform a new matrix using the built clustering.
- Parameters:
- Xarray-like of shape (n_samples, n_features) or (n_samples, n_samples)
A M by N array of M observations in N dimensions or a length M array of M one-dimensional observations.
- Returns:
- Yndarray of shape (n_samples, n_clusters) or (n_clusters,)
The pooled values for each feature cluster.
Examples using sklearn.cluster.FeatureAgglomeration
¶
Feature agglomeration vs. univariate selection