sklearn.manifold.Isomap

class sklearn.manifold.Isomap(n_neighbors=5, n_components=2, eigen_solver='auto', tol=0, max_iter=None, path_method='auto', neighbors_algorithm='auto', n_jobs=None, metric='minkowski', p=2, metric_params=None)[source]

Isomap Embedding

Non-linear dimensionality reduction through Isometric Mapping

Read more in the User Guide.

Parameters
n_neighborsinteger

number of neighbors to consider for each point.

n_componentsinteger

number of coordinates for the manifold

eigen_solver[‘auto’|’arpack’|’dense’]

‘auto’ : Attempt to choose the most efficient solver for the given problem.

‘arpack’ : Use Arnoldi decomposition to find the eigenvalues and eigenvectors.

‘dense’ : Use a direct solver (i.e. LAPACK) for the eigenvalue decomposition.

tolfloat

Convergence tolerance passed to arpack or lobpcg. not used if eigen_solver == ‘dense’.

max_iterinteger

Maximum number of iterations for the arpack solver. not used if eigen_solver == ‘dense’.

path_methodstring [‘auto’|’FW’|’D’]

Method to use in finding shortest path.

‘auto’ : attempt to choose the best algorithm automatically.

‘FW’ : Floyd-Warshall algorithm.

‘D’ : Dijkstra’s algorithm.

neighbors_algorithmstring [‘auto’|’brute’|’kd_tree’|’ball_tree’]

Algorithm to use for nearest neighbors search, passed to neighbors.NearestNeighbors instance.

n_jobsint or None, default=None

The number of parallel jobs to run. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors. See Glossary for more details.

metricstring, or callable, default=”minkowski”

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 metric is “precomputed”, X is assumed to be a distance matrix and must be square. X may be a Glossary.

New in version 0.22.

pint, default=2

Parameter for the Minkowski metric from sklearn.metrics.pairwise.pairwise_distances. When p = 1, this is equivalent to using manhattan_distance (l1), and euclidean_distance (l2) for p = 2. For arbitrary p, minkowski_distance (l_p) is used.

New in version 0.22.

metric_paramsdict, default=None

Additional keyword arguments for the metric function.

New in version 0.22.

Attributes
embedding_array-like, shape (n_samples, n_components)

Stores the embedding vectors.

kernel_pca_object

KernelPCA object used to implement the embedding.

nbrs_sklearn.neighbors.NearestNeighbors instance

Stores nearest neighbors instance, including BallTree or KDtree if applicable.

dist_matrix_array-like, shape (n_samples, n_samples)

Stores the geodesic distance matrix of training data.

References

R7f4d308f5054-1

Tenenbaum, J.B.; De Silva, V.; & Langford, J.C. A global geometric framework for nonlinear dimensionality reduction. Science 290 (5500)

Examples

>>> from sklearn.datasets import load_digits
>>> from sklearn.manifold import Isomap
>>> X, _ = load_digits(return_X_y=True)
>>> X.shape
(1797, 64)
>>> embedding = Isomap(n_components=2)
>>> X_transformed = embedding.fit_transform(X[:100])
>>> X_transformed.shape
(100, 2)

Methods

fit(self, X[, y])

Compute the embedding vectors for data X

fit_transform(self, X[, y])

Fit the model from data in X and transform X.

get_params(self[, deep])

Get parameters for this estimator.

reconstruction_error(self)

Compute the reconstruction error for the embedding.

set_params(self, \*\*params)

Set the parameters of this estimator.

transform(self, X)

Transform X.
__init__(self, n_neighbors=5, n_components=2, eigen_solver='auto', tol=0, max_iter=None, path_method='auto', neighbors_algorithm='auto', n_jobs=None, metric='minkowski', p=2, metric_params=None)[source]

Initialize self. See help(type(self)) for accurate signature.

fit(self, X, y=None)[source]

Compute the embedding vectors for data X

Parameters
X{array-like, sparse graph, BallTree, KDTree, NearestNeighbors}

Sample data, shape = (n_samples, n_features), in the form of a numpy array, sparse graph, precomputed tree, or NearestNeighbors object.

yIgnored
Returns
selfreturns an instance of self.
fit_transform(self, X, y=None)[source]

Fit the model from data in X and transform X.

Parameters
X{array-like, sparse graph, BallTree, KDTree}

Training vector, where n_samples in the number of samples and n_features is the number of features.

yIgnored
Returns
X_newarray-like, shape (n_samples, n_components)
get_params(self, deep=True)[source]

Get parameters for this estimator.

Parameters
deepboolean, optional

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

Returns
paramsmapping of string to any

Parameter names mapped to their values.

reconstruction_error(self)[source]

Compute the reconstruction error for the embedding.

Returns
reconstruction_errorfloat

Notes

The cost function of an isomap embedding is

E = frobenius_norm[K(D) - K(D_fit)] / n_samples

Where D is the matrix of distances for the input data X, D_fit is the matrix of distances for the output embedding X_fit, and K is the isomap kernel:

K(D) = -0.5 * (I - 1/n_samples) * D^2 * (I - 1/n_samples)

set_params(self, **params)[source]

Set the parameters of this estimator.

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

Returns
self
property training_data_

DEPRECATED: Attribute training_data_ was deprecated in version 0.22 and will be removed in 0.24.

transform(self, X)[source]

Transform X.

This is implemented by linking the points X into the graph of geodesic distances of the training data. First the n_neighbors nearest neighbors of X are found in the training data, and from these the shortest geodesic distances from each point in X to each point in the training data are computed in order to construct the kernel. The embedding of X is the projection of this kernel onto the embedding vectors of the training set.

Parameters
Xarray-like, shape (n_queries, n_features)

If neighbors_algorithm=’precomputed’, X is assumed to be a distance matrix or a sparse graph of shape (n_queries, n_samples_fit).

Returns
X_newarray-like, shape (n_queries, n_components)