giotto.diagrams.PersistenceEntropy¶

class giotto.diagrams.PersistenceEntropy(n_jobs=None)

Persistence entropies of persistence diagrams.

Given a persistence diagrams consisting of birth-death-dimension triples [b, d, q], subdiagrams corresponding to distinct homology dimensions are considered separately, and their respective persistence entropies are calculated as the (base e) entropies of the collections of differences d - b, normalized by the sum of all such differences.

Parameters
n_jobsint or None, optional, default: None

The number of jobs to use for the computation. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors.

Attributes
homology_dimensions_list

Homology dimensions seen in fit, sorted in ascending order.

Methods

 fit(self, X[, y]) Store all observed homology dimensions in homology_dimensions_. fit_transform(self, X[, y]) Fit to data, then transform it. get_params(self[, deep]) Get parameters for this estimator. set_params(self, \*\*params) Set the parameters of this estimator. transform(self, X[, y]) Compute the persistence entropies of diagrams in X.
__init__(self, n_jobs=None)

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

fit(self, X, y=None)

Store all observed homology dimensions in homology_dimensions_. Then, return the estimator.

This method is there to implement the usual scikit-learn API and hence work in pipelines.

Parameters
Xndarray, shape (n_samples, n_features, 3)

Input data. Array of persistence diagrams, each a collection of triples [b, d, q] representing persistent topological features through their birth (b), death (d) and homology dimension (q).

yNone

There is no need for a target in a transformer, yet the pipeline API requires this parameter.

Returns
selfobject
fit_transform(self, X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters
Xnumpy array of shape [n_samples, n_features]

Training set.

ynumpy array of shape [n_samples]

Target values.

Returns
X_newnumpy array of shape [n_samples, n_features_new]

Transformed array.

get_params(self, deep=True)

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.

set_params(self, **params)

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
transform(self, X, y=None)

Compute the persistence entropies of diagrams in X.

Parameters
Xndarray, shape (n_samples, n_features, 3)

Input data. Array of persistence diagrams, each a collection of triples [b, d, q] representing persistent topological features through their birth (b), death (d) and homology dimension (q).

yNone

There is no need for a target in a transformer, yet the pipeline API requires this parameter.

Returns
Xtndarray, shape (n_samples, n_homology_dimensions)

Persistence entropies: one value per sample and per homology dimension seen in fit. Index i along axis 1 corresponds to the i-th homology dimension in homology_dimensions_.