FlagserPersistence¶

class
gtda.homology.
FlagserPersistence
(homology_dimensions=0, 1, directed=True, filtration='max', coeff=2, max_edge_weight=inf, infinity_values=None, reduced_homology=True, max_entries= 1, n_jobs=None)[source]¶ Persistence diagrams resulting from filtrations of directed or undirected flag complexes 1.
Given a weighted directed or undirected graph, information about the appearance and disappearance of topological features (technically, homology classes) of various dimension and at different scales is summarised in the corresponding persistence diagram.
Important note:
Persistence diagrams produced by this class must be interpreted with care due to the presence of padding triples which carry no information. See
transform
for additional information.
 Parameters
homology_dimensions (list or tuple, optional, default:
(0, 1)
) – Dimensions (nonnegative integers) of the topological features to be detected.directed (bool, optional, default:
True
) –If
True
,transform
computes the persistence diagrams of the filtered directed flag complexes arising from the input collection of weighted directed graphs. IfFalse
,transform
computes the persistence diagrams of the filtered undirected flag complexes obtained by regarding all input weighted graphs as undirected, and:if max_edge_weight is
numpy.inf
, it is sufficient to pass a collection of (dense or sparse) uppertriangular matrices;if max_edge_weight is finite, it is recommended to pass either a collection of symmetric dense matrices, or a collection of sparse uppertriangular matrices.
filtration (string, optional, default:
'max'
) – Algorithm determining the filtration values of higher order simplices from the weights of the vertices and edges. Possible values are: [‘dimension’, ‘zero’, ‘max’, ‘max3’, ‘max_plus_one’, ‘product’, ‘sum’, ‘pmean’, ‘pmoment’, ‘remove_edges’, ‘vertex_degree’]coeff (int prime, optional, default:
2
) – Compute homology with coefficients in the prime field \(\mathbb{F}_p = \{ 0, \ldots, p  1 \}\) where \(p\) equals coeff.max_edge_weight (float, optional, default:
numpy.inf
) – Maximum edge weight to be considered in the filtration. All edge weights greater than this value will be considered as absent from the filtration and topological features at scales larger than this value will not be detected.infinity_values (float or None, default:
None
) – Which death value to assign to features which are still alive at filtration value max_edge_weight.None
means that this death value is declared to be equal to max_edge_weight.reduced_homology (bool, optional, default:
True
) – IfTrue
, the earliestborn triple in homology dimension 0 which has infinite death is discarded from each diagram computed intransform
.max_entries (int, optional, default:
1
) – Number controlling the degree of precision in the matrix reductions performed by the the backend. Corresponds to the parameterapproximation
inpyflagser.flagser_weighted
andpyflagser.flagser_unweighted
. Increase for higher precision, decrease for faster computation. A good value is often100000
in hard problems. A negative value computes highest possible precision.n_jobs (int or None, optional, default:
None
) – The number of jobs to use for the computation.None
means 1 unless in ajoblib.parallel_backend
context.1
means using all processors.

infinity_values_
¶ Effective death value to assign to features which are still alive at filtration value max_edge_weight.
 Type
float
See also
VietorisRipsPersistence
,SparseRipsPersistence
,WeakAlphaPersistence
,EuclideanCechPersistence
,ConsistentRescaling
,ConsecutiveRescaling
Notes
The pyflagser Python package is used for binding Flagser, a C++ backend for computing the (persistent) homology of (filtered) directed flag complexes. For more details, please refer to the flagser documentation.
References
 1
D. Luetgehetmann, D. Govc, J. P. Smith, and R. Levi, “Computing persistent homology of directed flag complexes”, Algorithms, 13(1), 2020.

__init__
(homology_dimensions=0, 1, directed=True, filtration='max', coeff=2, max_edge_weight=inf, infinity_values=None, reduced_homology=True, max_entries= 1, n_jobs=None)[source]¶ Initialize self. See help(type(self)) for accurate signature.

fit
(X, y=None)[source]¶ Calculate
infinity_values_
. Then, return the estimator.This method is here to implement the usual scikitlearn API and hence work in pipelines.
 Parameters
X (ndarray or list of length n_samples) – Input collection of adjacency matrices of weighted directed or undirected graphs. Can be either a 3D ndarray whose zeroth dimension has size
n_samples
, or a list containingn_samples
2D ndarrays/sparse matrices. In each adjacency matrix, diagonal elements are vertex weights and offdiagonal elements are edges weights. It is assumed that a vertex weight cannot be larger than the weight of the edges it forms. The way zero values are handled depends on the format of the matrix. If the matrix is a densenumpy.ndarray
, zero values denote zeroweighted edges. If the matrix is a sparsescipy.sparse
matrix, explicitly stored offdiagonal zeros and all diagonal zeros denote zeroweighted edges. Offdiagonal values that have not been explicitly stored are treated byscipy.sparse
as zeros but will be understood as infinitelyvalued edges, i.e., edges absent from the filtration.y (None) – There is no need for a target in a transformer, yet the pipeline API requires this parameter.
 Returns
self
 Return type
object

fit_transform
(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
X (ndarray or list of length n_samples) – Input collection of adjacency matrices of weighted directed or undirected graphs. Can be either a 3D ndarray whose zeroth dimension has size
n_samples
, or a list containingn_samples
2D ndarrays/sparse matrices. In each adjacency matrix, diagonal elements are vertex weights and offdiagonal elements are edges weights. It is assumed that a vertex weight cannot be larger than the weight of the edges it forms. The way zero values are handled depends on the format of the matrix. If the matrix is a densenumpy.ndarray
, zero values denote zeroweighted edges. If the matrix is a sparsescipy.sparse
matrix, explicitly stored offdiagonal zeros and all diagonal zeros denote zeroweighted edges. Offdiagonal values that have not been explicitly stored are treated byscipy.sparse
as zeros but will be understood as infinitelyvalued edges, i.e., edges absent from the filtration.y (None) – There is no need for a target in a transformer, yet the pipeline API requires this parameter.
 Returns
Xt – Array of persistence diagrams computed from the feature arrays or distance matrices in X.
n_features
equals \(\sum_q n_q\), where \(n_q\) is the maximum number of topological features in dimension \(q\) across all samples in X. Return type
ndarray of shape (n_samples, n_features, 3)

fit_transform_plot
(X, y=None, sample=0, **plot_params)¶ Fit to data, then apply
transform_plot
. Parameters
X (ndarray of shape (n_samples, ..)) – Input data.
y (ndarray of shape (n_samples,) or None) – Target values for supervised problems.
sample (int) – Sample to be plotted.
**plot_params – Optional plotting parameters.
 Returns
Xt – Transformed onesample slice from the input.
 Return type
ndarray of shape (1, ..)

get_params
(deep=True)¶ Get parameters for this estimator.
 Parameters
deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.
 Returns
params – Parameter names mapped to their values.
 Return type
mapping of string to any

static
plot
(Xt, sample=0, homology_dimensions=None, plotly_params=None)[source]¶ Plot a sample from a collection of persistence diagrams, with homology in multiple dimensions.
 Parameters
Xt (ndarray of shape (n_samples, n_features, 3)) – Collection of persistence diagrams, such as returned by
transform
.sample (int, optional, default:
0
) – Index of the sample in Xt to be plotted.homology_dimensions (list, tuple or None, optional, default:
None
) – Which homology dimensions to include in the plot.None
means plotting all dimensions present inXt[sample]
.plotly_params (dict or None, optional, default:
None
) – Custom parameters to configure the plotly figure. Allowed keys are"traces"
and"layout"
, and the corresponding values should be dictionaries containing keyword arguments as would be fed to theupdate_traces
andupdate_layout
methods ofplotly.graph_objects.Figure
.
 Returns
fig – Plotly figure.
 Return type
plotly.graph_objects.Figure
object

set_params
(**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. Parameters
**params (dict) – Estimator parameters.
 Returns
self – Estimator instance.
 Return type
object

transform
(X, y=None)[source]¶ For each adjacency matrix in X, compute the relevant persistence diagram as an array of triples [b, d, q]. Each triple represents a persistent topological feature in dimension q (belonging to homology_dimensions) which is born at b and dies at d. Only triples in which b < d are meaningful. Triples in which b and d are equal (“diagonal elements”) may be artificially introduced during the computation for padding purposes, since the number of nontrivial persistent topological features is typically not constant across samples. They carry no information and hence should be effectively ignored by any further computation.
 Parameters
X (ndarray or list of length n_samples) – Input collection of adjacency matrices of weighted directed or undirected graphs. Can be either a 3D ndarray whose zeroth dimension has size
n_samples
, or a list containingn_samples
2D ndarrays/sparse matrices. In each adjacency matrix, diagonal elements are vertex weights and offdiagonal elements are edges weights. It is assumed that a vertex weight cannot be larger than the weight of the edges it forms. The way zero values are handled depends on the format of the matrix. If the matrix is a densenumpy.ndarray
, zero values denote zeroweighted edges. If the matrix is a sparsescipy.sparse
matrix, explicitly stored offdiagonal zeros and all diagonal zeros denote zeroweighted edges. Offdiagonal values that have not been explicitly stored are treated byscipy.sparse
as zeros but will be understood as infinitelyvalued edges, i.e., edges absent from the filtration.y (None) – There is no need for a target in a transformer, yet the pipeline API requires this parameter.
 Returns
Xt – Array of persistence diagrams computed from the feature arrays or distance matrices in X.
n_features
equals \(\sum_q n_q\), where \(n_q\) is the maximum number of topological features in dimension \(q\) across all samples in X. Return type
ndarray of shape (n_samples, n_features, 3)

transform_plot
(X, sample=0, **plot_params)¶ Take a onesample slice from the input collection and transform it. Before returning the transformed object, plot the transformed sample.
 Parameters
X (ndarray of shape (n_samples, ..)) – Input data.
sample (int) – Sample to be plotted.
**plot_params – Optional plotting parameters.
 Returns
Xt – Transformed onesample slice from the input.
 Return type
ndarray of shape (1, ..)