TopOMetry
latest
Installation:
Installation and dependencies
Optional dependencies
Getting started:
About TopOMetry
Quick-start cheat-sheet
Tutorials:
Quick-start with the MNIST digits dataset
Using TopOMetry for document embedding
Using TopOMetry’s classes: Kernel, EigenDecomposition and Project
Estimating intrinsic dimensionalities
Evaluating embeddings
RNA velocity with scVelo and TopOMetry
Embedding to non-euclidean spaces with MAP
API:
TopOGraph
API Reference
TopOMetry
Index
Edit on GitHub
Index
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A
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
_
__delattr__ (topo.tpgraph.procrustes.ProcrustesResult attribute)
__dir__() (topo.tpgraph.procrustes.ProcrustesResult method)
__getattr__() (topo.tpgraph.procrustes.ProcrustesResult method)
__repr__() (topo.layouts.Projector method)
(topo.layouts.projector.Projector method)
(topo.spectral.eigen.EigenDecomposition method)
(topo.TopOGraph method)
(topo.topograph.TopOGraph method)
(topo.tpgraph.intrinsic_dim.IntrinsicDim method)
(topo.tpgraph.IntrinsicDim method)
(topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
(topo.tpgraph.procrustes.ProcrustesResult method)
__setattr__ (topo.tpgraph.procrustes.ProcrustesResult attribute)
__version__ (in module topo)
(in module topo.version)
_adap_bw() (in module topo.tpgraph.kernels)
_calculate_imputation_error() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
_check_arraytypes() (in module topo.tpgraph.procrustes)
_compute_id() (topo.tpgraph.intrinsic_dim.IntrinsicDim method)
(topo.tpgraph.IntrinsicDim method)
_compute_kernel_from_version_knn() (topo.TopOGraph method)
(topo.topograph.TopOGraph method)
_connected_components() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
_dense_degree() (in module topo.spectral._spectral)
_dense_diffusion() (in module topo.spectral._spectral)
_dense_diffusion_symmetric() (in module topo.spectral._spectral)
_dense_normalized_random_walk_laplacian() (in module topo.spectral._spectral)
_dense_symmetric_normalized_laplacian() (in module topo.spectral._spectral)
_dense_unnormalized_laplacian() (in module topo.spectral._spectral)
_get_dist_to_k_nearest_neighbor() (in module topo.tpgraph.intrinsic_dim)
_get_dist_to_median_nearest_neighbor() (in module topo.tpgraph.intrinsic_dim)
_get_landmarks() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
_HAS_PYMDE (in module topo.layouts.projector)
_have_annoy (in module topo.layouts.projector)
_have_faiss (in module topo.layouts.projector)
_have_hnswlib (in module topo.layouts.projector)
_have_nmslib (in module topo.layouts.projector)
_have_numba (in module topo.base)
(in module topo.base.dists)
_HAVE_SCANPY (in module topo)
(in module topo.single_cell)
_hide_zero_padding() (in module topo.tpgraph.procrustes)
_metric_info (topo.base.ann.FAISSTransformer property)
_mock_identity (in module topo.base.dists)
_more_tags() (topo.base.ann.FAISSTransformer method)
_optimize_layout_aligned_euclidean_single_epoch() (in module topo.spectral.umap_layouts)
_optimize_layout_euclidean_densmap_epoch_init() (in module topo.spectral.umap_layouts)
_optimize_layout_euclidean_single_epoch() (in module topo.spectral.umap_layouts)
_orthogonal() (in module topo.tpgraph.procrustes)
_parse_backend() (topo.layouts.Projector method)
(topo.layouts.projector.Projector method)
(topo.TopOGraph method)
(topo.topograph.TopOGraph method)
(topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
_parse_random_state() (topo.TopOGraph method)
(topo.topograph.TopOGraph method)
(topo.tpgraph.intrinsic_dim.IntrinsicDim method)
(topo.tpgraph.IntrinsicDim method)
_remove_anchor_anchor_edges() (in module topo.layouts.projector)
_replicate_normalize_densities() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
_scale_array() (in module topo.tpgraph.procrustes)
_set_diag() (in module topo.spectral._spectral)
_setup_input_array_lower() (in module topo.tpgraph.procrustes)
_sparse_degree() (in module topo.spectral._spectral)
_sparse_diffusion() (in module topo.spectral._spectral)
_sparse_diffusion_symmetric() (in module topo.spectral._spectral)
_sparse_normalized_random_walk_laplacian() (in module topo.spectral._spectral)
_sparse_symmetrized_normalized_laplacian() (in module topo.spectral._spectral)
_sparse_unnormalized_laplacian() (in module topo.spectral._spectral)
_transform() (topo.base.ann.AnnoyTransformer method)
(topo.base.ann.FAISSTransformer method)
_translate_array() (in module topo.tpgraph.procrustes)
_zero_padding() (in module topo.tpgraph.procrustes)
A
A (topo.tpgraph.Kernel property)
(topo.tpgraph.kernels.Kernel property)
adjacency() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
annotate_heatmap() (in module topo.plot)
AnnoyTransformer (class in topo.base.ann)
approx_log_Gamma() (in module topo.base.sparse)
arr_intersect() (in module topo.base.sparse)
arr_union() (in module topo.base.sparse)
arr_unique() (in module topo.base.sparse)
C
cknn_graph() (in module topo.tpgraph)
(in module topo.tpgraph.cknn)
clip() (in module topo.spectral.umap_layouts)
component_layout() (in module topo.spectral.eigen)
compute_error() (in module topo.tpgraph.procrustes)
compute_G_from_H() (in module topo.eval.rmetric)
compute_kernel() (in module topo.tpgraph)
(in module topo.tpgraph.kernels)
compute_membership_strengths() (in module topo.tpgraph.fuzzy)
create_density_plot() (in module topo.plot)
(in module topo.utils.umap_utils)
csr_unique() (in module topo.utils.umap_utils)
D
decay_plot() (in module topo.plot)
degree (topo.tpgraph.Kernel property)
(topo.tpgraph.kernels.Kernel property)
degree() (in module topo.spectral)
(in module topo.spectral._spectral)
diff_op() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
diffusion_operator() (in module topo.spectral)
(in module topo.spectral._spectral)
DM() (in module topo.spectral)
(in module topo.spectral._spectral)
draw_edges() (in module topo.plot)
draw_simple_ellipse() (in module topo.plot)
E
EIGEN_SOLVERS (in module topo.spectral.eigen)
eigendecompose() (in module topo.spectral.eigen)
EigenDecomposition (class in topo.spectral.eigen)
eigenspectrum() (topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
eigsorted() (in module topo.eval.rmetric)
(in module topo.plot)
(in module topo.utils)
(in module topo.utils._utils)
eval_density_at_point() (in module topo.plot)
(in module topo.utils.umap_utils)
eval_gaussian() (in module topo.plot)
(in module topo.utils.umap_utils)
eval_models_layouts() (in module topo.pipes)
(topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
explained_variance() (in module topo.pipes)
F
FAISSTransformer (class in topo.base.ann)
fast_knn_indices() (in module topo.layouts)
(in module topo.utils.umap_utils)
filter() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
find_ab_params() (in module topo.layouts)
(in module topo.layouts.graph_utils)
fit() (topo.base.ann.AnnoyTransformer method)
(topo.base.ann.FAISSTransformer method)
(topo.base.ann.HNSWlibTransformer method)
(topo.base.ann.NMSlibTransformer method)
(topo.eval.RiemannMetric method)
(topo.eval.rmetric.RiemannMetric method)
(topo.layouts.Projector method)
(topo.layouts.projector.Projector method)
(topo.spectral.eigen.EigenDecomposition method)
(topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
(topo.tpgraph.GeneralizedProcrustes method)
(topo.tpgraph.intrinsic_dim.IntrinsicDim method)
(topo.tpgraph.IntrinsicDim method)
(topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
(topo.tpgraph.procrustes.GeneralizedProcrustes method)
fit_transform() (topo.base.ann.AnnoyTransformer method)
(topo.base.ann.FAISSTransformer method)
(topo.base.ann.HNSWlibTransformer method)
(topo.base.ann.NMSlibTransformer method)
(topo.layouts.Projector method)
(topo.layouts.projector.Projector method)
(topo.spectral.eigen.EigenDecomposition method)
(topo.TopOGraph method)
(topo.topograph.TopOGraph method)
(topo.tpgraph.GeneralizedProcrustes method)
(topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
(topo.tpgraph.procrustes.GeneralizedProcrustes method)
fit_transform_procrustes() (in module topo.tpgraph)
(in module topo.tpgraph.procrustes)
fsa_global() (in module topo.tpgraph.intrinsic_dim)
fsa_local() (in module topo.tpgraph.intrinsic_dim)
fuzzy_embedding() (in module topo.layouts)
(in module topo.layouts.map)
fuzzy_simplicial_set() (in module topo.layouts)
(in module topo.tpgraph)
(in module topo.tpgraph.fuzzy)
G
gaussian_potential() (in module topo.plot)
general_sset_intersection() (in module topo.base.sparse)
general_sset_union() (in module topo.base.sparse)
generalized() (in module topo.tpgraph.procrustes)
GeneralizedProcrustes (class in topo.tpgraph)
(class in topo.tpgraph.procrustes)
geodesic_correlation() (in module topo.eval)
(in module topo.eval.local_scores)
geodesic_distance() (in module topo.eval)
(in module topo.eval.local_scores)
get_cmap() (in module topo.plot)
get_detG() (topo.eval.RiemannMetric method)
(topo.eval.rmetric.RiemannMetric method)
get_dual_rmetric() (topo.eval.RiemannMetric method)
(topo.eval.rmetric.RiemannMetric method)
get_eccentricity() (in module topo.eval)
(in module topo.eval.rmetric)
(in module topo.utils)
(in module topo.utils._utils)
get_indices_distances() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
get_indices_distances_from_sparse_matrix() (in module topo.utils)
(in module topo.utils._utils)
get_landmark_indices() (in module topo.utils)
(in module topo.utils._utils)
get_mdimG() (topo.eval.RiemannMetric method)
(topo.eval.rmetric.RiemannMetric method)
get_rmetric() (topo.eval.RiemannMetric method)
(topo.eval.rmetric.RiemannMetric method)
get_sparse_matrix_from_indices_distances() (in module topo.utils)
(in module topo.utils._utils)
get_sparse_row() (in module topo.base.ann)
global_loss_() (in module topo.eval.global_scores)
global_score() (in module topo.pipes)
global_score_laplacian() (in module topo.eval)
(in module topo.eval.global_scores)
global_score_pca() (in module topo.eval)
(in module topo.eval.global_scores)
graph_laplacian() (in module topo.spectral)
(in module topo.spectral._spectral)
H
heatmap() (in module topo.plot)
HNSWlibTransformer (class in topo.base.ann)
hyperboloid() (in module topo.plot)
I
impute() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
ind_dist_grad() (topo.base.ann.HNSWlibTransformer method)
(topo.base.ann.NMSlibTransformer method)
INT32_MAX (in module topo.layouts)
(in module topo.layouts.graph_utils)
(in module topo.tpgraph.fuzzy)
INT32_MIN (in module topo.layouts)
(in module topo.layouts.graph_utils)
(in module topo.tpgraph.fuzzy)
interpolate() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
IntrinsicDim (class in topo.tpgraph)
(class in topo.tpgraph.intrinsic_dim)
is_connected() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
Isomap() (in module topo.layouts)
(in module topo.layouts.isomap)
K
K (topo.tpgraph.Kernel property)
(topo.tpgraph.kernels.Kernel property)
Kernel (class in topo.tpgraph)
(class in topo.tpgraph.kernels)
knn (topo.tpgraph.Kernel property)
(topo.tpgraph.kernels.Kernel property)
kNN() (in module topo.base)
(in module topo.base.ann)
knn_kendall_tau() (in module topo.eval.local_scores)
knn_spearman_r() (in module topo.eval)
(in module topo.eval.local_scores)
L
L (topo.tpgraph.Kernel property)
(topo.tpgraph.kernels.Kernel property)
laplacian() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
LE() (in module topo.spectral)
(in module topo.spectral._spectral)
list_eigenbases() (topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
local_eigengap_experimental() (in module topo.tpgraph.intrinsic_dim)
log_beta() (in module topo.base.sparse)
log_single_beta() (in module topo.base.sparse)
M
make_epochs_per_sample() (in module topo.layouts)
(in module topo.layouts.graph_utils)
MIN_K_DIST_SCALE (in module topo.tpgraph.fuzzy)
mk_faiss_index() (topo.base.ann.FAISSTransformer method)
mle_global() (in module topo.tpgraph.intrinsic_dim)
mle_local() (in module topo.tpgraph.intrinsic_dim)
module
topo
topo.base
topo.base.ann
topo.base.dists
topo.base.sparse
topo.eval
topo.eval.global_scores
topo.eval.local_scores
topo.eval.rmetric
topo.layouts
topo.layouts.graph_utils
topo.layouts.isomap
topo.layouts.map
topo.layouts.projector
topo.pipes
topo.plot
topo.single_cell
topo.spectral
topo.spectral._spectral
topo.spectral.eigen
topo.spectral.locally
topo.spectral.umap_layouts
topo.topograph
topo.tpgraph
topo.tpgraph.cknn
topo.tpgraph.fuzzy
topo.tpgraph.intrinsic_dim
topo.tpgraph.kernels
topo.tpgraph.procrustes
topo.utils
topo.utils._utils
topo.utils.umap_utils
topo.version
multi_component_layout() (in module topo.spectral.eigen)
N
NMSlibTransformer (class in topo.base.ann)
norm() (in module topo.utils.umap_utils)
NPY_INFINITY (in module topo.tpgraph.fuzzy)
O
optimize_layout_aligned_euclidean() (in module topo.spectral)
(in module topo.spectral.umap_layouts)
optimize_layout_euclidean() (in module topo.layouts)
(in module topo.spectral)
(in module topo.spectral.umap_layouts)
optimize_layout_generic() (in module topo.layouts)
(in module topo.spectral)
(in module topo.spectral.umap_layouts)
optimize_layout_inverse() (in module topo.layouts)
(in module topo.spectral)
(in module topo.spectral.umap_layouts)
or_else_csrs() (in module topo.base.ann)
orthogonal() (in module topo.tpgraph.procrustes)
P
P (topo.tpgraph.Kernel property)
(topo.tpgraph.kernels.Kernel property)
plot_all_scores() (in module topo.plot)
plot_bases_scores() (in module topo.plot)
plot_cov_ellipse() (in module topo.plot)
plot_dimensionality_histograms() (in module topo.plot)
plot_dimensionality_histograms_multiple() (in module topo.plot)
plot_eigenspectrum() (topo.spectral.eigen.EigenDecomposition method)
(topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
plot_eigenvectors() (in module topo.plot)
plot_graphs_scores() (in module topo.plot)
plot_id() (topo.tpgraph.intrinsic_dim.IntrinsicDim method)
(topo.tpgraph.IntrinsicDim method)
plot_layouts_scores() (in module topo.plot)
plot_point_cov() (in module topo.plot)
plot_riemann_metric() (in module topo.plot)
plot_scores() (in module topo.plot)
poincare() (in module topo.plot)
postprocess_knn_csr() (in module topo.base.ann)
preprocess() (in module topo.single_cell)
print_eval_results() (in module topo.utils)
(in module topo.utils._utils)
procrustes() (in module topo.tpgraph.procrustes)
ProcrustesResult (class in topo.tpgraph.procrustes)
project() (topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
Projector (class in topo.layouts)
(class in topo.layouts.projector)
PYAMG_LOADED (in module topo.spectral.eigen)
R
rdist() (in module topo.spectral.umap_layouts)
read_pkl() (in module topo)
(in module topo.utils)
(in module topo.utils._utils)
rescale() (topo.spectral.eigen.EigenDecomposition method)
resistance_distance() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
results() (topo.spectral.eigen.EigenDecomposition method)
riemann_metric() (in module topo.eval.rmetric)
RiemannMetric (class in topo.eval)
(class in topo.eval.rmetric)
run_models() (topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
S
scatter() (in module topo.plot)
scatter3d() (in module topo.plot)
setup_input_arrays() (in module topo.tpgraph.procrustes)
setup_input_arrays_multi() (in module topo.tpgraph.procrustes)
shortest_paths() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
simplicial_set_embedding() (in module topo.layouts)
(in module topo.layouts.graph_utils)
SMOOTH_K_TOLERANCE (in module topo.tpgraph.fuzzy)
smooth_knn_dist() (in module topo.tpgraph.fuzzy)
SP (topo.tpgraph.Kernel property)
(topo.tpgraph.kernels.Kernel property)
sparse_bray_curtis() (in module topo.base.sparse)
sparse_canberra() (in module topo.base.sparse)
sparse_chebyshev() (in module topo.base.sparse)
sparse_correlation() (in module topo.base.sparse)
sparse_cosine() (in module topo.base.sparse)
sparse_dice() (in module topo.base.sparse)
sparse_diff() (in module topo.base.sparse)
sparse_euclidean() (in module topo.base.sparse)
sparse_hamming() (in module topo.base.sparse)
sparse_hellinger() (in module topo.base.sparse)
sparse_jaccard() (in module topo.base.sparse)
sparse_kulsinski() (in module topo.base.sparse)
sparse_ll_dirichlet() (in module topo.base.sparse)
sparse_manhattan() (in module topo.base.sparse)
sparse_matching() (in module topo.base.sparse)
sparse_minkowski() (in module topo.base.sparse)
sparse_mul() (in module topo.base.sparse)
sparse_named_distances (in module topo.base.sparse)
sparse_need_n_features (in module topo.base.sparse)
sparse_rogers_tanimoto() (in module topo.base.sparse)
sparse_russellrao() (in module topo.base.sparse)
sparse_sokal_michener() (in module topo.base.sparse)
sparse_sokal_sneath() (in module topo.base.sparse)
SPARSE_SPECIAL_METRICS (in module topo.base.sparse)
sparse_sum() (in module topo.base.sparse)
sparsify() (topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
spectral_clustering() (in module topo.spectral._spectral)
spectral_layout() (in module topo.layouts)
(in module topo.spectral.eigen)
(topo.spectral.eigen.EigenDecomposition method)
(topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
sphere() (in module topo.plot)
sphere_projection() (in module topo.plot)
submatrix() (in module topo.utils.umap_utils)
subsample_square_csr_to_indices() (in module topo.utils)
(in module topo.utils._utils)
T
tau_rand() (in module topo.utils.umap_utils)
tau_rand_int() (in module topo.utils.umap_utils)
test_efficiency() (topo.base.ann.HNSWlibTransformer method)
(topo.base.ann.NMSlibTransformer method)
topo
module
topo.base
module
topo.base.ann
module
topo.base.dists
module
topo.base.sparse
module
topo.eval
module
topo.eval.global_scores
module
topo.eval.local_scores
module
topo.eval.rmetric
module
topo.layouts
module
topo.layouts.graph_utils
module
topo.layouts.isomap
module
topo.layouts.map
module
topo.layouts.projector
module
topo.pipes
module
topo.plot
module
topo.single_cell
module
topo.spectral
module
topo.spectral._spectral
module
topo.spectral.eigen
module
topo.spectral.locally
module
topo.spectral.umap_layouts
module
topo.topograph
module
topo.tpgraph
module
topo.tpgraph.cknn
module
topo.tpgraph.fuzzy
module
topo.tpgraph.intrinsic_dim
module
topo.tpgraph.kernels
module
topo.tpgraph.procrustes
module
topo.utils
module
topo.utils._utils
module
topo.utils.umap_utils
module
topo.version
module
TopOGraph (class in topo)
,
[1]
(class in topo.topograph)
toroid() (in module topo.plot)
torus_euclidean_grad() (in module topo.utils.umap_utils)
transform() (topo.base.ann.AnnoyTransformer method)
(topo.base.ann.FAISSTransformer method)
(topo.base.ann.HNSWlibTransformer method)
(topo.base.ann.NMSlibTransformer method)
(topo.eval.RiemannMetric method)
(topo.eval.rmetric.RiemannMetric method)
(topo.layouts.Projector method)
(topo.layouts.projector.Projector method)
(topo.spectral.eigen.EigenDecomposition method)
(topo.TopOGraph method)
,
[1]
(topo.topograph.TopOGraph method)
(topo.tpgraph.GeneralizedProcrustes method)
(topo.tpgraph.intrinsic_dim.IntrinsicDim method)
(topo.tpgraph.IntrinsicDim method)
(topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
(topo.tpgraph.procrustes.GeneralizedProcrustes method)
ts() (in module topo.layouts)
(in module topo.utils.umap_utils)
two_to_3d_hyperboloid() (in module topo.plot)
U
update_search() (topo.base.ann.HNSWlibTransformer method)
(topo.base.ann.NMSlibTransformer method)
W
weighted_degree (topo.tpgraph.Kernel property)
(topo.tpgraph.kernels.Kernel property)
write_pkl() (topo.TopOGraph method)
(topo.topograph.TopOGraph method)
(topo.tpgraph.Kernel method)
(topo.tpgraph.kernels.Kernel method)
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