Index

_

__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) __version__ (in module topo) (in module topo.version) _A (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _adap_bw() (in module topo.tpgraph.kernels) _automated_sizing() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _calculate_imputation_error() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) _center() (in module topo.eval.rmetric) _clusters (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _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 (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _connected_components() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) _consolidate_macros_via_conductance() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _cosine_distance_to_angle_from_sparse_triplets() (in module topo.tpgraph.kernels) _cosine_knn_requires_unit_vectors() (in module topo.tpgraph.kernels) _csr() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _Dd (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _degree (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _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) _eigengap_k() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _ellipse_from_G() (in module topo.eval.rmetric) _ensure_array() (in module topo.eval.rmetric) _ensure_csr() (in module topo.eval.topo_metrics) _ensure_nonneg_and_finite() (in module topo.tpgraph.kernels) _first_non_none() (in module topo.single_cell) _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) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _have_faiss (in module topo.layouts.projector) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _have_hnswlib (in module topo.layouts.projector) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _have_nmslib (in module topo.layouts.projector) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _have_numba (in module topo.base) (in module topo.base.dists)

_HAVE_SCANPY (in module topo) (in module topo.single_cell) _HAVE_SK (in module topo.eval.rmetric) _id_details (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _K (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _kernel_msZ (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _kernel_Z (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _knn_msZ (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _knn_Z (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _L (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _louvain_micro() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _maybe_l2_normalize_rows() (in module topo.tpgraph.kernels) _mbkm() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _noANN_lib() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _normalized_laplacian() (topo.TopOGraph method) (topo.topograph.TopOGraph 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.layouts) (in module topo.spectral.umap_layouts) _P (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _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) _prepare_colors() (in module topo.eval.rmetric) _project_spd() (in module topo.eval.rmetric) _remove_anchor_anchor_edges() (in module topo.layouts.projector) _replicate_normalize_densities() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) _sample_densities (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _scaffold_components_dm (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _scaffold_components_ms (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _scaling_values() (in module topo.eval.rmetric) _select_P_operator() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _SP (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) _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) _symmetrize() (in module topo.eval.rmetric) _symmetrize_geometric() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _to_float32_csr() (topo.TopOGraph method) (topo.topograph.TopOGraph method) _top_eigs_of_P() (in module topo.eval.topo_metrics) _topk_support_from_row() (in module topo.eval.topo_metrics) _uom_active_mode (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _uom_axis_slices (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) _upper_triangle_vec() (in module topo.eval.topo_metrics) _weighted_degree (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute)

A

A (topo.tpgraph.Kernel property) (topo.tpgraph.kernels.Kernel property) adaptive_bw (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) adaptive_bw_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) adaptive_bw_nbr_expanded_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) adjacency() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) alpha_decaying (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute)

anisotropy (topo.spectral.eigen.EigenDecomposition attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) annotate_heatmap() (in module topo.plot) 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) automated_scaffold_sizing() (in module topo.tpgraph) (in module topo.tpgraph.intrinsic_dim)

B

backend (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) base_kernel (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) base_kernel_version (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) base_knn (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)

base_knn_graph (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) base_metric (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) base_nbrs_class (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) BaseKernelDict (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) bases_graph_verbose (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)

C

cache (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) cache_input (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) calculate_deformation() (in module topo.eval.rmetric) checkpoints_ (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) cknn (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) cknn_graph() (in module topo.tpgraph) (in module topo.tpgraph.cknn) clip() (in module topo.spectral.umap_layouts) ClustersDict (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) commute_time_trace_gap() (in module topo.eval.topo_metrics)

component_layout() (in module topo.spectral.eigen) components_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) components_indices_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) 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) current_eigenbasis (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) current_graphkernel (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)

D

D_inv_sqrt_ (topo.spectral.eigen.EigenDecomposition attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) 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) delta (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) dens_dict (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) dense (topo.base.ann.NMSlibTransformer attribute)

diff_op() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) diff_t (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) diffusion_coordinates() (in module topo.eval.topo_metrics) diffusion_distance_from_eigs() (in module topo.eval.topo_metrics) diffusion_operator (topo.spectral.eigen.EigenDecomposition attribute) diffusion_operator() (in module topo.spectral) (in module topo.spectral._spectral) diffusion_rank_biased_overlap() (in module topo.eval.topo_metrics) draw_edges() (in module topo.plot) draw_simple_ellipse() (in module topo.plot) drop_first (topo.spectral.eigen.EigenDecomposition attribute)

E

efC (topo.base.ann.HNSWlibTransformer attribute) (topo.base.ann.NMSlibTransformer attribute) efS (topo.base.ann.HNSWlibTransformer attribute) (topo.base.ann.NMSlibTransformer attribute) EIGEN_SOLVERS (in module topo.spectral.eigen) eigen_tol (topo.spectral.eigen.EigenDecomposition attribute) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) eigenbasis (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) eigenbasis_knn_graph (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) EigenbasisDict (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) eigendecompose() (in module topo.spectral.eigen) EigenDecomposition (class in topo.spectral.eigen) eigengap (topo.spectral.eigen.EigenDecomposition attribute) eigenmap_method (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) eigensolver (topo.spectral.eigen.EigenDecomposition attribute) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)

eigenspectrum() (topo.TopOGraph method), [1] (topo.topograph.TopOGraph method) eigenvalues (topo.spectral.eigen.EigenDecomposition attribute) (topo.TopOGraph property) (topo.topograph.TopOGraph property) eigenvectors (topo.spectral.eigen.EigenDecomposition attribute) eigsorted() (in module topo.eval.rmetric) embedding (topo.spectral.eigen.EigenDecomposition attribute) enforce_min_eigs (topo.spectral.eigen.EigenDecomposition attribute) estimate_eigengap (topo.spectral.eigen.EigenDecomposition attribute) euclidean() (in module topo.base.dists) 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) expand_nbr_search (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) expanded_k_neighbor_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) explained_variance() (in module topo.pipes)

F

fast_knn_indices() (in module topo.layouts) (in module topo.utils.umap_utils) filter() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) filter_signal() (topo.TopOGraph method) (topo.topograph.TopOGraph method) find_ab_params() (in module topo.layouts) (in module topo.layouts.graph_utils) find_ideal_projection() (topo.TopOGraph method) (topo.topograph.TopOGraph method) fit() (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.intrinsic_dim.IntrinsicDim method) (topo.tpgraph.IntrinsicDim method) (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method)

fit_transform() (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.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) fsa_global() (in module topo.tpgraph.intrinsic_dim) fsa_local() (in module topo.tpgraph.intrinsic_dim) fuzzy (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) 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) 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) 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_P() (in module topo.eval.topo_metrics) 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)

global_dimensionality (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) global_id (topo.TopOGraph property) (topo.topograph.TopOGraph property) (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) global_id_fsa() (topo.TopOGraph method) (topo.topograph.TopOGraph method) global_id_mle() (topo.TopOGraph method) (topo.topograph.TopOGraph method) 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_kernel_version (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) graph_knn (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) graph_laplacian() (in module topo.spectral) (in module topo.spectral._spectral) graph_metric (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) GraphKernelDict (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) grid_search() (in module topo.base) (in module topo.base.ann)

H

heatmap() (in module topo.plot)

HNSWlibTransformer (class in topo.base.ann) hyperboloid() (in module topo.plot)

I

id_headroom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) id_ks (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) id_max_components (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) id_method (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) id_metric (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) id_min_components (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) id_quantile (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) impute() (topo.TopOGraph method) (topo.topograph.TopOGraph method) (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) include_init_snapshot (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute)

ind_dist_grad() (topo.base.ann.HNSWlibTransformer method) (topo.base.ann.NMSlibTransformer method) init (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) init_Y_ (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) 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) keep_estimator (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) 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_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) knn_kendall_tau() (in module topo.eval) (in module topo.eval.local_scores) knn_msZ (topo.TopOGraph property) (topo.topograph.TopOGraph property)

knn_msZ_uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) knn_spearman_r() (in module topo.eval) (in module topo.eval.local_scores) knn_X (topo.TopOGraph property) (topo.topograph.TopOGraph property) knn_X_uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) knn_Z (topo.TopOGraph property) (topo.topograph.TopOGraph property) knn_Z_uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) kwargs (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute)

L

L (topo.eval.RiemannMetric attribute) (topo.eval.rmetric.RiemannMetric attribute) (topo.tpgraph.Kernel property) (topo.tpgraph.kernels.Kernel property) landmark_method (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) landmarks (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) landmarks_ (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) laplacian (topo.spectral.eigen.EigenDecomposition attribute) laplacian() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) laplacian_type (topo.spectral.eigen.EigenDecomposition attribute) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) layout_verbose (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)

LE() (in module topo.spectral) (in module topo.spectral._spectral) list_eigenbases() (topo.TopOGraph method), [1] (topo.topograph.TopOGraph method) load_topograph() (in module topo) (in module topo.topograph) local_dimensionality (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) local_id (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) local_ids (topo.TopOGraph property) (topo.topograph.TopOGraph property) LocalScoresDict (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) log_beta() (in module topo.base.sparse) log_single_beta() (in module topo.base.sparse) low_memory (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)

M

M (topo.base.ann.HNSWlibTransformer attribute) m (topo.base.ann.HNSWlibTransformer attribute) M (topo.base.ann.NMSlibTransformer attribute) (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) m (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) M (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) make_epochs_per_sample() (in module topo.layouts) (in module topo.layouts.graph_utils) mdimG (topo.eval.RiemannMetric attribute) (topo.eval.rmetric.RiemannMetric attribute) method (topo.base.ann.NMSlibTransformer attribute) (topo.spectral.eigen.EigenDecomposition attribute) methods (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) metric (topo.base.ann.HNSWlibTransformer attribute) (topo.base.ann.NMSlibTransformer attribute) (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) min_eigs (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) MIN_K_DIST_SCALE (in module topo.tpgraph.fuzzy) 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.eval.topo_metrics 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.umap_layouts topo.topograph topo.tpgraph topo.tpgraph.cknn topo.tpgraph.fuzzy topo.tpgraph.intrinsic_dim topo.tpgraph.kernels topo.utils topo.utils._utils topo.utils.umap_utils topo.version

msTopoMAP (topo.TopOGraph property) (topo.topograph.TopOGraph property) msTopoMAP_snapshots (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) msTopoPaCMAP (topo.TopOGraph property) (topo.topograph.TopOGraph property) msZ_uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) multi_component_layout() (in module topo.spectral.eigen) multiscale_diffusion_emd() (in module topo.eval.topo_metrics)

N

N (topo.base.ann.HNSWlibTransformer attribute) (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) (topo.spectral.eigen.EigenDecomposition attribute) n (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) N (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) n_components (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) (topo.spectral.eigen.EigenDecomposition attribute) n_eigs (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) n_jobs (topo.base.ann.HNSWlibTransformer attribute) (topo.base.ann.NMSlibTransformer attribute) (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute)

n_k (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) n_landmarks (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) n_neighbors (topo.base.ann.HNSWlibTransformer attribute) (topo.base.ann.NMSlibTransformer attribute) (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) nbrs_backend (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) NMSlibTransformer (class in topo.base.ann) norm() (in module topo.utils.umap_utils) NPY_INFINITY (in module topo.tpgraph.fuzzy) num_iters (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute)

O

omega_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) omega_nbr_expanded_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) 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)

P

p (topo.base.ann.HNSWlibTransformer attribute) (topo.base.ann.NMSlibTransformer attribute) P (topo.tpgraph.Kernel property) (topo.tpgraph.kernels.Kernel property) P_of_msZ (topo.TopOGraph property) (topo.topograph.TopOGraph property) P_of_msZ_uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) P_of_X (topo.TopOGraph property) (topo.topograph.TopOGraph property) P_of_X_uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) P_of_Z (topo.TopOGraph property) (topo.topograph.TopOGraph property) P_of_Z_uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) pairwise (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) plot (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) 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_metric_contraction_expansion() (in module topo.eval.rmetric) plot_point_cov() (in module topo.plot) plot_riemann_metric() (in module topo.plot) plot_riemann_metric_global() (in module topo.eval.rmetric) plot_riemann_metric_localized() (in module topo.eval.rmetric) plot_scores() (in module topo.plot) plt (in module topo.eval.rmetric) poincare() (in module topo.plot) powered_operator (topo.spectral.eigen.EigenDecomposition attribute) project() (topo.TopOGraph method), [1] (topo.topograph.TopOGraph method) projection_method (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) projection_methods (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) ProjectionDict (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) Projector (class in topo.layouts) (class in topo.layouts.projector) pseudotime() (topo.TopOGraph method) (topo.topograph.TopOGraph method) PYAMG_LOADED (in module topo.spectral.eigen)

R

random_state (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) (topo.spectral.eigen.EigenDecomposition attribute) (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) rank_diffusion_correlation() (in module topo.eval.topo_metrics) rdist() (in module topo.spectral.umap_layouts) rescale() (topo.spectral.eigen.EigenDecomposition method) resistance_distance() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) results() (topo.spectral.eigen.EigenDecomposition method)

return_evals (topo.spectral.eigen.EigenDecomposition attribute) rho_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) riemann_diagnostics() (topo.TopOGraph method) (topo.topograph.TopOGraph method) riemann_metric() (in module topo.eval.rmetric) RiemannMetric (class in topo.eval) (class in topo.eval.rmetric) RiemannMetricDict (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) rowwise_js_similarity() (in module topo.eval.topo_metrics) run_models() (topo.TopOGraph method), [1] (topo.topograph.TopOGraph method) runtimes (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)

S

save_callback (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) save_every (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) save_limit (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) save_topograph() (in module topo) (in module topo.topograph) scatter() (in module topo.plot) scatter3d() (in module topo.plot) semi_aniso (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) set_refined_from_precomputed() (topo.TopOGraph method) (topo.topograph.TopOGraph method) shortest_paths() (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) sigma (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) sigma_ (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) 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) space (topo.base.ann.HNSWlibTransformer attribute) (topo.base.ann.NMSlibTransformer attribute) 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_neighborhood_f1() (in module topo.eval.topo_metrics) sparse_poincare() (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) SpecLayout (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) 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) spectral_procrustes() (in module topo.eval.topo_metrics) spectral_scaffold() (topo.TopOGraph method) (topo.topograph.TopOGraph method) spectral_selectivity() (topo.TopOGraph method) (topo.topograph.TopOGraph method) spectral_similarity() (in module topo.eval.topo_metrics) sphere() (in module topo.plot) sphere_projection() (in module topo.plot) submatrix() (in module topo.utils.umap_utils) symmetrize (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute)

T

t (topo.spectral.eigen.EigenDecomposition attribute) tau_rand() (in module topo.utils.umap_utils) tau_rand_int() (in module topo.utils.umap_utils) temp_file (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) 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.eval.topo_metrics 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.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.utils module topo.utils._utils module topo.utils.umap_utils module topo.version module topo_preserve_score() (in module topo.eval.topo_metrics) TopOGraph (class in topo), [1] (class in topo.topograph) TopoMAP (topo.TopOGraph property) (topo.topograph.TopOGraph property) TopoMAP_snapshots (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) TopoPaCMAP (topo.TopOGraph property) (topo.topograph.TopOGraph property) toroid() (in module topo.plot) torus_euclidean_grad() (in module topo.utils.umap_utils) transform() (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.intrinsic_dim.IntrinsicDim method) (topo.tpgraph.IntrinsicDim method) (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method) ts() (in module topo.layouts) (in module topo.utils.umap_utils) two_to_3d_hyperboloid() (in module topo.plot)

U

uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_BaseKernel_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_comp_labels_ (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_components_ (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_DMEig_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_eigenvalues_dm_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_eigenvalues_ms_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_enabled (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_find_components() (topo.TopOGraph method) (topo.topograph.TopOGraph method) uom_Kernel_msZ_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)

uom_Kernel_Z_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_knn_msZ_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_knn_X_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_knn_Z_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_msDMEig_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_msZ_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) uom_Z_list (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) update_search() (topo.base.ann.HNSWlibTransformer method) (topo.base.ann.NMSlibTransformer method) use_angular (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute) use_k (topo.tpgraph.intrinsic_dim.IntrinsicDim attribute) (topo.tpgraph.IntrinsicDim attribute)

V

verbose (topo.base.ann.HNSWlibTransformer attribute) (topo.base.ann.NMSlibTransformer attribute) (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) (topo.spectral.eigen.EigenDecomposition attribute) (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute)

verbosity (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute) visualize_optimization() (topo.TopOGraph method) (topo.topograph.TopOGraph method)

W

weight (topo.spectral.eigen.EigenDecomposition attribute) weighted_degree (topo.tpgraph.Kernel property) (topo.tpgraph.kernels.Kernel property)

write_pkl() (topo.TopOGraph method), [1] (topo.topograph.TopOGraph method) (topo.tpgraph.Kernel method) (topo.tpgraph.kernels.Kernel method)

X

X (topo.tpgraph.Kernel attribute) (topo.tpgraph.kernels.Kernel attribute)

Y

Y (topo.eval.RiemannMetric attribute) (topo.eval.rmetric.RiemannMetric attribute) Y() (topo.TopOGraph method) (topo.topograph.TopOGraph method)

Y_ (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute) Y_aux_ (topo.layouts.Projector attribute) (topo.layouts.projector.Projector attribute)

Z

Z_uom (topo.TopOGraph attribute) (topo.topograph.TopOGraph attribute)