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Table of Contents
Installation
Implemented Algorithms
Typical usage of the package
Modules (API reference)
Tutorial: Density Based Clustering
Tutorial: Information Imbalance
Tutorial: Intrinsic dimension
Tutorial: Using DADApy to analyse a molecular dynamics trajectory of a small peptide
Tutorial: Intrinsic dimension estimation for discrete metrics
Tutorial: Differentiable Information Imbalance
Hands-on tutorial at SISSA
Citing DADApy
dadapy
Index
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Index
_
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B
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C
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D
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F
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I
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L
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M
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N
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R
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S
_
_utils.utils
module
B
bord_indices (clustering.Clustering attribute)
C
cluster_assignment (clustering.Clustering attribute)
cluster_centers (clustering.Clustering attribute)
cluster_indices (clustering.Clustering attribute)
clustering
module
Clustering (class in clustering)
compute_all_distances() (in module _utils.utils)
compute_clustering_ADP() (clustering.Clustering method)
compute_clustering_ADP_pure_python() (clustering.Clustering method)
compute_clustering_DP() (clustering.Clustering method)
compute_cross_nn_distances() (in module _utils.utils)
compute_DecGraph() (clustering.Clustering method)
compute_density_kNN() (density_estimation.DensityEstimation method)
compute_density_kpeaks() (density_estimation.DensityEstimation method)
compute_density_kstarNN() (density_estimation.DensityEstimation method)
compute_density_PAk() (density_estimation.DensityEstimation method)
compute_id_2NN() (id_estimation.IdEstimation method)
compute_id_2NN_wprior() (id_estimation.IdEstimation method)
compute_id_binomial_k() (id_estimation.IdEstimation method)
compute_id_binomial_rk() (id_estimation.IdEstimation method)
compute_nn_distances() (in module _utils.utils)
compute_NN_PBC() (in module _utils.utils)
D
density_estimation
module
DensityEstimation (class in density_estimation)
F
from_all_distances_to_nndistances() (in module _utils.utils)
I
id_estimation
module
IdEstimation (class in id_estimation)
L
log_den (density_estimation.DensityEstimation attribute)
log_den_bord (clustering.Clustering attribute)
log_den_bord_err (clustering.Clustering attribute)
log_den_err (density_estimation.DensityEstimation attribute)
M
module
_utils.utils
clustering
density_estimation
id_estimation
N
N_clusters (clustering.Clustering attribute)
R
return_entropy() (density_estimation.DensityEstimation method)
return_id_scaling_2NN() (id_estimation.IdEstimation method)
return_id_scaling_gride() (id_estimation.IdEstimation method)
return_interpolated_density_kNN() (density_estimation.DensityEstimation method)
return_interpolated_density_kstarNN() (density_estimation.DensityEstimation method)
return_interpolated_density_PAk() (density_estimation.DensityEstimation method)
S
set_id() (id_estimation.IdEstimation method)
set_kstar() (density_estimation.DensityEstimation method)
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