├── .gitattributes ├── .gitignore ├── .idea ├── codeStyles │ └── codeStyleConfig.xml └── inspectionProfiles │ ├── Project_Default.xml │ └── profiles_settings.xml ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE.txt ├── Makefile ├── README.rst ├── ci_scripts ├── install.sh ├── success.sh └── test.sh ├── doc ├── .gitignore ├── Makefile ├── _static │ └── .gitkeep ├── api.rst ├── basic_usage.rst ├── basic_usage_bokeh_example.html ├── benchmarking.rst ├── bokeh_digits_plot.py ├── clustering.rst ├── conf.py ├── doc_requirements.txt ├── faq.rst ├── how_umap_works.rst ├── images │ ├── BasicUsage_13_1.png │ ├── BasicUsage_18_0.png │ ├── BasicUsage_20_1.png │ ├── BasicUsage_26_1.png │ ├── BasicUsage_6_1.png │ ├── SupervisedUMAP_10_1.png │ ├── SupervisedUMAP_15_1.png │ ├── SupervisedUMAP_22_1.png │ ├── SupervisedUMAP_31_0.png │ ├── SupervisedUMAP_33_0.png │ ├── UMAPTransform_15_0.png │ ├── UMAPTransform_21_0.png │ ├── clustering_10_1.png │ ├── clustering_16_1.png │ ├── clustering_27_1.png │ ├── clustering_31_1.png │ ├── clustering_6_1.png │ ├── how_umap_works_basic_graph.png │ ├── how_umap_works_fuzzy_open_cover.png │ ├── how_umap_works_local_metric_open_cover.png │ ├── how_umap_works_open_cover.png │ ├── how_umap_works_raw_data.png │ ├── how_umap_works_raw_graph.png │ ├── how_umap_works_umap_graph.png │ ├── how_umap_works_umap_graph_layout.png │ ├── how_umap_works_umap_layout.png │ ├── how_umap_works_umap_open_cover.png │ ├── how_umap_works_uniform_distribution_cover.png │ ├── parameters_13_1.png │ ├── parameters_13_2.png │ ├── parameters_13_3.png │ ├── parameters_13_4.png │ ├── parameters_13_5.png │ ├── parameters_13_6.png │ ├── parameters_13_7.png │ ├── parameters_16_1.png │ ├── parameters_16_2.png │ ├── parameters_16_3.png │ ├── parameters_16_4.png │ ├── parameters_16_5.png │ ├── parameters_16_6.png │ ├── parameters_19_1.png │ ├── parameters_21_1.png │ ├── parameters_32_1.png │ ├── parameters_32_2.png │ ├── parameters_32_3.png │ ├── parameters_32_4.png │ ├── parameters_32_5.png │ ├── parameters_8_1.png │ ├── performance_14_1.png │ ├── performance_17_1.png │ ├── performance_20_1.png │ ├── simplices.png │ └── umap_vae_pca.png ├── index.rst ├── logo.png ├── make.bat ├── parameters.rst ├── supervised.rst └── transform.rst ├── docs_requirements.txt ├── examples ├── README.txt ├── digits │ ├── digits.html │ └── digits.py ├── iris │ ├── iris.html │ └── iris.py ├── plot_algorithm_comparison.py ├── plot_fashion-mnist_example.py ├── plot_feature_extraction_classification.py └── plot_mnist_example.py ├── gpumap ├── __init__.py ├── compute_membership_strengths_gpu.py ├── distances.py ├── gpumap_.py ├── nearest_neighbors_gpu.py ├── nndescent.py ├── optimize_layout_gpu.py ├── rp_tree.py ├── smooth_knn_dist_gpu.py ├── sparse.py ├── spectral.py ├── tests │ ├── __init__.py │ ├── digits_embedding_42.npy │ └── test_umap.py ├── utils.py └── validation.py ├── images ├── iris.png ├── mnist_digits.png ├── sklearn_digits.png ├── 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