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geomstats · May 16, 2022 · efbc7bc · efbc7bc
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diff --git a/rsonthal_xfcui/CSphd.csv → ...sonthal__xfcui__Tree-Embeddings/CSphd.csv b/rsonthal_xfcui/CSphd.csv → ...sonthal__xfcui__Tree-Embeddings/CSphd.csv
diff --git a/rsonthal_xfcui/TreeEmbed.py → ...thal__xfcui__Tree-Embeddings/TreeEmbed.py b/rsonthal_xfcui/TreeEmbed.py → ...thal__xfcui__Tree-Embeddings/TreeEmbed.py
diff --git a/rsonthal_xfcui/TreeEmbeddings.ipynb → ...cui__Tree-Embeddings/TreeEmbeddings.ipynb b/rsonthal_xfcui/TreeEmbeddings.ipynb → ...cui__Tree-Embeddings/TreeEmbeddings.ipynb
diff --git a/rsonthal_xfcui/TreeRepresentation.py → ...ui__Tree-Embeddings/TreeRepresentation.py b/rsonthal_xfcui/TreeRepresentation.py → ...ui__Tree-Embeddings/TreeRepresentation.py
diff --git a/rsonthal_xfcui/TreeSpace.py → ...thal__xfcui__Tree-Embeddings/TreeSpace.py b/rsonthal_xfcui/TreeSpace.py → ...thal__xfcui__Tree-Embeddings/TreeSpace.py
diff --git a/rsonthal_xfcui/prior.py → ...rsonthal__xfcui__Tree-Embeddings/prior.py b/rsonthal_xfcui/prior.py → ...rsonthal__xfcui__Tree-Embeddings/prior.py
diff --git a/rsonthal_xfcui/utilities.py → ...thal__xfcui__Tree-Embeddings/utilities.py b/rsonthal_xfcui/utilities.py → ...thal__xfcui__Tree-Embeddings/utilities.py
diff --git a/..._Regression_on_Riemannian_Manifolds.ipynb → ..._Regression_on_Riemannian_Manifolds.ipynb b/..._Regression_on_Riemannian_Manifolds.ipynb → ..._Regression_on_Riemannian_Manifolds.ipynb
diff --git a/...ger/data/MNIST/raw/t10k-images-idx3-ubyte → ...SNE/data/MNIST/raw/t10k-images-idx3-ubyte b/...ger/data/MNIST/raw/t10k-images-idx3-ubyte → ...SNE/data/MNIST/raw/t10k-images-idx3-ubyte
diff --git a/.../data/MNIST/raw/t10k-images-idx3-ubyte.gz → .../data/MNIST/raw/t10k-images-idx3-ubyte.gz b/.../data/MNIST/raw/t10k-images-idx3-ubyte.gz → .../data/MNIST/raw/t10k-images-idx3-ubyte.gz
diff --git a/...ger/data/MNIST/raw/t10k-labels-idx1-ubyte → ...SNE/data/MNIST/raw/t10k-labels-idx1-ubyte b/...ger/data/MNIST/raw/t10k-labels-idx1-ubyte → ...SNE/data/MNIST/raw/t10k-labels-idx1-ubyte
diff --git a/.../data/MNIST/raw/t10k-labels-idx1-ubyte.gz → .../data/MNIST/raw/t10k-labels-idx1-ubyte.gz b/.../data/MNIST/raw/t10k-labels-idx1-ubyte.gz → .../data/MNIST/raw/t10k-labels-idx1-ubyte.gz
diff --git a/...er/data/MNIST/raw/train-images-idx3-ubyte → ...NE/data/MNIST/raw/train-images-idx3-ubyte b/...er/data/MNIST/raw/train-images-idx3-ubyte → ...NE/data/MNIST/raw/train-images-idx3-ubyte
diff --git a/...data/MNIST/raw/train-images-idx3-ubyte.gz → ...data/MNIST/raw/train-images-idx3-ubyte.gz b/...data/MNIST/raw/train-images-idx3-ubyte.gz → ...data/MNIST/raw/train-images-idx3-ubyte.gz
diff --git a/...er/data/MNIST/raw/train-labels-idx1-ubyte → ...NE/data/MNIST/raw/train-labels-idx1-ubyte b/...er/data/MNIST/raw/train-labels-idx1-ubyte → ...NE/data/MNIST/raw/train-labels-idx1-ubyte
diff --git a/...data/MNIST/raw/train-labels-idx1-ubyte.gz → ...data/MNIST/raw/train-labels-idx1-ubyte.gz b/...data/MNIST/raw/train-labels-idx1-ubyte.gz → ...data/MNIST/raw/train-labels-idx1-ubyte.gz
diff --git a/andberger/img/crypto.svg → ...n__hauberg__Riemannian-SNE/img/crypto.svg b/andberger/img/crypto.svg → ...n__hauberg__Riemannian-SNE/img/crypto.svg
diff --git a/andberger/img/intro_figure.svg → ...berg__Riemannian-SNE/img/intro_figure.svg b/andberger/img/intro_figure.svg → ...berg__Riemannian-SNE/img/intro_figure.svg
diff --git a/andberger/img/mnist6.svg → ...n__hauberg__Riemannian-SNE/img/mnist6.svg b/andberger/img/mnist6.svg → ...n__hauberg__Riemannian-SNE/img/mnist6.svg
diff --git a/andberger/img/mnist6_plane.svg → ...berg__Riemannian-SNE/img/mnist6_plane.svg b/andberger/img/mnist6_plane.svg → ...berg__Riemannian-SNE/img/mnist6_plane.svg
diff --git a/andberger/models/euclidean.py → ...uberg__Riemannian-SNE/models/euclidean.py b/andberger/models/euclidean.py → ...uberg__Riemannian-SNE/models/euclidean.py
diff --git a/andberger/models/riesne_model.py → ...rg__Riemannian-SNE/models/riesne_model.py b/andberger/models/riesne_model.py → ...rg__Riemannian-SNE/models/riesne_model.py
diff --git a/andberger/models/sphere.py → ..._hauberg__Riemannian-SNE/models/sphere.py b/andberger/models/sphere.py → ..._hauberg__Riemannian-SNE/models/sphere.py
diff --git a/andberger/rie_sne.ipynb → ...on__hauberg__Riemannian-SNE/rie_sne.ipynb b/andberger/rie_sne.ipynb → ...on__hauberg__Riemannian-SNE/rie_sne.ipynb
diff --git a/andberger/riesne.py → ...rgsson__hauberg__Riemannian-SNE/riesne.py b/andberger/riesne.py → ...rgsson__hauberg__Riemannian-SNE/riesne.py
diff --git a/andberger/riesne_utils.py → ...__hauberg__Riemannian-SNE/riesne_utils.py b/andberger/riesne_utils.py → ...__hauberg__Riemannian-SNE/riesne_utils.py
diff --git a/Neural_SEED_smORFs.ipynb b/Neural_SEED_smORFs.ipynb
diff --git a/NeuroSEED-master/.vscode/launch.json b/NeuroSEED-master/.vscode/launch.json
diff --git a/NeuroSEED-master/strings_subset.pkl b/NeuroSEED-master/strings_subset.pkl
diff --git a/NeuroSEED-master/strings_test.pkl b/NeuroSEED-master/strings_test.pkl
diff --git a/...Brownian_motion_on_manifold_sampler.ipynb → ...Brownian_motion_on_manifold_sampler.ipynb b/...Brownian_motion_on_manifold_sampler.ipynb → ...Brownian_motion_on_manifold_sampler.ipynb
diff --git a/david-klindt_TEDDY/data_helper.py → ...logical-Ensemble-Detection/data_helper.py b/david-klindt_TEDDY/data_helper.py → ...logical-Ensemble-Detection/data_helper.py
diff --git a/david-klindt_TEDDY/geomstats_additions.py → ...Ensemble-Detection/geomstats_additions.py b/david-klindt_TEDDY/geomstats_additions.py → ...Ensemble-Detection/geomstats_additions.py
diff --git a/david-klindt_TEDDY/model.py → ...__Topological-Ensemble-Detection/model.py b/david-klindt_TEDDY/model.py → ...__Topological-Ensemble-Detection/model.py
diff --git a/..._TEDDY/results/setting=T2+R2_run=0.pickle → ...ection/results/setting=T2+R2_run=0.pickle b/..._TEDDY/results/setting=T2+R2_run=0.pickle → ...ection/results/setting=T2+R2_run=0.pickle
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diff --git a/NeuroSEED-master/closest_string/test.py → ...n-Hyperbolic-Space/closest_string/test.py b/NeuroSEED-master/closest_string/test.py → ...n-Hyperbolic-Space/closest_string/test.py
diff --git a/...-master/closest_string/triplet/dataset.py → ...c-Space/closest_string/triplet/dataset.py b/...-master/closest_string/triplet/dataset.py → ...c-Space/closest_string/triplet/dataset.py
diff --git a/...losest_string/triplet/models/cnn/train.py → ...losest_string/triplet/models/cnn/train.py b/...losest_string/triplet/models/cnn/train.py → ...losest_string/triplet/models/cnn/train.py
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diff --git a/...ED-master/closest_string/triplet/train.py → ...lic-Space/closest_string/triplet/train.py b/...ED-master/closest_string/triplet/train.py → ...lic-Space/closest_string/triplet/train.py
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diff --git a/...tance/task/dataset_generator_synthetic.py → ...tance/task/dataset_generator_synthetic.py b/...tance/task/dataset_generator_synthetic.py → ...tance/task/dataset_generator_synthetic.py
diff --git a/NeuroSEED-master/edit_distance/train.py → ...n-Hyperbolic-Space/edit_distance/train.py b/NeuroSEED-master/edit_distance/train.py → ...n-Hyperbolic-Space/edit_distance/train.py
diff --git a/NeuroSEED-master/generate_dataset.py → ...g-in-Hyperbolic-Space/generate_dataset.py b/NeuroSEED-master/generate_dataset.py → ...g-in-Hyperbolic-Space/generate_dataset.py
diff --git a/...-master/hierarchical_clustering/README.md → ...c-Space/hierarchical_clustering/README.md b/...-master/hierarchical_clustering/README.md → ...c-Space/hierarchical_clustering/README.md
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diff --git a/...cal_clustering/relaxed/unionfind/setup.py → ...cal_clustering/relaxed/unionfind/setup.py b/...cal_clustering/relaxed/unionfind/setup.py → ...cal_clustering/relaxed/unionfind/setup.py
diff --git a/...l_clustering/relaxed/unionfind/test_uf.py → ...l_clustering/relaxed/unionfind/test_uf.py b/...l_clustering/relaxed/unionfind/test_uf.py → ...l_clustering/relaxed/unionfind/test_uf.py
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diff --git a/...oSEED-master/multiple_alignment/README.md → ...rbolic-Space/multiple_alignment/README.md b/...oSEED-master/multiple_alignment/README.md → ...rbolic-Space/multiple_alignment/README.md
diff --git a/...ltiple_alignment/guide_tree/guide_tree.py → ...ltiple_alignment/guide_tree/guide_tree.py b/...ltiple_alignment/guide_tree/guide_tree.py → ...ltiple_alignment/guide_tree/guide_tree.py
diff --git a/...ple_alignment/steiner_string/baselines.py → ...ple_alignment/steiner_string/baselines.py b/...ple_alignment/steiner_string/baselines.py → ...ple_alignment/steiner_string/baselines.py
diff --git a/...iner_string/models/convolutional/model.py → ...iner_string/models/convolutional/model.py b/...iner_string/models/convolutional/model.py → ...iner_string/models/convolutional/model.py
diff --git a/...iner_string/models/convolutional/train.py → ...iner_string/models/convolutional/train.py b/...iner_string/models/convolutional/train.py → ...iner_string/models/convolutional/train.py
diff --git a/...e_alignment/steiner_string/models/loss.py → ...e_alignment/steiner_string/models/loss.py b/...e_alignment/steiner_string/models/loss.py → ...e_alignment/steiner_string/models/loss.py
diff --git a/...gnment/steiner_string/models/mlp/model.py → ...gnment/steiner_string/models/mlp/model.py b/...gnment/steiner_string/models/mlp/model.py → ...gnment/steiner_string/models/mlp/model.py
diff --git a/...gnment/steiner_string/models/mlp/train.py → ...gnment/steiner_string/models/mlp/train.py b/...gnment/steiner_string/models/mlp/train.py → ...gnment/steiner_string/models/mlp/train.py
diff --git a/.../steiner_string/models/msa_autoencoder.py → .../steiner_string/models/msa_autoencoder.py b/.../steiner_string/models/msa_autoencoder.py → .../steiner_string/models/msa_autoencoder.py
diff --git a/...steiner_string/models/pair_autoencoder.py → ...steiner_string/models/pair_autoencoder.py b/...steiner_string/models/pair_autoencoder.py → ...steiner_string/models/pair_autoencoder.py
diff --git a/...ltiple_alignment/steiner_string/parser.py → ...ltiple_alignment/steiner_string/parser.py b/...ltiple_alignment/steiner_string/parser.py → ...ltiple_alignment/steiner_string/parser.py
diff --git a/..._alignment/steiner_string/task/dataset.py → ..._alignment/steiner_string/task/dataset.py b/..._alignment/steiner_string/task/dataset.py → ..._alignment/steiner_string/task/dataset.py
diff --git a/...r_string/task/dataset_generator_genome.py → ...r_string/task/dataset_generator_genome.py b/...r_string/task/dataset_generator_genome.py → ...r_string/task/dataset_generator_genome.py
diff --git a/...ultiple_alignment/steiner_string/train.py → ...ultiple_alignment/steiner_string/train.py b/...ultiple_alignment/steiner_string/train.py → ...ultiple_alignment/steiner_string/train.py
diff --git a/NeuroSEED-master/neuroSEED.py → ...mbedding-in-Hyperbolic-Space/neuroSEED.py b/NeuroSEED-master/neuroSEED.py → ...mbedding-in-Hyperbolic-Space/neuroSEED.py
diff --git a/NeuroSEED-master/njtree.dnd → ...-Embedding-in-Hyperbolic-Space/njtree.dnd b/NeuroSEED-master/njtree.dnd → ...-Embedding-in-Hyperbolic-Space/njtree.dnd
diff --git a/...EED-master/smorf_use_backend_functions.py → ...olic-Space/smorf_use_backend_functions.py b/...EED-master/smorf_use_backend_functions.py → ...olic-Space/smorf_use_backend_functions.py
diff --git a/...ormatics_algorithms/test_edit_distance.py → ...ormatics_algorithms/test_edit_distance.py b/...ormatics_algorithms/test_edit_distance.py → ...ormatics_algorithms/test_edit_distance.py
diff --git a/...rmatics_algorithms/test_exact_matching.py → ...rmatics_algorithms/test_exact_matching.py b/...rmatics_algorithms/test_exact_matching.py → ...rmatics_algorithms/test_exact_matching.py
diff --git a/...est_closest_dataset_generation_genomic.py → ...est_closest_dataset_generation_genomic.py b/...est_closest_dataset_generation_genomic.py → ...est_closest_dataset_generation_genomic.py
diff --git a/...t_closest_dataset_generation_synthetic.py → ...t_closest_dataset_generation_synthetic.py b/...t_closest_dataset_generation_synthetic.py → ...t_closest_dataset_generation_synthetic.py
diff --git a/...sest_string_tests/test_closest_testing.py → ...sest_string_tests/test_closest_testing.py b/...sest_string_tests/test_closest_testing.py → ...sest_string_tests/test_closest_testing.py
diff --git a/...distance_functions/test_distance_torch.py → ...distance_functions/test_distance_torch.py b/...distance_functions/test_distance_torch.py → ...distance_functions/test_distance_torch.py
diff --git a/...sts/test_ed_dataset_generation_genomic.py → ...sts/test_ed_dataset_generation_genomic.py b/...sts/test_ed_dataset_generation_genomic.py → ...sts/test_ed_dataset_generation_genomic.py
diff --git a/...s/test_ed_dataset_generation_synthetic.py → ...s/test_ed_dataset_generation_synthetic.py b/...s/test_ed_dataset_generation_synthetic.py → ...s/test_ed_dataset_generation_synthetic.py
diff --git a/...s/edit_distance_tests/test_ed_training.py → ...s/edit_distance_tests/test_ed_training.py b/...s/edit_distance_tests/test_ed_training.py → ...s/edit_distance_tests/test_ed_training.py
diff --git a/...sts/test_hc_dataset_generation_genomic.py → ...sts/test_hc_dataset_generation_genomic.py b/...sts/test_hc_dataset_generation_genomic.py → ...sts/test_hc_dataset_generation_genomic.py
diff --git a/...s/test_hc_dataset_generation_synthetic.py → ...s/test_hc_dataset_generation_synthetic.py b/...s/test_hc_dataset_generation_synthetic.py → ...s/test_hc_dataset_generation_synthetic.py
diff --git a/...ing_tests/test_hc_unsupervised_testing.py → ...ing_tests/test_hc_unsupervised_testing.py b/...ing_tests/test_hc_unsupervised_testing.py → ...ing_tests/test_hc_unsupervised_testing.py
diff --git a/...alignment_tests/test_msa_guide_testing.py → ...alignment_tests/test_msa_guide_testing.py b/...alignment_tests/test_msa_guide_testing.py → ...alignment_tests/test_msa_guide_testing.py
diff --git a/...ts/test_msa_steiner_dataset_generation.py → ...ts/test_msa_steiner_dataset_generation.py b/...ts/test_msa_steiner_dataset_generation.py → ...ts/test_msa_steiner_dataset_generation.py
diff --git a/...gnment_tests/test_msa_steiner_training.py → ...gnment_tests/test_msa_steiner_training.py b/...gnment_tests/test_msa_steiner_training.py → ...gnment_tests/test_msa_steiner_training.py
diff --git a/...oSEED-master/tutorial/closest_diagram.png → ...rbolic-Space/tutorial/closest_diagram.png b/...oSEED-master/tutorial/closest_diagram.png → ...rbolic-Space/tutorial/closest_diagram.png
diff --git a/NeuroSEED-master/tutorial/closest_real.png → ...yperbolic-Space/tutorial/closest_real.png b/NeuroSEED-master/tutorial/closest_real.png → ...yperbolic-Space/tutorial/closest_real.png
diff --git a/...EED-master/tutorial/closest_synthetic.png → ...olic-Space/tutorial/closest_synthetic.png b/...EED-master/tutorial/closest_synthetic.png → ...olic-Space/tutorial/closest_synthetic.png
diff --git a/NeuroSEED-master/tutorial/cover.png → ...ng-in-Hyperbolic-Space/tutorial/cover.png b/NeuroSEED-master/tutorial/cover.png → ...ng-in-Hyperbolic-Space/tutorial/cover.png
diff --git a/NeuroSEED-master/tutorial/edit_diagram.PNG → ...yperbolic-Space/tutorial/edit_diagram.PNG b/NeuroSEED-master/tutorial/edit_diagram.PNG → ...yperbolic-Space/tutorial/edit_diagram.PNG
diff --git a/NeuroSEED-master/tutorial/edit_dimension.png → ...erbolic-Space/tutorial/edit_dimension.png b/NeuroSEED-master/tutorial/edit_dimension.png → ...erbolic-Space/tutorial/edit_dimension.png
diff --git a/NeuroSEED-master/tutorial/edit_real.PNG → ...n-Hyperbolic-Space/tutorial/edit_real.PNG b/NeuroSEED-master/tutorial/edit_real.PNG → ...n-Hyperbolic-Space/tutorial/edit_real.PNG
diff --git a/NeuroSEED-master/tutorial/edit_synthetic.PNG → ...erbolic-Space/tutorial/edit_synthetic.PNG b/NeuroSEED-master/tutorial/edit_synthetic.PNG → ...erbolic-Space/tutorial/edit_synthetic.PNG
diff --git a/NeuroSEED-master/tutorial/hc_animals.png → ...-Hyperbolic-Space/tutorial/hc_animals.png b/NeuroSEED-master/tutorial/hc_animals.png → ...-Hyperbolic-Space/tutorial/hc_animals.png
diff --git a/NeuroSEED-master/tutorial/hc_average.png → ...-Hyperbolic-Space/tutorial/hc_average.png b/NeuroSEED-master/tutorial/hc_average.png → ...-Hyperbolic-Space/tutorial/hc_average.png
diff --git a/NeuroSEED-master/tutorial/hyphc_plots.png → ...Hyperbolic-Space/tutorial/hyphc_plots.png b/NeuroSEED-master/tutorial/hyphc_plots.png → ...Hyperbolic-Space/tutorial/hyphc_plots.png
diff --git a/...D-master/tutorial/microbiome_analysis.png → ...ic-Space/tutorial/microbiome_analysis.png b/...D-master/tutorial/microbiome_analysis.png → ...ic-Space/tutorial/microbiome_analysis.png
diff --git a/...oSEED-master/tutorial/msa_guide_table.png → ...rbolic-Space/tutorial/msa_guide_table.png b/...oSEED-master/tutorial/msa_guide_table.png → ...rbolic-Space/tutorial/msa_guide_table.png
diff --git a/...D-master/tutorial/msa_steiner_diagram.png → ...ic-Space/tutorial/msa_steiner_diagram.png b/...D-master/tutorial/msa_steiner_diagram.png → ...ic-Space/tutorial/msa_steiner_diagram.png
diff --git a/...EED-master/tutorial/msa_steiner_table.png → ...olic-Space/tutorial/msa_steiner_table.png b/...EED-master/tutorial/msa_steiner_table.png → ...olic-Space/tutorial/msa_steiner_table.png
diff --git a/...ioinformatics_algorithms/edit_distance.py → ...ioinformatics_algorithms/edit_distance.py b/...ioinformatics_algorithms/edit_distance.py → ...ioinformatics_algorithms/edit_distance.py
diff --git a/...oinformatics_algorithms/exact_matching.py → ...oinformatics_algorithms/exact_matching.py b/...oinformatics_algorithms/exact_matching.py → ...oinformatics_algorithms/exact_matching.py
diff --git a/...nformatics_algorithms/inexact_matching.py → ...nformatics_algorithms/inexact_matching.py b/...nformatics_algorithms/inexact_matching.py → ...nformatics_algorithms/inexact_matching.py
diff --git a/...-master/util/data_handling/data_loader.py → ...c-Space/util/data_handling/data_loader.py b/...-master/util/data_handling/data_loader.py → ...c-Space/util/data_handling/data_loader.py
diff --git a/...l/data_handling/data_loader_calculator.py → ...l/data_handling/data_loader_calculator.py b/...l/data_handling/data_loader_calculator.py → ...l/data_handling/data_loader_calculator.py
diff --git a/...er/util/data_handling/string_generator.py → ...ce/util/data_handling/string_generator.py b/...er/util/data_handling/string_generator.py → ...ce/util/data_handling/string_generator.py
diff --git a/.../distance_functions/distance_functions.py → .../distance_functions/distance_functions.py b/.../distance_functions/distance_functions.py → .../distance_functions/distance_functions.py
diff --git a/...til/distance_functions/distance_matrix.py → ...til/distance_functions/distance_matrix.py b/...til/distance_functions/distance_matrix.py → ...til/distance_functions/distance_matrix.py
diff --git a/...il/distance_functions/geometric_median.py → ...il/distance_functions/geometric_median.py b/...il/distance_functions/geometric_median.py → ...il/distance_functions/geometric_median.py
diff --git a/NeuroSEED-master/util/ml_and_math/layers.py → ...perbolic-Space/util/ml_and_math/layers.py b/NeuroSEED-master/util/ml_and_math/layers.py → ...perbolic-Space/util/ml_and_math/layers.py
diff --git a/...master/util/ml_and_math/loss_functions.py → ...-Space/util/ml_and_math/loss_functions.py b/...master/util/ml_and_math/loss_functions.py → ...-Space/util/ml_and_math/loss_functions.py
diff --git a/NeuroSEED-master/util/ml_and_math/math.py → ...Hyperbolic-Space/util/ml_and_math/math.py b/NeuroSEED-master/util/ml_and_math/math.py → ...Hyperbolic-Space/util/ml_and_math/math.py
diff --git a/...oSEED-master/util/ml_and_math/poincare.py → ...rbolic-Space/util/ml_and_math/poincare.py b/...oSEED-master/util/ml_and_math/poincare.py → ...rbolic-Space/util/ml_and_math/poincare.py