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BaseAutoencoder.__init__ |
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BaseAutoencoder._build_network |
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BaseLoss.compute_paired_loss |
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BasePipeline.__init__ |
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BasePreprocessor._split_data_package |
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BasePreprocessor._is_image_data |
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BasePreprocessor._remove_nans |
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BasePreprocessor._normalize_image_data |
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BasePreprocessor._get_translation_keys |
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BasePreprocessor._get_user_translation_keys |
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BasePreprocessor.format_reconstruction |
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BasePreprocessor.filter_imgdata_list |
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45 |
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BaseTrainer.__init__ |
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8 |
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BaseTrainer.setup_trainer |
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12 |
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BaseTrainer._setup_fabric |
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BaseTrainer._init_loaders |
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BaseTrainer._input_validation |
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BaseTrainer._handle_reproducibility |
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14 |
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BaseTrainer._seed_worker |
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BaseTrainer._init_model_architecture |
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BaseTrainer._should_checkpoint |
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BaseTrainer.train |
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BaseTrainer.decode |
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BaseTrainer.predict |
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BaseTrainer.purge |
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33 |
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BaseVisualizer.__init__ |
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BaseVisualizer.__setitem__ |
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BaseVisualizer.visualize |
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BaseVisualizer.show_latent_space |
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BaseVisualizer.show_weights |
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BaseVisualizer.show_evaluation |
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BaseVisualizer.save_plots |
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39 |
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BaseVisualizer._make_loss_format |
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BaseVisualizer._make_loss_plot |
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BaseVisualizer._plot_model_weights |
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62 |
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BaseVisualizer._collect_all_metadata |
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36 |
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33 |
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9 |
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SchemaPrinterMixin.get_params |
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4 |
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SchemaPrinterMixin.print_schema |
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DataInfo.validate_selected_layers |
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3 |
3 |
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DataInfo._forbid_user_k_filter |
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3 |
3 |
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| src / autoencodix / configs / default_config.py |
DataInfo.validate_image_resize |
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7 |
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DefaultConfig.handle_backward_compatibility |
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8 |
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DefaultConfig.validate_data_config |
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20 |
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DefaultConfig.determine_case |
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25 |
11 |
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DefaultConfig.validate_ratios |
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4 |
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100% |
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DefaultConfig.validate_float_precision |
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4 |
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DefaultConfig.validate_gpu_strategy |
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3 |
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0 |
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| src / autoencodix / configs / default_config.py |
DefaultConfig.validate_k_filter_with_nonzero_var |
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6 |
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83% |
| src / autoencodix / configs / default_config.py |
DefaultConfig.get_params |
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4 |
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100% |
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DefaultConfig.print_schema |
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13 |
4 |
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(no function) |
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125 |
0 |
0 |
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(no function) |
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4 |
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0 |
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9 |
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0 |
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| src / autoencodix / configs / ontix_config.py |
OntixConfig.validate_nested_scaling |
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5 |
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(no function) |
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7 |
0 |
0 |
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100% |
| src / autoencodix / configs / stackix_config.py |
StackixConfig._force_save_memory_false |
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4 |
4 |
0 |
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| src / autoencodix / configs / stackix_config.py |
(no function) |
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8 |
0 |
0 |
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(no function) |
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5 |
0 |
0 |
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(no function) |
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4 |
0 |
0 |
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100% |
| src / autoencodix / configs / xmodalix_config.py |
XModalixConfig._force_save_memory_false |
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4 |
4 |
0 |
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XModalixEvaluator.__init__ |
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XModalixEvaluator._get_clin_data |
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XModalixEvaluator._enrich_results |
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XModalixEvaluator._expand_reference_methods |
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XModalixEvaluator._load_input_for_ml |
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Imagix.__init__ |
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DisentanglixLoss.__init__ |
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DisentanglixLoss.forward |
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DisentanglixLoss._compute_losses |
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DisentanglixLoss._forward_with_annealing |
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MaskixLoss.__init__ |
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MaskixLoss._validate_model_output |
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MaskixLoss._validate_loss_config |
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MaskixLoss.forward |
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VanillixLoss.forward |
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VarixLoss.__init__ |
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VarixLoss._compute_losses |
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VarixLoss.forward |
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XModalLoss.__init__ |
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XModalLoss.forward |
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XModalLoss._calc_class_loss |
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63 |
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XModalLoss._calc_paired_loss |
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XModalLoss._combine_sub_losses |
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XModalLoss._store_sub_losses |
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XModalLoss._calc_adversial_loss |
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Maskix.__init__ |
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Maskix.impute |
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CaptumForward.forward |
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ImageVAEArchitecture.__init__ |
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ImageVAEArchitecture._build_network |
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ImageVAEArchitecture._get_spatial_dim |
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ImageVAEArchitecture.encode |
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ImageVAEArchitecture.reparameterize |
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ImageVAEArchitecture.get_latent_space |
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ImageVAEArchitecture.decode |
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ImageVAEArchitecture.translate |
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ImageVAEArchitecture.forward |
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ImageVAEFastArchitecture.__init__ |
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ImageVAEFastArchitecture._build_network |
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ImageVAEFastArchitecture._get_spatial_dim |
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ImageVAEFastArchitecture.encode |
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ImageVAEFastArchitecture.reparameterize |
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ImageVAEFastArchitecture.get_latent_space |
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ImageVAEFastArchitecture.decode |
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ImageVAEFastArchitecture.translate |
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ImageVAEFastArchitecture.forward |
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LayerFactory.get_layer_dimensions |
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LayerFactory.create_layer |
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LayerFactory.create_maskix_layer |
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MaskixArchitectureVanilla.__init__ |
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MaskixArchitectureVanilla._build_network |
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MaskixArchitectureVanilla._build_custom |
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MaskixArchitectureVanilla._build_scMAE |
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MaskixArchitectureVanilla.encode |
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MaskixArchitectureVanilla.get_latent_space |
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MaskixArchitectureVanilla.decode |
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MaskixArchitectureVanilla.forward |
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OntixArchitecture.__init__ |
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OntixArchitecture._make_masks |
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OntixArchitecture._build_network |
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OntixArchitecture.encode |
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OntixArchitecture.reparameterize |
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OntixArchitecture.decode |
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OntixArchitecture.forward |
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OntixArchitecture.get_latent_space |
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VanillixArchitecture.__init__ |
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VanillixArchitecture._build_network |
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VanillixArchitecture.encode |
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VanillixArchitecture.get_latent_space |
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VanillixArchitecture.decode |
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VanillixArchitecture.forward |
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(no function) |
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14 |
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VarixArchitecture.__init__ |
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11 |
1 |
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VarixArchitecture._build_network |
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19 |
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VarixArchitecture.encode |
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8 |
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VarixArchitecture.reparameterize |
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3 |
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0 |
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VarixArchitecture.get_latent_space |
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3 |
3 |
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VarixArchitecture.decode |
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1 |
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VarixArchitecture.forward |
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4 |
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(no function) |
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15 |
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(no function) |
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0 |
0 |
0 |
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100% |
| src / autoencodix / ontix.py |
Ontix.__init__ |
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13 |
13 |
0 |
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Ontix._read_ont_file |
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10 |
10 |
0 |
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(no function) |
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27 |
0 |
0 |
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Stackix.__init__ |
|
4 |
4 |
0 |
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Stackix._process_latent_results |
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11 |
11 |
0 |
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(no function) |
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30 |
0 |
0 |
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100% |
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(no function) |
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5 |
0 |
0 |
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100% |
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GeneralTrainer.__init__ |
|
15 |
4 |
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73% |
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GeneralTrainer._init_buffers |
|
11 |
1 |
0 |
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91% |
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GeneralTrainer._init_buffers.make_tensor_buffer |
|
7 |
4 |
0 |
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43% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._init_buffers.make_numpy_buffer |
|
1 |
0 |
0 |
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100% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._init_buffers.make_split_buffers |
|
1 |
0 |
0 |
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100% |
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GeneralTrainer._ontix_hook |
|
1 |
0 |
0 |
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100% |
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GeneralTrainer.train |
|
17 |
1 |
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94% |
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GeneralTrainer.maskix_hook |
|
1 |
0 |
0 |
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100% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._train_epoch |
|
24 |
1 |
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96% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._validate_epoch |
|
20 |
1 |
0 |
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95% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._log_losses |
|
4 |
0 |
0 |
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100% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._store_checkpoint |
|
6 |
1 |
0 |
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83% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._capture_dynamics |
|
20 |
9 |
0 |
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55% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._dynamics_to_result |
|
6 |
0 |
0 |
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100% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer._dynamics_to_result.maybe_add |
|
2 |
1 |
0 |
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50% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer.predict |
|
18 |
18 |
0 |
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0% |
| src / autoencodix / trainers / _general_trainer.py |
GeneralTrainer.decode |
|
5 |
5 |
0 |
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0% |
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GeneralTrainer.get_model |
|
1 |
1 |
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0% |
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GeneralTrainer.purge |
|
9 |
9 |
0 |
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0% |
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(no function) |
|
30 |
0 |
0 |
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100% |
| src / autoencodix / trainers / _maskix_trainer.py |
MaskixTrainer.__init__ |
|
7 |
7 |
0 |
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0% |
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MaskixTrainer._validate_masking_fn |
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10 |
10 |
0 |
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MaskixTrainer.maskix_hook |
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3 |
3 |
0 |
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MaskixTrainer._maskix_hook |
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6 |
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0 |
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(no function) |
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13 |
0 |
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OntixTrainer.__init__ |
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1 |
1 |
0 |
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0% |
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OntixTrainer._ontix_hook |
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4 |
4 |
0 |
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OntixTrainer._validate_masks |
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2 |
2 |
0 |
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OntixTrainer._apply_weight_masks |
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3 |
3 |
0 |
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0% |
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(no function) |
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13 |
0 |
0 |
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100% |
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StackixOrchestrator.__init__ |
|
24 |
24 |
0 |
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0% |
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StackixOrchestrator.set_testset |
|
1 |
1 |
0 |
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0% |
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StackixOrchestrator._train_modality |
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6 |
6 |
0 |
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0% |
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StackixOrchestrator._train_distributed |
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29 |
29 |
0 |
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StackixOrchestrator._train_sequential |
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6 |
6 |
0 |
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StackixOrchestrator._extract_latent_spaces |
|
35 |
35 |
0 |
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0% |
| src / autoencodix / trainers / _stackix_orchestrator.py |
StackixOrchestrator.train_modalities |
|
10 |
10 |
0 |
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0% |
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StackixOrchestrator.prepare_latent_datasets |
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12 |
12 |
0 |
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StackixOrchestrator.predict_modalities |
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6 |
6 |
0 |
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StackixOrchestrator.reconstruct_from_stack |
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17 |
17 |
0 |
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0% |
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(no function) |
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SingleCellDataReader.read_data |
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get_dataset |
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show_figure |
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Loader.load |
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flip_labels |
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find_translation_keys |
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preprocess_explanations |
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42 |
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AnnDataConverter._numeric_ds_to_adata |
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AnnDataConverter._parse_multimodal |
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AnnDataConverter.dataset_to_adata |
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generate_example_data |
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28 |
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generate_multi_bulk_example |
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generate_default_bulk_bulk_example |
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generate_default_sc_sc_example |
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generate_default_img_bulk_example |
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generate_default_sc_img_example |
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generate_default_img_img_example |
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generate_raw_datapackage |
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generate_multi_sc_example |
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46 |
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Vanillix_EncoderSingleDim.__init__ |
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4 |
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Vanillix_EncoderSingleDim.forward |
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make_DeepLiftShap_Vanillix_dim |
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make_feature_importance_Vanillix |
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get_top_kgenes_per_latent_dimension |
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2 |
2 |
0 |
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plot_union_top_genes_heatmap |
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16 |
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| src / autoencodix / utils / feature_importance.py |
get_top_genes_per_dimension |
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4 |
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run_go_enrichment |
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5 |
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plot_GO_log_odds_all |
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18 |
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do_miraculix_visualization |
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3 |
3 |
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| src / autoencodix / utils / feature_importance.py |
do_feature_importance_Vanillix |
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24 |
24 |
0 |
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| src / autoencodix / utils / feature_importance.py |
Varix_EncoderSingleDim.__init__ |
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7 |
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| src / autoencodix / utils / feature_importance.py |
Varix_EncoderSingleDim.forward |
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make_DeepLiftShap_Varix_dim |
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| src / autoencodix / utils / feature_importance.py |
make_feature_importance_Varix |
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36 |
36 |
0 |
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| src / autoencodix / utils / feature_importance.py |
do_feature_importance_Varix |
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23 |
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0 |
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| src / autoencodix / utils / feature_importance.py |
make_IntegratedGradients_Varix_dim |
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5 |
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| src / autoencodix / utils / feature_importance.py |
make_IntegratedGradients_Vanillix_dim |
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5 |
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0 |
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| src / autoencodix / utils / feature_importance.py |
(no function) |
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39 |
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| src / autoencodix / utils / prompts.py |
(no function) |
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1 |
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100% |
| src / autoencodix / vanillix.py |
Vanillix.__init__ |
|
2 |
0 |
0 |
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100% |
| src / autoencodix / vanillix.py |
Vanillix.sample_latent_space |
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16 |
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| src / autoencodix / vanillix.py |
(no function) |
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27 |
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0 |
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100% |
| src / autoencodix / varix.py |
Varix.__init__ |
|
2 |
2 |
0 |
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| src / autoencodix / varix.py |
(no function) |
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27 |
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| src / autoencodix / visualize / __init__.py |
(no function) |
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4 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer.__init__ |
|
1 |
1 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer.__setitem__ |
|
1 |
1 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer.visualize |
|
10 |
10 |
0 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer.show_latent_space |
|
87 |
87 |
0 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer.show_weights |
|
6 |
6 |
0 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer._plot_2D |
|
65 |
65 |
0 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer._plot_latent_clustermap |
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11 |
11 |
0 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer._plot_latent_ridge |
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40 |
40 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer._plot_latent_ridge.label |
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3 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer._plot_evaluation |
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21 |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer._total_correlation |
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| src / autoencodix / visualize / _general_visualizer.py |
GeneralVisualizer._coverage_calc |
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8 |
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| src / autoencodix / visualize / _general_visualizer.py |
(no function) |
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32 |
0 |
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100% |
| src / autoencodix / visualize / _imagix_visualizer.py |
ImagixVisualizer.__init__ |
|
1 |
1 |
0 |
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| src / autoencodix / visualize / _imagix_visualizer.py |
ImagixVisualizer.__setitem__ |
|
1 |
1 |
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| src / autoencodix / visualize / _imagix_visualizer.py |
ImagixVisualizer.visualize |
|
4 |
4 |
0 |
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| src / autoencodix / visualize / _imagix_visualizer.py |
ImagixVisualizer.show_weights |
|
1 |
1 |
0 |
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| src / autoencodix / visualize / _imagix_visualizer.py |
ImagixVisualizer.show_image_recon_grid |
|
24 |
24 |
0 |
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| src / autoencodix / visualize / _imagix_visualizer.py |
(no function) |
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15 |
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100% |
| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer.__init__ |
|
1 |
1 |
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| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer.__setitem__ |
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1 |
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| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer.visualize |
|
13 |
13 |
0 |
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| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer.show_latent_space |
|
84 |
84 |
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| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer.show_weights |
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| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer.show_image_translation |
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51 |
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| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer.show_2D_translation |
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41 |
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| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer._plot_translate_latent |
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| src / autoencodix / visualize / _xmodal_visualizer.py |
XModalVisualizer._plot_latent_ridge_multi |
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XModalVisualizer._plot_latent_ridge_multi.label |
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XModalVisualizer._plot_evaluation |
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Visualizer.__init__ |
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Visualizer.__setitem__ |
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Visualizer.visualize |
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5 |
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Visualizer.save_plots |
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Visualizer.show_loss |
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16 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.show_latent_space |
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94 |
94 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.show_weights |
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6 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.plot_model_weights |
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62 |
62 |
0 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.plot_2D |
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40 |
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0 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.plot_latent_ridge |
|
30 |
30 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.plot_latent_ridge.label |
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3 |
3 |
0 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.make_loss_plot |
|
22 |
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0 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.make_loss_format |
|
26 |
26 |
0 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.plot_evaluation |
|
15 |
15 |
0 |
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| src / autoencodix / visualize / visualize.py |
Visualizer.show_evaluation |
|
27 |
27 |
0 |
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| src / autoencodix / visualize / visualize.py |
Visualizer._total_correlation |
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3 |
3 |
0 |
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| src / autoencodix / visualize / visualize.py |
Visualizer._coverage_calc |
|
8 |
8 |
0 |
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| src / autoencodix / visualize / visualize.py |
(no function) |
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41 |
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0 |
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100% |
| src / autoencodix / xmodalix.py |
XModalix.__init__ |
|
4 |
4 |
0 |
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| src / autoencodix / xmodalix.py |
XModalix.show_result |
|
7 |
7 |
0 |
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| src / autoencodix / xmodalix.py |
XModalix._process_latent_results |
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26 |
26 |
0 |
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| src / autoencodix / xmodalix.py |
XModalix._validate_prediction_data |
|
2 |
2 |
0 |
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| src / autoencodix / xmodalix.py |
XModalix._predict |
|
2 |
2 |
0 |
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| src / autoencodix / xmodalix.py |
XModalix.predict |
|
18 |
18 |
0 |
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0% |
| src / autoencodix / xmodalix.py |
XModalix.sample_latent_space |
|
1 |
1 |
0 |
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0% |
| src / autoencodix / xmodalix.py |
(no function) |
|
35 |
0 |
0 |
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100% |
| src / tests / __init__.py |
(no function) |
|
0 |
0 |
0 |
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100% |