├── .github ├── ISSUE_TEMPLATE │ ├── ---bug-report.md │ ├── ---feature-request.md │ └── ---question.md └── workflows │ ├── lint.yaml │ ├── python-publish.yml │ └── test.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE.txt ├── MANIFEST.in ├── Makefile ├── README.md ├── _config.yml ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── conf.py │ ├── fuse.data.datasets.caching.rst │ ├── fuse.data.datasets.caching.tests.rst │ ├── fuse.data.datasets.rst │ ├── fuse.data.datasets.tests.rst │ ├── fuse.data.ops.rst │ ├── fuse.data.ops.tests.rst │ ├── fuse.data.pipelines.rst │ ├── fuse.data.pipelines.tests.rst │ ├── fuse.data.rst │ ├── fuse.data.tests.rst │ ├── fuse.data.utils.rst │ ├── fuse.data.utils.tests.rst │ ├── fuse.dl.lightning.rst │ ├── fuse.dl.losses.rst │ ├── fuse.dl.losses.segmentation.rst │ ├── fuse.dl.models.backbones.rst │ ├── fuse.dl.models.heads.rst │ ├── fuse.dl.models.rst │ ├── fuse.dl.rst │ ├── fuse.dl.templates.rst │ ├── fuse.dl.tests.rst │ ├── fuse.eval.examples.rst │ ├── fuse.eval.metrics.libs.rst │ ├── fuse.eval.metrics.rst │ ├── fuse.eval.metrics.segmentation.rst │ ├── fuse.eval.metrics.survival.rst │ ├── fuse.eval.rst │ ├── fuse.eval.tests.rst │ ├── fuse.rst │ ├── fuse.utils.config_tools.rst │ ├── fuse.utils.config_tools.tests.rst │ ├── fuse.utils.cpu_profiling.rst │ ├── fuse.utils.cpu_profiling.tests.rst │ ├── fuse.utils.data.rst │ ├── fuse.utils.data.tests.rst │ ├── fuse.utils.file_io.rst │ ├── fuse.utils.file_io.tests.rst │ ├── fuse.utils.multiprocessing.rst │ ├── fuse.utils.rand.rst │ ├── fuse.utils.rand.tests.rst │ ├── fuse.utils.remote_execution.rst │ ├── fuse.utils.rst │ ├── fuse.utils.tests.rst │ ├── fuse_examples.imaging.classification.bright.eval.rst │ ├── fuse_examples.imaging.classification.bright.rst │ ├── fuse_examples.imaging.classification.cmmd.rst │ ├── fuse_examples.imaging.classification.isic.rst │ ├── fuse_examples.imaging.classification.knight.eval.rst │ ├── fuse_examples.imaging.classification.knight.rst │ ├── fuse_examples.imaging.classification.mnist.rst │ ├── fuse_examples.imaging.classification.rst │ ├── fuse_examples.imaging.classification.stoic21.rst │ ├── fuse_examples.imaging.hello_world.rst │ ├── fuse_examples.imaging.rst │ ├── fuse_examples.multimodality.ehr_transformer.rst │ ├── fuse_examples.multimodality.image_clinical.rst │ ├── fuse_examples.multimodality.rst │ ├── fuse_examples.rst │ ├── fuse_examples.tests.rst │ ├── fuseimg.data.ops.rst │ ├── fuseimg.data.ops.tests.rst │ ├── fuseimg.data.rst │ ├── fuseimg.datasets.rst │ ├── fuseimg.datasets.tests.rst │ ├── fuseimg.eval.rst │ ├── fuseimg.rst │ ├── fuseimg.utils.align.rst │ ├── fuseimg.utils.rst │ ├── index.rst │ ├── modules.rst │ ├── run_all_unit_tests.rst │ └── setup.rst ├── fuse ├── __init__.py ├── data │ ├── README.md │ ├── __init__.py │ ├── datasets │ │ ├── __init__.py │ │ ├── caching │ │ │ ├── __init__.py │ │ │ ├── object_caching_handlers.py │ │ │ ├── samples_cacher.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_sample_caching.py │ │ ├── dataset_base.py │ │ ├── dataset_default.py │ │ ├── dataset_wrap_seq_to_dict.py │ │ ├── sample_caching_audit.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_dataset_default.py │ │ │ ├── test_dataset_default_audit_feature.py │ │ │ └── test_dataset_wrap_seq_to_dict.py │ ├── key_types.py │ ├── key_types_for_testing.py │ ├── ops │ │ ├── __init__.py │ │ ├── caching_tools.py │ │ ├── hashable_class.py │ │ ├── op_base.py │ │ ├── ops_aug_common.py │ │ ├── ops_aug_tabular.py │ │ ├── ops_cast.py │ │ ├── ops_common.py │ │ ├── ops_common_for_testing.py │ │ ├── ops_debug.py │ │ ├── ops_read.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_op_base.py │ │ │ ├── test_ops_aug_common.py │ │ │ ├── test_ops_cast.py │ │ │ ├── test_ops_common.py │ │ │ └── test_ops_read.py │ ├── patterns.py │ ├── pipelines │ │ ├── __init__.py │ │ ├── pipeline_default.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ └── test_pipeline_default.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_initialization.py │ │ └── test_version.py │ ├── tokenizers │ │ ├── __init__.py │ │ └── modular_tokenizer │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── inject_utils.py │ │ │ ├── modular_tokenizer.py │ │ │ ├── op.py │ │ │ ├── scripts │ │ │ ├── add_multi_tokenizer_special_tokens.py │ │ │ ├── add_tokenizer_to_multi_tokenizer.py │ │ │ └── create_multi_tokenizer.py │ │ │ └── special_tokens.py │ └── utils │ │ ├── __init__.py │ │ ├── collates.py │ │ ├── export.py │ │ ├── sample.py │ │ ├── samplers.py │ │ ├── split.py │ │ └── tests │ │ ├── __init__.py │ │ ├── test_collates.py │ │ ├── test_dataset_export.py │ │ └── test_samplers.py ├── dl │ ├── README.md │ ├── __init__.py │ ├── cross_validation │ │ └── pipeline.py │ ├── lightning │ │ ├── __init__.py │ │ ├── pl_epoch_summary.py │ │ ├── pl_funcs.py │ │ └── pl_module.py │ ├── losses │ │ ├── __init__.py │ │ ├── contrastive │ │ │ └── contrastive_loss.py │ │ ├── loss_base.py │ │ ├── loss_default.py │ │ ├── loss_extract.py │ │ ├── loss_warm_up.py │ │ ├── loss_wrap_to_dict.py │ │ └── segmentation │ │ │ ├── __init__.py │ │ │ └── loss_dice.py │ ├── models │ │ ├── __init__.py │ │ ├── backbones │ │ │ ├── __init__.py │ │ │ ├── backbone_inception_resnet_v2.py │ │ │ ├── backbone_mlp.py │ │ │ ├── backbone_mvit.py │ │ │ ├── backbone_resnet.py │ │ │ ├── backbone_resnet_3d.py │ │ │ ├── backbone_transformer.py │ │ │ ├── backbone_unet3d.py │ │ │ └── backbone_vit.py │ │ ├── heads │ │ │ ├── __init__.py │ │ │ ├── common.py │ │ │ ├── head_dense_segmentation.py │ │ │ ├── head_global_pooling_classifier.py │ │ │ ├── heads_1D.py │ │ │ └── heads_3D.py │ │ ├── model_ensemble.py │ │ ├── model_multihead.py │ │ ├── model_multistream.py │ │ ├── model_siamese.py │ │ └── model_wrapper.py │ ├── templates │ │ ├── __init__.py │ │ └── walkthrough_template.py │ └── tests │ │ ├── __init__.py │ │ ├── test_cat.py │ │ ├── test_loss_wrapper.py │ │ └── test_vit.py ├── doc │ ├── FuseMedML-logo.png │ └── coding_style.md ├── eval │ ├── README.md │ ├── __init__.py │ ├── evaluator.py │ ├── examples │ │ ├── __init__.py │ │ ├── examples.py │ │ ├── examples_segmentation.py │ │ ├── examples_seq_gen.py │ │ ├── examples_stats.py │ │ └── inputs │ │ │ ├── detection │ │ │ ├── example_coco_new.json │ │ │ └── instances_val2014_fakesegm100_results.json │ │ │ ├── ensemble │ │ │ └── mnist │ │ │ │ └── test_dir │ │ │ │ ├── 0 │ │ │ │ └── test_set_infer.gz │ │ │ │ ├── 1 │ │ │ │ └── test_set_infer.gz │ │ │ │ ├── 2 │ │ │ │ └── test_set_infer.gz │ │ │ │ ├── 3 │ │ │ │ └── test_set_infer.gz │ │ │ │ └── 4 │ │ │ │ └── test_set_infer.gz │ │ │ ├── example0.pickle │ │ │ ├── example1_predictions.csv │ │ │ ├── example1_targets.csv │ │ │ ├── example2_predictions_fold0.csv │ │ │ ├── example2_predictions_fold1.csv │ │ │ ├── example2_targets.csv │ │ │ ├── example7_predictions.csv │ │ │ └── semantic_segmentation │ │ │ ├── labeled │ │ │ ├── id_0 │ │ │ │ └── seg.nii.gz │ │ │ ├── id_1 │ │ │ │ └── seg.nii.gz │ │ │ ├── id_2 │ │ │ │ └── seg.nii.gz │ │ │ └── id_3 │ │ │ │ └── seg.nii.gz │ │ │ └── predicted │ │ │ ├── id_0.nii.gz │ │ │ ├── id_1.nii.gz │ │ │ ├── id_2.nii.gz │ │ │ └── id_3.nii.gz │ ├── metric_diagram.png │ ├── metrics │ │ ├── __init__.py │ │ ├── classification │ │ │ ├── metrics_calibration_common.py │ │ │ ├── metrics_classification_common.py │ │ │ ├── metrics_ensembling_common.py │ │ │ ├── metrics_model_comparison_common.py │ │ │ └── metrics_thresholding_common.py │ │ ├── detection │ │ │ └── metrics_detection_common.py │ │ ├── libs │ │ │ ├── __init__.py │ │ │ ├── calibration.py │ │ │ ├── classification.py │ │ │ ├── efficient_active_ranking_pairwise_model.py │ │ │ ├── efficient_ranking_batch_rank.py │ │ │ ├── ensembling.py │ │ │ ├── instance_segmentation.py │ │ │ ├── model_comparison.py │ │ │ ├── pairwise_ranking.py │ │ │ ├── segmentation.py │ │ │ ├── stat.py │ │ │ ├── survival.py │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_ranking.py │ │ │ └── thresholding.py │ │ ├── metrics_common.py │ │ ├── metrics_model_comparison.py │ │ ├── ranking │ │ │ └── __init__.py │ │ ├── regression │ │ │ ├── __init__.py │ │ │ └── metrics.py │ │ ├── segmentation │ │ │ ├── __init__.py │ │ │ ├── metrics_instance_segmentation_common.py │ │ │ └── metrics_segmentation_common.py │ │ ├── sequence_gen │ │ │ └── metrics_seq_gen_common.py │ │ ├── stat │ │ │ └── metrics_stat_common.py │ │ ├── survival │ │ │ ├── __init__.py │ │ │ └── metrics_survival.py │ │ └── utils.py │ └── tests │ │ ├── __init__.py │ │ └── test_eval.py ├── requirements.txt ├── requirements_dev.txt ├── utils │ ├── README.md │ ├── __init__.py │ ├── add_preamble.py │ ├── config_tools │ │ ├── __init__.py │ │ ├── config_tools.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── base_conf_example │ │ │ ├── base_conf_example.py │ │ │ ├── some_conf_internal_include │ │ │ ├── some_conf_internal_include.py │ │ │ ├── some_conf_no_include.py │ │ │ └── test_config.py │ ├── cpu_profiling │ │ ├── __init__.py │ │ ├── profiler.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_profiler.py │ │ │ └── test_timer.py │ │ └── timer.py │ ├── data │ │ ├── __init__.py │ │ ├── collate.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ └── test_collate.py │ ├── dl │ │ ├── checkpoint.py │ │ └── torch_utils.py │ ├── file_io │ │ ├── __init__.py │ │ ├── atomic_file.py │ │ ├── compressed.py │ │ ├── file_io.py │ │ ├── path.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_hdf5.py │ │ │ └── test_path.py │ ├── gpu.py │ ├── interface_validator.py │ ├── misc │ │ ├── context.py │ │ ├── func_util.py │ │ ├── misc.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ └── test_pretty_dataframe.py │ ├── multiprocessing │ │ ├── __init__.py │ │ ├── helpers.py │ │ ├── linux_shared_memory.py │ │ └── run_multiprocessed.py │ ├── ndict.py │ ├── rand │ │ ├── __init__.py │ │ ├── param_sampler.py │ │ ├── seed.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_param_sampler.py │ │ │ └── test_seed.py │ ├── remote_execution │ │ ├── __init__.py │ │ ├── check_available_port.sh │ │ ├── remote_execution.py │ │ ├── script_runner.sh │ │ ├── script_runner_DETACHED.sh │ │ └── shell_handler.py │ ├── tests │ │ ├── __init__.py │ │ ├── decorators.py │ │ ├── test_interface_validator.py │ │ ├── test_ndict.py │ │ └── test_utils_hierarchical_dict.py │ ├── utils_debug.py │ ├── utils_hierarchical_dict.py │ └── utils_logger.py └── version.py ├── fuse_examples ├── __init__.py ├── imaging │ ├── __init__.py │ ├── classification │ │ ├── __init__.py │ │ ├── bright │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ └── eval │ │ │ │ ├── __init__.py │ │ │ │ ├── baseline │ │ │ │ ├── validation_baseline_task1_predictions.csv │ │ │ │ ├── validation_baseline_task2_predictions.csv │ │ │ │ └── validation_results │ │ │ │ │ ├── results.csv │ │ │ │ │ └── results.md │ │ │ │ ├── eval.py │ │ │ │ ├── example │ │ │ │ ├── example_targets.csv │ │ │ │ ├── example_task1_predictions.csv │ │ │ │ ├── example_task2_predictions.csv │ │ │ │ └── results │ │ │ │ │ ├── results.csv │ │ │ │ │ └── results.md │ │ │ │ └── validation_targets.csv │ │ ├── cmmd │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── conf │ │ │ │ └── config.yaml │ │ │ └── runner.py │ │ ├── isic │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── golden_members.py │ │ │ └── isic_runner.py │ │ ├── knight │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── baseline │ │ │ │ ├── config.yaml │ │ │ │ ├── fuse_baseline.py │ │ │ │ ├── splits_final.pkl │ │ │ │ └── utils.py │ │ │ ├── download_data.sh │ │ │ ├── eval │ │ │ │ ├── __init__.py │ │ │ │ ├── baseline │ │ │ │ │ ├── validation_baseline_task1_predictions.csv │ │ │ │ │ ├── validation_baseline_task2_predictions.csv │ │ │ │ │ ├── validation_results_task1 │ │ │ │ │ │ ├── results.csv │ │ │ │ │ │ ├── results.md │ │ │ │ │ │ └── task1_roc.png │ │ │ │ │ └── validation_results_task2 │ │ │ │ │ │ ├── results.csv │ │ │ │ │ │ ├── results.md │ │ │ │ │ │ └── task2_roc.png │ │ │ │ ├── eval.py │ │ │ │ └── example │ │ │ │ │ ├── example_targets.csv │ │ │ │ │ ├── example_task1_predictions.csv │ │ │ │ │ ├── example_task2_predictions.csv │ │ │ │ │ └── results │ │ │ │ │ ├── results.csv │ │ │ │ │ ├── results.md │ │ │ │ │ ├── task1_roc.png │ │ │ │ │ └── task2_roc.png │ │ │ ├── make_predictions_file.py │ │ │ └── make_targets_file.py │ │ ├── mnist │ │ │ ├── __init__.py │ │ │ ├── lenet.py │ │ │ ├── run_mnist_custom_pl_imp.py │ │ │ └── simple_mnist_starter.py │ │ └── stoic21 │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── dataset.py │ │ │ └── runner_stoic21.py │ ├── hello_world │ │ ├── __init__.py │ │ ├── hello_world.ipynb │ │ └── hello_world_utils.py │ ├── ml_pipelines │ │ ├── README.md │ │ ├── mnist │ │ │ ├── funcs.py │ │ │ └── run_mnist_pipeline.py │ │ └── stoic21 │ │ │ └── run_stoic_pipeline.py │ ├── oai_example │ │ ├── README.md │ │ ├── __init__.py │ │ ├── data │ │ │ ├── data_ops.py │ │ │ ├── oai_ds.py │ │ │ └── seg_ds.py │ │ ├── downstream │ │ │ ├── classification.py │ │ │ ├── classification_config.yaml │ │ │ ├── segmentation.py │ │ │ └── segmentation_config.yaml │ │ └── self_supervised │ │ │ ├── dino.py │ │ │ └── dino_config.yaml │ └── segmentation │ │ └── picai │ │ ├── conf │ │ └── config_template.yaml │ │ ├── runner.py │ │ └── unet.py ├── multimodality │ ├── __init__.py │ ├── ehr_transformer │ │ ├── Fig1.jpg │ │ ├── Fig2.jpg │ │ ├── README.md │ │ ├── __init__.py │ │ ├── config.yaml │ │ ├── dataset.py │ │ ├── main_train.py │ │ ├── model.py │ │ └── utils.py │ └── image_clinical │ │ ├── __init__.py │ │ ├── arch.png │ │ ├── dataset.py │ │ └── multimodality_image_clinical.ipynb ├── requirements.txt └── tests │ ├── __init__.py │ ├── test_classification_bright,py │ ├── test_classification_cmmd.py │ ├── test_classification_isic.py │ ├── test_classification_knight.py │ ├── test_classification_mnist.py │ ├── test_classification_stoic21.py │ ├── test_ehr_transformer.py │ ├── test_notebook_hello_world.py │ └── test_segmentation_picai.py ├── fuseimg ├── README.md ├── __init__.py ├── data │ ├── __init__.py │ └── ops │ │ ├── __init__.py │ │ ├── aug │ │ ├── color.py │ │ └── geometry.py │ │ ├── color.py │ │ ├── debug_ops.py │ │ ├── image_loader.py │ │ ├── ops_common_imaging.py │ │ ├── ops_debug.py │ │ ├── shape_ops.py │ │ └── tests │ │ ├── __init__.py │ │ ├── test_ops.py │ │ └── test_pipeline_caching.py ├── datasets │ ├── __init__.py │ ├── cmmd.py │ ├── isic.py │ ├── kits21.py │ ├── kits21_example.ipynb │ ├── knight.py │ ├── mnist.py │ ├── picai.py │ ├── stoic21.py │ └── tests │ │ ├── __init__.py │ │ └── test_datasets.py ├── eval │ ├── __init__.py │ └── metrics_vis_2d.py ├── requirements.txt └── utils │ ├── __init__.py │ ├── align │ ├── __init__.py │ ├── utils_align_base.py │ └── utils_align_ecc.py │ ├── image_processing.py │ └── typing │ ├── key_types_imaging.py │ └── typed_element.py ├── make.bat ├── py.typed ├── pyproject.toml └── run_all_unit_tests.py /.github/ISSUE_TEMPLATE/---bug-report.md: -------------------------------------------------------------------------------- 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