├── .github ├── ISSUE_TEMPLATE │ ├── bug-report.yml │ ├── config.yml │ ├── documentation.yml │ └── feature-request.yml ├── pull_request_template.md └── workflows │ └── python-package.yml ├── .gitignore ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── SECURITY.md ├── docs ├── README_docs.md ├── docs │ ├── advanced │ │ ├── compatibility_with_huggingface.md │ │ ├── reproduction_of_results.md │ │ └── text_encoding.md │ ├── cli.md │ ├── data.md │ ├── evaluation.md │ ├── images │ │ ├── annotation_schemes.png │ │ ├── mlflow_1.png │ │ ├── mlflow_2.png │ │ ├── nerblackbox.png │ │ ├── nerblackbox_doccano.png │ │ ├── nerblackbox_hf.png │ │ ├── nerblackbox_labelstudio.png │ │ ├── nerblackbox_sources.png │ │ ├── package-16.svg │ │ ├── standard_pretokenized.png │ │ └── tensorboard.png │ ├── index.md │ ├── inference.md │ ├── preparation.md │ ├── python_api │ │ ├── annotation_tool.md │ │ ├── dataset.md │ │ ├── model.md │ │ ├── overview.md │ │ ├── store.md │ │ ├── text_encoder.md │ │ └── training.md │ ├── stylesheets │ │ └── extra.css │ └── training.md └── mkdocs.yml ├── e2e_tests ├── .gitignore ├── README_e2e_tests.rst ├── e2e_test_api.py ├── e2e_test_cli.py ├── e2e_test_evaluation.py └── utils.py ├── nerblackbox ├── MLproject ├── __about__.py ├── __init__.py ├── api │ ├── __init__.py │ ├── annotation_tool.py │ ├── dataset.py │ ├── model.py │ ├── store.py │ ├── training.py │ └── utils.py ├── cli.py ├── modules │ ├── __init__.py │ ├── annotation │ │ ├── __init__.py │ │ ├── annotation_tool_base.py │ │ ├── annotation_tool_doccano.py │ │ ├── annotation_tool_labelstudio.py │ │ ├── colors.py │ │ ├── file_conversion.py │ │ ├── io.py │ │ └── utils.py │ ├── data │ │ ├── datasets │ │ │ └── .gitignore │ │ ├── pretrained_models │ │ │ └── .gitignore │ │ ├── results │ │ │ └── .gitignore │ │ └── training_configs │ │ │ ├── .gitignore │ │ │ ├── default.ini │ │ │ ├── my_training_conll2003.ini │ │ │ ├── my_training_example.ini │ │ │ ├── my_training_sic.ini │ │ │ ├── my_training_suc.ini │ │ │ ├── my_training_swe_nerc.ini │ │ │ └── my_training_swedish_ner_corpus.ini │ ├── datasets │ │ ├── __init__.py │ │ ├── analyzer.py │ │ ├── formatter │ │ │ ├── __init__.py │ │ │ ├── auto_formatter.py │ │ │ ├── base_formatter.py │ │ │ ├── conll2003_formatter.py │ │ │ ├── huggingface_datasets_formatter.py │ │ │ ├── sic_formatter.py │ │ │ ├── suc_formatter.py │ │ │ ├── sucx_formatter.py │ │ │ ├── swe_nerc_formatter.py │ │ │ ├── swedish_ner_corpus_formatter.py │ │ │ └── util_functions.py │ │ └── plots.py │ ├── ner_training │ │ ├── __init__.py │ │ ├── annotation_tags │ │ │ ├── __init__.py │ │ │ ├── annotation.py │ │ │ ├── input_examples_utils.py │ │ │ ├── tags.py │ │ │ └── token_tags.py │ │ ├── callbacks │ │ │ ├── __init__.py │ │ │ ├── custom_early_stopping.py │ │ │ └── learning_rate_changer.py │ │ ├── data_preprocessing │ │ │ ├── __init__.py │ │ │ ├── data_preprocessor.py │ │ │ ├── text_encoder.py │ │ │ └── tools │ │ │ │ ├── __init__.py │ │ │ │ ├── csv_reader.py │ │ │ │ ├── encodings_dataset.py │ │ │ │ ├── input_example.py │ │ │ │ ├── input_examples_to_tensors.py │ │ │ │ └── utils.py │ │ ├── logging │ │ │ ├── __init__.py │ │ │ ├── default_logger.py │ │ │ └── mlflow_client.py │ │ ├── metrics │ │ │ ├── __init__.py │ │ │ ├── logged_metrics.py │ │ │ └── ner_metrics.py │ │ ├── ner_model.py │ │ ├── ner_model_evaluation.py │ │ ├── ner_model_train.py │ │ ├── ner_model_train2model.py │ │ └── single_run.py │ ├── scripts │ │ ├── __init__.py │ │ └── script_run_training.py │ ├── training_config │ │ ├── __init__.py │ │ ├── preset.py │ │ ├── training.py │ │ └── training_config.py │ ├── training_results.py │ └── utils │ │ ├── __init__.py │ │ ├── env_variable.py │ │ ├── parameters.py │ │ └── util_functions.py └── tests │ ├── __init__.py │ ├── test_analyzer.py │ ├── test_annotation.py │ ├── test_api_model.py │ ├── test_api_training.py │ ├── test_api_utils.py │ ├── test_data │ ├── .gitignore │ ├── final_data │ │ ├── test.csv │ │ ├── train.csv │ │ └── val.csv │ ├── formatted_data │ │ ├── ner_tag_mapping.json │ │ ├── test.csv │ │ ├── test_formatted.csv │ │ ├── train.csv │ │ ├── train_formatted.csv │ │ ├── val.csv │ │ └── val_formatted.csv │ ├── original_data │ │ ├── eng.testa │ │ ├── eng.testb │ │ ├── eng.train │ │ ├── sic-train.conll │ │ ├── suc-train.conll │ │ ├── swe_nerc-test.tsv │ │ ├── swe_nerc-train.tsv │ │ ├── swe_nerc-val.tsv │ │ ├── test_corpus.txt │ │ ├── train_corpus.txt │ │ ├── train_original.csv │ │ └── val_corpus.txt │ ├── test.csv │ ├── test_ner_metrics_entity.csv │ ├── test_ner_metrics_token.csv │ ├── train.csv │ ├── training_configs │ │ ├── default.ini │ │ └── test_training.ini │ └── val.csv │ ├── test_data_preprocessing.py │ ├── test_formatter.py │ ├── test_formatter_conll2003.py │ ├── test_formatter_huggingface_datasets.py │ ├── test_formatter_sic.py │ ├── test_formatter_suc.py │ ├── test_formatter_sucx.py │ ├── test_formatter_swe_nerc.py │ ├── test_formatter_swedish_ner_corpus.py │ ├── test_input_examples_utils.py │ ├── test_logged_metrics.py │ ├── test_ner_metrics.py │ ├── test_ner_model_evaluation.py │ ├── test_tags.py │ ├── test_text_encoder.py │ ├── test_token_tags.py │ ├── test_training.py │ ├── test_training_config.py │ ├── test_training_results.py │ ├── test_util_functions.py │ ├── test_utils.py │ └── utils.py ├── notebooks ├── .gitignore ├── README_notebooks.md ├── doccano.ini ├── doccano.ipynb ├── huggingface.ipynb ├── labelstudio.ini ├── labelstudio.ipynb └── utils.py ├── paper ├── experiments │ ├── experiments_appD.py │ ├── experiments_appG1.py │ ├── experiments_appG2.py │ ├── experiments_appG3.py │ ├── experiments_appH.py │ ├── experiments_appK.py │ ├── experiments_appL.py │ ├── experiments_main.py │ ├── experiments_main_results_epochs.py │ ├── experiments_scheme.py │ ├── global_variables.py │ └── helper_functions.py └── script_paper.py ├── pytest.ini ├── requirements.txt ├── requirements_dev.txt ├── setup.cfg ├── setup.py └── tox.ini 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