.dockerignore
.flake8
.gitignore
.readthedocs.yaml
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
README.md
install_requires.txt
mypy.ini
pyproject.toml
requirements-dev.txt
requirements.txt
setup.py
configs/base_train_selfsupervised.txt
configs/base_validate.txt
configs/default_regression_tests.yml
docs/Makefile
docs/conf.py
docs/index.rst
docs/main.md
docs/make.bat
docs/requirements.txt
docs/_static/css/overrides.css
docs/_templates/autoapi_templates/index.rst
examples/README.md
examples/cdb.csv
examples/cdb.dat
examples/cdb_2.csv
examples/cdb_old_broken_weights_in_config.dat
examples/complex_cdb.csv
examples/run_standalone_meta_annotations.py
examples/vocab.dat
examples/vocab_data.txt
examples/medmentions/medmentions.txt
medcat/LICENSE
medcat/__init__.py
medcat/cat.py
medcat/cdb.py
medcat/cdb_maker.py
medcat/config.py
medcat/config_meta_cat.py
medcat/config_rel_cat.py
medcat/config_transformers_ner.py
medcat/install_requires.txt
medcat/meta_cat.py
medcat/pipe.py
medcat/rel_cat.py
medcat/vocab.py
medcat.egg-info/PKG-INFO
medcat.egg-info/SOURCES.txt
medcat.egg-info/dependency_links.txt
medcat.egg-info/requires.txt
medcat.egg-info/top_level.txt
medcat/datasets/__init__.py
medcat/datasets/data_collator.py
medcat/datasets/helpers.py
medcat/datasets/medcat_annotations.py
medcat/datasets/medcat_annotations.py.lock
medcat/datasets/patient_concept_stream.py
medcat/datasets/transformers_ner.py
medcat/linking/__init__.py
medcat/linking/context_based_linker.py
medcat/linking/vector_context_model.py
medcat/ner/__init__.py
medcat/ner/transformers_ner.py
medcat/ner/vocab_based_annotator.py
medcat/ner/vocab_based_ner.py
medcat/pipeline/__init__.py
medcat/pipeline/pipe_runner.py
medcat/preprocessing/__init__.py
medcat/preprocessing/cleaners.py
medcat/preprocessing/iterators.py
medcat/preprocessing/taggers.py
medcat/preprocessing/tokenizers.py
medcat/stats/__init__.py
medcat/stats/kfold.py
medcat/stats/mctexport.py
medcat/stats/stats.py
medcat/tokenizers/__init__.py
medcat/tokenizers/meta_cat_tokenizers.py
medcat/tokenizers/transformers_ner.py
medcat/utils/__init__.py
medcat/utils/cdb_state.py
medcat/utils/cdb_utils.py
medcat/utils/checkpoint.py
medcat/utils/config_utils.py
medcat/utils/data_utils.py
medcat/utils/decorators.py
medcat/utils/filters.py
medcat/utils/hasher.py
medcat/utils/helpers.py
medcat/utils/make_vocab.py
medcat/utils/matutils.py
medcat/utils/medmentions.py
medcat/utils/memory_optimiser.py
medcat/utils/ml_utils.py
medcat/utils/model_creator.py
medcat/utils/normalizers.py
medcat/utils/other.py
medcat/utils/postprocessing.py
medcat/utils/preprocess_snomed.py
medcat/utils/preprocess_umls.py
medcat/utils/spacy_compatibility.py
medcat/utils/usage_monitoring.py
medcat/utils/vocab_utils.py
medcat/utils/meta_cat/__init__.py
medcat/utils/meta_cat/data_utils.py
medcat/utils/meta_cat/ml_utils.py
medcat/utils/meta_cat/models.py
medcat/utils/ner/__init__.py
medcat/utils/ner/deid.py
medcat/utils/ner/helpers.py
medcat/utils/ner/metrics.py
medcat/utils/ner/model.py
medcat/utils/regression/README.md
medcat/utils/regression/__init__.py
medcat/utils/regression/checking.py
medcat/utils/regression/regression_checker.py
medcat/utils/regression/results.py
medcat/utils/regression/targeting.py
medcat/utils/regression/utils.py
medcat/utils/relation_extraction/__init__.py
medcat/utils/relation_extraction/base_component.py
medcat/utils/relation_extraction/config.py
medcat/utils/relation_extraction/ml_utils.py
medcat/utils/relation_extraction/models.py
medcat/utils/relation_extraction/pad_seq.py
medcat/utils/relation_extraction/rel_dataset.py
medcat/utils/relation_extraction/tokenizer.py
medcat/utils/relation_extraction/bert/__init__.py
medcat/utils/relation_extraction/bert/config.py
medcat/utils/relation_extraction/bert/model.py
medcat/utils/relation_extraction/bert/tokenizer.py
medcat/utils/relation_extraction/llama/__init__.py
medcat/utils/relation_extraction/llama/config.py
medcat/utils/relation_extraction/llama/model.py
medcat/utils/relation_extraction/llama/tokenizer.py
medcat/utils/relation_extraction/modernbert/__init__.py
medcat/utils/relation_extraction/modernbert/config.py
medcat/utils/relation_extraction/modernbert/model.py
medcat/utils/relation_extraction/modernbert/tokenizer.py
medcat/utils/saving/__init__.py
medcat/utils/saving/coding.py
medcat/utils/saving/converter.py
medcat/utils/saving/envsnapshot.py
medcat/utils/saving/serializer.py
media/cat-logo.png
media/cat-logo.svg
media/news.md
media/data/medmentions_only_above_300.json
models/README.md
notebooks/BERT for NER.ipynb
notebooks/Prepare and load data into neo4j.ipynb
notebooks/TWDS - MedCAT & Neo4j Tutorial.ipynb
tests/__init__.py
tests/check_deprecations.py
tests/helper.py
tests/test_cat.py
tests/test_cdb.py
tests/test_cdb_maker.py
tests/test_config.py
tests/test_entity_linking.py
tests/test_meta_cat.py
tests/test_ner.py
tests/test_pipe.py
tests/test_pipe_runner.py
tests/test_rel_cat.py
tests/test_transformers_ner.py
tests/test_vocab.py
tests/model_creator/config_example.yml
tests/model_creator/medcat.txt
tests/model_creator/umls_sample.csv
tests/model_creator/wikipedia_sample.txt
tests/ner/test_transformers_ner.py
tests/preprocessing/__init__.py
tests/preprocessing/test_cleaners.py
tests/resources/deid_test_data.json
tests/resources/deid_train_data.json
tests/resources/jsonpickle_config.json
tests/resources/jsonpickle_meta_cat_config.json
tests/resources/jsonpickle_rel_cat_config.json
tests/resources/jsonpickle_tner_config.json
tests/resources/mct_export_for_meta_cat_test.json
tests/resources/medcat_rel_test.csv
tests/resources/medcat_rel_train.csv
tests/resources/medcat_trainer_export.json
tests/resources/medcat_trainer_export_FAKE_CONCEPTS.json
tests/resources/medcat_trainer_export_filtered.json
tests/resources/medcat_trainer_export_relations.json
tests/resources/test_categories.yml
tests/resources/checkpoints/cat_train/1643822916/checkpoint-2-18
tests/resources/checkpoints/cat_train/1643822916/checkpoint-2-20
tests/resources/checkpoints/cat_train/1643823460/checkpoint-2-18
tests/resources/checkpoints/cat_train/1643823460/checkpoint-2-20
tests/resources/checkpoints/cat_train_supervised/1643823460/checkpoint-1-1
tests/resources/ff_core_fake_dr/meta.json
tests/resources/model_compatibility/check_backwards_compatibility.sh
tests/resources/regression/run_regression.sh
tests/resources/regression/test_vocab.py
tests/resources/regression/creation/cat_creation.py
tests/resources/regression/creation/preprocessed4cdb.txt
tests/resources/regression/creation/selfsupervised_data.txt
tests/resources/regression/creation/supervised_mct_export.json
tests/resources/regression/creation/vocab_data.txt
tests/resources/regression/testing/test_model_regresssion.yml
tests/stats/__init__.py
tests/stats/helpers.py
tests/stats/test_kfold.py
tests/stats/test_mctexport.py
tests/utils/__init__.py
tests/utils/test_cdb_state.py
tests/utils/test_cdb_utils.py
tests/utils/test_checkpoint.py
tests/utils/test_config_utils.py
tests/utils/test_data_utils.py
tests/utils/test_decorators.py
tests/utils/test_hashing.py
tests/utils/test_helpers.py
tests/utils/test_memory_optimiser.py
tests/utils/test_normalizers.py
tests/utils/test_preprocess_snomed.py
tests/utils/test_spacy_compatibility.py
tests/utils/test_usage_monitoring.py
tests/utils/test_vocab_utils.py
tests/utils/ner/__init__.py
tests/utils/ner/test_deid.py
tests/utils/regression/__init__.py
tests/utils/regression/test_checking.py
tests/utils/regression/test_metadata.py
tests/utils/regression/test_results.py
tests/utils/regression/test_targeting.py
tests/utils/regression/test_utils.py
tests/utils/saving/__init__.py
tests/utils/saving/test_coding.py
tests/utils/saving/test_envsnapshot.py
tests/utils/saving/test_serialization.py
tutorial/README.md