.gitignore
.pre-commit-config.yaml
LICENSE
README.md
db_properties.ini
full_grid_search_config.ini
pyproject.toml
simple_grid_search_config.ini
.github/workflows/python-build.yml
.github/workflows/tests.yml
deepspeed_configs/zero1.json
deepspeed_configs/zero2.json
deepspeed_configs/zero3.json
images/cehr_bert_architecture.png
images/tokenization_att_generation.png
sample_configs/hf_cehrbert_finetuning_runner_config.yaml
sample_configs/hf_cehrbert_pretrain_runner_config.yaml
sample_configs/hf_cehrbert_pretrain_runner_meds_config.yaml
sample_data/finetune/full/fake_data.parquet
sample_data/finetune/test/fake_data.parquet
sample_data/finetune/train/fake_data.parquet
sample_data/pretrain/patient_sequence.parquet
src/cehrbert/__init__.py
src/cehrbert.egg-info/PKG-INFO
src/cehrbert.egg-info/SOURCES.txt
src/cehrbert.egg-info/dependency_links.txt
src/cehrbert.egg-info/entry_points.txt
src/cehrbert.egg-info/requires.txt
src/cehrbert.egg-info/top_level.txt
src/cehrbert/config/__init__.py
src/cehrbert/config/grid_search_config.py
src/cehrbert/config/output_names.py
src/cehrbert/data_generators/__init__.py
src/cehrbert/data_generators/data_classes.py
src/cehrbert/data_generators/data_generator_base.py
src/cehrbert/data_generators/graph_sample_method.py
src/cehrbert/data_generators/learning_objective.py
src/cehrbert/data_generators/tokenizer.py
src/cehrbert/data_generators/hf_data_generator/__init__.py
src/cehrbert/data_generators/hf_data_generator/hf_dataset.py
src/cehrbert/data_generators/hf_data_generator/hf_dataset_collator.py
src/cehrbert/data_generators/hf_data_generator/hf_dataset_mapping.py
src/cehrbert/data_generators/hf_data_generator/meds_utils.py
src/cehrbert/data_generators/hf_data_generator/patient_block.py
src/cehrbert/data_generators/hf_data_generator/meds_to_cehrbert_conversion_rules/__init__.py
src/cehrbert/data_generators/hf_data_generator/meds_to_cehrbert_conversion_rules/meds_to_cehrbert_base.py
src/cehrbert/data_generators/hf_data_generator/meds_to_cehrbert_conversion_rules/meds_to_cehrbert_micmic4.py
src/cehrbert/data_generators/hf_data_generator/meds_to_cehrbert_conversion_rules/meds_to_cehrbert_omop.py
src/cehrbert/evaluations/__init__.py
src/cehrbert/evaluations/evaluation.py
src/cehrbert/evaluations/evaluation_parameters.py
src/cehrbert/evaluations/evaluation_parse_args.py
src/cehrbert/evaluations/transfer_learning_evaluation.py
src/cehrbert/evaluations/model_evaluators/__init__.py
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src/cehrbert/evaluations/model_evaluators/hierarchical_bert_evaluators.py
src/cehrbert/evaluations/model_evaluators/model_evaluators.py
src/cehrbert/evaluations/model_evaluators/sequence_model_evaluators.py
src/cehrbert/keras_transformer/__init__.py
src/cehrbert/keras_transformer/bert.py
src/cehrbert/keras_transformer/extras.py
src/cehrbert/keras_transformer/position.py
src/cehrbert/med_extension/__init__.py
src/cehrbert/med_extension/schema_extension.py
src/cehrbert/models/__init__.py
src/cehrbert/models/bert_models.py
src/cehrbert/models/bert_models_visit_prediction.py
src/cehrbert/models/evaluation_models.py
src/cehrbert/models/hierachical_bert_model_v2.py
src/cehrbert/models/hierachical_phenotype_model_new.py
src/cehrbert/models/loss_schedulers.py
src/cehrbert/models/parse_args.py
src/cehrbert/models/hf_models/__init__.py
src/cehrbert/models/hf_models/config.py
src/cehrbert/models/hf_models/hf_cehrbert.py
src/cehrbert/models/hf_models/hf_modeling_outputs.py
src/cehrbert/models/hf_models/tokenization_hf_cehrbert.py
src/cehrbert/models/hf_models/tokenization_utils.py
src/cehrbert/models/layers/__init__.py
src/cehrbert/models/layers/custom_layers.py
src/cehrbert/models/layers/hierarchical_custom_layers.py
src/cehrbert/runners/__init__.py
src/cehrbert/runners/hf_cehrbert_finetune_runner.py
src/cehrbert/runners/hf_cehrbert_pretrain_runner.py
src/cehrbert/runners/hf_runner_argument_dataclass.py
src/cehrbert/runners/runner_util.py
src/cehrbert/tools/__init__.py
src/cehrbert/tools/download_omop_tables.py
src/cehrbert/trainers/__init__.py
src/cehrbert/trainers/model_trainer.py
src/cehrbert/trainers/train_cehr_bert.py
src/cehrbert/utils/__init__.py
src/cehrbert/utils/checkpoint_utils.py
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src/cehrbert/utils/model_utils.py
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tests/__init__.py
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tests/integration_tests/runners/__init__.py
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tests/integration_tests/runners/hf_cehrbert_pretrain_runner_test.py
tests/integration_tests/trainers/__init__.py
tests/integration_tests/trainers/train_cehr_bert_test.py
tests/unit_tests/__init__.py
tests/unit_tests/data_generators/__init__.py
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tests/unit_tests/data_generators/visit_prediction_learning_objective_test.py
tests/unit_tests/data_generators/hf_data_generator/__init__.py
tests/unit_tests/data_generators/hf_data_generator/hf_generate_start_end_index_mapping_test.py
tests/unit_tests/data_generators/hf_data_generator/hf_masked_language_modeling_mapping_test.py
tests/unit_tests/data_generators/hf_data_generator/hf_med_to_cehrbert_mapping_test.py
tests/unit_tests/data_generators/hf_data_generator/hf_sort_patient_sequence_dataset_mapping_test.py
tests/unit_tests/data_generators/hf_data_generator/meds_utils_test.py
tests/unit_tests/data_generators/hf_data_generator/omop_meds_generate_demographics_and_patient_blocks_test.py
tests/unit_tests/models/__init__.py
tests/unit_tests/models/concept_value_decoder_layer_test.py
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tests/unit_tests/utils/__init__.py
tests/unit_tests/utils/truncated_offline_statistics_test.py
tests/unit_tests/utils/truncated_online_statistics_test.py