├── .github └── workflows │ ├── python-build.yml │ └── tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── db_properties.ini ├── deepspeed_configs ├── zero1.json ├── zero2.json └── zero3.json ├── full_grid_search_config.ini ├── images ├── cehr_bert_architecture.png └── tokenization_att_generation.png ├── pyproject.toml ├── sample_configs ├── hf_cehrbert_finetuning_runner_config.yaml ├── hf_cehrbert_pretrain_runner_config.yaml └── hf_cehrbert_pretrain_runner_meds_config.yaml ├── sample_data ├── MIMIC-IV-meds │ └── meds_reader │ │ ├── .done │ │ ├── code │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── doses_per_24_hrs │ │ ├── data │ │ └── zdict │ │ ├── drg_mortality │ │ ├── data │ │ └── zdict │ │ ├── drg_severity │ │ ├── data │ │ └── zdict │ │ ├── emar_id │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── emar_seq │ │ ├── data │ │ └── zdict │ │ ├── frequency │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── hadm_id │ │ ├── data │ │ └── zdict │ │ ├── icustay_id │ │ ├── data │ │ └── zdict │ │ ├── insurance │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── language │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── link_order_id │ │ ├── data │ │ └── zdict │ │ ├── marital_status │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── meds_reader.length │ │ ├── meds_reader.null_map │ │ ├── data │ │ └── zdict │ │ ├── meds_reader.properties │ │ ├── meds_reader.version │ │ ├── metadata │ │ ├── .shards.json │ │ ├── codes.parquet │ │ ├── dataset.json │ │ └── subject_splits.parquet │ │ ├── numeric_value │ │ ├── data │ │ └── zdict │ │ ├── order_id │ │ ├── data │ │ └── zdict │ │ ├── ordercategorydescription │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── poe_id │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── priority │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── race │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── route │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── statusdescription │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── subject_id │ │ ├── text_value │ │ ├── data │ │ ├── dictionary │ │ └── zdict │ │ ├── time │ │ ├── data │ │ └── zdict │ │ └── unit │ │ ├── data │ │ ├── dictionary │ │ └── zdict ├── finetune │ ├── full │ │ └── fake_data.parquet │ ├── test │ │ └── fake_data.parquet │ └── train │ │ └── fake_data.parquet └── pretrain │ └── patient_sequence.parquet ├── simple_grid_search_config.ini ├── src └── cehrbert │ ├── __init__.py │ ├── cehrbert_utils.py │ ├── config │ ├── __init__.py │ ├── grid_search_config.py │ └── output_names.py │ ├── data_generators │ ├── __init__.py │ ├── data_classes.py │ ├── data_generator_base.py │ ├── graph_sample_method.py │ ├── hf_data_generator │ │ ├── __init__.py │ │ ├── cache_util.py │ │ ├── hf_dataset.py │ │ ├── hf_dataset_collator.py │ │ ├── hf_dataset_mapping.py │ │ ├── meds_to_cehrbert_conversion_rules │ │ │ ├── __init__.py │ │ │ ├── meds_to_cehrbert_base.py │ │ │ ├── meds_to_cehrbert_micmic4.py │ │ │ └── meds_to_cehrbert_omop.py │ │ ├── meds_utils.py │ │ ├── patient_block.py │ │ └── sample_packing_sampler.py │ ├── learning_objective.py │ └── tokenizer.py │ ├── evaluations │ ├── __init__.py │ ├── evaluation.py │ ├── evaluation_parameters.py │ ├── evaluation_parse_args.py │ ├── model_evaluators │ │ ├── __init__.py │ │ ├── bert_model_evaluators.py │ │ ├── frequency_model_evaluators.py │ │ ├── hierarchical_bert_evaluators.py │ │ ├── model_evaluators.py │ │ └── sequence_model_evaluators.py │ └── transfer_learning_evaluation.py │ ├── keras_transformer │ ├── __init__.py │ ├── bert.py │ ├── extras.py │ └── position.py │ ├── linear_prob │ ├── __init__.py │ ├── compute_cehrbert_features.py │ └── train_with_cehrbert_features.py │ ├── med_extension │ ├── __init__.py │ └── schema_extension.py │ ├── models │ ├── __init__.py │ ├── bert_models.py │ ├── bert_models_visit_prediction.py │ ├── evaluation_models.py │ ├── hf_models │ │ ├── __init__.py │ │ ├── config.py │ │ ├── hf_cehrbert.py │ │ ├── hf_modeling_outputs.py │ │ ├── tokenization_hf_cehrbert.py │ │ └── tokenization_utils.py │ ├── hierachical_bert_model_v2.py │ ├── hierachical_phenotype_model_new.py │ ├── layers │ │ ├── __init__.py │ │ ├── custom_layers.py │ │ └── hierarchical_custom_layers.py │ ├── loss_schedulers.py │ └── parse_args.py │ ├── runners │ ├── __init__.py │ ├── data_utils.py │ ├── hf_cehrbert_finetune_runner.py │ ├── hf_cehrbert_pretrain_runner.py │ ├── hf_runner_argument_dataclass.py │ ├── hyperparameter_search_util.py │ ├── runner_util.py │ └── sample_packing_trainer.py │ ├── scripts │ └── create_cehrbert_pretraining_data.sh │ ├── tools │ ├── __init__.py │ └── download_omop_tables.py │ ├── trainers │ ├── __init__.py │ ├── model_trainer.py │ └── train_cehr_bert.py │ └── utils │ ├── __init__.py │ ├── checkpoint_utils.py │ ├── logging_utils.py │ ├── model_utils.py │ └── stat_utils.py └── tests ├── __init__.py ├── integration_tests ├── __init__.py ├── runners │ ├── __init__.py │ ├── hf_cehrbert_pretrain_runner_meds_test.py │ ├── hf_cehrbert_pretrain_runner_sample_packing_test.py │ ├── hf_cehrbert_pretrain_runner_streaming_test.py │ └── hf_cehrbert_pretrain_runner_test.py └── trainers │ ├── __init__.py │ └── train_cehr_bert_test.py └── unit_tests ├── __init__.py ├── data_generators ├── __init__.py ├── bert_masked_language_modeling_learning_objective_test.py ├── hf_data_generator │ ├── __init__.py │ ├── hf_dataset_mapping_test.py │ ├── hf_generate_start_end_index_mapping_test.py │ ├── hf_masked_language_modeling_mapping_test.py │ ├── hf_med_to_cehrbert_mapping_test.py │ ├── hf_sort_patient_sequence_dataset_mapping_test.py │ ├── meds_utils_test.py │ ├── omop_meds_generate_demographics_and_patient_blocks_test.py │ └── patient_block_test.py └── visit_prediction_learning_objective_test.py ├── models ├── __init__.py ├── concept_value_decoder_layer_test.py └── hf_models │ ├── __init__.py │ ├── hf_cehrbert_test.py │ ├── numeric_concept_statistics_test.py │ └── tokenization_hf_cehrbert_test.py └── utils ├── __init__.py 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