.gitignore
.pre-commit-config.yaml
LICENSE
README.md
constraints.txt
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/MIMIC-IV-meds/meds_reader/.done
sample_data/MIMIC-IV-meds/meds_reader/meds_reader.length
sample_data/MIMIC-IV-meds/meds_reader/meds_reader.properties
sample_data/MIMIC-IV-meds/meds_reader/meds_reader.version
sample_data/MIMIC-IV-meds/meds_reader/subject_id
sample_data/MIMIC-IV-meds/meds_reader/code/data
sample_data/MIMIC-IV-meds/meds_reader/code/dictionary
sample_data/MIMIC-IV-meds/meds_reader/code/zdict
sample_data/MIMIC-IV-meds/meds_reader/doses_per_24_hrs/data
sample_data/MIMIC-IV-meds/meds_reader/doses_per_24_hrs/zdict
sample_data/MIMIC-IV-meds/meds_reader/drg_mortality/data
sample_data/MIMIC-IV-meds/meds_reader/drg_mortality/zdict
sample_data/MIMIC-IV-meds/meds_reader/drg_severity/data
sample_data/MIMIC-IV-meds/meds_reader/drg_severity/zdict
sample_data/MIMIC-IV-meds/meds_reader/emar_id/data
sample_data/MIMIC-IV-meds/meds_reader/emar_id/dictionary
sample_data/MIMIC-IV-meds/meds_reader/emar_id/zdict
sample_data/MIMIC-IV-meds/meds_reader/emar_seq/data
sample_data/MIMIC-IV-meds/meds_reader/emar_seq/zdict
sample_data/MIMIC-IV-meds/meds_reader/frequency/data
sample_data/MIMIC-IV-meds/meds_reader/frequency/dictionary
sample_data/MIMIC-IV-meds/meds_reader/frequency/zdict
sample_data/MIMIC-IV-meds/meds_reader/hadm_id/data
sample_data/MIMIC-IV-meds/meds_reader/hadm_id/zdict
sample_data/MIMIC-IV-meds/meds_reader/icustay_id/data
sample_data/MIMIC-IV-meds/meds_reader/icustay_id/zdict
sample_data/MIMIC-IV-meds/meds_reader/insurance/data
sample_data/MIMIC-IV-meds/meds_reader/insurance/dictionary
sample_data/MIMIC-IV-meds/meds_reader/insurance/zdict
sample_data/MIMIC-IV-meds/meds_reader/language/data
sample_data/MIMIC-IV-meds/meds_reader/language/dictionary
sample_data/MIMIC-IV-meds/meds_reader/language/zdict
sample_data/MIMIC-IV-meds/meds_reader/link_order_id/data
sample_data/MIMIC-IV-meds/meds_reader/link_order_id/zdict
sample_data/MIMIC-IV-meds/meds_reader/marital_status/data
sample_data/MIMIC-IV-meds/meds_reader/marital_status/dictionary
sample_data/MIMIC-IV-meds/meds_reader/marital_status/zdict
sample_data/MIMIC-IV-meds/meds_reader/meds_reader.null_map/data
sample_data/MIMIC-IV-meds/meds_reader/meds_reader.null_map/zdict
sample_data/MIMIC-IV-meds/meds_reader/metadata/.shards.json
sample_data/MIMIC-IV-meds/meds_reader/metadata/codes.parquet
sample_data/MIMIC-IV-meds/meds_reader/metadata/dataset.json
sample_data/MIMIC-IV-meds/meds_reader/metadata/subject_splits.parquet
sample_data/MIMIC-IV-meds/meds_reader/numeric_value/data
sample_data/MIMIC-IV-meds/meds_reader/numeric_value/zdict
sample_data/MIMIC-IV-meds/meds_reader/order_id/data
sample_data/MIMIC-IV-meds/meds_reader/order_id/zdict
sample_data/MIMIC-IV-meds/meds_reader/ordercategorydescription/data
sample_data/MIMIC-IV-meds/meds_reader/ordercategorydescription/dictionary
sample_data/MIMIC-IV-meds/meds_reader/ordercategorydescription/zdict
sample_data/MIMIC-IV-meds/meds_reader/poe_id/data
sample_data/MIMIC-IV-meds/meds_reader/poe_id/dictionary
sample_data/MIMIC-IV-meds/meds_reader/poe_id/zdict
sample_data/MIMIC-IV-meds/meds_reader/priority/data
sample_data/MIMIC-IV-meds/meds_reader/priority/dictionary
sample_data/MIMIC-IV-meds/meds_reader/priority/zdict
sample_data/MIMIC-IV-meds/meds_reader/race/data
sample_data/MIMIC-IV-meds/meds_reader/race/dictionary
sample_data/MIMIC-IV-meds/meds_reader/race/zdict
sample_data/MIMIC-IV-meds/meds_reader/route/data
sample_data/MIMIC-IV-meds/meds_reader/route/dictionary
sample_data/MIMIC-IV-meds/meds_reader/route/zdict
sample_data/MIMIC-IV-meds/meds_reader/statusdescription/data
sample_data/MIMIC-IV-meds/meds_reader/statusdescription/dictionary
sample_data/MIMIC-IV-meds/meds_reader/statusdescription/zdict
sample_data/MIMIC-IV-meds/meds_reader/text_value/data
sample_data/MIMIC-IV-meds/meds_reader/text_value/dictionary
sample_data/MIMIC-IV-meds/meds_reader/text_value/zdict
sample_data/MIMIC-IV-meds/meds_reader/time/data
sample_data/MIMIC-IV-meds/meds_reader/time/zdict
sample_data/MIMIC-IV-meds/meds_reader/unit/data
sample_data/MIMIC-IV-meds/meds_reader/unit/dictionary
sample_data/MIMIC-IV-meds/meds_reader/unit/zdict
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/cehrbert_utils.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/baseline_evaluation/__init__.py
src/cehrbert/baseline_evaluation/evaluation.py
src/cehrbert/baseline_evaluation/evaluation_parse_args.py
src/cehrbert/baseline_evaluation/transfer_learning_evaluation.py
src/cehrbert/baseline_evaluation/model_evaluators/__init__.py
src/cehrbert/baseline_evaluation/model_evaluators/frequency_model_evaluators.py
src/cehrbert/baseline_evaluation/model_evaluators/model_evaluators.py
src/cehrbert/data_generators/__init__.py
src/cehrbert/data_generators/hf_data_generator/__init__.py
src/cehrbert/data_generators/hf_data_generator/cache_util.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/sample_packing_sampler.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/linear_prob/__init__.py
src/cehrbert/linear_prob/compute_cehrbert_features.py
src/cehrbert/linear_prob/train_with_cehrbert_features.py
src/cehrbert/med_extension/__init__.py
src/cehrbert/med_extension/schema_extension.py
src/cehrbert/models/__init__.py
src/cehrbert/models/evaluation_models.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/runners/__init__.py
src/cehrbert/runners/data_utils.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/hyperparameter_search_util.py
src/cehrbert/runners/runner_util.py
src/cehrbert/runners/sample_packing_trainer.py
src/cehrbert/scripts/create_cehrbert_pretraining_data.sh
src/cehrbert/tools/__init__.py
src/cehrbert/tools/download_omop_tables.py
src/cehrbert/utils/__init__.py
src/cehrbert/utils/model_utils.py
src/cehrbert/utils/stat_utils.py
tests/__init__.py
tests/integration_tests/__init__.py
tests/integration_tests/runners/__init__.py
tests/integration_tests/runners/hf_cehrbert_pretrain_runner_meds_test.py
tests/integration_tests/runners/hf_cehrbert_pretrain_runner_sample_packing_test.py
tests/integration_tests/runners/hf_cehrbert_pretrain_runner_streaming_test.py
tests/integration_tests/runners/hf_cehrbert_pretrain_runner_test.py
tests/unit_tests/__init__.py
tests/unit_tests/data_generators/__init__.py
tests/unit_tests/data_generators/hf_data_generator/__init__.py
tests/unit_tests/data_generators/hf_data_generator/hf_dataset_mapping_test.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/data_generators/hf_data_generator/patient_block_test.py
tests/unit_tests/models/__init__.py
tests/unit_tests/models/hf_models/__init__.py
tests/unit_tests/models/hf_models/hf_cehrbert_test.py
tests/unit_tests/models/hf_models/numeric_concept_statistics_test.py
tests/unit_tests/models/hf_models/tokenization_hf_cehrbert_test.py
tests/unit_tests/utils/__init__.py
tests/unit_tests/utils/truncated_offline_statistics_test.py
tests/unit_tests/utils/truncated_online_statistics_test.py