.flake8
.gitignore
.mypy.ini
.pre-commit-config.yaml
LICENSE
README.md
_config.yml
pyproject.toml
setup.py
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/build.yaml
.github/workflows/tests.yaml
native/.bazelrc
native/.clang-format
native/.clang-tidy
native/BUILD
native/WORKSPACE
native/backupbazelrc
native/civil_day_caster.hh
native/clmbr_dictionary.hh
native/compute_statistics.cc
native/constdb.cc
native/constdb.hh
native/convert_dictionary_formats.cc
native/count_codes_and_values.cc
native/count_codes_and_values.hh
native/count_codes_and_values_test.cc
native/cpu_jax_extension.cc
native/create_dictionary.cc
native/create_dictionary.hh
native/create_survival_dictionary.cc
native/create_survival_dictionary.hh
native/csv.cc
native/csv.hh
native/csv_test.cc
native/database.cc
native/database.hh
native/database_test.cc
native/database_test_helper.cc
native/database_test_helper.hh
native/dataloader_extension.cc
native/dataloader_extension.hh
native/datasets_extension.cc
native/datasets_extension.hh
native/dictionary.cc
native/dictionary.hh
native/dictionary_test.cc
native/embedding_dot.cu
native/embedding_dot.hh
native/exp_mean.cu
native/exp_mean.hh
native/extension.cc
native/extension_test.py
native/filesystem_caster.hh
native/flatmap.hh
native/gather_scatter.cu
native/gather_scatter.hh
native/jax_extension.cc
native/jax_extension.hh
native/join_csvs.cc
native/join_csvs.hh
native/join_csvs_test.cc
native/local_attention.cu
native/local_attention.hh
native/malloc_trim.hh
native/metrics_extension.cc
native/metrics_extension.hh
native/npy.hh
native/parse_utils.cc
native/parse_utils.hh
native/prepare_all.sh
native/prepare_notes_for_tokenization.cc
native/register_iterable.hh
native/simple_test.cc
native/stat_utils.hh
native/survival.hh
native/survival_metrics.cc
native/survival_metrics.hh
native/survival_test.cc
native/thread_utils.hh
src/femr/__init__.py
src/femr/jax.py
src/femr.egg-info/PKG-INFO
src/femr.egg-info/SOURCES.txt
src/femr.egg-info/dependency_links.txt
src/femr.egg-info/entry_points.txt
src/femr.egg-info/not-zip-safe
src/femr.egg-info/requires.txt
src/femr.egg-info/top_level.txt
src/femr/datasets/__init__.py
src/femr/datasets/fileio.py
src/femr/datasets/types.py
src/femr/etl_pipelines/__init__.py
src/femr/etl_pipelines/omop.py
src/femr/etl_pipelines/sickkids.py
src/femr/etl_pipelines/simple.py
src/femr/etl_pipelines/stanford.py
src/femr/extension/__init__.pyi
src/femr/extension/datasets.pyi
src/femr/extension/jax.pyi
src/femr/extractors/__init__.py
src/femr/extractors/csv.py
src/femr/extractors/omop.py
src/femr/featurizers/__init__.py
src/femr/featurizers/core.py
src/femr/featurizers/featurizers.py
src/femr/featurizers/featurizers_notes.py
src/femr/labelers/__init__.py
src/femr/labelers/core.py
src/femr/labelers/omop.py
src/femr/labelers/omop_inpatient_admissions.py
src/femr/labelers/omop_lab_values.py
src/femr/metrics/__init__.py
src/femr/models/__init__.py
src/femr/models/dataloader.py
src/femr/models/scripts.py
src/femr/models/transformer.py
src/femr/transforms/__init__.py
src/femr/transforms/notes.py
src/femr/transforms/sickkids.py
src/femr/transforms/stanford.py
tests/test_csvs.py
tests/test_datasets.py
tests/test_jax.py
tests/test_metrics.py
tests/test_transforms.py
tests/tools.py
tests/featurizers/test_OnlineStatistics.py
tests/featurizers/test_featurizers.py
tests/labelers/test_CodeLabelers.py
tests/labelers/test_InpatientAdmissionLabelers.py
tests/labelers/test_LabValueLabelers.py
tests/labelers/test_LabeledPatients.py
tests/labelers/test_NLabelerPerPatient.py
tests/labelers/test_OpioidOverdoseLabeler.py
tests/labelers/test_TimeHorizonEventLabeler.py
tools/omop/normalize_visit_detail.py
tools/stanford/download_bigquery.py
tools/stanford/flowsheet_cleaner.py
tutorials/0_Fundamental FEMR Schema, Patients And Events.ipynb
tutorials/1_run_featurizers.py
tutorials/2_train_baseline_models.py
tutorials/3_run_text_featurizer.py
tutorials/4_train_clmbr_model.py
tutorials/Simple FEMR Format.ipynb
tutorials/mimic_etl_tutorial.py