Index

A

Adapter (class in FastEHR.adapters.adapter) adapter (FastEHR.dataloader.foundational_loader.Collator attribute) (FastEHR.dataloader.foundational_loader.FoundationalDataModule attribute)

add_batch() (FastEHR.adapters.BEHRT.BehrtDFBuilder method)

B

batch_size (FastEHR.dataloader.foundational_loader.FoundationalDataModule attribute) BehrtDFBuilder (class in FastEHR.adapters.BEHRT)

build_table() (FastEHR.database.build_db.build_diagnosis_table.Diagnoses method) (FastEHR.database.build_db.build_static_table.Static method) (FastEHR.database.build_db.build_valued_event_tables.Measurements method)

C

class_token_id (FastEHR.adapters.BEHRT.BehrtDFBuilder attribute) collate_fn (FastEHR.dataloader.foundational_loader.FoundationalDataModule attribute) collate_fn() (FastEHR.dataloader.foundational_loader.Collator method) Collator (class in FastEHR.dataloader.foundational_loader) collector (FastEHR.dataloader.dataset.dataset_polars.PolarsDataset attribute) connect() (FastEHR.database.build_db.build_diagnosis_table.Diagnoses method) (FastEHR.database.build_db.build_static_table.Static method) (FastEHR.database.build_db.build_valued_event_tables.Measurements method) (FastEHR.database.collector.SQLiteDataCollector method) connection (FastEHR.database.build_db.build_diagnosis_table.Diagnoses attribute) (FastEHR.database.build_db.build_static_table.Static attribute) (FastEHR.database.build_db.build_valued_event_tables.Measurements attribute) (FastEHR.database.collector.SQLiteDataCollector attribute)

connection_token (FastEHR.database.build_db.build_diagnosis_table.Diagnoses attribute) (FastEHR.database.build_db.build_static_table.Static attribute) (FastEHR.database.build_db.build_valued_event_tables.Measurements attribute) context_time_scale (FastEHR.dataloader.foundational_loader.FoundationalDataModule property) convert_sample() (FastEHR.adapters.BEHRT.ConvertToBEHRT method) convert_to_supervised() (FastEHR.dataloader.foundational_loader.Collator static method) ConvertToBEHRT (class in FastEHR.adapters.BEHRT) create_behrt_tokenizer() (FastEHR.adapters.BEHRT.ConvertToBEHRT method) cursor (FastEHR.database.build_db.build_diagnosis_table.Diagnoses attribute) (FastEHR.database.build_db.build_static_table.Static attribute) (FastEHR.database.build_db.build_valued_event_tables.Measurements attribute) (FastEHR.database.collector.SQLiteDataCollector attribute)

D

db_path (FastEHR.database.build_db.build_diagnosis_table.Diagnoses attribute) (FastEHR.database.build_db.build_static_table.Static attribute) (FastEHR.database.build_db.build_valued_event_tables.Measurements attribute) (FastEHR.database.collector.SQLiteDataCollector attribute) decode() (FastEHR.dataloader.foundational_loader.FoundationalDataModule method) (FastEHR.dataloader.tokenizers_local.base.TokenizerBase method)

Diagnoses (class in FastEHR.database.build_db.build_diagnosis_table) disconnect() (FastEHR.database.build_db.build_diagnosis_table.Diagnoses method) (FastEHR.database.build_db.build_static_table.Static method) (FastEHR.database.build_db.build_valued_event_tables.Measurements method) (FastEHR.database.collector.SQLiteDataCollector method)

E

encode() (FastEHR.dataloader.foundational_loader.FoundationalDataModule method) (FastEHR.dataloader.tokenizers_local.base.TokenizerBase method)

event_frequency() (FastEHR.dataloader.tokenizers_local.base.TokenizerBase static method) extract_measurement_name() (FastEHR.database.build_db.build_valued_event_tables.Measurements static method)

F

FastEHR module FastEHR.adapters module FastEHR.adapters.adapter module FastEHR.adapters.BEHRT module FastEHR.database module FastEHR.database.build_db module FastEHR.database.build_db.build_diagnosis_table module FastEHR.database.build_db.build_static_table module FastEHR.database.build_db.build_valued_event_tables module FastEHR.database.collector module FastEHR.dataloader module FastEHR.dataloader.dataset module FastEHR.dataloader.dataset.dataset_polars module

FastEHR.dataloader.dataset.utils module FastEHR.dataloader.dataset.utils.dynamic module FastEHR.dataloader.foundational_loader module FastEHR.dataloader.tokenizers_local module FastEHR.dataloader.tokenizers_local.base module FastEHR.dataloader.tokenizers_local.tokenizers_local module FastEHR.dataloader.utils module FastEHR.dataloader.utils.study_criteria module fastehr_tokenizer (FastEHR.adapters.BEHRT.ConvertToBEHRT attribute) file_row_count_dict (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) fit() (FastEHR.dataloader.dataset.dataset_polars.PolarsDataset method) (FastEHR.dataloader.tokenizers_local.base.TokenizerBase method) (FastEHR.dataloader.tokenizers_local.tokenizers_local.NonTabular method) (FastEHR.dataloader.tokenizers_local.tokenizers_local.Tabular method) (FastEHR.dataloader.utils.study_criteria.index_inclusion_method method) fit_description (FastEHR.dataloader.tokenizers_local.base.TokenizerBase property) flush() (FastEHR.adapters.BEHRT.BehrtDFBuilder method) FoundationalDataModule (class in FastEHR.dataloader.foundational_loader) FoundationalDataset (class in FastEHR.dataloader.foundational_loader)

G

get_meta_information() (FastEHR.database.collector.SQLiteDataCollector method)

getitem() (FastEHR.dataloader.foundational_loader.FoundationalDataset method) global_diagnoses (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute)

I

id_prefix (FastEHR.adapters.BEHRT.BehrtDFBuilder attribute) index_inclusion_method (class in FastEHR.dataloader.utils.study_criteria)

is_supervised (FastEHR.dataloader.foundational_loader.FoundationalDataModule property) is_tabular (FastEHR.dataloader.tokenizers_local.tokenizers_local.NonTabular attribute) (FastEHR.dataloader.tokenizers_local.tokenizers_local.Tabular attribute)

M

max_seq_length (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) measurement_table_names (FastEHR.database.build_db.build_valued_event_tables.Measurements property) Measurements (class in FastEHR.database.build_db.build_valued_event_tables) meta_information (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) meta_measurement (FastEHR.dataloader.foundational_loader.FoundationalDataset property) meta_static (FastEHR.dataloader.foundational_loader.FoundationalDataset property) min_seq_len (FastEHR.adapters.BEHRT.BehrtDFBuilder attribute) min_workers (FastEHR.dataloader.foundational_loader.FoundationalDataModule attribute) module FastEHR FastEHR.adapters FastEHR.adapters.adapter FastEHR.adapters.BEHRT FastEHR.database FastEHR.database.build_db FastEHR.database.build_db.build_diagnosis_table FastEHR.database.build_db.build_static_table FastEHR.database.build_db.build_valued_event_tables FastEHR.database.collector FastEHR.dataloader FastEHR.dataloader.dataset FastEHR.dataloader.dataset.dataset_polars FastEHR.dataloader.dataset.utils FastEHR.dataloader.dataset.utils.dynamic FastEHR.dataloader.foundational_loader FastEHR.dataloader.tokenizers_local FastEHR.dataloader.tokenizers_local.base FastEHR.dataloader.tokenizers_local.tokenizers_local FastEHR.dataloader.utils FastEHR.dataloader.utils.study_criteria

N

next_id (FastEHR.adapters.BEHRT.BehrtDFBuilder attribute)

NonTabular (class in FastEHR.dataloader.tokenizers_local.tokenizers_local)

P

pad_token_id (FastEHR.adapters.BEHRT.BehrtDFBuilder attribute) parquet_path (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) path_to_data (FastEHR.database.build_db.build_diagnosis_table.Diagnoses attribute) (FastEHR.database.build_db.build_static_table.Static attribute) (FastEHR.database.build_db.build_valued_event_tables.Measurements attribute)

path_to_db (FastEHR.dataloader.dataset.dataset_polars.PolarsDataset attribute) PolarsDataset (class in FastEHR.dataloader.dataset.dataset_polars) preprocess_measurements() (in module FastEHR.dataloader.dataset.utils.dynamic)

Q

query_measurement_aggregations (FastEHR.database.build_db.build_valued_event_tables.Measurements property)

R

random_context_window (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute)

repeating_events (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) rows (FastEHR.adapters.BEHRT.BehrtDFBuilder attribute)

S

save_path (FastEHR.dataloader.dataset.dataset_polars.PolarsDataset attribute) seed (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) sep_token_id (FastEHR.adapters.BEHRT.BehrtDFBuilder attribute) special_tokens (FastEHR.adapters.BEHRT.ConvertToBEHRT attribute) SQLiteDataCollector (class in FastEHR.database.collector) standardise() (FastEHR.dataloader.foundational_loader.FoundationalDataModule method) standardise_values (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute)

Static (class in FastEHR.database.build_db.build_static_table) static_1hot (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) sub_dir (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) subsample (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) supervised (FastEHR.adapters.BEHRT.ConvertToBEHRT attribute) (FastEHR.dataloader.foundational_loader.Collator attribute) supervised_time_scale (FastEHR.dataloader.foundational_loader.Collator attribute) (FastEHR.dataloader.foundational_loader.FoundationalDataModule property)

T

Tabular (class in FastEHR.dataloader.tokenizers_local.tokenizers_local) test_dataloader() (FastEHR.dataloader.foundational_loader.FoundationalDataModule method) test_set (FastEHR.dataloader.foundational_loader.FoundationalDataModule attribute) time_scale (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) tokenizer (FastEHR.adapters.adapter.Adapter property) (FastEHR.adapters.BEHRT.ConvertToBEHRT attribute) (FastEHR.dataloader.foundational_loader.FoundationalDataModule attribute) (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute)

TokenizerBase (class in FastEHR.dataloader.tokenizers_local.base) total_samples (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute) train_dataloader() (FastEHR.dataloader.foundational_loader.FoundationalDataModule method) train_set (FastEHR.dataloader.foundational_loader.FoundationalDataModule attribute)

U

unstandardise() (FastEHR.dataloader.foundational_loader.FoundationalDataModule method)

V

val_dataloader() (FastEHR.dataloader.foundational_loader.FoundationalDataModule method) val_set (FastEHR.dataloader.foundational_loader.FoundationalDataModule attribute)

view_sample() (FastEHR.dataloader.foundational_loader.FoundationalDataset method) vocab_size (FastEHR.dataloader.tokenizers_local.base.TokenizerBase property)

W

warnings_raised (FastEHR.dataloader.foundational_loader.FoundationalDataset attribute)

Z

zfill (FastEHR.adapters.BEHRT.BehrtDFBuilder attribute)