pyhealth.datasets.MIMIC3Dataset#

The open Medical Information Mart for Intensive Care (MIMIC-III) database, refer to doc for more information. We process this database into well-structured dataset object and give user the best flexibility and convenience for supporting modeling and analysis.

class pyhealth.datasets.MIMIC3Dataset(root, tables, dataset_name=None, config_path=None, **kwargs)[source]#

Bases: BaseDataset

A dataset class for handling MIMIC-III data.

This class is responsible for loading and managing the MIMIC-III dataset, which includes tables such as patients, admissions, and icustays.

root#

The root directory where the dataset is stored.

Type:: str

tables#

A list of tables to be included in the dataset.

Type:: List[str]

dataset_name#

The name of the dataset.

Type:: Optional[str]

config_path#

The path to the configuration file.

Type:: Optional[str]

Examples

>>> from pyhealth.datasets import MIMIC3Dataset
>>> # Load MIMIC-III dataset with clinical tables
>>> dataset = MIMIC3Dataset(
...     root="/path/to/mimic-iii/1.4",
...     tables=["diagnoses_icd", "procedures_icd", "labevents"],
... )
>>> dataset.stats()

preprocess_noteevents(df)[source]#

Table-specific preprocess function which will be called by BaseDataset.load_table().

Preprocesses the noteevents table by ensuring that the charttime column is populated. If charttime is null, it uses chartdate with a default time of 00:00:00.

See: https://mimic.mit.edu/docs/iii/tables/noteevents/#chartdate-charttime-storetime.

Parameters:: df (pl.LazyFrame) – The input dataframe containing noteevents data.
Returns:: The processed dataframe with updated charttime values.
Return type:: pl.LazyFrame

clean_tmpdir()#

Cleans up the temporary directory within the cache.

Return type:: None

create_tmpdir()#

Creates and returns a new temporary directory within the cache.

Returns:: The path to the new temporary directory.
Return type:: Path

property default_task: Optional[BaseTask]#

Returns the default task for the dataset.

Returns:: The default task, if any.
Return type:: Optional[BaseTask]

get_patient(patient_id)#

Retrieves a Patient object for the given patient ID.

Parameters:: patient_id (str) – The ID of the patient to retrieve.
Returns:: The Patient object for the given ID.
Return type:: Patient
Raises:: AssertionError – If the patient ID is not found in the dataset.

property global_event_df: LazyFrame#

Returns the path to the cached event dataframe.

Returns:: The path to the cached event dataframe.
Return type:: Path

iter_patients(df=None)#

Yields Patient objects for each unique patient in the dataset.

Yields:: Iterator[Patient] – An iterator over Patient objects.
Return type:: Iterator[Patient]

load_data()#

Loads data from the specified tables.

Returns:: A concatenated lazy frame of all tables.
Return type:: dd.DataFrame

load_table(table_name)#

Loads a table and processes joins if specified.

Parameters:

table_name (str) – The name of the table to load.

Returns:

The processed Dask dataframe for the table.

Return type:

dd.DataFrame

Raises:

ValueError – If the table is not found in the config.
FileNotFoundError – If the source file (CSV/TSV or Parquet) for the table or join is not found.

set_task(task=None, num_workers=None, input_processors=None, output_processors=None, split=None)#

Processes the base dataset to generate the task-specific sample dataset. The cache structure is as follows:

{task_name}_{task_uuid}/        # Cached data for specific task based on task name, schema, and args
    task_df.ld/                 # Intermediate task dataframe based on schema
    samples_{proc_uuid}.ld/     # Final processed samples after applying processors
        schema.pkl              # Saved SampleBuilder schema
        split.npz               # Sample indices per split part (with split= only)
        *.bin                   # Processed sample files

Parameters:

task (Optional[BaseTask]) – The task to set. Uses default task if None.
num_workers (int) – Number of workers for multi-threading. Default is self.num_workers.
input_processors (Optional[Dict[str, FeatureProcessor]]) – Pre-fitted input processors. If provided, these will be used instead of creating new ones from task’s input_schema. Defaults to None.
output_processors (Optional[Dict[str, FeatureProcessor]]) – Pre-fitted output processors. If provided, these will be used instead of creating new ones from task’s output_schema. Defaults to None.
split (Optional[Split]) – Split the samples, e.g. by patient with PatientSplit, and fit every processor on the first (training) part only, so the other parts never shape preprocessing. The parts are used as the split returns them. Samples are streamed; nothing is loaded into memory beyond the per-sample index that processing already keeps. Defaults to None: fit on all samples and return one dataset, as before.

Returns:

The generated sample dataset, or, with split, a tuple with one dataset per part, training part first, whose processors were fitted on the training part.

Return type:

SampleDataset

Examples

>>> from pyhealth.datasets import PatientSplit
>>> train, val, test = dataset.set_task(  
...     task, split=PatientSplit(ratios=(0.7, 0.1, 0.2), seed=42)
... )

Raises:: AssertionError – If no default task is found and task is None.

stats()#

Prints statistics about the dataset.

Return type:: None

property unique_patient_ids: List[str]#

Returns a list of unique patient IDs.

Returns:: List of unique patient IDs.
Return type:: List[str]