README.md

metadata

tags:
  - medical

Dataset Usage

Description

The Mimic-IV dataset generate data by executing the Pipeline available on https://github.com/healthylaife/MIMIC-IV-Data-Pipeline.

Function Signature

load_dataset('thbndi/Mimic4Dataset', task, mimic_path=mimic_data, config_path=config_file, encoding=encod, generate_cohort=gen_cohort, val_size=size, cache_dir=cache)

Arguments

1. task (string) :

   • Description: Specifies the task you want to perform with the dataset.
   • Default: "Mortality"
   • Note: Possible Values : 'Phenotype', 'Length of Stay', 'Readmission', 'Mortality'

2. mimic_path (string) :

   • Description: Complete path to the Mimic-IV raw data on user's machine.
   • Note: You need to provide the appropriate path where the Mimic-IV data is stored. The path should end with the version of mimic (eg : mimiciv/2.2). Supported version : 2.2 and 1.0 as provided by the authors of the pipeline.

3. config_path (string) optionnal :

   • Description: Path to the configuration file for the cohort generation choices (more infos in '/config/readme.md').
   • Default: Configuration file provided in the 'config' folder.

4. encoding (string) optionnal :

   • Description: Data encoding option for the features.
   • Options: "concat", "aggreg", "tensor", "raw", "text"
   • Default: "concat"
   • Note: Choose one of the following options for data encoding:
     • "concat": Concatenates the one-hot encoded diagnoses, demographic data vector, and dynamic features at each measured time instant, resulting in a high-dimensional feature vector.
     • "aggreg": Concatenates the one-hot encoded diagnoses, demographic data vector, and dynamic features, where each item_id is replaced by the average of the measured time instants, resulting in a reduced-dimensional feature vector.
     • "tensor": Represents each feature as an 2D array. There are separate arrays for labels, demographic data ('DEMO'), diagnosis ('COND'), medications ('MEDS'), procedures ('PROC'), chart/lab events ('CHART/LAB'), and output events data ('OUT'). Dynamic features are represented as 2D arrays where each row contains values at a specific time instant.
     • "raw": Provide cohort from the pipeline without any encoding for custom data processing.
     • "text": Represents diagnoses as text suitable for BERT or other similar text-based models.
     • For 'concat' and 'aggreg' the composition of the vector is given in './data/dict/"task"/features_aggreg.csv' or './data/dict/"task"/features_concat.csv' file and in 'features_names' column of the dataset.

5. generate_cohort (bool) optionnal :

   • Description: Determines whether to generate a new cohort from Mimic-IV data.
   • Default: True
   • Note: Set it to True to generate a cohort, or False to skip cohort generation.

6. val_size, 'test_size' (float) optionnal :

   • Description: Proportion of the dataset used for validation during training.
   • Default: 0.1 for validation size and 0.2 for testing size.
   • Note: Can be set to 0.

7. cache_dir (string) optionnal :

   • Description: Directory where the processed dataset will be cached.
   • Note: Providing a cache directory for each encoding type can avoid errors when changing the encoding type.

Example Usage

import datasets
from datasets import load_dataset

# Example 1: Load dataset with default settings
dataset = load_dataset('thbndi/Mimic4Dataset', task="Mortality", mimic_path="/path/to/mimic_data")

# Example 2: Load dataset with custom settings
dataset = load_dataset('thbndi/Mimic4Dataset', task="Phenotype", mimic_path="/path/to/mimic_data", config_path="/path/to/config_file", encoding="aggreg", generate_cohort=False, val_size=0.2, cache_dir="/path/to/cache_dir")

Please note that the provided examples are for illustrative purposes only, and you should adjust the paths and settings based on your actual dataset and specific use case.