# Configuration File Instructions Below are the instructions to create a valid configuration file. ## Configuration File Structure The configuration file should be in YAML format (.config file) and follow the structure outlined below for **ICU Data**: ```yaml disease_label: mandatory only if the prediction task is Phenotype timePrediction: timeWindow: timebucket: radimp: predW: diagnosis: output: chart: proc: meds: disease_filter: icu_no_icu: groupingDiag: select_diag: select_med: select_proc: select_out: select_chart: outlier_removal: outlier: left_outlier: ``` The configuration file should be in YAML format (.config file) and follow the structure outlined below for **Non-ICU Data**: ```yaml disease_label: mandatory only if the prediction task is Phenotype timePrediction: timeWindow: timebucket: radimp: predW: diagnosis: lab: proc: meds: disease_filter: icu_no_icu: groupingDiag: groupingProc: groupingMed: select_diag: select_med: select_proc: select_lab: outlier_removal: outlier: left_outlier: ``` Replace the `` placeholders with the corresponding values specific to your use case. Detailed explanations of each variable and their valid values are provided in the next section. ## Variable Definitions and Valid Values - `disease_label` (string): Specifies the disease label for Phenotype prediction task. Don't provide the line if the task is not Phenotype. Valid values: CAD, Heart Failure, CKD, COPD. - `timePrediction` (integer): Specifies the time prediction (days). Valid values depend on the task: - For Phenotype task: 30 - For Mortality task: 0 - For Length of Stay task: Between 1 and 10 (inclusive) - For Readmission task: Between 10 and 150 (inclusive), multiple of 10 - `timeWindow` (string): Specifies the time window. Valid values: - For Phenotype or Readmission task: Last X hours (with 24 <= X >= 72) - For Mortality or Length of Stay tasks: First X hours (with 24 <= X >= 72) - `timebucket` (integer): Specifies the time bucket. Valid values: Between 1 and 6 (inclusive). - `radimp` (string): Specifies the imputation method. Valid values: - No Imputation - forward fill and mean - forward fill and median - `predW` (integer): Specifies the prediction window. Valid values depend on the task: - For Phenotype, Length of Stay, or Readmission tasks: 0 - For Mortality task: Between 2 and 8 (inclusive) - `diagnosis`, `output`, `chart`, `proc`, `meds`, `lab` (boolean): Specifies whether to include each respective feature. Valid values: True or False. - `disease_filter` (string): Specifies the disease filter if focusing on a cohort with a specific chronic disease. Valid values: - Heart Failure - COPD - CKD - CAD - No Disease Filter - `icu_no_icu` (string): Specifies the dataset type. Valid values: ICU. - `groupingDiag` (string): Specifies the grouping ICD option for diagnosis. Valid values: - Convert ICD-9 to ICD-10 and group ICD-10 codes - Keep both ICD-9 and ICD-10 codes - Convert ICD-9 to ICD-10 codes - `groupingMed`: Specifies if grouping Medication codes should be done to use Non propietary names : Valid values : Yes, No - `groupingProc` : Specifies the ICD codes version to perform grouping for procedures : Valid values : - ICD-9 and ICD-10 - ICD-10 - `select_diag`, `select_med`, `select_proc`, `select_out`, `select_chart`,`select_lab` (boolean): Specifies whether to do features selection as describe in https://github.com/healthylaife/MIMIC-IV-Data-Pipeline benchmark. Valid values: True or False. - `outlier_removal` (string): Specifies the outlier removal method. Valid values: - No outlier detection - Impute Outlier (default:98) - Remove outliers (default:98) - `outlier` (integer): Specifies the outlier threshold. Valid values: Between 90 and 99 (inclusive). - `left_outlier` (integer): Specifies the left outlier threshold. Valid values: Between 0 and 10 (inclusive). ## Example Configuration File Here's an example of a valid configuration file for **ICU Data**: ```yaml disease_label: CAD timePrediction: 30 timeWindow: Last 72 hours timebucket: 2 radimp: forward fill and mean predW: 0 diagnosis: True output: True chart: True proc: True meds: True disease_filter: No Disease Filter icu_no_icu: ICU groupingICD: Convert ICD-9 to ICD-10 and group ICD-10 codes select_diag: False select_med: False select_proc: False select_out: False select_chart: False outlier_removal: Impute Outlier (default:98) outlier: 98 left_outlier: 0 ``` Here's an example of a valid configuration file for **Non-ICU Data**: ```yaml timePrediction: 0 timeWindow: First 48 hours timebucket: 2 radimp: forward fill and mean predW: 2 diagnosis: True lab: True proc: False meds: False disease_filter: CKD icu_no_icu: ICU groupingDiag: Convert ICD-9 to ICD-10 and group ICD-10 codes select_diag: False select_med: False select_proc: False select_lab: False outlier_removal: Impute Outlier (default:98) outlier: 98 left_outlier: 0 groupingMed: Yes groupingProc: ICD-10 ``` Feel free to modify the values to fit your specific requirements. ## Usage Provide the full path of your configuration file while calling the loading dataset function with the parameter config_path=``. For more understanding of the configuration please refer to https://github.com/healthylaife/MIMIC-IV-Data-Pipeline.