| # 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: <disease_label> mandatory only if the prediction task is Phenotype | |
| timePrediction: <timePrediction> | |
| timeWindow: <timeWindow> | |
| timebucket: <timebucket> | |
| radimp: <radimp> | |
| predW: <predW> | |
| diagnosis: <diagnosis> | |
| output: <output> | |
| chart: <chart> | |
| proc: <proc> | |
| meds: <meds> | |
| disease_filter: <disease_filter> | |
| icu_no_icu: <icu_no_icu> | |
| groupingDiag: <groupingDiag> | |
| select_diag: <select_diag> | |
| select_med: <select_med> | |
| select_proc: <select_proc> | |
| select_out: <select_out> | |
| select_chart: <select_chart> | |
| outlier_removal: <outlier_removal> | |
| outlier: <outlier> | |
| left_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: <disease_label> mandatory only if the prediction task is Phenotype | |
| timePrediction: <timePrediction> | |
| timeWindow: <timeWindow> | |
| timebucket: <timebucket> | |
| radimp: <radimp> | |
| predW: <predW> | |
| diagnosis: <diagnosis> | |
| lab: <lab> | |
| proc: <proc> | |
| meds: <meds> | |
| disease_filter: <disease_filter> | |
| icu_no_icu: <icu_no_icu> | |
| groupingDiag: <groupingDiag> | |
| groupingProc: <groupingProc> | |
| groupingMed: <groupingMed> | |
| select_diag: <select_diag> | |
| select_med: <select_med> | |
| select_proc: <select_proc> | |
| select_lab: <select_lab> | |
| outlier_removal: <outlier_removal> | |
| outlier: <outlier> | |
| left_outlier: <left_outlier> | |
| ``` | |
| Replace the `<variable>` 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. 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=`<path_to_config_file>`. | |
| For more understanding of the configuration please refer to https://github.com/healthylaife/MIMIC-IV-Data-Pipeline. |