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