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Train - Clinical data, Train - Bacteria (Kaiju), Train - Bacteriophage…
Train - Clinical data
Features selected - Impute missing values by group mean
Train - Bacteria (Kaiju)
LIONESS with Spiec-Easi
Network Metrics calculation
Feature-selected -> PCA
Feature selected - Clinical -> Z-Score
Ricci-Curvature calculation
Edge weights - Did not use?
Train - Bacteriophage (DemoVir)
Z-score
SMOTE
Random Forest Hyper-parameter Tuning
Variable Importance - 100 iter - Top 50
Logistic regression - parameter tuning
Repeated Stratified KFold
Final Model fitting and testing
Balanced Random Forest - Parameter Tuning
Repeated Stratified KFold
Final model fitting and testing
Train - Test split
wilcoxon-test (p< 0.1)
Concatenate
CLR Transformation