Update function with imputation already handled.

machine_learning/helper.py

@@ -69,8 +69,6 @@ def insert_row(df, row):
 def run_all_models(input_csv):
     # Prepare data
     model_input = pd.read_csv(input_csv)
-    model_input.dropna(axis=1, how="all", inplace=True)
-    model_input.dropna(axis=0, how="any", subset=["target"], inplace=True)
 
     index_columns = ["local_segment", "local_segment_label", "local_segment_start_datetime", "local_segment_end_datetime"]
     model_input.set_index(index_columns, inplace=True)
@@ -78,6 +76,8 @@ def run_all_models(input_csv):
     data_x, data_y, data_groups = model_input.drop(["target", "pid"], axis=1), model_input["target"], model_input["pid"]
 
     categorical_feature_colnames = ["gender", "startlanguage"]
+    additional_categorical_features = [col for col in data_x.columns if "mostcommonactivity" in col or "homelabel" in col]
+    categorical_feature_colnames += additional_categorical_features
     categorical_features = data_x[categorical_feature_colnames].copy()
     mode_categorical_features = categorical_features.mode().iloc[0]
     # fillna with mode
@@ -90,8 +90,6 @@ def run_all_models(input_csv):
     numerical_features = data_x.drop(categorical_feature_colnames, axis=1)
 
     train_x = pd.concat([numerical_features, categorical_features], axis=1)
-    imputer = SimpleImputer(missing_values=np.nan, strategy='mean')
-    train_x_imputed = imputer.fit_transform(train_x)
 
     # Prepare cross validation
     logo = LeaveOneGroupOut()
@@ -106,7 +104,7 @@ def run_all_models(input_csv):
     lin_reg_rapids = linear_model.LinearRegression()
     lin_reg_scores = cross_val_score(
         lin_reg_rapids,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -120,7 +118,7 @@ def run_all_models(input_csv):
     ridge_reg = linear_model.Ridge(alpha=.5)
     ridge_reg_scores = cross_val_score(
         ridge_reg,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -134,7 +132,7 @@ def run_all_models(input_csv):
     lasso_reg = linear_model.Lasso(alpha=0.1)
     lasso_reg_score = cross_val_score(
         lasso_reg,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -148,7 +146,7 @@ def run_all_models(input_csv):
     bayesian_ridge_reg = linear_model.BayesianRidge()
     bayesian_ridge_reg_score = cross_val_score(
         bayesian_ridge_reg,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -162,7 +160,7 @@ def run_all_models(input_csv):
     ransac_reg = linear_model.RANSACRegressor()
     ransac_reg_score = cross_val_score(
         ransac_reg,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -176,7 +174,7 @@ def run_all_models(input_csv):
     svr = svm.SVR()
     svr_score = cross_val_score(
         svr,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -190,7 +188,7 @@ def run_all_models(input_csv):
     kridge = kernel_ridge.KernelRidge()
     kridge_score = cross_val_score(
         kridge,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -204,7 +202,7 @@ def run_all_models(input_csv):
     gpr = gaussian_process.GaussianProcessRegressor()
     gpr_score = cross_val_score(
         gpr,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -218,7 +216,7 @@ def run_all_models(input_csv):
     rfr = ensemble.RandomForestRegressor(max_features=0.3, n_jobs=-1)
     rfr_score = cross_val_score(
         rfr,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -232,7 +230,7 @@ def run_all_models(input_csv):
     xgb = XGBRegressor()
     xgb_score = cross_val_score(
         xgb,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,
@@ -246,7 +244,7 @@ def run_all_models(input_csv):
     ada = ensemble.AdaBoostRegressor()
     ada_score = cross_val_score(
         ada,
-        X=train_x_imputed,
+        X=train_x,
         y=data_y,
         groups=data_groups,
         cv=logo,