add small constant to MissForest to avoid zeros

BojarLab · Jul 17, 2023 · 213444b · 213444b
1 parent 00a80a0
commit 213444b
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/build/lib/glycowork/motif/processing.py b/build/lib/glycowork/motif/processing.py
@@ -483,6 +483,7 @@ def replace_zero_with_random_gaussian_knn(df, group_sizes, mean = 0.01,
 
     return df.T
 
+
 class MissForest:
     """Parameters
     (adapted from https://github.com/yuenshingyan/MissForest)
@@ -530,7 +531,8 @@ def fit_transform(self, X: pd.DataFrame) -> pd.DataFrame:
 
                     # Replace missing values in the current column with predictions
                     X_transform.loc[X_nan[column], column] = y_missing_pred
-
+        # Avoiding zeros
+        X_transform += 1e-6
         return X_transform
 
 

diff --git a/glycowork/motif/processing.py b/glycowork/motif/processing.py
@@ -483,6 +483,7 @@ def replace_zero_with_random_gaussian_knn(df, group_sizes, mean = 0.01,
 
     return df.T
 
+
 class MissForest:
     """Parameters
     (adapted from https://github.com/yuenshingyan/MissForest)
@@ -530,7 +531,8 @@ def fit_transform(self, X: pd.DataFrame) -> pd.DataFrame:
 
                     # Replace missing values in the current column with predictions
                     X_transform.loc[X_nan[column], column] = y_missing_pred
-
+        # Avoiding zeros
+        X_transform += 1e-6
         return X_transform