pandasdataframescikit-learnconcatenationscaling

Why is my data is not getting properly concatenated


I split the data using train test split after prerpcessing.

from sklearn.model_selection import train_test_split
X_train,X_test,y_train,y_test= train_test_split(X,y,test_size=0.2,random_state=42)

Then did robust scaling separately for the numerical columns in test and train

from sklearn.preprocessing import RobustScaler
robust = RobustScaler()
X_train_ = robust.fit_transform(X_train[numeric_columns])
X_test_ = robust.transform(X_test[numeric_columns])
X_train_sc_num=pd.DataFrame(X_train_,columns=[numeric_columns])
X_test_sc_num=pd.DataFrame(X_test_,columns=[numeric_columns])

Then did concatenation.

X_train_scaled=pd.concat([X_train_sc_num,X_train[categoric_columns]],axis=1)
X_test_scaled=pd.concat([X_test_sc_num,X_test[categoric_columns]],axis=1)

but the shape got broken and so many 'nan' values added in the categorical columns of the output data. The sahpe was (466,17)+(466,11), it should be (466,28), but it became (560,28).

How can I solve this issue?

I want to do Robust scale my data after Train_Test_split, but without touching my OHE columns,


Solution

  • Your issue might be arising from a couple of things.

    1. First of all, you're using columns=[numeric_columns], which would treat the list as a single column name. Instead, it should be just columns=numeric_columns.
    2. When creating the scaled DataFrames, you weren't preserving the index from the original data. To do this, you simply add an additional parameter index=X_train.index (or X_test, depending on the case) to the pd.DataFrame() initialization.

    Here is a reproducible example using this example data illustrating the steps you'd need to follow with your data:

    import numpy as np
    import pandas as pd
    from sklearn.model_selection import train_test_split
    from sklearn.preprocessing import RobustScaler
    
    # Create example data
    np.random.seed(42)
    n_samples = 466
    
    numerical_data = {"temperature": np.random.normal(14, 3, n_samples), "moisture": np.random.normal(96, 2, n_samples)}
    categorical_data = {"color": np.random.choice(["green", "yellow", "purple"], size=n_samples, p=[0.8, 0.1, 0.1])}
    
    # Create DataFrame
    df = pd.DataFrame({**numerical_data, **categorical_data})
    
    # Define numeric and categorical columns
    numerical_columns = numerical_data.keys()
    categorical_columns = categorical_data.keys()
    
    # One-hot encode categorical columns
    df_encoded = pd.get_dummies(df, columns=categorical_columns)
    
    # Split features and target (creating dummy target for example)
    y = np.random.randint(0, 2, n_samples)
    X = df_encoded
    
    # Split the data
    X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)
    
    # Get the one-hot encoded column names
    # In general, these will be different than categorical_columns, since you're doing OHE
    categorical_columns_encoded = [col for col in X_train.columns if col not in numerical_columns]
    
    # Initialize RobustScaler
    robust = RobustScaler()
    
    # Scale only numeric columns
    X_train_scaled_numeric = robust.fit_transform(X_train[numerical_columns])
    X_test_scaled_numeric = robust.transform(X_test[numerical_columns])
    
    # Create DataFrames with correct column names for scaled numeric data
    X_train_scaled_numeric_df = pd.DataFrame(
        X_train_scaled_numeric,
        columns=numerical_columns,
        index=X_train.index,  # Preserve the index
    )
    
    X_test_scaled_numeric_df = pd.DataFrame(
        X_test_scaled_numeric,
        columns=numerical_columns,
        index=X_test.index,  # Preserve the index
    )
    
    # Concatenate with categorical columns
    X_train_scaled = pd.concat([X_train_scaled_numeric_df, X_train[categorical_columns_encoded]], axis=1)
    X_test_scaled = pd.concat([X_test_scaled_numeric_df, X_test[categorical_columns_encoded]], axis=1)
    
    # Verify the shapes
    print("Original shapes:")
    print(f"X_train: {X_train.shape}")
    print(f"X_test: {X_test.shape}")
    print("\nScaled shapes:")
    print("X_train_scaled: {X_train_scaled.shape} = {X_train_scaled_numeric.shape} + {X_train[categorical_columns_encoded].shape}")
    print(f"X_test_scaled: {X_test_scaled.shape} = {X_test_scaled_numeric.shape} + {X_test[categorical_columns_encoded].shape}")
    
    # Verify no NaN values
    print("\nNaN check:")
    print("NaN in X_train_scaled:", X_train_scaled.isna().sum().sum())
    print("NaN in X_test_scaled:", X_test_scaled.isna().sum().sum())
    

    That would print:

    Original shapes:
    X_train: (372, 5)
    X_test: (94, 5)
    
    Scaled shapes:
    X_train_scaled: (372, 5) = (372, 2) + (372, 3)
    X_test_scaled: (94, 5) = (94, 2) + (94, 3)