I am working working with the World Happiness Report dataset from Kaggle. When using either cross_val_score or GridSearchCV from sklearn, I get very large negative r2 scores. My first thought was that the models I was using were SEVERELY over-fitting (it is a small dataset), but when I performed cross-validation using KFold to split the data, I got reasonable results.

You can view an example of what I am talking about in this Google Colab Notebook. The relevant code is also shown below.

Using cross_val_score

model = LinearRegression()
print(cross_val_score(model, X, y, scoring='r2', cv=5))

Output: [-5.57285067 -5.9477523 -6.23988074 -8.84930385 -2.39521998]

Using KFold

model = LinearRegression()
kf = KFold(n_splits=5, random_state=1, shuffle=True)
scores = []

for i, (train_index, test_index) in enumerate(kf.split(X)):
    X_train = X[train_index,:]
    y_train = y[train_index]
    X_test = X[test_index,:]
    y_test = y[test_index]

    model.fit(X_train, y_train)
    test_score = model.score(X_test, y_test)
    scores.append(round(test_score, 6))


Output: [0.829785, 0.774577, 0.762708, 0.661945, 0.727391]

Some Additional Observations

  • It doesn't seem to matter what type of model I use. I still get very large negative scores when using cross_val_score.
  • I created a synthetic dataset that was approximately the same size of the World Happiness dataset just to try some things out. In that case, I did not get large negative r2 scores from cross_val_score. This is shown in the Google Colab notebook that I shared above.
  • I notice that the magnitude of the negative results I get using cross_val_score is greatly affected by the number of folds I use. Increasing the number of folds significantly increases the magnitude.

Thanks in advance for your help!


2 Answers 2


you are fitting your whole data to it, it seems the cross_val_score awaits a predefined train_test_split object. Ignore the part with 'bla' :-). Btw. it is also the kaggle data. I used it in one of my own notebooks.


  • $\begingroup$ Thank you very much for your reply, but I don't think that it quite gets to the core of the issue. First, the primary purpose of cross-validation is to avoid needing to create a train-test split. New splits are created during cross-validation. Second, you are not providing a "train_test_split" object to cross_valscore. The objects X_train` and y_train are numpy arrays, just like the original X and y arrays. $\endgroup$
    – Beane
    Mar 7, 2021 at 17:00
  • $\begingroup$ Your comment did help me to discover the true source of the issue, however. The data is not shuffled by cross_val_score. I did not know this previously. Since the observations are provided in order of the target variable in this dataset, the folds created by cross-val_score each consider of similar observations and are not representative of the dataset as a whole. I was able to resolve the issue by shuffling the data before using cross_val_score. Thank you for taking the time to look at this! $\endgroup$
    – Beane
    Mar 7, 2021 at 17:00
  • $\begingroup$ Well if you see it that way: Xtrain is not a numpy array it is pandas DataFrame object... which is an array like shape. But I'm glad I could help even you tried to correct me in every sentence ... $\endgroup$ Mar 7, 2021 at 17:44
  • $\begingroup$ Please try not to take things so personally. I appreciate your effort to help, and was not trying to be critical of you, but the points I made were correct. In reference to your comment about arrays vs DataFrames... If you pass arrays to train_test_split, you will get back out arrays. If you pass in DataFrames, you will get back DataFrames. I said that X_train was an array because in my case, it was. I has created X to be an array, meaning that X_train was an array. (continued) $\endgroup$
    – Beane
    Mar 7, 2021 at 21:13
  • $\begingroup$ But if I has been working with DataFrames, my point still stands: The datatype of X and X_train will be the same (both arrays or both DataFrames). You suggested that cross_val_score expected a train_test_split object, but that is not the issue. The type of the objects are the same with or without using train_test_split. As I explained, the reason why train_test_split works in this situation is because it shuffles the rows before performing the split. $\endgroup$
    – Beane
    Mar 7, 2021 at 21:16

Solved! The issue is that the observations in this dataset are ordered with respect to the value of the target variable and cross_val_score does not shuffle the data provided to it. As a result, each fold contains a set of values that are similar to each other and don't represent the entire dataset.


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