I'm working on imputing null values in the Titanic dataset. The 'Embarked' column has some. I do NOT want to just set them all to the most common value, 'S'. I want to impute 'Embarked' based on its correlation with the other columns.

I have tried applying this formula to the 'Embarked' column:

def embark(e):
        if e == 'S': return 1
        if e == 'Q': return 2
        if e == 'C': return 3
        else: return 4

This allows me to check out data.corr(), but I think it's trickier than that since I'll get a different correlation with different value assignments (right??). I also thought about using a four-dimensional (for S,Q,C,NaN) one-hot vector, but I doubt that would work.

Is there a skLearn method that does this some way? Any further insights on the matter?


2 Answers 2


I suggest trying the sklearn module KNNImputer. KNN will use clustering to calculate the null/missing values based on the data that is available (non-null). It should handle numerical and categorical data. You may need to do some encoding on the non-null values first.

You can also look at creating and modelling with multiple imputed datasets using different imputation settings/values and then compare or combine the results. This will help deal with some of the problems inherent in imputation, such as

  • randomness
  • high sampling variability
  • standard error estimates, etc

Other options:

RandomForest fancyimpute

It is fine to impute the data in your test dataset also. Just be sure not to include the label or response in any of the imputation, as that value won't be available in a new dataset.

Also, any imputation method you use should be calculated on the train dataset and then applied to the test dataset. This will prevent data or information leakage between the 2 datasets, and will simulate model performance on any future datasets you use the model on.

One more thing: After imputing, you should look at the distributions of both train and test datasets to compare their distributions, you want them to match as closely as possible.







  • $\begingroup$ Thanks for the sources. I was going to use knnImputer, but what about for the test data that has NaN values? Do I preprocess the test data in the same way? I guess I would, right? $\endgroup$
    – JTalbott
    Commented Jul 14, 2020 at 18:59
  • $\begingroup$ Yes, you can impute the data in your test dataset, using the imputation calculated on the training dataset. I included more details in my answer above. $\endgroup$
    – Donald S
    Commented Jul 15, 2020 at 2:22

For your specific case I would recommend the "grouped mode" because that would be the value you are interested in imputing (I did the same for this kaggle challenge).

On more general terms we have to understand the scale of each variable. We often talk about categorical data but in more detail we have to differentiate between "nominal data" and "ordinal data".

Income brackets are ordinal, that means there is a clear numerical hierarchy, while other data such as the "Embarkment" here is more nominal, that means there is no order or numerical relation.

Therefore a correlation is impossible and it is more helpful to think in terms of grouped distributions.

What does that mean for imputation

Finally besides simply imputing the grouped mode (that is the most frequent value per group) you could try imputation algorithms like MICE which are in a way predicting the missing value based on other variables. This is possible for nominal as well as ordinal categorical factors.

Please be aware that imputation is highly depended on the question of why a value is missing. You have to make sure that the value is not MNAR before you try imputation at all.

  • $\begingroup$ Would I use the same methodology to replace the Null values in the test set? Because there are some FARE data values missing in the test, but they are all there in the train data. $\endgroup$
    – JTalbott
    Commented Jul 14, 2020 at 19:03
  • $\begingroup$ Yes but it is very important to fit the transformer on the training data only lest you introduce data leakage $\endgroup$
    – Fnguyen
    Commented Jul 14, 2020 at 19:27

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.