How To Handle Missing Values In Machine Learning Data With Weka

Last Updated on December 13, 2019

Data is rarely clean and often you can have corrupt or missing values.

It is important to identify, mark and handle missing data when developing machine learning models in order to get the very best performance.

In this post you will discover how to handle missing values in your machine learning data using Weka.

After reading this post you will know:

  • How to mark missing values in your dataset.
  • How to remove data with missing values from your dataset.
  • How to impute missing values.

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How To Handle Missing Data For Machine Learning in Weka

How To Handle Missing Data For Machine Learning in Weka
Photo by Peter Sitte, some rights reserved.

Predict the Onset of Diabetes

The problem used for this example is the Pima Indians onset of diabetes dataset.

It is a classification problem where each instance represents medical details for one patient and the task is to predict whether the patient will have an onset of diabetes within the next five years.

You can learn more about the dataset here:

You can also access this dataset in your Weka installation, under the data/ directory in the file called diabetes.arff.

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Mark Missing Values

The Pima Indians dataset is a good basis for exploring missing data.

Some attributes such as blood pressure (pres) and Body Mass Index (mass) have values of zero, which are impossible. These are examples of corrupt or missing data that must be marked manually.

You can mark missing values in Weka using the NumericalCleaner filter. The recipe below shows you how to use this filter to mark the 11 missing values on the Body Mass Index (mass) attribute.

1. Open the Weka Explorer.

2. Load the Pima Indians onset of diabetes dataset.

3. Click the “Choose” button for the Filter and select NumericalCleaner, it us under unsupervized.attribute.NumericalCleaner.

Weka Select NumericCleaner Data Filter

Weka Select NumericCleaner Data Filter

4. Click on the filter to configure it.

5. Set the attributeIndicies to 6, the index of the mass attribute.

6. Set minThreshold to 0.1E-8 (close to zero), which is the minimum value allowed for the attribute.

7. Set minDefault to NaN, which is unknown and will replace values below the threshold.

8. Click the “OK” button on the filter configuration.

9. Click the “Apply” button to apply the filter.

Click “mass” in the “attributes” pane and review the details of the “selected attribute”. Notice that the 11 attribute values that were formally set to 0 are not marked as Missing.

Weka Missing Data Marked

Weka Missing Data Marked

In this example we marked values below a threshold as missing.

You could just as easily mark them with a specific numerical value. You could also mark values missing between a upper and lower range of values.

Next, let’s look at how we can remove instances with missing values from our dataset.

Remove Missing Data

Now that you know how to mark missing values in your data, you need to learn how to handle them.

A simple way to handle missing data is to remove those instances that have one or more missing values.

You can do this in Weka using the RemoveWithValues filter.

Continuing on from the above recipe to mark missing values, you can remove missing values as follows:

1. Click the “Choose” button for the Filter and select RemoveWithValues, it us under unsupervized.instance.RemoveWithValues.

Weka Select RemoveWithValues Data Filter

Weka Select RemoveWithValues Data Filter

2. Click on the filter to configure it.

3. Set the attributeIndicies to 6, the index of the mass attribute.

4. Set matchMissingValues to “True”.

5. Click the “OK” button to use the configuration for the filter.

6. Click the “Apply” button to apply the filter.

Click “mass” in the “attributes” section and review the details of the “selected attribute”.

Notice that the 11 attribute values that were marked Missing have been removed from the dataset.

Weka Missing Values Removed

Weka Missing Values Removed

Note, you can undo this operation by clicking the “Undo” button.

Impute Missing Values

Instances with missing values do not have to be removed, you can replace the missing values with some other value.

This is called imputing missing values.

It is common to impute missing values with the mean of the numerical distribution. You can do this easily in Weka using the ReplaceMissingValues filter.

Continuing on from the first recipe above to mark missing values, you can impute the missing values as follows:

1. Click the “Choose” button for the Filter and select ReplaceMissingValues, it us under unsupervized.attribute.ReplaceMissingValues.

Weka ReplaceMissingValues Data Filter

Weka ReplaceMissingValues Data Filter

2. Click the “Apply” button to apply the filter to your dataset.

Click “mass” in the “attributes” section and review the details of the “selected attribute”.

Notice that the 11 attribute values that were marked Missing have been set to the mean value of the distribution.

Weka Imputed Values

Weka Imputed Values


In this post you discovered how you can handle missing data in your machine learning dataset using Weka.

Specifically, you learned:

  • How to mark corrupt values as missing in your dataset.
  • How to remove instances with missing values from your dataset.
  • How to impute mean values for missing values in your dataset.

Do you have any questions about missing data or about this tutorial? Ask your questions in the comments below and I will do my best to answer.

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46 Responses to How To Handle Missing Values In Machine Learning Data With Weka

  1. Avatar
    Ramesh September 6, 2016 at 4:54 pm #

    I am to ask a question when the data having missing numeric values(blank) is subjected to classification say Multilayer Perceptron, what value is taken for calculation by the WEKA.

    • Avatar
      Jason Brownlee September 7, 2016 at 10:25 am #

      Hi Ramesh, you can pre-process your data to impute missing values with a mean or other constant value.

  2. Avatar
    Enrique Ortega October 18, 2016 at 8:16 am #

    Hi, thank you for your instructions. Now that I have removed the instances with a particular missing attribute value, I would like to train with the remaining data to predict the missing values I just removed, how do I do that?

    • Avatar
      Jason Brownlee October 19, 2016 at 9:06 am #

      Hi Enrique, my best advice would be to save a copy of your transformed dataset.

      You can then load it in the future and use it in your Exploration and Experiments.

  3. Avatar
    Shah January 18, 2017 at 8:18 am #

    hi sir, thanks for such a fruitful demo. I wanted to ask if we can use KNN imputation with Weka. Or any other imputation based on nearest neighbors

  4. Avatar
    santanu chatterjee February 3, 2017 at 10:03 pm #

    I want to predict an attribute which is present in training dataset but absent in test dataset. Even if it is present, I tried using that brand instances as Null or missing values. I am using randomforest and it gats wrapped in inputmapped classifier and although it executes but it predicts only ? marks(i.e,. Null).

    the dataset that I am using contains importer names,unit,currency,duty values,brand specs(in text,some in numeric or real). The value that I am trying to predict is a text(nominal). Most of the text data can be easily lablled as binary data type.

  5. Avatar
    Mohammed February 21, 2017 at 8:48 am #


    Please send me a notification whenever a new post or newsletter is added.


  6. Avatar
    UK Student March 6, 2017 at 7:36 am #

    Hi Jason,

    Nice article, however, I feel like you missed a good point of explaining which step on missing data should be taken and so I am a tad confused.

    At what point would I prefer to remove samples that contain missing information over the choice of Imputing them?

    The removal of samples also leads me to the question of what is the minimum threshold of samples that you should retain in your dataset for it to still be representative of the objective you are attempting to carry out?

    • Avatar
      Jason Brownlee March 6, 2017 at 11:01 am #

      We cannot know which method will be “best” for a given problem.

      Try multiple approaches systematically and select the approach that gives the best predictive models on your problem.

      The amount of data require is also dependent on the complexity of the problem.

      Sorry, no easy answers. Lots of experimentation and trial-and-error required in applied machine learning. Develop a robust test harness!

  7. Avatar
    ram gopal v March 25, 2017 at 11:18 pm #

    In weka tool when i click on tree under classification it is not showing J48 How do i add it ?

  8. Avatar
    MarcusS April 19, 2017 at 1:53 am #

    Hello, in case of nominal attribute, how could I remove missing instances (e.g. flagged with “?”)? I didn’t find a filter. Applying the “Remove with values” should be able but it didn’t work. Thank you.

    • Avatar
      Jason Brownlee April 19, 2017 at 7:54 am #

      Are you able to use the pandas functions demonstrated in the tutorial?

      I believe the type of the column should not matter for the dataframe functions used.

  9. Avatar
    Neo July 8, 2017 at 11:03 am #

    Hi Jason,

    I wanna ask about missing data. I know sometimes missing data are too important for us to completely remove them from analysis. For instance I have a data set that has 30% of he overall data missing. I am trying to do a time series prediction and data are missing consistently for Saturdasy and Sundays for 5 years. I am employing a Kalman smoothing method to fill in the spaces for those two days…

    Do you think this method may be relatively okay? or do you think I should remove the rows with missing values?

    • Avatar
      Jason Brownlee July 9, 2017 at 10:51 am #

      Try different methods and see what works best for your problem. It’s hard (intractable!) to say what will work best a priori.

      • Avatar
        Neo July 9, 2017 at 7:42 pm #

        could you please mention a few evaluation (if any) techniques to check how well my method of replacing missing data worked? How do I know which is the best method since there’s no way I could ever know what this missing data are.

        Thank you in advance.

        • Avatar
          Jason Brownlee July 11, 2017 at 10:16 am #

          Yes, focus on the predictive skill of models trained with the data on which you performed the imputation.

  10. Avatar
    Leonardo July 25, 2017 at 5:59 am #

    Hi Jason,

    Good article 🙂

    I have some doubts. I generate my model, im missing atributes i insert the symbol “?”

    Do you know how Weka works when the value of attributes missing is “?”

    Can you give-me one paper that talk about this?

    Best Regards

    • Avatar
      Jason Brownlee July 25, 2017 at 9:49 am #

      Does this tutorial work for you?

      • Avatar
        Leonardo July 26, 2017 at 9:10 am #

        I am so sorry Jason, my Technique is different …

        I do not want to fill in the values, I want to leave them blank …

        Do you know how the algorithm works when I do this?

        Thanks again 🙂

        • Avatar
          Leonardo July 28, 2017 at 10:13 am #

          Hello Jason 🙂

          I learn 🙂 …

          If you use MLP the missing values are ignored by setting the input value to zero.

          If you use SMOreg or Linear Regression the missing values are for mean/mode imputation.

  11. Avatar
    alex s October 10, 2017 at 3:34 am #

    hi jason i am doing prediction with naive bayes and i have a lot of missing values in my dataset ,for this moment i use replace missing values and then pre-process and predict is it mayby better if i delete the attributes with 95% of missing values?

    • Avatar
      Jason Brownlee October 10, 2017 at 7:50 am #

      I would recommend trying a suite of different approaches and see what works best for your specific data.

      • Avatar
        alex s October 10, 2017 at 10:12 am #

        i don’t quite understand what is the difference between handling the missing values the way you did in the article as opposed to only using the “replace missing values” filter ?

  12. Avatar
    bayan November 22, 2018 at 5:51 am #

    i am faced problem

    i don have a missing value but the sign (?) is appear when apply in weka

  13. Avatar
    harsha tumati February 9, 2019 at 7:52 pm #

    when we are trying apply unsupervised attribute replacemissingvalues filter in weka ,i am able to get filled up miising value as output

  14. Avatar
    Xamo February 25, 2019 at 12:54 pm #

    Hi, I have trouble in handling missing value.

    The problem is regression, not classification. Is there any way to use Machine Learning to handle missing values?

    I am stumped.

    Thank you

    • Avatar
      Jason Brownlee February 25, 2019 at 2:18 pm #

      Yes, you can use the mean value as a good starting point.

  15. Avatar
    Arnab March 6, 2019 at 6:32 am #

    Hi Jason. Informative. Thanks. I wanted to ask how does the default settings of Weka (without filters) handle missing values? Are training/testing examples 1) Case-wise excluded (Any example with any missing predictor excluded) 2) Imputed from mean/median of the available feature attributes?

    • Avatar
      Jason Brownlee March 6, 2019 at 8:01 am #

      It uses the data as is I believe, e.g. “missing” values are treated as values.

      • Avatar
        Arnab March 6, 2019 at 9:31 am #

        Sorry didnt quite get it. Appreciate more clarity on it. How can “missing” value be treated as value? It is “missing” as implied

        • Avatar
          Jason Brownlee March 6, 2019 at 2:45 pm #

          In some cases a missing value may be marked with a value, e.g. “none” or “nan”. A method like a decision tree can then make split decisions based on this value.

          If the data is actually missing, then the row or value may simply be ignored by the algorithm, although it depends on the algorithm.

  16. Avatar
    Victor June 3, 2019 at 1:45 am #


    Im trying to perform imputation to missing data (initially to test the process this missing data is generated by randomly removing data from attributes in a dataSet). I want to do this by using an ANN. So my question is, if I train the ANN in weka setting the class to the actual class, can then use this ANN to predict the value of the missing one by then setting the class of the instance in this missing attribute? I´m trying to do this but I get a “no input instance format defined” error.

    If the answer is no, then, Do I have to train the ANN for each missing attribute, setting the data class in this specific attribute to this that is going to be predicted and then using the instance as an input once the ANN (or any other classificator) is arreado trained. For me, this means that there is a need to perform one training (one machine, in fact) for each missing attribute.

    I think that what I’m asking is to perform regression, but I do not found how to do this in weka.

    • Avatar
      Jason Brownlee June 3, 2019 at 6:43 am #

      The model would be trained to predict the missing value not the class value. E.g. an imputation method.

      Yes, a model will be trained for each feature I believe.

      • Avatar
        Victor June 5, 2019 at 5:05 am #

        Thnks a lot. I have finally decided to train one “Method” for each attribute in a batch single process to later perform a quick imputation.

        Really appreciate your answer!

  17. Avatar
    stellamaris July 25, 2019 at 5:30 am #

    done it successfully

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