The Model Performance Mismatch Problem (and what to do about it)

What To Do If Model Test Results Are Worse than Training.

The procedure when evaluating machine learning models is to fit and evaluate them on training data, then verify that the model has good skill on a held-back test dataset.

Often, you will get a very promising performance when evaluating the model on the training dataset and poor performance when evaluating the model on the test set.

In this post, you will discover techniques and issues to consider when you encounter this common problem.

After reading this post, you will know:

  • The problem of model performance mismatch that may occur when evaluating machine learning algorithms.
  • The causes of overfitting, under-representative data samples, and stochastic algorithms.
  • Ways to harden your test harness to avoid the problem in the first place.

This post was based on a reader question; thanks! Keep the questions coming!

Let’s get started.

The Model Performance Mismatch Problem (and what to do about it)

The Model Performance Mismatch Problem (and what to do about it)
Photo by Arapaoa Moffat, some rights reserved.


This post is divided into 4 parts; they are:

  1. Model Evaluation
  2. Model Performance Mismatch
  3. Possible Causes and Remedies
  4. More Robust Test Harness

Model Evaluation

When developing a model for a predictive modeling problem, you need a test harness.

The test harness defines how the sample of data from the domain will be used to evaluate and compare candidate models for your predictive modeling problem.

There are many ways to structure a test harness, and no single best way for all projects.

One popular approach is to use a portion of data for fitting and tuning the model and a portion for providing an objective estimate of the skill of the tuned model on out-of-sample data.

The data sample is split into a training and test dataset. The model is evaluated on the training dataset using a resampling method such as k-fold cross-validation, and the set itself may be further divided into a validation dataset used to tune the hyperparameters of the model.

The test set is held back and used to evaluate and compare tuned models.

For more on training, validation, and test sets, see the post:

Model Performance Mismatch

The resampling method will give you an estimate of the skill of your model on unseen data by using the training dataset.

The test dataset provides a second data point and ideally an objective idea of how well the model is expected to perform, corroborating the estimated model skill.

What if the estimate of model skill on the training dataset does not match the skill of the model on the test dataset?

The scores will not match in general. We do expect some differences because some small overfitting of the training dataset is inevitable given hyperparameter tuning, making the training scores optimistic.

But what if the difference is worryingly large?

  • Which score do you trust?
  • Can you still compare models using the test dataset?
  • Is the model tuning process invalidated?

It is a challenging and very common situation in applied machine learning.

We can call this concern the “model performance mismatch” problem.

Note: ideas of “large differences” in model performance are relative to your chosen performance measures, datasets, and models. We cannot talk objectively about differences in general, only relative differences that you must interpret yourself.

Possible Causes and Remedies

There are many possible causes for the model performance mismatch problem.

Ultimately, your goal is to have a test harness that you know allows you to make good decisions regarding which model and model configuration to use as a final model.

In this section, we will look at some possible causes, diagnostics, and techniques you can use to investigate the problem.

Let’s look at three main areas: model overfitting, the quality of the data sample, and the stochastic nature of the learning algorithm.

1. Model Overfitting

Perhaps the most common cause is that you have overfit the training data.

You have hit upon a model, a set of model hyperparameters, a view of the data, or a combination of these elements and more that just so happens to give a good skill estimate on the training dataset.

The use of k-fold cross-validation will help to some degree. The use of tuning models with a separate dataset too will help. Nevertheless, it is possible to keep pushing and overfit on the training dataset.

If this is the case, the test skill may be more representative of the true skill of the chosen model and configuration.

One simple (but not easy) way to diagnose whether you have overfit the training dataset, is to get another data point on model skill. Evaluate the chosen model on another set of data. For example, some ideas to try include:

  • Try a k-fold cross-validation evaluation of the model on the test dataset.
  • Try a fit of the model on the training dataset and an evaluation on the test and a new data sample.

If you’re overfit, you have options.

  • Perhaps you can scrap your current training dataset and collect a new training dataset.
  • Perhaps you can re-split your sample into train/test in a softer approach to getting a new training dataset.

I would suggest that the results that you have obtained to-date are suspect and should be re-considered. Especially those where you may have spent too long tuning.

Overfitting may be the ultimate cause for the discrepancy in model scores, though it may not be the area to attack first.

2. Unrepresentative Data Sample

It is possible that your training or test datasets are an unrepresentative sample of data from the domain.

This means that the sample size is too small or the examples in the sample do not effectively “cover” the cases observed in the broader domain.

This can be obvious to spot if you see noisy model performance results. For example:

  • A large variance on cross-validation scores.
  • A large variance on similar model types on the test dataset.

In addition, you will see the discrepancy between train and test scores.

Another good second test is to check summary statistics for each variable on the train and test sets, and ideally on the cross-validation folds. You are looking for a large variance in sample means and standard deviation.

The remedy is often to get a larger and more representative sample of data from the domain. Alternately, to use more discriminating methods in preparing the data sample and splits. Think stratified k-fold cross validation, but applied to input variables in an attempt to maintain population means and standard deviations for real-valued variables in addition to the distribution of categorical variables.

Often when I see overfitting on a project, it is because the test harness is not as robust as it should be, not because of hill climbing the test dataset.

3. Stochastic Algorithm

It is possible that you are seeing a discrepancy in model scores because of the stochastic nature of the algorithm.

Many machine learning algorithms involve a stochastic component. For example, the random initial weights in a neural network, the shuffling of data and in turn the gradient updates in stochastic gradient descent, and much more.

This means, that each time the same algorithm is run on the same data, different sequences of random numbers are used and, in turn, a different model with different skill will result.

You can learn more about this in the post:

This issue can be seen by the variance in model skill scores from cross-validation, much like having an unrepresentative data sample.

The difference here is that the variance can be cleared up by repeating the model evaluation process, e.g. cross-validation, in order to control for the randomness in training the model.

This is often called the multiple repeats k-fold cross-validation and is used for neural networks and stochastic optimization algorithms, when resources permit.

I have more on this approach to evaluating models in the post:

More Robust Test Harness

A lot of these problems can be addressed early by designing a robust test harness and then gathering evidence to demonstrate that indeed your test harness is robust.

This might include running experiments before you get started evaluating models for real. Experiments such:

  • A sensitivity analysis of train/test splits.
  • A sensitivity analysis of k values for cross-validation.
  • A sensitivity analysis of a given model’s behavior.
  • A sensitivity analysis on the number of repeats.

On this last point, see the post:

You are looking for:

  • Low variance and consistent mean in evaluation scores between tests in a cross-validation.
  • Correlated population means between model scores on train and test sets.

Use statistical tools like standard error and significance tests if needed.

Use a modern and un-tuned model that performs well in general for such testing, such as random forest.

  • If you discover a difference in skill scores between training and test sets, and it is consistent, that may be fine. You know what to expect.
  • If you measure a variance in mean skill scores within a given test, you have error bars you can use to interpret the results.

I would go so far as to say that without a robust test harness, the results you achieve will be a mess. You will not be able to effectively interpret them. There will be an element of risk (or fraud, if you’re an academic) in the presentation of the outcomes from a fragile test harness. And reproducibility/robustness is a massive problem in numerical fields like applied machine learning.

Finally, avoid using the test dataset too much. Once you have strong evidence that your harness is robust, do not touch the test dataset until it comes time for final model selection.

Further Reading

This section provides more resources on the topic if you are looking to go deeper.


In this post, you discovered the model performance mismatch problem where model performance differs greatly between training and test sets, and techniques to diagnose and address the issue.

Specifically, you learned:

  • The problem of model performance mismatch that may occur when evaluating machine learning algorithms.
  • The causes of overfitting, under-representative data samples, and stochastic algorithms.
  • Ways to harden your test harness to avoid the problem in the first place.

Do you have any questions?
Ask your questions in the comments below and I will do my best to answer.

19 Responses to The Model Performance Mismatch Problem (and what to do about it)

  1. Raj April 20, 2018 at 3:56 am #

    Thanks again for the nice post! I learn new things whenever I read your blogs.

    I have basic question here – Is there a way to check 100% coverage of training data before stratified k-fold cross validation? 100% coverage means training sample/data that will have all possible combinations/data/values of features to be considered for model, or is it something domain expert should confirm?

    • Jason Brownlee April 20, 2018 at 6:01 am #

      Normally we do not seek 100% coverage, instead we seek a statistically representative sample.

      We can explore whether we achieve this using summary statistics.

  2. Phuong Ho April 21, 2018 at 9:41 am #

    Thanks for the nice post. Can I have a question please:

    I am developing my model prediction using both plsr package (partial least square) and h2o package (deep machine learning). From the original data set, I split 80% for model training through 10-fold CV and retain 20% for testing. I repeat this 10 time (i.e. outer loop CV) and each time the data is shuffled before split into training (80%) and testing (20%). My observation is that the Rcv reported by the pls model is always higher than that of machine learning. However, on the outer loop, when I use the best model obtained during cross validation to predict the test data, the thing is opposite: the r-squared of machine learning is better than that of pls for all 10 repeats. Can I conclude that the CV of pls possibly overfits the data?

    Thanks, Phuong

    • Jason Brownlee April 22, 2018 at 5:56 am #

      I would change one thing.

      Discard all models trained during cross validation, then train a model on all training data and evaluate it on the hold out test set.

  3. Sajan May 20, 2019 at 7:43 pm #

    Hey Jason,

    I made a model with some 15 features and when made their dummies as their many features with categorical variables after which my model before training took input of around 680 features,

    When I tested on a few new data points to predict the rate from my model it showed an error of
    “Number of features of the model must match the input. Model n_features is 680 and input n_features is 41”

    What should I do in this situation?

    Before I tried managing my variables with one hot encoding, I got the result but they were absurd as they manage variables and number them alphabetically.

    Can you suggest me a way out of it?

    • Jason Brownlee May 21, 2019 at 6:35 am #

      The input to the model at inference time must undergo the same preparation as the training data.

  4. Hani Berkovich June 12, 2019 at 9:41 pm #

    Hi Jason,
    I developed nlp classification model,
    But I found issue:
    First of all I run the training process on all data and got model and probabilities per object,
    after that I took one object from base data and execute the model on it,
    I expected to get the same probabilities outputs but there are difference,
    Note –
    That for each run I got the same results every time,
    The difference is between training and useing with model,
    Thanks in advance 🙂

  5. Hani Berkovich June 13, 2019 at 4:35 pm #

    Thank you for your response,
    If the model is overfitting, Is it can to be that we will get other probabilities for same data?

  6. Hani Berkovich June 18, 2019 at 4:25 am #

    Thank you again,
    I mean to ask , that in case that my model is overfitting, One of symptom is the situation what I described, that I got other probabilities for same data
    When I build model and when I am using with this?

    • Jason Brownlee June 18, 2019 at 6:42 am #

      Sorry, I don’t follow, can you elaborate please?

  7. Hani Berkovich June 18, 2019 at 4:35 am #

    Note- that the data is same ,nothing change it

  8. Hani Berkovich June 23, 2019 at 10:00 pm #

    Hi Jason,
    Thank you a lot that you try to help,
    I explain you again my issue:
    I developed NLP ML algorithim and got strange situation :
    I build model with all data,
    Then take one of records (the data wasnt changed) and run the model on it, and got different results,
    Can you know something about this situation?
    Have you ever encountered such a thing?
    Thank you!!

    • Jason Brownlee June 24, 2019 at 6:29 am #

      What do you mean you took one record and ran the model on it?

      Retrained the model?
      Made a prediction?

  9. Hani Berkovich June 24, 2019 at 4:59 pm #

    Made a prediction,for test the model
    Thank you

  10. Amy August 5, 2019 at 10:50 am #

    Hi Jason,

    I would really appreciate if you can provide some insights on out of time validations.

    I have built a model to predict the users that will make a purchase in future using the historical data. My training and test data have the same time period and i want to make predictions for the future time. I am getting an accuracy of around 80 percent on test data but the real time performance is really poor i.e. around 50 percent.

    My intuition says that train, validation and test data should have different time period to get the good predictions.

    • Jason Brownlee August 5, 2019 at 2:02 pm #

      Perhaps use the models to make a forecast on out of sample data where the real values are available or can be acquired.

      Then compare each to see what type of errors the model is making.

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