Chapter 15 Stacked Models

In the previous chapters, you’ve learned how to train individual learners, which in the context of this chapter will be referred to as base learners. Stacking (sometimes called “stacked generalization”) involves training a new learning algorithm to combine the predictions of several base learners. First, the base learners are trained using the available training data, then a combiner or meta algorithm, called the super learner, is trained to make a final prediction based on the predictions of the base learners. Such stacked ensembles tend to outperform any of the individual base learners (e.g., a single RF or GBM) and have been shown to represent an asymptotically optimal system for learning (Laan, Polley, and Hubbard 2003).

15.1 Prerequisites

This chapter leverages the following packages, with the emphasis on h2o:

# Helper packages
library(rsample)   # for creating our train-test splits
library(recipes)   # for minor feature engineering tasks

# Modeling packages
library(h2o)       # for fitting stacked models

To illustrate key concepts we continue with the Ames housing example from previous chapters:

# Load and split the Ames housing data
ames <- AmesHousing::make_ames()
set.seed(123)  # for reproducibility
split <- initial_split(ames, strata = "Sale_Price")
ames_train <- training(split)
ames_test <- testing(split)

# Make sure we have consistent categorical levels
blueprint <- recipe(Sale_Price ~ ., data = ames_train) %>%
  step_other(all_nominal(), threshold = 0.005)

# Create training & test sets for h2o
train_h2o <- prep(blueprint, training = ames_train, retain = TRUE) %>%
  juice() %>%
test_h2o <- prep(blueprint, training = ames_train) %>%
  bake(new_data = ames_test) %>%

# Get response and feature names
Y <- "Sale_Price"
X <- setdiff(names(ames_train), Y)

15.2 The Idea

Leo Breiman, known for his work on classification and regression trees and random forests, formalized stacking in his 1996 paper on Stacked Regressions (Breiman 1996b). Although the idea originated in (Wolpert 1992) under the name “Stacked Generalizations”, the modern form of stacking that uses internal k-fold CV was Breiman’s contribution.

However, it wasn’t until 2007 that the theoretical background for stacking was developed, and also when the algorithm took on the cooler name, Super Learner (Van der Laan, Polley, and Hubbard 2007). Moreover, the authors illustrated that super learners will learn an optimal combination of the base learner predictions and will typically perform as well as or better than any of the individual models that make up the stacked ensemble. Until this time, the mathematical reasons for why stacking worked were unknown and stacking was considered a black art.

15.2.1 Common ensemble methods

Ensemble machine learning methods use multiple learning algorithms to obtain better predictive performance than could be obtained from any of the constituent learning algorithms. The idea of combining multiple models rather than selecting the single best is well-known and has been around for a long time. In fact, many of the popular modern machine learning algorithms (including ones in previous chapters) are actually ensemble methods.

For example, bagging (Chapter 10) and random forests (Chapter 11) are ensemble approaches that average the predictions from many decision trees to reduce prediction variance and are robust to outliers and noisy data; ultimately leading to greater predictive accuracy. Boosted decision trees (Chapter 12) are another ensemble approach that slowly learns unique patterns in the data by sequentially combining individual, shallow trees.

Stacking, on the other hand, is designed to ensemble a diverse group of strong learners.

15.2.2 Super learner algorithm

The super learner algorithm consists of three phases:

  1. Set up the ensemble
    • Specify a list of \(L\) base learners (with a specific set of model parameters).
    • Specify a meta learning algorithm. This can be any one of the algorithms discussed in the previous chapters but most often is some form of regularized regression.
  2. Train the ensemble
    • Train each of the \(L\) base learners on the training set.
    • Perform k-fold CV on each of the base learners and collect the cross-validated predictions from each (the same k-folds must be used for each base learner). These predicted values represent \(p_1, \dots, p_L\) in Eq. (15.1).
    • The \(N\) cross-validated predicted values from each of the \(L\) algorithms can be combined to form a new \(N \times L\) feature matrix (represented by \(Z\) in Eq. (15.1). This matrix, along with the original response vector (\(y\)), are called the “level-one” data. (\(N =\) number of rows in the training set.)
    \[\begin{equation} \tag{15.1} n \Bigg \{ \Bigg [ p_1 \Bigg ] \cdots \Bigg [ p_L \Bigg ] \Bigg [ y \Bigg ] \rightarrow n \Bigg \{ \overbrace{\Bigg [ \quad Z \quad \Bigg ]}^L \Bigg [ y \Bigg ] \end{equation}\]
    • Train the meta learning algorithm on the level-one data (\(y = f\left(Z\right)\)). The “ensemble model” consists of the \(L\) base learning models and the meta learning model, which can then be used to generate predictions on new data.
  3. Predict on new data.
    • To generate ensemble predictions, first generate predictions from the base learners.
    • Feed those predictions into the meta learner to generate the ensemble prediction.

Stacking never does worse than selecting the single best base learner on the training data (but not necessarily the validation or test data). The biggest gains are usually produced when stacking base learners that have high variability, and uncorrelated, predicted values. The more similar the predicted values are between the base learners, the less advantage there is to combining them.

15.2.3 Available packages

There are a few package implementations for model stacking in the R ecosystem. SuperLearner (Polley et al. 2019) provides the original Super Learner and includes a clean interface to 30+ algorithms. Package subsemble (LeDell et al. 2014) also provides stacking via the super learner algorithm discussed above; however, it also offers improved parallelization over the SuperLearner package and implements the subsemble algorithm (Sapp, Laan, and Canny 2014).42 Unfortunately, subsemble is currently only available via GitHub and is primarily maintained for backward compatibility rather than forward development. A third package, caretEnsemble (Deane-Mayer and Knowles 2016), also provides an approach for stacking, but it implements a bootsrapped (rather than cross-validated) version of stacking. The bootstrapped version will train faster since bootsrapping (with a train/test set) requires a fraction of the work of k-fold CV; however, the the ensemble performance often suffers as a result of this shortcut.

This chapter focuses on the use of h2o for model stacking. h2o provides an efficient implementation of stacking and allows you to stack existing base learners, stack a grid search, and also implements an automated machine learning search with stacked results. All three approaches will be discussed.

15.3 Stacking existing models

The first approach to stacking is to train individual base learner models separately and then stack them together. For example, say we found the optimal hyperparameters that provided the best predictive accuracy for the following algorithms:

  1. Regularized regression base learner.
  2. Random forest base learner.
  3. GBM base learner.
  4. XGBoost base learner.

We can train each of these models individually (see the code chunk below). However, to stack them later we need to do a few specific things:

  1. All models must be trained on the same training set.
  2. All models must be trained with the same number of CV folds.
  3. All models must use the same fold assignment to ensure the same observations are used (we can do this by using fold_assignment = "Modulo").
  4. The cross-validated predictions from all of the models must be preserved by setting keep_cross_validation_predictions = TRUE. This is the data which is used to train the meta learner algorithm in the ensemble.
# Train & cross-validate a GLM model
best_glm <- h2o.glm(
  x = X, y = Y, training_frame = train_h2o, alpha = 0.1,
  remove_collinear_columns = TRUE, nfolds = 10, fold_assignment = "Modulo",
  keep_cross_validation_predictions = TRUE, seed = 123

# Train & cross-validate a RF model
best_rf <- h2o.randomForest(
  x = X, y = Y, training_frame = train_h2o, ntrees = 1000, mtries = 20,
  max_depth = 30, min_rows = 1, sample_rate = 0.8, nfolds = 10,
  fold_assignment = "Modulo", keep_cross_validation_predictions = TRUE,
  seed = 123, stopping_rounds = 50, stopping_metric = "RMSE",
  stopping_tolerance = 0

# Train & cross-validate a GBM model
best_gbm <- h2o.gbm(
  x = X, y = Y, training_frame = train_h2o, ntrees = 5000, learn_rate = 0.01,
  max_depth = 7, min_rows = 5, sample_rate = 0.8, nfolds = 10,
  fold_assignment = "Modulo", keep_cross_validation_predictions = TRUE,
  seed = 123, stopping_rounds = 50, stopping_metric = "RMSE",
  stopping_tolerance = 0

# Train & cross-validate an XGBoost model
best_xgb <- h2o.xgboost(
  x = X, y = Y, training_frame = train_h2o, ntrees = 5000, learn_rate = 0.05,
  max_depth = 3, min_rows = 3, sample_rate = 0.8, categorical_encoding = "Enum",
  nfolds = 10, fold_assignment = "Modulo", 
  keep_cross_validation_predictions = TRUE, seed = 123, stopping_rounds = 50,
  stopping_metric = "RMSE", stopping_tolerance = 0

We can now use h2o.stackedEnsemble() to stack these models. Note how we feed the base learner models into the base_models = list() argument. Here, we apply a random forest model as the metalearning algorithm. However, you could also apply regularized regression, GBM, or a neural network as the metalearner (see ?h2o.stackedEnsemble for details).

# Train a stacked tree ensemble
ensemble_tree <- h2o.stackedEnsemble(
  x = X, y = Y, training_frame = train_h2o, model_id = "my_tree_ensemble",
  base_models = list(best_glm, best_rf, best_gbm, best_xgb),
  metalearner_algorithm = "drf"

Since our ensemble is built on the CV results of the base learners, but has no cross-validation results of its own, we’ll use the test data to compare our results. If we assess the performance of our base learners on the test data we see that the stochastic GBM base learner has the lowest RMSE of 20859.92. The stacked model achieves a small 1% performance gain with an RMSE of 20664.56.

# Get results from base learners
get_rmse <- function(model) {
  results <- h2o.performance(model, newdata = test_h2o)
list(best_glm, best_rf, best_gbm, best_xgb) %>%
## [1] 30024.67 23075.24 20859.92 21391.20

# Stacked results
h2o.performance(ensemble_tree, newdata = test_h2o)@metrics$RMSE
## [1] 20664.56

We previously stated that the biggest gains are usually produced when we are stacking base learners that have high variability, and uncorrelated, predicted values. If we assess the correlation of the CV predictions we can see strong correlation across the base learners, especially with three tree-based learners. Consequentley, stacking provides less advantage in this situation since the base learners have highly correlated predictions; however, a 1% performance improvement can still be considerable improvement depending on the business context.

  GLM_pred = as.vector(h2o.getFrame(best_glm@model$cross_validation_holdout_predictions_frame_id$name)),
  RF_pred = as.vector(h2o.getFrame(best_rf@model$cross_validation_holdout_predictions_frame_id$name)),
  GBM_pred = as.vector(h2o.getFrame(best_gbm@model$cross_validation_holdout_predictions_frame_id$name)),
  XGB_pred = as.vector(h2o.getFrame(best_xgb@model$cross_validation_holdout_predictions_frame_id$name))
) %>% cor()
##           GLM_pred   RF_pred  GBM_pred  XGB_pred
## GLM_pred 1.0000000 0.9390229 0.9291982 0.9345048
## RF_pred  0.9390229 1.0000000 0.9920349 0.9821944
## GBM_pred 0.9291982 0.9920349 1.0000000 0.9854160
## XGB_pred 0.9345048 0.9821944 0.9854160 1.0000000

15.5 Automated machine learning

Our final topic to discuss involves performing an automated search across multiple base learners and then stack the resulting models (this is sometimes referred to as automated machine learning or AutoML). This is very much like the grid searches that we have been performing for base learners and discussed in Chapters 4-14; however, rather than search across a variety of parameters for a single base learner, we want to perform a search across a variety of hyperparameter settings for many different base learners.

There are several competitors that provide licensed software that help automate the end-to-end machine learning process to include feature engineering, model validation procedures, model selection, hyperparameter optimization, and more. Open source applications are more limited and tend to focus on automating the model building, hyperparameter configurations, and comparison of model performance.

Although AutoML has made it easy for non-experts to experiment with machine learning, there is still a significant amount of knowledge and background in data science that is required to produce high-performing machine learning models. AutoML is more about freeing up your time (which is quite valuable). The machine learning process is often long, iterative, and repetitive and AutoML can also be a helpful tool for the advanced user, by simplifying the process of performing a large number of modeling-related tasks that would typically require hours/days writing many lines of code. This can free up the user’s time to focus on other tasks in the data science pipeline such as data-preprocessing, feature engineering, model interpretability, and model deployment.

h2o provides an open source implementation of AutoML with the h2o.automl() function. The current version of h2o.automl() trains and cross-validates a random forest, an extremely-randomized forest, a random grid of GBMs, a random grid of DNNs, and then trains a stacked ensemble using all of the models; see ?h2o::h2o.automl for details.

By default, h2o.automl() will search for 1 hour but you can control how long it searches by adjusting a variety of stopping arguments (e.g., max_runtime_secs, max_models, and stopping_tolerance).

The following performs an automated search for two hours, which ended up assessing 80 models. h2o.automl() will automatically use the same folds for stacking so you do not need to specify fold_assignment = "Modulo". This allows for consistent model comparison across the same CV sets. We see that most of the leading models are GBM variants and achieve an RMSE in the 22000–23000 range. As you probably noticed, this was not as good as some of our best models we found using our own GBM grid searches (reference Chapter 12). However, we could start this AutoML procedure and then spend our two hours performing other tasks while h2o automatically assesses these 80 models. The AutoML procedure then provides us direction for further analysis. In this case, we could start by further assessing the hyperparameter settings in the top five GBM models to see if there were common attributes that could point us to additional grid searches worth exploring.

# Use AutoML to find a list of candidate models (i.e., leaderboard)
auto_ml <- h2o.automl(
  x = X, y = Y, training_frame = train_h2o, nfolds = 5, 
  max_runtime_secs = 60 * 120, max_models = 50,
  keep_cross_validation_predictions = TRUE, sort_metric = "RMSE", seed = 123,
  stopping_rounds = 50, stopping_metric = "RMSE", stopping_tolerance = 0

# Assess the leader board; the following truncates the results to show the top 
# and bottom 15 models. You can get the top model with auto_ml@leader
auto_ml@leaderboard %>% %>%
  dplyr::select(model_id, rmse) %>%
##                                               model_id   rmse
## 1                     XGBoost_1_AutoML_20190220_084553   22229.97
## 2            GBM_grid_1_AutoML_20190220_084553_model_1   22437.26
## 3            GBM_grid_1_AutoML_20190220_084553_model_3   22777.57
## 4                         GBM_2_AutoML_20190220_084553   22785.60
## 5                         GBM_3_AutoML_20190220_084553   23133.59
## 6                         GBM_4_AutoML_20190220_084553   23185.45
## 7                     XGBoost_2_AutoML_20190220_084553   23199.68
## 8                     XGBoost_1_AutoML_20190220_075753   23231.28
## 9                         GBM_1_AutoML_20190220_084553   23326.57
## 10           GBM_grid_1_AutoML_20190220_075753_model_2   23330.42
## 11                    XGBoost_3_AutoML_20190220_084553   23475.23
## 12       XGBoost_grid_1_AutoML_20190220_084553_model_3   23550.04
## 13      XGBoost_grid_1_AutoML_20190220_075753_model_15   23640.95
## 14       XGBoost_grid_1_AutoML_20190220_084553_model_8   23646.66
## 15       XGBoost_grid_1_AutoML_20190220_084553_model_6   23682.37
## ...                                                ...        ...
## 65           GBM_grid_1_AutoML_20190220_084553_model_5   33971.32
## 66           GBM_grid_1_AutoML_20190220_075753_model_8   34489.39
## 67  DeepLearning_grid_1_AutoML_20190220_084553_model_3   36591.73
## 68           GBM_grid_1_AutoML_20190220_075753_model_6   36667.56
## 69      XGBoost_grid_1_AutoML_20190220_084553_model_13   40416.32
## 70           GBM_grid_1_AutoML_20190220_075753_model_9   47744.43
## 71    StackedEnsemble_AllModels_AutoML_20190220_084553   49856.66
## 72    StackedEnsemble_AllModels_AutoML_20190220_075753   59127.09
## 73 StackedEnsemble_BestOfFamily_AutoML_20190220_084553   76714.90
## 74 StackedEnsemble_BestOfFamily_AutoML_20190220_075753   76748.40
## 75           GBM_grid_1_AutoML_20190220_075753_model_5   78465.26
## 76           GBM_grid_1_AutoML_20190220_075753_model_3   78535.34
## 77           GLM_grid_1_AutoML_20190220_075753_model_1   80284.34
## 78           GLM_grid_1_AutoML_20190220_084553_model_1   80284.34
## 79       XGBoost_grid_1_AutoML_20190220_075753_model_4   92559.44
## 80      XGBoost_grid_1_AutoML_20190220_075753_model_10  125384.88


Breiman, Leo. 1996b. “Stacked Regressions.” Machine Learning 24 (1). Springer: 49–64.

Deane-Mayer, Zachary A., and Jared E. Knowles. 2016. CaretEnsemble: Ensembles of Caret Models.

Laan, Mark J. van der, Eric C. Polley, and Alan E. Hubbard. 2003. “Super Learner.” Statistical Applications in Genetics and Molecular Biology 6 (1).

LeDell, Erin, Stephanie Sapp, Mark van der Laan, and Maintainer Erin LeDell. 2014. Package “Subsemble”.

Polley, Eric, Erin LeDell, Chris Kennedy, and Mark van der Laan. 2019. SuperLearner: Super Learner Prediction.

Sapp, Stephanie, Mark J van der Laan, and John Canny. 2014. “Subsemble: An Ensemble Method for Combining Subset-Specific Algorithm Fits.” Journal of Applied Statistics 41 (6). Taylor & Francis: 1247–59.

Van der Laan, Mark J, Eric C Polley, and Alan E Hubbard. 2007. “Super Learner.” Statistical Applications in Genetics and Molecular Biology 6 (1). De Gruyter.

Wolpert, David H. 1992. “Stacked Generalization.” Neural Networks 5: 241–59.

  1. The subsemble algorithm is a general subset ensemble prediction method, which can be used for small, moderate, or large data sets. Subsemble partitions the full data set into subsets of observations, fits a specified underlying algorithm on each subset, and uses a unique form of k-fold CV to output a prediction function that combines the subset-specific fits.