A Brief Introduction to caretEnsemble

Zach Deane-Mayer

2024-09-12

caretEnsemble is a package for making ensembles of caret models. You should already be somewhat familiar with the caret package before trying out caretEnsemble.

caretEnsemble has 3 primary functions: caretList, caretEnsemble and caretStack. caretList is used to build lists of caret models on the same training data, with the same re-sampling parameters. caretEnsemble and caretStack are used to create ensemble models from such lists of caret models. caretEnsemble uses a glm to create a simple linear blend of models and caretStack uses a caret model to combine the outputs from several component caret models.

caretList

caretList is a flexible function for fitting many different caret models, with the same resampling parameters, to the same dataset. It returns a convenient list of caret objects which can later be passed to caretEnsemble and caretStack. caretList has almost exactly the same arguments as train (from the caret package), with the exception that the trControl argument comes last. It can handle both the formula interface and the explicit x, y interface to train. As in caret, the formula interface introduces some overhead and the x, y interface is preferred.

caretEnsemble has 2 arguments that can be used to specify which models to fit: methodList and tuneList. methodList is a simple character vector of methods that will be fit with the default train parameters, while tuneList can be used to customize the call to each component model and will be discussed in more detail later. First, lets build an example dataset (adapted from the caret vignette):

data(Sonar, package = "mlbench")
set.seed(107L)
inTrain <- caret::createDataPartition(y = Sonar$Class, p = 0.75, list = FALSE)
training <- Sonar[inTrain, ]
testing <- Sonar[-inTrain, ]

model_list <- caretEnsemble::caretList(
  Class ~ .,
  data = training,
  methodList = c("glmnet", "rpart")
)
print(summary(model_list))
#> The following models were ensembled: glmnet, rpart  
#> 
#> Model accuracy:
#>    model_name metric     value         sd
#>        <char> <char>     <num>      <num>
#> 1:     glmnet    ROC 0.8599370 0.09069233
#> 2:      rpart    ROC 0.7495693 0.10710959

(As with train, the formula interface is convenient but introduces move overhead. For large datasets the explicitly passing x and y is preferred). We can use the predict function to extract predictions from this object for new data:

p <- predict(model_list, newdata = head(testing))
knitr::kable(p, format = "markdown")

glmnet	rpart
0.9398307	0.1250000
0.1428399	0.1250000
0.2041884	0.8181818
0.5180661	0.8181818
0.5951758	0.8181818
0.5055788	0.8181818

If you desire more control over the model fit, use the caretModelSpec to construct a list of model specifications for the tuneList argument. This argument can be used to fit several different variants of the same model, and can also be used to pass arguments through train down to the component functions (e.g. trace=FALSE for nnet):

model_list_big <- caretEnsemble::caretList(
  Class ~ .,
  data = training,
  methodList = c("glmnet", "rpart"),
  tuneList = list(
    rf1 = caretEnsemble::caretModelSpec(method = "rf", tuneGrid = data.frame(.mtry = 2L)),
    rf2 = caretEnsemble::caretModelSpec(method = "rf", tuneGrid = data.frame(.mtry = 10L), preProcess = "pca"),
    nn = caretEnsemble::caretModelSpec(method = "nnet", tuneLength = 2L, trace = FALSE)
  )
)
print(summary(model_list_big))
#> The following models were ensembled: rf1, rf2, nn, glmnet, rpart  
#> 
#> Model accuracy:
#>    model_name metric     value         sd
#>        <char> <char>     <num>      <num>
#> 1:         rf    ROC 0.9233333 0.03092727
#> 2:         rf    ROC 0.8573319 0.06415653
#> 3:       nnet    ROC 0.8746849 0.04153548
#> 4:     glmnet    ROC 0.8589216 0.03577354
#> 5:      rpart    ROC 0.7144048 0.12164189

Finally, you should note that caretList does not support custom caret models. Fitting those models are beyond the scope of this vignette, but if you do so, you can manually add them to the model list (e.g. model_list_big[["my_custom_model"]] <- my_custom_model). Just be sure to use the same re-sampling indexes in trControl as you use in the caretList models!

caretEnsemble

caretList is the preferred way to construct list of caret models in this package, as it will ensure the resampling indexes are identical across all models. Lets take a closer look at our list of models:

lattice::xyplot(caret::resamples(model_list))

As you can see from this plot, these 2 models are uncorrelated, and the rpart model is occasionally anti-predictive, with a one re-sample showing AUC of 0.46.

We can confirm the 2 model”s correlation with the modelCor function from caret (caret has a lot of convenient functions for analyzing lists of models):

caret::modelCor(caret::resamples(model_list))
#>           glmnet     rpart
#> glmnet 1.0000000 0.5172171
#> rpart  0.5172171 1.0000000

These 2 models make a good candidate for an ensemble: their predictions are fairly uncorrelated, but their overall accuracy is similar. We do a simple, linear greedy optimization on AUC using caretEnsemble:

greedy_ensemble <- caretEnsemble::caretEnsemble(model_list)
print(summary(greedy_ensemble))
#> The following models were ensembled: glmnet, rpart  
#> 
#> Model Importance:
#> glmnet_M glmnet_R  rpart_M  rpart_R 
#>   0.3533   0.3942   0.1271   0.1254 
#> 
#> Model accuracy:
#>    model_name metric     value         sd
#>        <char> <char>     <num>      <num>
#> 1:   ensemble    ROC 0.8788866 0.05319158
#> 2:     glmnet    ROC 0.8599370 0.09069233
#> 3:      rpart    ROC 0.7495693 0.10710959

model_preds <- predict(model_list, newdata = testing, excluded_class_id = 2L)
ens_preds <- predict(greedy_ensemble, newdata = testing, excluded_class_id = 2L)
model_preds$ensemble <- ens_preds
auc <- caTools::colAUC(model_preds, testing$Class)
print(auc)
#>            glmnet     rpart  ensemble
#> M vs. R 0.8472222 0.7746914 0.8657407

The ensemble has an AUC on the training set resamples of 0.87 which is about 1.9% better than the best individual model.

Note that the levels for the Sonar Data are “M” and “R”, where M is level 1 and R is level 2. “M” stands for “metal cylinder” and “R” stands for rock. M is the positive class, so we exclude class 2L from our predictions. You can set excluded_class_id = 0L

p <- predict(greedy_ensemble, newdata = head(testing), excluded_class_id = 0L)
knitr::kable(p, format = "markdown")

M	R
0.2801736	0.7198264
0.8619769	0.1380231
0.6300334	0.3699666
0.4009026	0.5990974
0.3446125	0.6553875
0.4100184	0.5899816

We can also use varImp to extract the variable importances from each member of the ensemble, as well as the final ensemble model:

round(caret::varImp(greedy_ensemble), 4L)
#> glmnet_M glmnet_R  rpart_M  rpart_R 
#>   0.3331   0.3802   0.1441   0.1426

caretStack

glm_ensemble <- caretEnsemble::caretStack(model_list, method = "glm")
model_preds2 <- model_preds
model_preds2$ensemble <- predict(glm_ensemble, newdata = testing, excluded_class_id = 2L)
print(caTools::colAUC(model_preds2, testing$Class))
#>            glmnet     rpart ensemble
#> M vs. R 0.8472222 0.7746914 0.867284
CF <- coef(glm_ensemble$ens_model$finalModel)[-1L]
print(CF / sum(CF))
#>    glmnet     rpart 
#> 0.7154119 0.2845881

Note that glm_ensemble$ens_model is a regular caret object of class train. The glm-weighted model weights (glm vs rpart) and test-set AUCs are extremely similar to the caretEnsemble greedy optimization.

We can also use more sophisticated ensembles than simple linear weights, but these models are much more susceptible to over-fitting, and generally require large sets of resamples to train on (n=50 or higher for bootstrap samples). Lets try one anyways:

gbm_ensemble <- caretEnsemble::caretStack(
  model_list,
  method = "gbm",
  verbose = FALSE,
  tuneLength = 5L
)
model_preds3 <- model_preds
model_preds3$ensemble <- predict(gbm_ensemble, newdata = testing, excluded_class_id = 2L)
caTools::colAUC(model_preds3, testing$Class)
#>            glmnet     rpart  ensemble
#> M vs. R 0.8472222 0.7746914 0.8657407

In this case, the sophisticated ensemble is no better than a simple weighted linear combination. Non-linear ensembles seem to work best when you have:

1. Lots of data.
2. Lots of models with similar accuracy.
3. Your models are uncorrelated: each one seems to capture a different aspect of the data, and different models perform best on different subsets of the data.