# Chapter 4 Ensemble Machine Learning

Rachael Phillips

Based on the sl3 R package by Jeremy Coyle, Nima Hejazi, Ivana Malenica, and Oleg Sofrygin.

Updated: 2020-01-17

## 4.1 Learning Objectives

By the end of this chapter you will be able to:

1. Select a loss function that is appropriate for the functional parameter to be estimated.
2. Assemble an ensemble of learners based on the properties that identify what features they support.
3. Customize learner hyperparameters to incorporate a diversity of different settings.
4. Select a subset of available covariates and pass only those variables to the modeling algorithm.
5. Fit an ensemble with nested cross-validation to obtain an estimate of the performance of the ensemble itself.
6. Obtain sl3 variable importance metrics.
7. Interpret the discrete and continuous super learner fits.
8. Rationalize the need to remove bias from the super learner to make an optimal bias–variance tradeoff for the parameter of interest.

## 4.2 Introduction

In Chapter 1, we introduced the road map for targeted learning as a general template to translate real-world data applications into formal statistical estimation problems. The first steps of this roadmap define the statistical estimation problem, which establish

1. Data as a realization of a random variable, or equivalently, an outcome of a particular experiment.
2. A statistical model, representing the true knowledge about the data-generating experiment.
3. A translation of the scientific question, which is often causal, into a target parameter.

Note that if the target parameter is causal, step 3 also requires establishing identifiability of the target quantity from the observed data distribution, under possible non-testable assumptions that may not necessarily be reasonable. Still, the target quantity does have a valid statistical interpretation. See causal target parameters for more detail on causal models and identifiability.

Now that we have defined the statistical estimation problem, we are ready to construct the TMLE; an asymptotically linear and efficient substitution estimator of this target quantity. The first step in this estimation procedure is an initial estimate of the data-generating distribution, or the relevant part of this distribution that is needed to evaluate the target parameter. For this initial estimation, we use the Super Learner (van der Laan, Polley, and Hubbard 2007). The super learner provides an important step in creating a robust estimator. It is a loss-function-based tool that uses cross-validation to obtain the best prediction of our target parameter, based on a weighted average of a library of machine learning algorithms. This library of machine learning algorithms consists of functions (“learners” in the sl3 nomenclature) that we think might be consistent with the true data-generating distribution. The ensembling of algorithms with weights (“metalearning” in the sl3 nomenclature) has been shown to be adaptive and robust, even in small samples (Polley and van der Laan 2010). The Super Learner has been proven to be asymptotically as accurate as the best possible prediction algorithm in the library (van der Laan and Dudoit 2003; van der Vaart, Dudoit, and van der Laan 2006).

### 4.2.1 Background

A loss function $$L$$ is defined as a function of the observed data and a candidate parameter value $$\psi$$, which has unknown true value $$\psi_0$$, $$L(\psi)(O)$$. We can estimate the loss by substituting the empirical distribution $$P_n$$ for the true (but unknown) distribution of the observed data $$P_0$$. A valid loss function will have expectation (risk) that is minimized at the true value of the parameter $$\psi_0$$. For example, the conditional mean minimizes the risk of the squared error loss. Thus, it is a valid loss function when estimating the conditional mean.

The discrete super learner, or cross-validation selector, is the algorithm in the library that minimizes the cross-validated empirical risk. The cross-validated empirical risk of an algorithm is defined as the empirical mean over a validation sample of the loss of the algorithm fitted on the training sample, averaged across the splits of the data.

The continuous/ensemble super learner is a weighted average of the library of algorithms, where the weights are chosen to minimize the cross-validated empirical risk of the library. Restricting the weights to be positive and sum to one (i.e., a convex combination) has been shown to improve upon the discrete super learner (Polley and van der Laan 2010; van der Laan, Polley, and Hubbard 2007). This notion of weighted combinations was introduced in Wolpert (1992) for neural networks and adapted for regressions in Breiman (1996).

For more detail on super learner we refer the reader to van der Laan, Polley, and Hubbard (2007) and Polley and van der Laan (2010). The optimality results for the cross-validation selector among a family of algorithms were established in van der Laan and Dudoit (2003) and extended in van der Vaart, Dudoit, and van der Laan (2006).

## 4.3 Basic Implementation

We begin by illustrating the basic functionality of the Super Learner algorithm as implemented in sl3. The sl3 implementation consists of the following steps:

1. Load the necessary libraries and data
2. Define the machine learning task
3. Make a super learner by creating library of base learners and a metalearner
4. Train the super learner on the machine learning task
5. Obtain predicted values

### 4.3.1 WASH Benefits Study Example

Using the WASH data, we are interested in predicting weight-for-height z-score whz using the available covariate data. Let’s begin!

### 0. Load the necessary libraries and data

First, we will load the relevant R packages, set a seed, and load the data.

library(here)
library(data.table)
library(knitr)
library(kableExtra)
library(tidyverse)
library(origami)
library(SuperLearner)
library(sl3)

set.seed(7194)

# load data set and take a peek
stringsAsFactors = TRUE)
kable(digits = 4) %>%
scroll_box(width = "100%", height = "300px")
whz tr fracode month aged sex momage momedu momheight hfiacat Nlt18 Ncomp watmin elec floor walls roof asset_wardrobe asset_table asset_chair asset_khat asset_chouki asset_tv asset_refrig asset_bike asset_moto asset_sewmach asset_mobile
0.00 Control N05265 9 268 male 30 Primary (1-5y) 146.40 Food Secure 3 11 0 1 0 1 1 0 1 1 1 0 1 0 0 0 0 1
-1.16 Control N05265 9 286 male 25 Primary (1-5y) 148.75 Moderately Food Insecure 2 4 0 1 0 1 1 0 1 0 1 1 0 0 0 0 0 1
-1.05 Control N08002 9 264 male 25 Primary (1-5y) 152.15 Food Secure 1 10 0 0 0 1 1 0 0 1 0 1 0 0 0 0 0 1
-1.26 Control N08002 9 252 female 28 Primary (1-5y) 140.25 Food Secure 3 5 0 1 0 1 1 1 1 1 1 0 0 0 1 0 0 1
-0.59 Control N06531 9 336 female 19 Secondary (>5y) 150.95 Food Secure 2 7 0 1 0 1 1 1 1 1 1 1 0 0 0 0 0 1
-0.51 Control N06531 9 304 male 20 Secondary (>5y) 154.20 Severely Food Insecure 0 3 1 1 0 1 1 0 0 0 0 1 0 0 0 0 0 1

### 1. Define the machine learning task

To define the machine learning “task” (predict weight-for-height z-score whz using the available covariate data), we need to create an sl3_Task object. The sl3_Task keeps track of the roles the variables play in the machine learning problem, the data, and any metadata (e.g., observational-level weights, id, offset).

# specify the outcome and covariates
outcome <- "whz"
covars <- colnames(washb_data)[-which(names(washb_data) == outcome)]

data = washb_data,
covariates = covars,
outcome = outcome
)
Warning in process_data(data, nodes, column_names = column_names, flag = flag, :
Missing covariate data detected: imputing covariates.

This warning is important. The task just imputed missing covariates for us. Specifically, for each covariate column with missing values, sl3 uses the median to impute missing continuous covariates, and the mode to impute binary or categorical covariates. Also, for each covariate column with missing values, sl3 adds an additional column indicating whether or not the value was imputed, which is particularly handy when the missingness in the data might be informative.

Also, notice that we did not specify the number of folds, or the loss function in the task. The default cross-validation scheme is V-fold, with the number of folds $$V=10$$.

Let’s visualize our washb_task.

washb_task
A sl3 Task with 4695 obs and these nodes:
$covariates [1] "tr" "fracode" "month" "aged" [5] "sex" "momage" "momedu" "momheight" [9] "hfiacat" "Nlt18" "Ncomp" "watmin" [13] "elec" "floor" "walls" "roof" [17] "asset_wardrobe" "asset_table" "asset_chair" "asset_khat" [21] "asset_chouki" "asset_tv" "asset_refrig" "asset_bike" [25] "asset_moto" "asset_sewmach" "asset_mobile" "delta_momage" [29] "delta_momheight"$outcome
[1] "whz"

$id NULL$weights
NULL

$offset NULL ### 2. Make a super learner Now that we have defined our machine learning problem with the task, we are ready to “make” the super learner. This requires specification of • A library of base learning algorithms that we think might be consistent with the true data-generating distribution. • A metalearner, to ensemble the base learners. We might also incorporate • Feature selection, to pass only a subset of the predictors to the algorithm. • Hyperparameter specification, to tune base learners. Learners have properties that indicate what features they support. We may use sl3_list_properties() to get a list of all properties supported by at least one learner. sl3_list_properties()  [1] "binomial" "categorical" "continuous" [4] "cv" "density" "ids" [7] "multivariate_outcome" "offset" "preprocessing" [10] "timeseries" "weights" "wrapper"  Since we have a continuous outcome, we may identify the learners that support this outcome type with sl3_list_learners(). sl3_list_learners("continuous")  [1] "Lrnr_arima" "Lrnr_bartMachine" [3] "Lrnr_bilstm" "Lrnr_caret" [5] "Lrnr_condensier" "Lrnr_dbarts" [7] "Lrnr_earth" "Lrnr_expSmooth" [9] "Lrnr_gam" "Lrnr_gbm" [11] "Lrnr_glm" "Lrnr_glm_fast" [13] "Lrnr_glmnet" "Lrnr_grf" [15] "Lrnr_h2o_glm" "Lrnr_h2o_grid" [17] "Lrnr_hal9001" "Lrnr_HarmonicReg" [19] "Lrnr_lstm" "Lrnr_mean" [21] "Lrnr_nnls" "Lrnr_optim" [23] "Lrnr_pkg_SuperLearner" "Lrnr_pkg_SuperLearner_method" [25] "Lrnr_pkg_SuperLearner_screener" "Lrnr_polspline" [27] "Lrnr_randomForest" "Lrnr_ranger" [29] "Lrnr_rpart" "Lrnr_rugarch" [31] "Lrnr_screener_corP" "Lrnr_screener_corRank" [33] "Lrnr_screener_randomForest" "Lrnr_solnp" [35] "Lrnr_stratified" "Lrnr_svm" [37] "Lrnr_tsDyn" "Lrnr_xgboost"  Now that we have an idea of some learners, we can construct them using the make_learner function. # choose base learners lrnr_glm <- make_learner(Lrnr_glm) lrnr_mean <- make_learner(Lrnr_mean) lrnr_glmnet <- make_learner(Lrnr_glmnet) We can customize learner hyperparameters to incorporate a diversity of different settings. Documentation for the learners and their hyperparameters can be found in the sl3 Learners Reference. We can also include learners from the SuperLearner R package. lrnr_ranger100 <- make_learner(Lrnr_ranger, num.trees = 100) lrnr_hal_simple <- make_learner(Lrnr_hal9001, degrees = 1, n_folds = 2) lrnr_gam <- Lrnr_pkg_SuperLearner$new("SL.gam")
lrnr_bayesglm <- Lrnr_pkg_SuperLearner$new("SL.bayesglm") Are you interested in creating a new base learning algorithm? If so, instructions are provided in Defining New sl3 Learners. In order to assemble the library of learners, we need to “stack” them together. A Stack is a special learner and it has the same interface as all other learners. What makes a stack special is that it combines multiple learners by training them simultaneously, so that their predictions can be either combined or compared. stack <- make_learner( Stack, lrnr_glm, lrnr_mean, lrnr_ranger100, lrnr_glmnet, lrnr_gam, lrnr_bayesglm ) We will fit a non-negative least squares metalearner using Lrnr_nnls. Note that any learner can be used as a metalearner. Lrnr_nnls is a solid choice for a metalearner, since it creates a convex combination of the learners when combining them. To metalearner <- make_learner(Lrnr_nnls) We can optionally select a subset of available covariates and pass only those variables to the modeling algorithm. Let’s consider screening covariates based on their correlation with our outcome of interest (cor.test p-value $$\leq 0.1$$). screen_cor <- Lrnr_pkg_SuperLearner_screener$new("screen.corP")
# which covariates are selected on the full data?
screen_cor$train(washb_task) [1] "Lrnr_pkg_SuperLearner_screener_screen.corP"$selected
[1] "tr"             "fracode"        "aged"           "momage"
[5] "momedu"         "momheight"      "hfiacat"        "Nlt18"
[9] "elec"           "floor"          "walls"          "asset_wardrobe"
[13] "asset_table"    "asset_chair"    "asset_khat"     "asset_chouki"
[17] "asset_tv"       "asset_refrig"   "asset_moto"     "asset_sewmach"
[21] "asset_mobile"  

To “pipe” only the selected covariates to the modeling algorithm, we need to make a Pipeline, which is a just set of learners to be fit sequentially, where the fit from one learner is used to define the task for the next learner. Note the difference between Pipeline and Stack here- one is necessary in order to define a sequential process, whereas the other one establishes parallel function of learners.

cor_pipeline <- make_learner(Pipeline, screen_cor, stack)

Now our learners will be preceded by a screening step.

We also consider the original stack, just to compare how the feature selection methods perform in comparison to the methods without feature selection.

Analogous to what we have seen before, we have to stack the pipeline and original stack together, so we may use them as base learners in our super learner.

fancy_stack <- make_learner(Stack, cor_pipeline, stack)
# we can visualize the stack
plot(dt_stack, color = FALSE, height = "400px", width = "100%")

In the above plot, we visualize the super learner, which we can see has 10 realizations of the stack and a separate hold-out (the top branch of the figure) that will not be used to fit the super learner.

We have made a library/stack of base learners and a metalearner, so we are ready to make the super learner. The super learner algorithm fits a metalearner on the validation-set predictions.

sl <- make_learner(Lrnr_sl,
learners = fancy_stack,
metalearner = metalearner
)
# we can visualize the super learner
plot(dt_sl, color = FALSE, height = "400px", width = "100%")

### 3. Train the super learner on the machine learning task

The super learner algorithm fits a metalearner on the validation-set predictions in a cross-validated manner, thereby avoiding overfitting. This procedure is referred to as the continuous super learner. The cross-validation selector, or discrete super learner, is the base learner with the lowest cross-validated risk.

Now we are ready to “train” our super learner on our sl3_task object, washb_task.

sl_fit <- sl$train(washb_task) ### 4. Obtain predicted values Now that we have fit the super learner, we are ready to obtain our predicted values for each subject. sl_preds <- sl_fit$predict()
head(sl_preds)
[1] -0.5350742 -0.8963147 -0.7691624 -0.7668657 -0.6906887 -0.7220518

We can also obtain a summary of the results.

sl_fit_summary <- sl_fit$print() [1] "SuperLearner:" List of 2$ : chr "Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)"
$: chr "Stack" [1] "Lrnr_nnls_FALSE" lrnrs 1: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_glm_TRUE 2: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_mean 3: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_ranger_100_TRUE_1 4: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_glmnet_NULL_deviance_10_1_100_TRUE 5: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_pkg_SuperLearner_SL.gam 6: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_pkg_SuperLearner_SL.bayesglm 7: Stack_Lrnr_glm_TRUE 8: Stack_Lrnr_mean 9: Stack_Lrnr_ranger_100_TRUE_1 10: Stack_Lrnr_glmnet_NULL_deviance_10_1_100_TRUE 11: Stack_Lrnr_pkg_SuperLearner_SL.gam 12: Stack_Lrnr_pkg_SuperLearner_SL.bayesglm weights 1: 0.00000000 2: 0.00000000 3: 0.06062127 4: 0.18182887 5: 0.17455573 6: 0.00000000 7: 0.00000000 8: 0.01491966 9: 0.32501659 10: 0.00000000 11: 0.24360058 12: 0.00000000 [1] "Cross-validated risk (MSE, squared error loss):" learner 1: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_glm_TRUE 2: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_mean 3: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_ranger_100_TRUE_1 4: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_glmnet_NULL_deviance_10_1_100_TRUE 5: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_pkg_SuperLearner_SL.gam 6: Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_pkg_SuperLearner_SL.bayesglm 7: Stack_Lrnr_glm_TRUE 8: Stack_Lrnr_mean 9: Stack_Lrnr_ranger_100_TRUE_1 10: Stack_Lrnr_glmnet_NULL_deviance_10_1_100_TRUE 11: Stack_Lrnr_pkg_SuperLearner_SL.gam 12: Stack_Lrnr_pkg_SuperLearner_SL.bayesglm 13: SuperLearner coefficients mean_risk SE_risk fold_SD fold_min_risk fold_max_risk 1: NA 1.015128 0.02363317 0.07629401 0.8927540 1.131594 2: NA 1.065282 0.02502664 0.09191791 0.9264292 1.196647 3: NA 1.024937 0.02365692 0.08231236 0.8778104 1.154654 4: NA 1.011705 0.02358588 0.07881693 0.8822292 1.130762 5: NA 1.011497 0.02357149 0.07449866 0.8919503 1.132290 6: NA 1.015119 0.02363328 0.07631510 0.8926608 1.131570 7: NA 1.018612 0.02380402 0.07799191 0.8956048 1.134940 8: NA 1.065282 0.02502664 0.09191791 0.9264292 1.196647 9: NA 1.016893 0.02349240 0.08138677 0.8775006 1.139465 10: NA 1.012390 0.02358515 0.07971601 0.8827155 1.130114 11: NA 1.012122 0.02358982 0.07486427 0.8981537 1.135950 12: NA 1.018596 0.02380414 0.07801948 0.8954820 1.134909 13: NA 1.005375 0.02338984 0.07833095 0.8754770 1.128689 From the table of the printed super learner fit, we note that the super learner had a mean risk of 1.005375 and that this ensemble weighted the ranger and glmnet learners highest while not weighting the mean learner highly. We can also see that the glmnet learner had the lowest cross-validated mean risk, thus making it the cross-validated selector (or the discrete super learner). The mean risk of the (continuous) super learner is calculated using the hold-out set that we visualized in the plot above. ## 4.4 Cross-validated Super Learner We can cross-validate the super learner to see how well the super learner performs on unseen data, and obtain an estimate of the cross-validated risk of the super learner. This estimation procedure requires an “external” layer of cross-validation, also called nested cross-validation, which involves setting aside a separate holdout sample that we don’t use to fit the super learner. This external cross validation procedure may also incorporate 10 folds, which is the default in sl3. However, we will incorporate 2 outer/external folds of cross-validation for computational efficiency. We also need to specify a loss function to evaluate super learner. Documentation for the available loss functions can be found in the sl3 Loss Function Reference. washb_task_new <- make_sl3_Task( data = washb_data, covariates = covars, outcome = outcome, folds = make_folds(washb_data, fold_fun = folds_vfold, V = 2) ) Warning in process_data(data, nodes, column_names = column_names, flag = flag, : Missing covariate data detected: imputing covariates. CVsl_fancy <- CV_lrnr_sl(sl_fit, washb_task_new, loss_squared_error) CVsl_fancy %>% kable(digits = 4) %>% kableExtra:::kable_styling(fixed_thead = T) %>% scroll_box(width = "100%", height = "300px") learner coefficients mean_risk SE_risk fold_SD fold_min_risk fold_max_risk Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_glm_TRUE NA 1.0300 0.0238 0.0075 1.0247 1.0353 Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_mean NA 1.0663 0.0250 0.0034 1.0639 1.0687 Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_ranger_100_TRUE_1 NA 1.0447 0.0239 0.0008 1.0441 1.0452 Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_glmnet_NULL_deviance_10_1_100_TRUE NA 1.0199 0.0236 0.0020 1.0185 1.0213 Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_pkg_SuperLearner_SL.gam NA 1.0309 0.0238 0.0076 1.0255 1.0363 Pipeline(Lrnr_pkg_SuperLearner_screener_screen.corP->Stack)_Lrnr_pkg_SuperLearner_SL.bayesglm NA 1.0299 0.0238 0.0073 1.0247 1.0351 Stack_Lrnr_glm_TRUE NA 1.0360 0.0246 0.0160 1.0246 1.0473 Stack_Lrnr_mean NA 1.0663 0.0250 0.0034 1.0639 1.0687 Stack_Lrnr_ranger_100_TRUE_1 NA 1.0297 0.0236 0.0034 1.0273 1.0321 Stack_Lrnr_glmnet_NULL_deviance_10_1_100_TRUE NA 1.0199 0.0236 0.0021 1.0184 1.0213 Stack_Lrnr_pkg_SuperLearner_SL.gam NA 1.0398 0.0277 0.0288 1.0195 1.0602 Stack_Lrnr_pkg_SuperLearner_SL.bayesglm NA 1.0359 0.0247 0.0159 1.0246 1.0472 SuperLearner NA 1.0156 0.0235 0.0017 1.0144 1.0169 ## 4.5 Variable Importance Measures with sl3 Variable importance can be interesting and informative. The sl3 varimp function returns a table with variables listed in decreasing order of importance, in which the measure of importance is based on a risk difference between the learner fit with a permuted covariate and the learner fit with the true covariate, across all covariates. In this manner, the larger the risk difference, the more important the variable is in the prediction. Let’s explore the sl3 variable importance measurements for the washb data. washb_varimp <- varimp(sl_fit, loss_squared_error) washb_varimp %>% kable(digits = 4) %>% kableExtra:::kable_styling(fixed_thead = T) %>% scroll_box(width = "100%", height = "300px") X risk_diff aged 0.0358 momedu 0.0071 asset_refrig 0.0059 month 0.0053 momheight 0.0052 tr 0.0049 asset_chair 0.0027 Nlt18 0.0017 elec 0.0015 asset_moto 0.0014 momage 0.0012 hfiacat 0.0011 fracode 0.0010 asset_khat 0.0010 asset_chouki 0.0009 asset_wardrobe 0.0006 sex 0.0006 asset_sewmach 0.0005 walls 0.0004 floor 0.0003 delta_momage -0.0001 watmin -0.0002 asset_table -0.0002 asset_bike -0.0002 roof -0.0002 asset_mobile -0.0003 delta_momheight -0.0003 asset_tv -0.0010 Ncomp -0.0017 ## 4.6 Exercise 1 – Predicting Myocardial Infarction with sl3 Answer the questions below to predict myocardial infarction (mi) using the available covariate data. Thanks to Professor David Benkeser at Emory University for making the this Cardiovascular Health Study (CHS) data easily accessible. # load the data set db_data <- url("https://raw.githubusercontent.com/benkeser/sllecture/master/chspred.csv") chspred <- read_csv(file = db_data, col_names = TRUE) # take a quick peek head(chspred) %>% kable(digits = 4) %>% kableExtra:::kable_styling(fixed_thead = T) %>% scroll_box(width = "100%", height = "300px") waist alcoh hdl beta smoke ace ldl bmi aspirin gend age estrgn glu ins cysgfr dm fetuina whr hsed race logcystat logtrig logcrp logcre health logkcal sysbp mi 110.1642 0.0000 66.4974 0 0 1 114.2162 27.9975 0 0 73.5179 0 159.9314 70.3343 75.0078 1 0.1752 1.1690 1 1 -0.3420 5.4063 2.0126 -0.6739 0 4.3926 177.1345 0 89.9763 0.0000 50.0652 0 0 0 103.7766 20.8931 0 0 61.7723 0 153.3888 33.9695 82.7433 1 0.5717 0.9011 0 0 -0.0847 4.8592 3.2933 -0.5551 1 6.2071 136.3742 0 106.1941 8.4174 40.5059 0 0 0 165.7158 28.4554 1 1 72.9312 0 121.7145 -17.3017 74.6989 0 0.3517 1.1797 0 1 -0.4451 4.5088 0.3013 -0.0115 0 6.7320 135.1993 0 90.0566 0.0000 36.1750 0 0 0 45.2035 23.9608 0 0 79.1191 0 53.9691 11.7315 95.7823 0 0.5439 1.1360 0 0 -0.4807 5.1832 3.0243 -0.5751 1 7.3972 139.0182 0 78.6143 2.9790 71.0642 0 1 0 131.3121 10.9656 0 1 69.0179 0 94.3153 9.7112 72.7109 0 0.4916 1.1028 1 0 0.3121 4.2190 -0.7057 0.0053 1 8.2779 88.0470 0 91.6593 0.0000 59.4963 0 0 0 171.1872 29.1317 0 1 81.8346 0 212.9066 -28.2269 69.2184 1 0.4621 0.9529 1 0 -0.2872 5.1773 0.9705 0.2127 1 5.9942 69.5943 0 1. Create an sl3 task, setting myocardial infarction mi as the outcome and using all available covariate data. 2. Make a library of seven relatively fast base learning algorithms (i.e., do not consider BART or HAL). Customize hyperparameters for one of your learners. Feel free to use learners from sl3 or SuperLearner. You may use the same base learning library that is presented above. 3. Incorporate feature selection with the SuperLearner screener screen.corP. 4. Fit the metalearning step with non-negative least squares, Lrnr_nnls. 5. With the metalearner and base learners, make the super learner and train it on the task. 6. Print your super learner fit by calling print() with $.
7. Cross-validate your super learner fit to see how well it performs on unseen data. Specify loss_squared_error as the loss function to evaluate the super learner.

## 4.11 Concluding Remarks

The general ensemble learning approach of super learner can be applied to a diversity of estimation and prediction problems that can be defined by a loss function. We just discussed conditional mean estimation, and in the appendix we delve into prediction of a conditional density, and the optimal individualized treatment rule. Plug-in estimators of the estimand are desirable because a plug-in estimator respects both the local and global constraints of the statistical model. We could just plug-in the estimator returned by Super Learner; however, this is problematic because the Super Learner estimators are trading off bias and variance in an optimal way and as a result their bias is essentially the rate of convergence of these algorithms, which is always slower than $$1/\sqrt{n}$$. Therefore, if we plug-in the estimator returned by super learner into the target parameter mapping, we would end up with an estimator which has the same bias as what we plugged in, which is greater than $$1/\sqrt{n}$$. Thus, we end up with an estimator which is not asymptotically normal, since it does not converge to the estimand at $$1/\sqrt{n}$$ rate.

An asymptotically linear estimator has no meaningful bias ($< 1/$), and can be written as an empirical mean in first order of a function of the data, the influence curve, plus some negligible remainder term. Once an estimator is asymptotically linear with an influence curve it’s normally distributed, so the standardized estimator converges to a normal distribution with mean 0 and variance is the variance of the influence curve. Thus, it is advantageous to construct asymptotically linear estimators since they permit formal statistical inference. Among the class of regular asymptotically linear estimators, there is an optimal estimator which is an efficient estimator, and that’s the one with influence curve equal to the canonical gradient of the path-wise derivative of the target parameter. The canonical gradient is the direction of the path through the data distribution where the parameter is steepest. An estimator is efficient if and only if is asymptotically linear with influence curve equal to the canonical gradient. One can calculate the canonical gradient with the statistical model and the statistical target parameter. Techniques for calculating the canonical gradient entail projecting an initial gradient on the tangent space of the model at the particular distribution in the model in which you want to calculate the canonical gradient.

Now we know what it takes to construct an efficient estimator. Namely, we need to construct an estimator which is asymptotically linear with influence curve the canonical gradient. There are three general classes of estimators which succeed in constructing asymptotically linear estimators: (1) the one-step estimator, but it is not a plug-in estimator; (2) the targeted maximum likelihood estimator, which is a super learner targeted towards the target parameter and it is a plug-in estimator; and (3) estimating equation based estimators, which use the canonical gradient but as an estimating function in the target parameter. In the chapters that follow, we focus on the targeted maximum likelihood estimator and the targeted minimum loss-based estimator, both referred to as TMLE.

## 4.12 Appendix

### 4.12.1 Exercise 1 Solution

Here is a potential solution to (Exercise 1 – Predicting Myocardial Infarction with sl3)(???).

chspred_task <- make_sl3_Task(
data = chspred,
outcome = "mi"
)

glm_learner <- Lrnr_glm$new() lasso_learner <- Lrnr_glmnet$new(alpha = 1)
ridge_learner <- Lrnr_glmnet$new(alpha = 0) enet_learner <- Lrnr_glmnet$new(alpha = 0.5)
curated_glm_learner <- Lrnr_glm_fast$new(formula = "mi ~ smoke + beta + waist") mean_learner <- Lrnr_mean$new() # That is one mean learner!
glm_fast_learner <- Lrnr_glm_fast$new() ranger_learner <- Lrnr_ranger$new()
svm_learner <- Lrnr_svm$new() xgb_learner <- Lrnr_xgboost$new()

screen_cor <- Lrnr_pkg_SuperLearner_screener$new("screen.corP") glm_pipeline <- make_learner(Pipeline, screen_cor, glm_learner) stack <- make_learner( Stack, glm_pipeline, glm_learner, lasso_learner, ridge_learner, enet_learner, curated_glm_learner, mean_learner, glm_fast_learner, ranger_learner, svm_learner, xgb_learner ) metalearner <- make_learner(Lrnr_nnls) sl <- Lrnr_sl$new(
learners = stack,
metalearner = metalearner
)
sl_fit <- sl$train(task) sl_fit$print()

CVsl

### 4.12.2 Exercise 2 Solution

Here’s a potential solution to (Exercise 2)(???).

### 4.12.3 Exercise 3 Solution

Here’s a potential solution to the (Exercise 3)(???).

### References

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

Polley, Eric C, and Mark J van der Laan. 2010. “Super Learner in Prediction.” bepress.

van der Laan, Mark J, and Sandrine Dudoit. 2003. “Unified Cross-Validation Methodology for Selection Among Estimators and a General Cross-Validated Adaptive Epsilon-Net Estimator: Finite Sample Oracle Inequalities and Examples.” bepress.

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

van der Vaart, Aad W, Sandrine Dudoit, and Mark J van der Laan. 2006. “Oracle Inequalities for Multi-Fold Cross Validation.” Statistics & Decisions 24 (3). Oldenbourg Wissenschaftsverlag: 351–71.

Wolpert, David H. 1992. “Stacked Generalization.” Neural Networks 5 (2). Elsevier: 241–59.