The Explainable Ensemble Trees (e2tree) key idea consists of the definition of an algorithm to represent every ensemble approach based on decision trees model using a single tree-like structure. The goal is to explain the results from the esemble algorithm while preserving its level of accuracy, which always outperforms those provided by a decision tree. The proposed method is based on identifying the relationship tree-like structure explaining the classification or regression paths summarizing the whole ensemble process. There are two main advantages of e2tree: - building an explainable tree that ensures the predictive performance of an RF model - allowing the decision-maker to manage with an intuitive structure (such as a tree-like structure).
In this example, we focus on Random Forest but, again, the algorithm can be generalized to every ensemble approach based on decision trees.
You can install the developer version of e2tree from GitHub with:
install.packages("remotes")
remotes::install_github("massimoaria/e2tree")require(e2tree)
require(randomForest)
require(dplyr)
require(ggplot2)
if (!(require(rsample, quietly=TRUE))){install.packages("rsample"); require(rsample, quietly=TRUE)}
options(dplyr.summarise.inform = FALSE)The package is still under development and therefore, for the time being, there are the following limitations:
Only ensembles trained with the randomForest package are supported. Additional packages and approaches will be supported in the future;
Currently e2tree works only in the case of classification problems. It will gradually be extended to other problems related to the nature of the response variable: regression, counting, multivariate response, etc.
In this example, we want to show the main functions of the e2tree package.
Starting from the IRIS dataset, we will train an ensemble tree using the randomForest package and then subsequently use e2tree to obtain an explainable tree synthesis of the ensemble classifier.
# Set random seed to make results reproducible:
set.seed(0)
# Initialize the split
iris_split <- iris %>% initial_split(prop = 0.6)
iris_split
#> <Training/Testing/Total>
#> <90/60/150>
# Assign the data to the correct sets
training <- iris_split %>% training()
validation <- iris_split %>% testing()
response_training <- training[,5]
response_validation <- validation[,5]Train an Random Forest model with 1000 weak learners
# Perform training:
ensemble = randomForest(Species ~ ., data = training, importance = TRUE, proximity = TRUE)Here, we create the dissimilarity matrix between observations through the createDisMatrix function
D = createDisMatrix(ensemble, data = training, label = "Species", parallel = list(active = FALSE, no_cores = NULL))
#> Parallel mode OFF (1 core)
#> Classification Framework
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#>
#> Attaching package: 'Rcpp'
#> The following object is masked from 'package:rsample':
#>
#> populate
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#dis <- 1-rf$proximitysetting e2tree parameters
setting=list(impTotal=0.1, maxDec=0.01, n=2, level=5)Build an explainable tree for RF
tree <- e2tree(Species ~ ., data = training, D, ensemble, setting)Plot the Explainable Ensemble Tree
expl_plot <- rpart2Tree(tree, ensemble)
rpart.plot::rpart.plot(expl_plot)
Let’s have a look at the output
tree %>% glimpse()
#> List of 7
#> $ tree :'data.frame': 11 obs. of 21 variables:
#> ..$ node : num [1:11] 1 2 3 6 12 13 26 27 54 55 ...
#> ..$ n : int [1:11] 90 33 57 28 22 6 2 4 2 2 ...
#> ..$ pred : chr [1:11] "setosa" "setosa" "virginica" "versicolor" ...
#> ..$ prob : num [1:11] 0.367 1 0.561 0.893 1 ...
#> ..$ impTotal : num [1:11] 0.723 0.029 0.627 0.437 0.206 ...
#> ..$ impChildren : num [1:11] 0.408 NA 0.29 0.306 NA ...
#> ..$ decImp : num [1:11] 0.315 NA 0.338 0.132 NA ...
#> ..$ decImpSur : num [1:11] 0.2072 NA 0.3285 0.0744 NA ...
#> ..$ variable : chr [1:11] "Petal.Length" NA "Petal.Width" "Petal.Length" ...
#> ..$ split : num [1:11] 57 NA 97 68 NA 71 NA 72 NA NA ...
#> ..$ splitLabel : chr [1:11] "Petal.Length <=1.9" NA "Petal.Width <=1.7" "Petal.Length <=4.7" ...
#> ..$ variableSur : chr [1:11] "Petal.Width" NA "Petal.Length" "Sepal.Length" ...
#> ..$ splitLabelSur: chr [1:11] "Petal.Width <=0.6" NA "Petal.Length <=4.7" "Sepal.Length <=5.8" ...
#> ..$ parent : num [1:11] 0 1 1 3 6 6 13 13 27 27 ...
#> ..$ children :List of 11
#> .. ..$ : num [1:2] 2 3
#> .. ..$ : logi NA
#> .. ..$ : num [1:2] 6 7
#> .. ..$ : num [1:2] 12 13
#> .. ..$ : logi NA
#> .. ..$ : num [1:2] 26 27
#> .. ..$ : logi NA
#> .. ..$ : num [1:2] 54 55
#> .. ..$ : logi NA
#> .. ..$ : logi NA
#> .. ..$ : logi NA
#> ..$ terminal : logi [1:11] FALSE TRUE FALSE FALSE TRUE FALSE ...
#> ..$ obs :List of 11
#> .. ..$ : int [1:90] 1 2 3 4 5 6 7 8 9 10 ...
#> .. ..$ : int [1:33] 4 5 8 11 14 17 21 23 26 27 ...
#> .. ..$ : int [1:57] 1 2 3 6 7 9 10 12 13 15 ...
#> .. ..$ : int [1:28] 2 6 7 10 12 13 20 22 24 33 ...
#> .. ..$ : int [1:22] 2 6 7 10 13 20 24 33 51 54 ...
#> .. ..$ : int [1:6] 12 22 50 69 79 89
#> .. ..$ : int [1:2] 12 50
#> .. ..$ : int [1:4] 22 69 79 89
#> .. ..$ : int [1:2] 22 79
#> .. ..$ : int [1:2] 69 89
#> .. ..$ : int [1:29] 1 3 9 15 16 18 19 25 28 31 ...
#> ..$ path : chr [1:11] "" "Petal.Length <=1.9" "!Petal.Length <=1.9" "!Petal.Length <=1.9 & Petal.Width <=1.7" ...
#> ..$ ncat : num [1:11] -1 NA -1 -1 NA -1 NA -1 NA NA ...
#> ..$ pred_val : num [1:11] 1 1 3 2 2 2 2 3 2 3 ...
#> ..$ yval2 : num [1:11, 1:8] 1 1 3 2 2 2 2 3 2 3 ...
#> .. ..- attr(*, "dimnames")=List of 2
#> $ csplit : NULL
#> $ splits : num [1:5, 1:5] 90 57 28 6 4 -1 -1 -1 -1 -1 ...
#> ..- attr(*, "dimnames")=List of 2
#> .. ..$ : chr [1:5] "Petal.Length" "Petal.Width" "Petal.Length" "Petal.Length" ...
#> .. ..$ : chr [1:5] "count" "ncat" "improve" "index" ...
#> $ call : language e2tree(formula = Species ~ ., data = training, D = D, ensemble = ensemble, setting = setting)
#> $ terms :Classes 'terms', 'formula' language Species ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width
#> .. ..- attr(*, "variables")= language list(Species, Sepal.Length, Sepal.Width, Petal.Length, Petal.Width)
#> .. ..- attr(*, "factors")= int [1:5, 1:4] 0 1 0 0 0 0 0 1 0 0 ...
#> .. .. ..- attr(*, "dimnames")=List of 2
#> .. ..- attr(*, "term.labels")= chr [1:4] "Sepal.Length" "Sepal.Width" "Petal.Length" "Petal.Width"
#> .. ..- attr(*, "order")= int [1:4] 1 1 1 1
#> .. ..- attr(*, "intercept")= int 1
#> .. ..- attr(*, "response")= int 1
#> .. ..- attr(*, ".Environment")=<environment: 0x139e68640>
#> .. ..- attr(*, "predvars")= language list(Species, Sepal.Length, Sepal.Width, Petal.Length, Petal.Width)
#> .. ..- attr(*, "dataClasses")= Named chr [1:5] "factor" "numeric" "numeric" "numeric" ...
#> .. .. ..- attr(*, "names")= chr [1:5] "Species" "Sepal.Length" "Sepal.Width" "Petal.Length" ...
#> $ control:List of 5
#> ..$ impTotal: num 0.1
#> ..$ maxDec : num 0.01
#> ..$ n : num 2
#> ..$ level : num 5
#> ..$ tMax : num 63
#> $ N : num [1:11] 1 2 3 6 12 13 26 27 54 55 ...
#> - attr(*, "xlevels")= list()
#> - attr(*, "ylevels")= chr [1:3] "virginica" "versicolor" "setosa"
#> - attr(*, "class")= chr [1:2] "list" "e2tree"Prediction with the new tree (example on training)
pred <- ePredTree(tree, training[,-5], target="virginica")Comparison of predictions (training sample) of RF and e2tree
table(pred$fit, ensemble$predicted)
#>
#> setosa versicolor virginica
#> setosa 33 0 0
#> versicolor 0 24 2
#> virginica 0 1 30Comparison of predictions (training sample) of RF and correct response
table(ensemble$predicted, response_training)
#> response_training
#> setosa versicolor virginica
#> setosa 33 0 0
#> versicolor 0 23 2
#> virginica 0 2 30Comparison of predictions (training sample) of e2tree and correct response
table(pred$fit,response_training)
#> response_training
#> setosa versicolor virginica
#> setosa 33 0 0
#> versicolor 0 25 1
#> virginica 0 0 31Variable Importance
ensemble_imp <- ensemble$importance %>% as.data.frame %>%
mutate(Variable = rownames(ensemble$importance),
RF_Var_Imp = round(MeanDecreaseAccuracy,2)) %>%
select(Variable, RF_Var_Imp)
V <- vimp(tree, training)
#V <- V$vimp %>%
# select(Variable,MeanImpurityDecrease, `ImpDec_ setosa`, `ImpDec_ versicolor`,`ImpDec_ virginica`) %>%
# mutate_at(c("MeanImpurityDecrease","ImpDec_ setosa", "ImpDec_ versicolor","ImpDec_ virginica"), round,2) %>%
# left_join(ensemble_imp, by = "Variable") %>%
# select(Variable, RF_Var_Imp, MeanImpurityDecrease, starts_with("ImpDec")) %>%
# rename(ETree_Var_Imp = MeanImpurityDecrease)
V
#> $vimp
#> # A tibble: 2 × 9
#> Variable MeanImpurityDecrease MeanAccuracyDecrease `ImpDec_ setosa`
#> <chr> <dbl> <dbl> <dbl>
#> 1 Petal.Length 0.366 2.22e- 2 0.315
#> 2 Petal.Width 0.214 1.41e-16 NA
#> # ℹ 5 more variables: `ImpDec_ versicolor` <dbl>, `ImpDec_ virginica` <dbl>,
#> # `AccDec_ setosa` <dbl>, `AccDec_ versicolor` <dbl>,
#> # `AccDec_ virginica` <dbl>
#>
#> $g_imp
#>
#> $g_acc
Comparison with the validation sample
ensemble.pred <- predict(ensemble, validation[,-5], proximity = TRUE)
pred_val<- ePredTree(tree, validation[,-5], target="virginica")Comparison of predictions (sample validation) of RF and e2tree
table(pred_val$fit, ensemble.pred$predicted)
#>
#> setosa versicolor virginica
#> setosa 17 0 0
#> versicolor 0 26 0
#> virginica 0 0 17Comparison of predictions (validation sample) of RF and correct response
table(ensemble.pred$predicted, response_validation)
#> response_validation
#> setosa versicolor virginica
#> setosa 17 0 0
#> versicolor 0 24 2
#> virginica 0 1 16
ensemble.prob <- predict(ensemble, validation[,-5], proximity = TRUE, type="prob")
roc_ensemble<- roc(response_validation, ensemble.prob$predicted[,"virginica"], target="virginica")
roc_ensemble$auc
#> [1] 0.9874563Comparison of predictions (validation sample) of e2tree and correct response
table(pred_val$fit, response_validation)
#> response_validation
#> setosa versicolor virginica
#> setosa 17 0 0
#> versicolor 0 24 2
#> virginica 0 1 16
roc_res <- roc(response_validation, pred_val$score, target="virginica")
roc_res$auc
#> [1] 0.9325268