Outline

• Classification and regression tree
• Random forest

Supervised machine learning and unsupervised machine learning

1. Classification (supervised machine learning):
   • With the class label known, build a model (classifier) to predict a future observation.
2. Clustering (unsupervised machine learning)
   • Without knowing the class label, cluster the data according to their similarity.

Classification (supervised machine learning)

Clustering (unsupervised machine learning)

Decision Tree (what the result looks like)

library(ElemStatLearn)
library(rpart)
library(rpart.plot)
afit <- rpart(as.factor(svi) ~ . - train, data = prostate)
rpart.plot(afit)

• Target: build up a prediction rule to determine svi = 1 or 0
• Top node:
  • 0: predicted svi status if a new subject falls into this node
  • 0.22: probablity svi = 1
  • 100%: all 97 subjects
• Bottom left:
  • 0: predicted svi status if a new subject falls into this node
  • 0.11: probablity svi = 1
  • 87%: 84 subjects fall into this node
• Bottom right:
  • 1: predicted svi status if a new subject falls into this node
  • 0.92: probablity svi = 1
  • 13%: 13 subjects fall into this node

Decision Tree

• Decision tree is a supervised learning algorithm (having a pre-defined labels).
• It works for both categorical and continuous input and output variables.
• In this technique, we split the population or sample into two or more homogeneous sets (or sub-populations) based on the best splitter.

Motivating example

• Sample size n = 30
• Variables (features): three variables
  • Gender (Boy/ Girl)
  • Class (IX or X)
  • Height (5 to 6 ft)
• Outcome (labels): 15 out of these 30 play cricket in leisure time.

Purpose: predict whether a student will play cricket in his/her leisure time, based on his/her three variables.

Decision tree

• Decision tree identifies the most significant variable and it’s value that gives best homogeneous sets of population.

Questions:

• What does the decision tree structure look like?
• How to define homogeneous?
• How to make a prediction for a new person?

Decision tree structure

Terminology:

• Root Node: It represents entire population or sample and no split yet.
• Splitting: Dividing a node into two or more sub-nodes.
• Decision Node: When a sub-node splits into further sub-nodes, then it is called decision node.
• Leaf/ Terminal Node: Nodes do not split is called Leaf or Terminal node.
• Pruning: When we remove sub-nodes of a decision node, this process is called pruning. You can say opposite process of splitting.
• Branch / Sub-Tree: A sub section of entire tree is called branch or sub-tree.
• Parent and Child Node: A node, which is divided into sub-nodes is called parent node of sub-nodes where as sub-nodes are the child of parent node.

How does a tree decide where to split?

Goodness of split (GOS) criteria - impurity

Details: - Selects the split and cutoff which result in most pure subset of nodes. - explores to split all available nodes. - explores to split all possible cutoffs for each node.

Recommended measure of GOS (impurity)

• Gini Index
• Entropy
• Interpretation about impurity:
  • 0 indicates pure
  • large value indicates impure.

Gini Index

Assume:

• outcome variable \(Y\) is binary (\(Y = 0\) or \(Y = 1\)).
• \(t\) is a node

\[M_{Gini}(t) = 1 - P(Y = 0 | X \in t)^2 - P(Y = 1 | X \in t)^2\]

Gini Index

• root: \[M_{Gini}(R) = 1 - 0.5^2 - 0.5^2 = 0.5\]
• Gender:Female: \[M_{Gini}(G:F) = 1 - 0.2^2 - 0.8^2 = 0.32\]
• Gender:Male: \[M_{Gini}(G:M) = 1 - 0.65^2 - 0.35^2 = 0.455\]
• Class:IX: \[M_{Gini}(C:4) = 1 - 0.43^2 - 0.57^2 = 0.4902\]
• Class:X: \[M_{Gini}(C:5) = 1 - 0.56^2 - 0.44^2 = 0.4928\]
• Height:5.5+: \[M_{Gini}(H:5.5+) = 1 - 0.56^2 - 0.44^2 = 0.4928\]
• Height:5.5-: \[M_{Gini}(H:5.5-) = 1 - 0.42^2 - 0.58^2 = 0.4872\]

Goodness of split (GOS) criteria using Gini Index

Given an impurity function \(M(t)\), the GOS criterion is to find the split \(t_L\) and \(t_R\) of note \(t\) such that the impurity measure is maximally decreased:

\[\arg \max_{t_R, t_L} M(t) - [P(X\in t_L|X\in t) M(t_L) + P(X\in t_R|X\in t) M(t_R)]\]

• If split on Gender: \[M_{Gini}(R) - \frac{10}{30}M_{Gini}(G:F) - \frac{20}{30}M_{Gini}(G:M) = 0.5 - 10/30\times 0.32 - 20/30\times 0.455 = 0.09 \]

• If split on Class: \[M_{Gini}(R) - \frac{14}{30}M_{Gini}(C:4) - \frac{16}{30}M_{Gini}(C:5) = 0.5 - 14/30\times 0.4902 - 16/30\times 0.4928 = 0.008 \]

• If split on Height:5.5 \[M_{Gini}(R) - \frac{12}{30}M_{Gini}(H:5.5-) - \frac{18}{30}M_{Gini}(H:5.5+) = 0.5 - 12/30*0.4872 - 18/30*0.4928 = 0.00944 \]

Therefore, we will split based on Gender (maximized decrease).

• Why 5.5? Actually we need to search all possible height cutoffs to select the best cutoff.

Entropy

Assume:

• outcome variable \(Y\) is binary (\(Y = 0\) or \(Y = 1\)).
• \(t\) is a node

\[M_{entropy}(t) = - P(Y = 0 | X \in t)\log P(Y = 0 | X \in t) - P(Y = 1 | X \in t)\log P(Y = 1 | X \in t)\]

Entropy

• root: \[M_{entropy}(R) = -0.5 \times \log(0.5) -0.5 \times \log(0.5) = 0.6931472\]
• Gender:Female: \[M_{entropy}(G:F) = -0.2 \times \log(0.2) -0.8 \times \log(0.8) = 0.5004024\]
• Gender:Male: \[M_{entropy}(G:M) = -0.65 \times \log(0.65) -0.35 \times \log(0.35) = 0.6474466\]
• Class:IX: \[M_{entropy}(C:4) = -0.43 \times \log(0.43) -0.57 \times \log(0.57) = 0.6833149\]
• Class:X: \[M_{entropy}(C:5) = -0.56 \times \log(0.56) -0.44 \times \log(0.44) = 0.6859298\]
• Height:5.5+: \[M_{entropy}(H:5.5+) = -0.56 \times \log(0.56) -0.44 \times \log(0.44) = 0.6859298\]
• Height:5.5-: \[M_{entropy}(H:5.5-) = -0.42 \times \log(0.42) -0.58 \times \log(0.58) = 0.680292\]

Goodness of split (GOS) criteria using entropy

Given an impurity function \(M(t)\), the GOS criterion is to find the split \(t_L\) and \(t_R\) of note \(t\) such that the impurity measure is maximally decreased:

\[\arg \max_{t_R, t_L} M(t) - [P(X\in t_L|X\in t) M(t_L) + P(X\in t_R|X\in t) M(t_R)]\]

• If split on Gender: \[M_{entropy}(R) - \frac{10}{30}M_{entropy}(G:F) - \frac{20}{30}M_{entropy}(G:M) = 0.6931472 - 10/30\times 0.5004024 - 20/30\times 0.6474466 = 0.09471533 \]

• If split on Class: \[M_{entropy}(R) - \frac{14}{30}M_{entropy}(C:4) - \frac{16}{30}M_{entropy}(C:5) = 0.6931472 - 14/30\times 0.6833149 - 16/30\times 0.6859298 = 0.008437687 \]

• If split on Height:5.5 \[M_{entropy}(R) - \frac{12}{30}M_{entropy}(H:5.5-) - \frac{18}{30}M_{entropy}(H:5.5+) = 0.6931472 - 12/30 \times 0.680292 - 18/30\times 0.6859298 = 0.00947252 \]

Therefore, we will split based on Gender (maximized decrease).

Summary of impurity measurement

• Categorical outcome
  • Gini Index
  • Entropy
  • Chi-Square
• Continuous outcome
  • Reduction in Variance

Complexity for each split:

• \(O(np)\)
  • for each variable, search for all possible cutoffs (n).
  • Repeat this for all variables (p of them).

Decision tree

How to make a prediction:

\[\hat{p}_{mk} = \frac{1}{N_m} \sum_{x_i \in t_m} \mathbb{I}(y_i = k)\]

E.g. if a new subject (G:Male, Class:X, H:5.8ft) falls into a terminal node, we just do a majority vote.

Regression Trees vs Classification Trees

• Regression trees
  • dependent variable is continuous
  • predictive value at a terminal node: mean response of observation falling in that region \[\hat{c}_{m} = ave(y_i|x_i \in T_m)\]
• Classification trees
  • dependent variable is categorical
  • predictive value at a terminal node: mode of observations falling in that region

Prostate cancer example

library(ElemStatLearn)
library(rpart)
library(rpart.plot)
head(prostate)

##       lcavol  lweight age      lbph svi       lcp gleason pgg45       lpsa
## 1 -0.5798185 2.769459  50 -1.386294   0 -1.386294       6     0 -0.4307829
## 2 -0.9942523 3.319626  58 -1.386294   0 -1.386294       6     0 -0.1625189
## 3 -0.5108256 2.691243  74 -1.386294   0 -1.386294       7    20 -0.1625189
## 4 -1.2039728 3.282789  58 -1.386294   0 -1.386294       6     0 -0.1625189
## 5  0.7514161 3.432373  62 -1.386294   0 -1.386294       6     0  0.3715636
## 6 -1.0498221 3.228826  50 -1.386294   0 -1.386294       6     0  0.7654678
##   train
## 1  TRUE
## 2  TRUE
## 3  TRUE
## 4  TRUE
## 5  TRUE
## 6  TRUE

Training set and testing set

For supervised machine learning, usually we split the data into the training set and the testing set.

• Training set: to build the classifier (build the decision rule in the CART model)
• Testing set: evaluate the performance of the classifier from the training set.

Apply cart

prostate_train <- subset(prostate, subset = train==TRUE)
prostate_test <- subset(prostate, subset = train==FALSE)

afit <- rpart(as.factor(svi) ~ . - train, data = prostate_train) ## svi as binary outcome
#afit <- rpart(svi ~ . - train, data = prostate_train) ## svi as continuous outcome
afit

## n= 67 
## 
## node), split, n, loss, yval, (yprob)
##       * denotes terminal node
## 
## 1) root 67 15 0 (0.77611940 0.22388060)  
##   2) lcavol< 2.523279 52  3 0 (0.94230769 0.05769231) *
##   3) lcavol>=2.523279 15  3 1 (0.20000000 0.80000000) *

Visualize cart result

rpart.plot(afit)

• Top node:
  • 0: predicted svi status if a new subject falls into this node
  • 0.22: probablity svi = 1
  • 100%: all 67 subjects
• Bottom left:
  • 0: predicted svi status if a new subject falls into this node
  • 0.06: probablity svi = 1
  • 78%: 52 subjects fall into this node
• Bottom right:
  • 1: predicted svi status if a new subject falls into this node
  • 0.80: probablity svi = 1
  • 22%: 15 subjects fall into this node

predicting the testing dataset using CART subject

predProb_cart <- predict(object = afit, newdata = prostate_test)
head(predProb_cart)

##            0          1
## 7  0.9423077 0.05769231
## 9  0.9423077 0.05769231
## 10 0.9423077 0.05769231
## 15 0.9423077 0.05769231
## 22 0.9423077 0.05769231
## 25 0.9423077 0.05769231

atable <- table(predictLabel = predProb_cart[,"1"]>0.5, trueLabel = prostate_test$svi)
atable

##             trueLabel
## predictLabel  0  1
##        FALSE 21  4
##        TRUE   3  2

## accuracy
sum(diag(atable)) / sum(atable)

## [1] 0.7666667

Overfitting problem

Pruning the tree (to reduce overfitting)

• Brieman et al (1984) proposed a backward node recombinaiton strategy called minimal cost-complexity pruning.
• The subtrees are nested sequence: \[T_{max} = T_1 \subset T_2 \subset \ldots \subset T_m\]

• The cost-complexity of \(T\) is \[C_\alpha (T) = \hat{R}(T) + \alpha |T|,\] where

• \(\hat{R}(T)\) is the error rate estimated based on tree \(T\).
• \(T\) is the tree structure.
• \(|T|\) is the number of terminal nodes of \(T\).
• \(\alpha\) is a positive complexity parameter that balance between bias and variance (complexity).
• \(\alpha\) is estimated from cross-validation.

• Another way is to set \(\alpha = \frac{R(T_i) - R(T_{i-1})}{|T_{i-1}| - |T_{i}|}\)

Titanic example (Will be on HW)

library(titanic)
dim(titanic_train)

## [1] 891  12

head(titanic_train)

##   PassengerId Survived Pclass
## 1           1        0      3
## 2           2        1      1
## 3           3        1      3
## 4           4        1      1
## 5           5        0      3
## 6           6        0      3
##                                                  Name    Sex Age SibSp Parch
## 1                             Braund, Mr. Owen Harris   male  22     1     0
## 2 Cumings, Mrs. John Bradley (Florence Briggs Thayer) female  38     1     0
## 3                              Heikkinen, Miss. Laina female  26     0     0
## 4        Futrelle, Mrs. Jacques Heath (Lily May Peel) female  35     1     0
## 5                            Allen, Mr. William Henry   male  35     0     0
## 6                                    Moran, Mr. James   male  NA     0     0
##             Ticket    Fare Cabin Embarked
## 1        A/5 21171  7.2500              S
## 2         PC 17599 71.2833   C85        C
## 3 STON/O2. 3101282  7.9250              S
## 4           113803 53.1000  C123        S
## 5           373450  8.0500              S
## 6           330877  8.4583              Q

Bagging

Bagging

1. Create Multiple DataSets:
   • Sampling with replacement on the original data
   • Taking row and column fractions less than 1 helps in making robust models, less prone to overfitting
2. Build Multiple Classifiers:
   • Classifiers are built on each data set.
3. Combine Classifiers:
   • The predictions of all the classifiers are combined using a mean, median or mode value depending on the problem at hand.
   • The combined values are generally more robust than a single model.

Random forest

Random forest algorithm

Assume number of cases in the training set is N, and number of features is M.

1. Repeat the following procedures B = 500 times (each time is a CART algorithm):
   1. Sample N cases with replacement.
   2. Sample m<M features without replacement.
   3. Apply the CART algorithm without pruning.
2. Predict new data by aggregating the predictions of the B trees (i.e., majority votes for classification, average for regression).

Random forest

Random Forest on prostate cancer example

library("randomForest")

## randomForest 4.6-14

## Type rfNews() to see new features/changes/bug fixes.

prostate_train <- subset(prostate, subset = train==TRUE)
prostate_test <- subset(prostate, subset = train==FALSE)

rffit <- randomForest(as.factor(svi) ~ . - train, data = prostate_train)
rffit

## 
## Call:
##  randomForest(formula = as.factor(svi) ~ . - train, data = prostate_train) 
##                Type of random forest: classification
##                      Number of trees: 500
## No. of variables tried at each split: 2
## 
##         OOB estimate of  error rate: 13.43%
## Confusion matrix:
##    0 1 class.error
## 0 49 3  0.05769231
## 1  6 9  0.40000000

Random Forest on prostate prediction

pred_rf <- predict(rffit, prostate_test)

ctable <- table(pred_rf, trueLabel = prostate_test$svi)
ctable

##        trueLabel
## pred_rf  0  1
##       0 22  4
##       1  2  2

## accuracy
sum(diag(ctable)) / sum(ctable)

## [1] 0.8

Random Forest importance score

library(ggplot2)

## 
## Attaching package: 'ggplot2'

## The following object is masked from 'package:randomForest':
## 
##     margin

imp <- importance(rffit)
impData <- data.frame(cov = rownames(imp), importance=imp[,1])

ggplot(impData) + aes(x=cov, y=importance, fill=cov) + geom_bar(stat="identity")

How to calculate Random Forest importance score

• Within each tree \(t\),
  • \(\hat{y}_i^{(t)}\): predicted class before permuting
  • \(\hat{y}_{i,\pi_j}^{(t)}\): predicted class after permuting \(x_j\) \[VI^{(t)}(x_j) = \frac{1}{|n^{(t)}|} \sum_{i \in n^{(t)}} I(y_i = \hat{y}_i^{(t)}) - \frac{1}{|n^{(t)}|} \sum_{i \in n^{(t)}} I(y_i = \hat{y}_{i,\pi_j}^{(t)})\]
• Raw importance: \[VI(x_j) = \frac{\sum_{t=1}^B VI^{(t)}(x_j)}{B}\]
• Scaled improtance: importance() funciton in R: \[z_j = \frac{VI(x_j)}{\hat{\sigma}/\sqrt{B}}\]

Will be on homework

Apply random forest on Titanic dataset to predict survival.

• What are the importance factors?
• How does the performance compare to CART.

References

• https://www.analyticsvidhya.com/blog/2016/04/complete-tutorial-tree-based-modeling-scratch-in-python/

• https://www.statistik.uni-dortmund.de/useR-2008/slides/Strobl+Zeileis.pdf

• Element of stat learning https://web.stanford.edu/~hastie/ElemStatLearn/