17_decision_trees_nb.py

# # Decision Trees
# 
# *Adapted from Chapter 8 of [An Introduction to Statistical Learning](http://www-bcf.usc.edu/~gareth/ISL/)*

# Why are we learning about decision trees?
# 
# - Can be applied to both regression and classification problems
# - Many useful properties
# - Very popular
# - Basis for more sophisticated models
# - Have a different way of "thinking" than the other models we have studied

# ## Lesson objectives
# 
# Students will be able to:
# 
# - Explain how a decision tree is created
# - Build a decision tree model in scikit-learn
# - Tune a decision tree model and explain how tuning impacts the model
# - Interpret a tree diagram
# - Describe the key differences between regression and classification trees
# - Decide whether a decision tree is an appropriate model for a given problem

# # Part 1: Regression trees
# 
# Major League Baseball player data from 1986-87:
# 
# - **Years** (x-axis): number of years playing in the major leagues
# - **Hits** (y-axis): number of hits in the previous year
# - **Salary** (color): low salary is blue/green, high salary is red/yellow

# ![Salary data](images/salary_color.png)

# Group exercise:
# 
# - The data above is our **training data**.
# - We want to build a model that predicts the Salary of **future players** based on Years and Hits.
# - We are going to "segment" the feature space into regions, and then use the **mean Salary in each region** as the predicted Salary for future players.
# - Intuitively, you want to **maximize** the similarity (or "homogeneity") within a given region, and **minimize** the similarity between different regions.
# 
# Rules for segmenting:
# 
# - You can only use **straight lines**, drawn one at a time.
# - Your line must either be **vertical or horizontal**.
# - Your line **stops** when it hits an existing line.

# ![Salary regions](images/salary_regions.png)

# Above are the regions created by a computer:
# 
# - $R_1$: players with **less than 5 years** of experience, mean Salary of **\$166,000 **
# - $R_2$: players with **5 or more years** of experience and **less than 118 hits**, mean Salary of **\$403,000 **
# - $R_3$: players with **5 or more years** of experience and **118 hits or more**, mean Salary of **\$846,000 **
# 
# **Note:** Years and Hits are both integers, but the convention is to use the **midpoint** between adjacent values to label a split.
# 
# These regions are used to make predictions on **out-of-sample data**. Thus, there are only three possible predictions! (Is this different from how **linear regression** makes predictions?)
# 
# Below is the equivalent regression tree:

# ![Salary tree](images/salary_tree.png)

# The first split is **Years < 4.5**, thus that split goes at the top of the tree. When a splitting rule is **True**, you follow the left branch. When a splitting rule is **False**, you follow the right branch.
# 
# For players in the **left branch**, the mean Salary is \$166,000, thus you label it with that value. (Salary has been divided by 1000 and log-transformed to 5.11.)
# 
# For players in the **right branch**, there is a further split on **Hits < 117.5**, dividing players into two more Salary regions: \$403,000 (transformed to 6.00), and \$846,000 (transformed to 6.74).

# ![Salary tree annotated](images/salary_tree_annotated.png)

# **What does this tree tell you about your data?**
# 
# - Years is the most important factor determining Salary, with a lower number of Years corresponding to a lower Salary.
# - For a player with a lower number of Years, Hits is not an important factor determining Salary.
# - For a player with a higher number of Years, Hits is an important factor determining Salary, with a greater number of Hits corresponding to a higher Salary.
# 
# **Question:** What do you like and dislike about decision trees so far?

# ## Building a regression tree by hand
# 
# Your **training data** is a tiny dataset of [used vehicle sale prices](https://raw.githubusercontent.com/justmarkham/DAT8/master/data/vehicles_train.csv). Your goal is to **predict price** for testing data.
# 
# 1. Read the data into a Pandas DataFrame.
# 2. Explore the data by sorting, plotting, or split-apply-combine (aka `group_by`).
# 3. Decide which feature is the most important predictor, and use that to create your first splitting rule.
#     - Only binary splits are allowed.
# 4. After making your first split, split your DataFrame into two parts, and then explore each part to figure out what other splits to make.
# 5. Stop making splits once you are convinced that it strikes a good balance between underfitting and overfitting.
#     - Your goal is to build a model that generalizes well.
#     - You are allowed to split on the same variable multiple times!
# 6. Draw your tree, labeling the leaves with the mean price for the observations in that region.
#     - Make sure nothing is backwards: You follow the **left branch** if the rule is true, and the **right branch** if the rule is false.

# ## How does a computer build a regression tree?
# 
# **Ideal approach:** Consider every possible partition of the feature space (computationally infeasible)
# 
# **"Good enough" approach:** recursive binary splitting
# 
# 1. Begin at the top of the tree.
# 2. For **every feature**, examine **every possible cutpoint**, and choose the feature and cutpoint such that the resulting tree has the lowest possible mean squared error (MSE). Make that split.
# 3. Examine the two resulting regions, and again make a **single split** (in one of the regions) to minimize the MSE.
# 4. Keep repeating step 3 until a **stopping criterion** is met:
#     - maximum tree depth (maximum number of splits required to arrive at a leaf)
#     - minimum number of observations in a leaf

# ### Demo: Choosing the ideal cutpoint for a given feature

# vehicle data
import pandas as pd
url = 'https://raw.githubusercontent.com/justmarkham/DAT8/master/data/vehicles_train.csv'
train = pd.read_csv(url)


# before splitting anything, just predict the mean of the entire dataset
train['prediction'] = train.price.mean()
train


# calculate RMSE for those predictions
from sklearn import metrics
import numpy as np
np.sqrt(metrics.mean_squared_error(train.price, train.prediction))


# define a function that calculates the RMSE for a given split of miles
def mileage_split(miles):
    lower_mileage_price = train[train.miles < miles].price.mean()
    higher_mileage_price = train[train.miles >= miles].price.mean()
    train['prediction'] = np.where(train.miles < miles, lower_mileage_price, higher_mileage_price)
    return np.sqrt(metrics.mean_squared_error(train.price, train.prediction))


# calculate RMSE for tree which splits on miles < 50000
print 'RMSE:', mileage_split(50000)
train


# calculate RMSE for tree which splits on miles < 100000
print 'RMSE:', mileage_split(100000)
train


# check all possible mileage splits
mileage_range = range(train.miles.min(), train.miles.max(), 1000)
RMSE = [mileage_split(miles) for miles in mileage_range]


# allow plots to appear in the notebook
import matplotlib.pyplot as plt
plt.rcParams['figure.figsize'] = (6, 4)
plt.rcParams['font.size'] = 14


# plot mileage cutpoint (x-axis) versus RMSE (y-axis)
plt.plot(mileage_range, RMSE)
plt.xlabel('Mileage cutpoint')
plt.ylabel('RMSE (lower is better)')


# **Recap:** Before every split, this process is repeated for every feature, and the feature and cutpoint that produces the lowest MSE is chosen.

# ## Building a regression tree in scikit-learn

# encode car as 0 and truck as 1
train['vtype'] = train.vtype.map({'car':0, 'truck':1})


# define X and y
feature_cols = ['year', 'miles', 'doors', 'vtype']
X = train[feature_cols]
y = train.price


# instantiate a DecisionTreeRegressor (with random_state=1)
from sklearn.tree import DecisionTreeRegressor
treereg = DecisionTreeRegressor(random_state=1)
treereg


# use leave-one-out cross-validation (LOOCV) to estimate the RMSE for this model
from sklearn.cross_validation import cross_val_score
scores = cross_val_score(treereg, X, y, cv=14, scoring='mean_squared_error')
np.mean(np.sqrt(-scores))


# ## What happens when we grow a tree too deep?
# 
# - Left: Regression tree for Salary **grown deeper**
# - Right: Comparison of the **training, testing, and cross-validation errors** for trees with different numbers of leaves

# ![Salary tree grown deep](images/salary_tree_deep.png)

# The **training error** continues to go down as the tree size increases (due to overfitting), but the lowest **cross-validation error** occurs for a tree with 3 leaves.

# ## Tuning a regression tree
# 
# Let's try to reduce the RMSE by tuning the **max_depth** parameter:

# try different values one-by-one
treereg = DecisionTreeRegressor(max_depth=1, random_state=1)
scores = cross_val_score(treereg, X, y, cv=14, scoring='mean_squared_error')
np.mean(np.sqrt(-scores))


# Or, we could write a loop to try a range of values:

# list of values to try
max_depth_range = range(1, 8)

# list to store the average RMSE for each value of max_depth
RMSE_scores = []

# use LOOCV with each value of max_depth
for depth in max_depth_range:
    treereg = DecisionTreeRegressor(max_depth=depth, random_state=1)
    MSE_scores = cross_val_score(treereg, X, y, cv=14, scoring='mean_squared_error')
    RMSE_scores.append(np.mean(np.sqrt(-MSE_scores)))


# plot max_depth (x-axis) versus RMSE (y-axis)
plt.plot(max_depth_range, RMSE_scores)
plt.xlabel('max_depth')
plt.ylabel('RMSE (lower is better)')


# max_depth=3 was best, so fit a tree using that parameter
treereg = DecisionTreeRegressor(max_depth=3, random_state=1)
treereg.fit(X, y)


# "Gini importance" of each feature: the (normalized) total reduction of error brought by that feature
pd.DataFrame({'feature':feature_cols, 'importance':treereg.feature_importances_})


# ## Creating a tree diagram

# create a Graphviz file
from sklearn.tree import export_graphviz
export_graphviz(treereg, out_file='tree_vehicles.dot', feature_names=feature_cols)

# At the command line, run this to convert to PNG:
#   dot -Tpng tree_vehicles.dot -o tree_vehicles.png


# ![Tree for vehicle data](images/tree_vehicles.png)

# Reading the internal nodes:
# 
# - **samples:** number of observations in that node before splitting
# - **mse:** MSE calculated by comparing the actual response values in that node against the mean response value in that node
# - **rule:** rule used to split that node (go left if true, go right if false)
# 
# Reading the leaves:
# 
# - **samples:** number of observations in that node
# - **value:** mean response value in that node
# - **mse:** MSE calculated by comparing the actual response values in that node against "value"

# ## Making predictions for the testing data

# read the testing data
url = 'https://raw.githubusercontent.com/justmarkham/DAT8/master/data/vehicles_test.csv'
test = pd.read_csv(url)
test['vtype'] = test.vtype.map({'car':0, 'truck':1})
test


# **Question:** Using the tree diagram above, what predictions will the model make for each observation?

# use fitted model to make predictions on testing data
X_test = test[feature_cols]
y_test = test.price
y_pred = treereg.predict(X_test)
y_pred


# calculate RMSE
np.sqrt(metrics.mean_squared_error(y_test, y_pred))


# calculate RMSE for your own tree!
y_test = [3000, 6000, 12000]
y_pred = [0, 0, 0]
from sklearn import metrics
np.sqrt(metrics.mean_squared_error(y_test, y_pred))


# # Part 2: Classification trees
# 
# **Example:** Predict whether Barack Obama or Hillary Clinton will win the Democratic primary in a particular county in 2008:

# ![Obama-Clinton decision tree](images/obama_clinton_tree.jpg)

# **Questions:**
# 
# - What are the observations? How many observations are there?
# - What is the response variable?
# - What are the features?
# - What is the most predictive feature?
# - Why does the tree split on high school graduation rate twice in a row?
# - What is the class prediction for the following county: 15% African-American, 90% high school graduation rate, located in the South, high poverty, high population density?
# - What is the predicted probability for that same county?

# ## Comparing regression trees and classification trees
# 
# |regression trees|classification trees|
# |---|---|
# |predict a continuous response|predict a categorical response|
# |predict using mean response of each leaf|predict using most commonly occuring class of each leaf|
# |splits are chosen to minimize MSE|splits are chosen to minimize Gini index (discussed below)|

# ## Splitting criteria for classification trees
# 
# Common options for the splitting criteria:
# 
# - **classification error rate:** fraction of training observations in a region that don't belong to the most common class
# - **Gini index:** measure of total variance across classes in a region

# ### Example of classification error rate
# 
# Pretend we are predicting whether someone buys an iPhone or an Android:
# 
# - At a particular node, there are **25 observations** (phone buyers), of whom **10 bought iPhones and 15 bought Androids**.
# - Since the majority class is **Android**, that's our prediction for all 25 observations, and thus the classification error rate is **10/25 = 40%**.
# 
# Our goal in making splits is to **reduce the classification error rate**. Let's try splitting on gender:
# 
# - **Males:** 2 iPhones and 12 Androids, thus the predicted class is Android
# - **Females:** 8 iPhones and 3 Androids, thus the predicted class is iPhone
# - Classification error rate after this split would be **5/25 = 20%**
# 
# Compare that with a split on age:
# 
# - **30 or younger:** 4 iPhones and 8 Androids, thus the predicted class is Android
# - **31 or older:** 6 iPhones and 7 Androids, thus the predicted class is Android
# - Classification error rate after this split would be **10/25 = 40%**
# 
# The decision tree algorithm will try **every possible split across all features**, and choose the split that **reduces the error rate the most.**

# ### Example of Gini index
# 
# Calculate the Gini index before making a split:
# 
# $$1 - \left(\frac {iPhone} {Total}\right)^2 - \left(\frac {Android} {Total}\right)^2 = 1 - \left(\frac {10} {25}\right)^2 - \left(\frac {15} {25}\right)^2 = 0.48$$
# 
# - The **maximum value** of the Gini index is 0.5, and occurs when the classes are perfectly balanced in a node.
# - The **minimum value** of the Gini index is 0, and occurs when there is only one class represented in a node.
# - A node with a lower Gini index is said to be more "pure".
# 
# Evaluating the split on **gender** using Gini index:
# 
# $$\text{Males: } 1 - \left(\frac {2} {14}\right)^2 - \left(\frac {12} {14}\right)^2 = 0.24$$
# $$\text{Females: } 1 - \left(\frac {8} {11}\right)^2 - \left(\frac {3} {11}\right)^2 = 0.40$$
# $$\text{Weighted Average: } 0.24 \left(\frac {14} {25}\right) + 0.40 \left(\frac {11} {25}\right) = 0.31$$
# 
# Evaluating the split on **age** using Gini index:
# 
# $$\text{30 or younger: } 1 - \left(\frac {4} {12}\right)^2 - \left(\frac {8} {12}\right)^2 = 0.44$$
# $$\text{31 or older: } 1 - \left(\frac {6} {13}\right)^2 - \left(\frac {7} {13}\right)^2 = 0.50$$
# $$\text{Weighted Average: } 0.44 \left(\frac {12} {25}\right) + 0.50 \left(\frac {13} {25}\right) = 0.47$$
# 
# Again, the decision tree algorithm will try **every possible split**, and will choose the split that **reduces the Gini index (and thus increases the "node purity") the most.**

# ### Comparing classification error rate and Gini index
# 
# - Gini index is generally preferred because it will make splits that **increase node purity**, even if that split does not change the classification error rate.
# - Node purity is important because we're interested in the **class proportions** in each region, since that's how we calculate the **predicted probability** of each class.
# - scikit-learn's default splitting criteria for classification trees is Gini index.
# 
# Note: There is another common splitting criteria called **cross-entropy**. It's numerically similar to Gini index, but slower to compute, thus it's not as popular as Gini index.

# ## Building a classification tree in scikit-learn

# We'll build a classification tree using the Titanic data:

# read in the data
url = 'https://raw.githubusercontent.com/justmarkham/DAT8/master/data/titanic.csv'
titanic = pd.read_csv(url)

# encode female as 0 and male as 1
titanic['Sex'] = titanic.Sex.map({'female':0, 'male':1})

# fill in the missing values for age with the median age
titanic.Age.fillna(titanic.Age.median(), inplace=True)

# create a DataFrame of dummy variables for Embarked
embarked_dummies = pd.get_dummies(titanic.Embarked, prefix='Embarked')
embarked_dummies.drop(embarked_dummies.columns[0], axis=1, inplace=True)

# concatenate the original DataFrame and the dummy DataFrame
titanic = pd.concat([titanic, embarked_dummies], axis=1)

# print the updated DataFrame
titanic.head()


# - **Survived:** 0=died, 1=survived (response variable)
# - **Pclass:** 1=first class, 2=second class, 3=third class
#     - What will happen if the tree splits on this feature?
# - **Sex:** 0=female, 1=male
# - **Age:** numeric value
# - **Embarked:** C or Q or S

# define X and y
feature_cols = ['Pclass', 'Sex', 'Age', 'Embarked_Q', 'Embarked_S']
X = titanic[feature_cols]
y = titanic.Survived


# fit a classification tree with max_depth=3 on all data
from sklearn.tree import DecisionTreeClassifier
treeclf = DecisionTreeClassifier(max_depth=3, random_state=1)
treeclf.fit(X, y)


# create a Graphviz file
export_graphviz(treeclf, out_file='tree_titanic.dot', feature_names=feature_cols)

# At the command line, run this to convert to PNG:
#   dot -Tpng tree_titanic.dot -o tree_titanic.png


# ![Tree for Titanic data](images/tree_titanic.png)

# Notice the split in the bottom right: the **same class** is predicted in both of its leaves. That split didn't affect the **classification error rate**, though it did increase the **node purity**, which is important because it increases the accuracy of our predicted probabilities.

# compute the feature importances
pd.DataFrame({'feature':feature_cols, 'importance':treeclf.feature_importances_})


# # Part 3: Comparing decision trees with other models
# 
# **Advantages of decision trees:**
# 
# - Can be used for regression or classification
# - Can be displayed graphically
# - Highly interpretable
# - Can be specified as a series of rules, and more closely approximate human decision-making than other models
# - Prediction is fast
# - Features don't need scaling
# - Automatically learns feature interactions
# - Tends to ignore irrelevant features
# - Non-parametric (will outperform linear models if relationship between features and response is highly non-linear)

# ![Trees versus linear models](images/tree_vs_linear.png)

# **Disadvantages of decision trees:**
# 
# - Performance is (generally) not competitive with the best supervised learning methods
# - Can easily overfit the training data (tuning is required)
# - Small variations in the data can result in a completely different tree (high variance)
# - Recursive binary splitting makes "locally optimal" decisions that may not result in a globally optimal tree
# - Doesn't tend to work well if the classes are highly unbalanced
# - Doesn't tend to work well with very small datasets