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Python Machine Learning

Organize data using effective pre-processing

techniques and use the best practices to
evaluate your machine learning models

Sebastian Raschka

If you want to nd out how to use Python to start answering

critical questions of your data, pick up Python Machine
Learningwhether you want to start from scratch or want
to extend your data science knowledge, this is an essential
and unmissable resource.

What you will learn from this book

Python Machine Learning

Python Machine Learning

ee

Unlock deeper insights into machine learning with this vital guide
to cutting-edge predictive analytics
Foreword by Dr. Randal S. Olson
Artificial Intelligence and Machine Learning Researcher, University of Pennsylvania

Sebastian Raschka

In this package, you will find:

The author biography

A preview chapter from the book, Chapter 3 'A Tour of Machine Learning
Classifiers Using Scikit-learn'
A synopsis of the books content
More information on Python Machine Learning

About the Author

Sebastian Raschka is a PhD student at Michigan State University, who develops

new computational methods in the field of computational biology. He has been

ranked as the number one most influential data scientist on GitHub by Analytics
Vidhya. He has a yearlong experience in Python programming and he has conducted
several seminars on the practical applications of data science and machine learning.
Talking and writing about data science, machine learning, and Python really
motivated Sebastian to write this book in order to help people develop data-driven
solutions without necessarily needing to have a machine learning background.
He has also actively contributed to open source projects and methods that he
implemented, which are now successfully used in machine learning competitions,
such as Kaggle. In his free time, he works on models for sports predictions, and if he
is not in front of the computer, he enjoys playing sports.

Preface
I probably don't need to tell you that machine learning has become one of the most
exciting technologies of our time and age. Big companies, such as Google, Facebook,
Apple, Amazon, IBM, and many more, heavily invest in machine learning research
and applications for good reasons. Although it may seem that machine learning has
become the buzzword of our time and age, it is certainly not a hype. This exciting
field opens the way to new possibilities and has become indispensable to our daily
lives. Talking to the voice assistant on our smart phones, recommending the right
product for our customers, stopping credit card fraud, filtering out spam from our
e-mail inboxes, detecting and diagnosing medical diseases, the list goes on and on.
If you want to become a machine learning practitioner, a better problem solver, or
maybe even consider a career in machine learning research, then this book is for you!
However, for a novice, the theoretical concepts behind machine learning can be quite
overwhelming. Yet, many practical books that have been published in recent years
will help you get started in machine learning by implementing powerful learning
algorithms. In my opinion, the use of practical code examples serve an important
purpose. They illustrate the concepts by putting the learned material directly into
action. However, remember that with great power comes great responsibility! The
concepts behind machine learning are too beautiful and important to be hidden in
a black box. Thus, my personal mission is to provide you with a different book; a
book that discusses the necessary details regarding machine learning concepts, offers
intuitive yet informative explanations on how machine learning algorithms work,
how to use them, and most importantly, how to avoid the most common pitfalls.
If you type "machine learning" as a search term in Google Scholar, it returns an
overwhelmingly large number-1,800,000 publications. Of course, we cannot discuss
all the nitty-gritty details about all the different algorithms and applications that have
emerged in the last 60 years. However, in this book, we will embark on an exciting
journey that covers all the essential topics and concepts to give you a head start in this
field. If you find that your thirst for knowledge is not satisfied, there are many useful
resources that can be used to follow up on the essential breakthroughs in this field.

Preface

If you have already studied machine learning theory in detail, this book will show
you how to put your knowledge into practice. If you have used machine learning
techniques before and want to gain more insight into how machine learning really
works, this book is for you! Don't worry if you are completely new to the machine
learning field; you have even more reason to be excited. I promise you that machine
learning will change the way you think about the problems you want to solve and
will show you how to tackle them by unlocking the power of data.
Before we dive deeper into the machine learning field, let me answer your most
important question, "why Python?" The answer is simple: it is powerful yet very
accessible. Python has become the most popular programming language for data
science because it allows us to forget about the tedious parts of programming and
offers us an environment where we can quickly jot down our ideas and put concepts
directly into action.
Reflecting on my personal journey, I can truly say that the study of machine learning
made me a better scientist, thinker, and problem solver. In this book, I want to
share this knowledge with you. Knowledge is gained by learning, the key is our
enthusiasm, and the true mastery of skills can only be achieved by practice. The road
ahead may be bumpy on occasions, and some topics may be more challenging than
others, but I hope that you will embrace this opportunity and focus on the reward.
Remember that we are on this journey together, and throughout this book, we will
add many powerful techniques to your arsenal that will help us solve even the
toughest problems the data-driven way.

What this book covers

Chapter 1, Giving Computers the Ability to Learn from Data, introduces you to the
main subareas of machine learning to tackle various problem tasks. In addition, it
discusses the essential steps for creating a typical machine learning model building
pipeline that will guide us through the following chapters.
Chapter 2, Training Machine Learning Algorithms for Classification, goes back to
the origin of machine learning and introduces binary perceptron classifiers and
adaptive linear neurons. This chapter is a gentle introduction to the fundamentals
of pattern classification and focuses on the interplay of optimization algorithms and
machine learning.
Chapter 3, A Tour of Machine Learning Classifiers Using Scikit-learn, describes the
essential machine learning algorithms for classification and provides practical
examples using one of the most popular and comprehensive open source machine
learning libraries, scikit-learn.

Preface

Chapter 4, Building Good Training Sets Data Preprocessing, discusses how to deal with
the most common problems in unprocessed datasets, such as missing data. It also
discusses several approaches to identify the most informative features in datasets
and teaches you how to prepare variables of different types as proper inputs for
machine learning algorithms.
Chapter 5, Compressing Data via Dimensionality Reduction, describes the essential
techniques to reduce the number of features in a dataset to smaller sets while
retaining most of their useful and discriminatory information. It discusses the
standard approach to dimensionality reduction via principal component analysis
and compares it to supervised and nonlinear transformation techniques.
Chapter 6, Learning Best Practices for Model Evaluation and Hyperparameter Tuning,
discusses the do's and don'ts for estimating the performances of predictive models.
Moreover, it discusses different metrics for measuring the performance of our
models and techniques to fine-tune machine learning algorithms.
Chapter 7, Combining Different Models for Ensemble Learning, introduces you to the
different concepts of combining multiple learning algorithms effectively. It teaches
you how to build ensembles of experts to overcome the weaknesses of individual
learners, resulting in more accurate and reliable predictions.
Chapter 8, Applying Machine Learning to Sentiment Analysis, discusses the essential
steps to transform textual data into meaningful representations for machine learning
algorithms to predict the opinions of people based on their writing.
Chapter 9, Embedding a Machine Learning Model into a Web Application, continues with
the predictive model from the previous chapter and walks you through the essential
steps of developing web applications with embedded machine learning models.
Chapter 10, Predicting Continuous Target Variables with Regression Analysis, discusses
the essential techniques for modeling linear relationships between target and
response variables to make predictions on a continuous scale. After introducing
different linear models, it also talks about polynomial regression and
tree-based approaches.
Chapter 11, Working with Unlabeled Data Clustering Analysis, shifts the focus to a
different subarea of machine learning, unsupervised learning. We apply algorithms
from three fundamental families of clustering algorithms to find groups of objects
that share a certain degree of similarity.

Preface

Chapter 12, Training Artificial Neural Networks for Image Recognition, extends the
concept of gradient-based optimization, which we first introduced in Chapter 2,
Training Machine Learning Algorithms for Classification, to build powerful, multilayer
neural networks based on the popular backpropagation algorithm.
Chapter 13, Parallelizing Neural Network Training with Theano, builds upon the
knowledge from the previous chapter to provide you with a practical guide for
training neural networks more efficiently. The focus of this chapter is on Theano, an
open source Python library that allows us to utilize multiple cores of modern GPUs.

A Tour of Machine Learning

Classiers Using Scikit-learn
In this chapter, we will take a tour through a selection of popular and powerful
machine learning algorithms that are commonly used in academia as well as in the
industry. While learning about the differences between several supervised learning
algorithms for classification, we will also develop an intuitive appreciation of their
individual strengths and weaknesses. Also, we will take our first steps with the
scikit-learn library, which offers a user-friendly interface for using those algorithms
efficiently and productively.
The topics that we will learn about throughout this chapter are as follows:

Introduction to the concepts of popular classification algorithms

Using the scikit-learn machine learning library

Questions to ask when selecting a machine learning algorithm

Choosing a classication algorithm

Choosing an appropriate classification algorithm for a particular problem task
requires practice: each algorithm has its own quirks and is based on certain
assumptions. To restate the "No Free Lunch" theorem: no single classifier works best
across all possible scenarios. In practice, it is always recommended that you compare
the performance of at least a handful of different learning algorithms to select the
best model for the particular problem; these may differ in the number of features
or samples, the amount of noise in a dataset, and whether the classes are linearly
separable or not.

[ 49 ]

A Tour of Machine Learning Classifiers Using Scikit-learn

Eventually, the performance of a classifier, computational power as well as

predictive power, depends heavily on the underlying data that are available for
learning. The five main steps that are involved in training a machine learning
algorithm can be summarized as follows:
1. Selection of features.
2. Choosing a performance metric.
3. Choosing a classifier and optimization algorithm.
4. Evaluating the performance of the model.
5. Tuning the algorithm.
Since the approach of this book is to build machine learning knowledge step by step,
we will mainly focus on the principal concepts of the different algorithms in this
chapter and revisit topics such as feature selection and preprocessing, performance
metrics, and hyperparameter tuning for more detailed discussions later in this book.

First steps with scikit-learn

In Chapter 2, Training Machine Learning Algorithms for Classification, you learned about
two related learning algorithms for classification: the perceptron rule and Adaline,
which we implemented in Python by ourselves. Now we will take a look at the
scikit-learn API, which combines a user-friendly interface with a highly optimized
implementation of several classification algorithms. However, the scikit-learn library
offers not only a large variety of learning algorithms, but also many convenient
functions to preprocess data and to fine-tune and evaluate our models. We will
discuss this in more detail together with the underlying concepts in Chapter 4,
Building Good Training Sets Data Preprocessing, and Chapter 5, Compressing
Data via Dimensionality Reduction.

Training a perceptron via scikit-learn

To get started with the scikit-learn library, we will train a perceptron model
similar to the one that we implemented in Chapter 2, Training Machine Learning
Algorithms for Classification. For simplicity, we will use the already familiar Iris
dataset throughout the following sections. Conveniently, the Iris dataset is already
available via scikit-learn, since it is a simple yet popular dataset that is frequently
used for testing and experimenting with algorithms. Also, we will only use two
features from the Iris flower dataset for visualization purposes.

[ 50 ]

Chapter 3

We will assign the petal length and petal width of the 150 flower samples to the feature
matrix X and the corresponding class labels of the flower species to the vector y:
>>>
>>>
>>>
>>>
>>>

from sklearn import datasets

import numpy as np
iris = datasets.load_iris()
X = iris.data[:, [2, 3]]
y = iris.target

If we executed np.unique(y) to return the different class labels stored in iris.

target, we would see that the Iris flower class names, Iris-Setosa, Iris-Versicolor,
and Iris-Virginica, are already stored as integers (0, 1, 2), which is recommended
for the optimal performance of many machine learning libraries.
To evaluate how well a trained model performs on unseen data, we will further split
the dataset into separate training and test datasets. Later in Chapter 5, Compressing
Data via Dimensionality Reduction, we will discuss the best practices around model
evaluation in more detail:
>>> from sklearn.cross_validation import train_test_split
>>> X_train, X_test, y_train, y_test = train_test_split(
...
X, y, test_size=0.3, random_state=0)

Using the train_test_split function from scikit-learn's cross_validation

module, we randomly split the X and y arrays into 30 percent test data (45 samples)
and 70 percent training data (105 samples).
Many machine learning and optimization algorithms also require feature scaling
for optimal performance, as we remember from the gradient descent example
in Chapter 2, Training Machine Learning Algorithms for Classification. Here, we will
standardize the features using the StandardScaler class from scikit-learn's
preprocessing module:
>>>
>>>
>>>
>>>
>>>

from sklearn.preprocessing import StandardScaler

sc = StandardScaler()
sc.fit(X_train)
X_train_std = sc.transform(X_train)
X_test_std = sc.transform(X_test)

[ 51 ]

A Tour of Machine Learning Classifiers Using Scikit-learn

Using the preceding code, we loaded the StandardScaler class from the
preprocessing module and initialized a new StandardScaler object that we assigned
to the variable sc. Using the fit method, StandardScaler estimated the parameters
(sample mean) and (standard deviation) for each feature dimension from the
training data. By calling the transform method, we then standardized the training
data using those estimated parameters and . Note that we used the same
scaling parameters to standardize the test set so that both the values in the training
and test dataset are comparable to each other.
Having standardized the training data, we can now train a perceptron model. Most
algorithms in scikit-learn already support multiclass classification by default via the
One-vs.-Rest (OvR) method, which allows us to feed the three flower classes to the
perceptron all at once. The code is as follows:
>>> from sklearn.linear_model import Perceptron
>>> ppn = Perceptron(n_iter=40, eta0=0.1, random_state=0)
>>> ppn.fit(X_train_std, y_train)

The scikit-learn interface reminds us of our perceptron implementation in Chapter 2,

Training Machine Learning Algorithms for Classification: after loading the Perceptron
class from the linear_model module, we initialized a new Perceptron object and
trained the model via the fit method. Here, the model parameter eta0 is equivalent
to the learning rate eta that we used in our own perceptron implementation, and the
parameter n_iter defines the number of epochs (passes over the training set). As
we remember from Chapter 2, Training Machine Learning Algorithms for Classification,
finding an appropriate learning rate requires some experimentation. If the learning
rate is too large, the algorithm will overshoot the global cost minimum. If the
learning rate is too small, the algorithm requires more epochs until convergence,
which can make the learning slowespecially for large datasets. Also, we used the
random_state parameter for reproducibility of the initial shuffling of the training
dataset after each epoch.
Having trained a model in scikit-learn, we can make predictions via the predict
method, just like in our own perceptron implementation in Chapter 2, Training
Machine Learning Algorithms for Classification. The code is as follows:
>>> y_pred = ppn.predict(X_test_std)
>>> print('Misclassified samples: %d' % (y_test != y_pred).sum())
Misclassified samples: 4

[ 52 ]

Chapter 3

On executing the preceding code, we see that the perceptron misclassifies 4 out of the
45 flower samples. Thus, the misclassification error on the test dataset is 0.089 or 8.9
percent ( 4 / 45 0.089 ) .
Instead of the misclassification error, many machine learning
practitioners report the classification accuracy of a model, which is
simply calculated as follows:
1 - misclassification error = 0.911 or 91.1 percent.

Scikit-learn also implements a large variety of different performance metrics that are
available via the metrics module. For example, we can calculate the classification
accuracy of the perceptron on the test set as follows:
>>> from sklearn.metrics import accuracy_score
>>> print('Accuracy: %.2f' % accuracy_score(y_test, y_pred))
0.91

Here, y_test are the true class labels and y_pred are the class labels that we
predicted previously.
Note that we evaluate the performance of our models based
on the test set in this chapter. In Chapter 5, Compressing Data via
Dimensionality Reduction, you will learn about useful techniques,
including graphical analysis such as learning curves, to detect
and prevent overfitting. Overfitting means that the model
captures the patterns in the training data well, but fails to
generalize well to unseen data.

Finally, we can use our plot_decision_regions function from Chapter 2, Training

Machine Learning Algorithms for Classification, to plot the decision regions of our
newly trained perceptron model and visualize how well it separates the different
flower samples. However, let's add a small modification to highlight the samples
from the test dataset via small circles:
from matplotlib.colors import ListedColormap
import matplotlib.pyplot as plt
def plot_decision_regions(X, y, classifier,
test_idx=None, resolution=0.02):
# setup marker generator and color map

[ 53 ]

A Tour of Machine Learning Classifiers Using Scikit-learn

markers = ('s', 'x', 'o', '^', 'v')
colors = ('red', 'blue', 'lightgreen', 'gray', 'cyan')
cmap = ListedColormap(colors[:len(np.unique(y))])
# plot the decision surface
x1_min, x1_max = X[:, 0].min() - 1, X[:, 0].max() + 1
x2_min, x2_max = X[:, 1].min() - 1, X[:, 1].max() + 1
xx1, xx2 = np.meshgrid(np.arange(x1_min, x1_max, resolution),
np.arange(x2_min, x2_max, resolution))
Z = classifier.predict(np.array([xx1.ravel(), xx2.ravel()]).T)
Z = Z.reshape(xx1.shape)
plt.contourf(xx1, xx2, Z, alpha=0.4, cmap=cmap)
plt.xlim(xx1.min(), xx1.max())
plt.ylim(xx2.min(), xx2.max())
# plot all samples
X_test, y_test = X[test_idx, :], y[test_idx]
for idx, cl in enumerate(np.unique(y)):
plt.scatter(x=X[y == cl, 0], y=X[y == cl, 1],
alpha=0.8, c=cmap(idx),
marker=markers[idx], label=cl)
# highlight test samples
if test_idx:
X_test, y_test = X[test_idx, :], y[test_idx]
plt.scatter(X_test[:, 0], X_test[:, 1], c='',
alpha=1.0, linewidth=1, marker='o',
s=55, label='test set')

With the slight modification that we made to the plot_decision_regions function

(highlighted in the preceding code), we can now specify the indices of the samples
that we want to mark on the resulting plots. The code is as follows:
>>>
>>>
>>>
...
...
...
>>>
>>>
>>>
>>>

X_combined_std = np.vstack((X_train_std, X_test_std))

y_combined = np.hstack((y_train, y_test))
plot_decision_regions(X=X_combined_std,
y=y_combined,
classifier=ppn,
test_idx=range(105,150))
plt.xlabel('petal length [standardized]')
plt.ylabel('petal width [standardized]')
plt.legend(loc='upper left')
plt.show()

[ 54 ]

Chapter 3

As we can see in the resulting plot, the three flower classes cannot be perfectly
separated by a linear decision boundaries:

We remember from our discussion in Chapter 2, Training Machine Learning Algorithms

for Classification, that the perceptron algorithm never converges on datasets that
aren't perfectly linearly separable, which is why the use of the perceptron algorithm
is typically not recommended in practice. In the following sections, we will look at
more powerful linear classifiers that converge to a cost minimum even if the classes
are not perfectly linearly separable.
The Perceptron as well as other scikit-learn functions and
classes have additional parameters that we omit for clarity.
You can read more about those parameters using the help
function in Python (for example, help(Perceptron)) or by
going through the excellent scikit-learn online documentation
at http://scikit-learn.org/stable/.

[ 55 ]

A Tour of Machine Learning Classifiers Using Scikit-learn

Modeling class probabilities via logistic

regression
Although the perceptron rule offers a nice and easygoing introduction to machine
learning algorithms for classification, its biggest disadvantage is that it never
converges if the classes are not perfectly linearly separable. The classification task
in the previous section would be an example of such a scenario. Intuitively, we can
think of the reason as the weights are continuously being updated since there is
always at least one misclassified sample present in each epoch. Of course, you can
change the learning rate and increase the number of epochs, but be warned that the
perceptron will never converge on this dataset. To make better use of our time, we
will now take a look at another simple yet more powerful algorithm for linear and
binary classification problems: logistic regression. Note that, in spite of its name,
logistic regression is a model for classification, not regression.

Logistic regression intuition and conditional

probabilities
Logistic regression is a classification model that is very easy to implement but
performs very well on linearly separable classes. It is one of the most widely used
algorithms for classification in industry. Similar to the perceptron and Adaline, the
logistic regression model in this chapter is also a linear model for binary classification
that can be extended to multiclass classification via the OvR technique.
To explain the idea behind logistic regression as a probabilistic model, let's first
introduce the odds ratio, which is the odds in favor of a particular event. The odds
p

ratio can be written as (1 p ) , where p stands for the probability of the positive
event. The term positive event does not necessarily mean good, but refers to the event
that we want to predict, for example, the probability that a patient has a certain
disease; we can think of the positive event as class label y = 1 . We can then further
define the logit function, which is simply the logarithm of the odds ratio (log-odds):

logit ( p ) = log

[ 56 ]

p
(1 p )

Chapter 3

The logit function takes input values in the range 0 to 1 and transforms them to
values over the entire real number range, which we can use to express a linear
relationship between feature values and the log-odds:
n

logit ( p ( y = 1| x ) ) = w0 x0 + w1 x1 +  + wm xm = wm xm = w T x
i =0

Here, p ( y = 1| x ) is the conditional probability that a particular sample belongs to

class 1 given its features x.
Now what we are actually interested in is predicting the probability that a certain
sample belongs to a particular class, which is the inverse form of the logit function. It
is also called the logistic function, sometimes simply abbreviated as sigmoid function
due to its characteristic S-shape.

( z) =

1
1 + e z

Here, z is the net input, that is, the linear combination of weights and sample features
and can be calculated as z = w T x = w0 + w1 x1 +  + wm xm .
Now let's simply plot the sigmoid function for some values in the range -7 to 7 to see
what it looks like:
>>>
>>>
>>>
...
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>

import matplotlib.pyplot as plt

import numpy as np
def sigmoid(z):
return 1.0 / (1.0 + np.exp(-z))
z = np.arange(-7, 7, 0.1)
phi_z = sigmoid(z)
plt.plot(z, phi_z)
plt.axvline(0.0, color='k')
plt.axhspan(0.0, 1.0, facecolor='1.0', alpha=1.0, ls='dotted')
plt.axhline(y=0.5, ls='dotted', color='k')
plt.yticks([0.0, 0.5, 1.0])
plt.ylim(-0.1, 1.1)
plt.xlabel('z')
plt.ylabel('$\phi (z)$')
plt.show()

[ 57 ]

A Tour of Machine Learning Classifiers Using Scikit-learn

As a result of executing the previous code example, we should now see the S-shaped
(sigmoidal) curve:

We can see that ( z ) approaches 1 if z goes towards infinity ( z ), since e

becomes very small for large values of z. Similarly, ( z ) goes towards 0 for z
as the result of an increasingly large denominator. Thus, we conclude that this
sigmoid function takes real number values as input and transforms them to values in
the range [0, 1] with an intercept at ( z ) = 0.5 .
z

To build some intuition for the logistic regression model, we can relate it to our
previous Adaline implementation in Chapter 2, Training Machine Learning Algorithms
for Classification. In Adaline, we used the identity function ( z ) = z as the activation
function. In logistic regression, this activation function simply becomes the sigmoid
function that we defined earlier, which is illustrated in the following figure:
1

Error

w0
x1
x2

w1
w2

..
.

wm

S
Net input
function

xm

[ 58 ]

y
Sigmoid
function

Quantizer

Chapter 3

The output of the sigmoid function is then interpreted as the probability of particular
sample belonging to class 1 ( z ) = P ( y = 1| x; w ) , given its features x parameterized by
the weights w. For example, if we compute ( z ) = 0.8 for a particular flower sample,
it means that the chance that this sample is an Iris-Versicolor flower is 80 percent.
Similarly, the probability that this flower is an Iris-Setosa flower can be calculated as
P ( y = 0 | x; w ) = 1 P ( y = 1| x; w ) = 0.2 or 20 percent. The predicted probability can then
simply be converted into a binary outcome via a quantizer (unit step function):

1 if ( z ) 0.5
y =
0 otherwise
If we look at the preceding sigmoid plot, this is equivalent to the following:

1
y =
0

if z 0.0
otherwise

In fact, there are many applications where we are not only interested in the predicted
class labels, but where estimating the class-membership probability is particularly
useful. Logistic regression is used in weather forecasting, for example, to not
only predict if it will rain on a particular day but also to report the chance of rain.
Similarly, logistic regression can be used to predict the chance that a patient has a
particular disease given certain symptoms, which is why logistic regression enjoys
wide popularity in the field of medicine.

Learning the weights of the logistic cost

function
You learned how we could use the logistic regression model to predict probabilities
and class labels. Now let's briefly talk about the parameters of the model, for
example, weights w. In the previous chapter, we defined the sum-squared-error
cost function:

J (w) =
i

(( )

1
z (i ) y (i )
2

[ 59 ]

A Tour of Machine Learning Classifiers Using Scikit-learn

We minimized this in order to learn the weights w for our Adaline classification
model. To explain how we can derive the cost function for logistic regression,
let's first define the likelihood L that we want to maximize when we build a
logistic regression model, assuming that the individual samples in our dataset are
independent of one another. The formula is as follows:

i =1

i =1

y( )

1 y ( )

( ( )) ( ( ))

L ( w ) = P ( y | x; w ) = P y ( ) | x ( ) ; w = z ( )
i

1 z( )
i

In practice, it is easier to maximize the (natural) log of this equation, which is called
the log-likelihood function:
n

( ( )) + (1 y ) log (1 ( z ))

l ( w ) = log L ( w ) = log z (i )
i =1

(i )

(i )

Firstly, applying the log function reduces the potential for numerical underflow,
which can occur if the likelihoods are very small. Secondly, we can convert the
product of factors into a summation of factors, which makes it easier to obtain
the derivative of this function via the addition trick, as you may remember
from calculus.
Now we could use an optimization algorithm such as gradient ascent to maximize
this log-likelihood function. Alternatively, let's rewrite the log-likelihood as a cost
function J that can be minimized using gradient descent as in Chapter 2, Training
Machine Learning Algorithms for Classification:
n

( ( )) (1 y ) log (1 ( z ))

J ( w ) = log z (i )
i =1

(i )

(i )

To get a better grasp on this cost function, let's take a look at the cost that we
calculate for one single-sample instance:

J ( ( z ) , y; w ) = y log ( ( z ) ) (1 y ) log (1 ( z ) )

[ 60 ]

Chapter 3

Looking at the preceding equation, we can see that the first term becomes zero if

y = 0 , and the second term becomes zero if y = 1 , respectively:

log ( ( z ) )
if y = 1
J ( ( z ) , y ; w ) =
log (1 ( z ) ) if y = 0
The following plot illustrates the cost for the classification of a single-sample instance
for different values of ( z ) :

We can see that the cost approaches 0 (plain blue line) if we correctly predict that
a sample belongs to class 1. Similarly, we can see on the y axis that the cost also
approaches 0 if we correctly predict y = 0 (dashed line). However, if the prediction
is wrong, the cost goes towards infinity. The moral is that we penalize wrong
predictions with an increasingly larger cost.

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A Tour of Machine Learning Classifiers Using Scikit-learn

Training a logistic regression model with

scikit-learn
If we were to implement logistic regression ourselves, we could simply substitute
the cost function J in our Adaline implementation from Chapter 2, Training Machine
Learning Algorithms for Classification, by the new cost function:

( ( )) + (1 y ) log (1 ( z ))

J ( w ) = y (i ) log z (i )
i

(i )

(i )

This would compute the cost of classifying all training samples per epoch and we
would end up with a working logistic regression model. However, since scikit-learn
implements a highly optimized version of logistic regression that also supports
multiclass settings off-the-shelf, we will skip the implementation and use the
sklearn.linear_model.LogisticRegression class as well as the familiar fit
method to train the model on the standardized flower training dataset:
>>> from sklearn.linear_model import LogisticRegression
>>> lr = LogisticRegression(C=1000.0, random_state=0)
>>> lr.fit(X_train_std, y_train)
>>> plot_decision_regions(X_combined_std,
...
y_combined, classifier=lr,
...
test_idx=range(105,150))
>>> plt.xlabel('petal length [standardized]')
>>> plt.ylabel('petal width [standardized]')
>>> plt.legend(loc='upper left')
>>> plt.show()

After fitting the model on the training data, we plotted the decision regions, training
samples and test samples, as shown here:

[ 62 ]

Chapter 3

Looking at the preceding code that we used to train the LogisticRegression

model, you might now be wondering, "What is this mysterious parameter C?"
We will get to this in a second, but let's briefly go over the concept of overfitting
and regularization in the next subsection first.
Furthermore, we can predict the class-membership probability of the samples via
the predict_proba method. For example, we can predict the probabilities of the
first Iris-Setosa sample:
>>> lr.predict_proba(X_test_std[0,:])

This returns the following array:

array([[

0.000,

0.063,

0.937]])

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A Tour of Machine Learning Classifiers Using Scikit-learn

The preceding array tells us that the model predicts a chance of 93.7 percent that the
sample belongs to the Iris-Virginica class, and a 6.3 percent chance that the sample is
a Iris-Versicolor flower.
We can show that the weight update in logistic regression via gradient descent is
indeed equal to the equation that we used in Adaline in Chapter 2, Training Machine
Learning Algorithms for Classification. Let's start by calculating the partial derivative of
the log-likelihood function with respect to the jth weight:

1
1
(1 y )
l ( w ) = y
( z)

w j

z
w
(
)
(
)
j

Before we continue, let's calculate the partial derivative of the sigmoid function first:

1
1
1
=
( z) =
e z =
2
z

z
z
z 1 + e
1 + e z
(1 + e )

1
z
1+ e

= ( z ) (1 ( z ) )

Now we can resubstitute ( z ) = ( z ) (1 ( z ) ) in our first equation to obtain

z
the following:

1
1
(1 y )
( z)
y

1 ( z ) w j
( z)

1
1
= y
(1 y )
z
( z ) (1 ( z ) )
1 ( z)
w j
( z)

= y (1 ( z ) ) (1 y ) ( z ) x j
= ( y ( z )) x j

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Chapter 3

Remember that the goal is to find the weights that maximize the log-likelihood so
that we would perform the update for each weight as follows:
n

( ) ) x( )

w j := w j + y (i ) z (i )
i =1

Since we update all weights simultaneously, we can write the general update rule
as follows:

w := w + w
We define w as follows:

w = l ( w )
Since maximizing the log-likelihood is equal to minimizing the cost function J that
we defined earlier, we can write the gradient descent update rule as follows:

w j =

( ) )

n
J
= y (i ) z (i ) x(i )
w j
i =1

w := w + w , w = J ( w )
This is equal to the gradient descent rule in Adaline in Chapter 2, Training Machine
Learning Algorithms for Classification.

Tackling overtting via regularization

Overfitting is a common problem in machine learning, where a model performs well
on training data but does not generalize well to unseen data (test data). If a model
suffers from overfitting, we also say that the model has a high variance, which can
be caused by having too many parameters that lead to a model that is too complex
given the underlying data. Similarly, our model can also suffer from underfitting
(high bias), which means that our model is not complex enough to capture the
pattern in the training data well and therefore also suffers from low performance
on unseen data.

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A Tour of Machine Learning Classifiers Using Scikit-learn

Although we have only encountered linear models for classification so far, the
problem of overfitting and underfitting can be best illustrated by using a more
complex, nonlinear decision boundary as shown in the following figure:

Variance measures the consistency (or variability) of the model

prediction for a particular sample instance if we would retrain
the model multiple times, for example, on different subsets of
the training dataset. We can say that the model is sensitive to the
randomness in the training data. In contrast, bias measures how far
off the predictions are from the correct values in general if we rebuild
the model multiple times on different training datasets; bias is the
measure of the systematic error that is not due to randomness.

One way of finding a good bias-variance tradeoff is to tune the complexity of

the model via regularization. Regularization is a very useful method to handle
collinearity (high correlation among features), filter out noise from data, and
eventually prevent overfitting. The concept behind regularization is to introduce
additional information (bias) to penalize extreme parameter weights. The most
common form of regularization is the so-called L2 regularization (sometimes also
called L2 shrinkage or weight decay), which can be written as follows:

w =

[ 66 ]

w
j =1

2
j

Chapter 3

Here,

is the so-called regularization parameter.

Regularization is another reason why feature scaling such as
standardization is important. For regularization to work properly,
we need to ensure that all our features are on comparable scales.

In order to apply regularization, we just need to add the regularization term to the
cost function that we defined for logistic regression to shrink the weights:

( ( ( )) + (1 y ) ( log (1 ( z )))) + 2 w

n
J ( w ) = log z (i )
i =1

(i )

Via the regularization parameter , we can then control how well we fit the training
data while keeping the weights small. By increasing the value of , we increase the
regularization strength.
The parameter C that is implemented for the LogisticRegression class in
scikit-learn comes from a convention in support vector machines, which will be
the topic of the next section. C is directly related to the regularization parameter ,
which is its inverse:

C=

So we can rewrite the regularized cost function of logistic regression as follows:

( ( ( )) + (1 y )) ( log (1 ( z ))) + 12 w

n
J ( w ) = C log z (i )
i =1

(i )

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A Tour of Machine Learning Classifiers Using Scikit-learn

Consequently, decreasing the value of the inverse regularization parameter C means

that we are increasing the regularization strength, which we can visualize by plotting
the L2 regularization path for the two weight coefficients:
>>>
>>>
...
...
...
...
>>>
>>>
...
>>>
...
>>>
>>>
>>>
>>>
>>>

weights, params = [], []

for c in np.arange(-5, 5):
lr = LogisticRegression(C=10**c, random_state=0)
lr.fit(X_train_std, y_train)
weights.append(lr.coef_[1])
params.append(10**c)
weights = np.array(weights)
plt.plot(params, weights[:, 0],
label='petal length')
plt.plot(params, weights[:, 1], linestyle='--',
label='petal width')
plt.ylabel('weight coefficient')
plt.xlabel('C')
plt.legend(loc='upper left')
plt.xscale('log')
plt.show()

By executing the preceding code, we fitted ten logistic regression models with
different values for the inverse-regularization parameter C. For the purposes of
illustration, we only collected the weight coefficients of the class 2 vs. all classifier.
Remember that we are using the OvR technique for multiclass classification.
As we can see in the resulting plot, the weight coefficients shrink if we decrease the
parameter C, that is, if we increase the regularization strength:

[ 68 ]

Chapter 3

Since an in-depth coverage of the individual classification algorithms

exceeds the scope of this book, I warmly recommend Dr. Scott
Menard's Logistic Regression: From Introductory to Advanced Concepts
and Applications, Sage Publications, to readers who want to learn more
about logistic regression.

Maximum margin classication with

support vector machines
Another powerful and widely used learning algorithm is the support vector
machine (SVM), which can be considered as an extension of the perceptron. Using
the perceptron algorithm, we minimized misclassification errors. However, in SVMs,
our optimization objective is to maximize the margin. The margin is defined as the
distance between the separating hyperplane (decision boundary) and the training
samples that are closest to this hyperplane, which are the so-called support vectors.
This is illustrated in the following figure:

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A Tour of Machine Learning Classifiers Using Scikit-learn

Maximum margin intuition

The rationale behind having decision boundaries with large margins is that they tend
to have a lower generalization error whereas models with small margins are more
prone to overfitting. To get an intuition for the margin maximization, let's take a
closer look at those positive and negative hyperplanes that are parallel to the decision
boundary, which can be expressed as follows:

w0 + w T x pos = 1

(1)

w0 + w T xneg = 1

( 2)

If we subtract those two linear equations (1) and (2) from each other, we get:

w T ( x pos xneg ) = 2
We can normalize this by the length of the vector w, which is defined as follows:

w =

m
j =1

w2j

So we arrive at the following equation:

w T ( x pos xneg )
w

2
w

The left side of the preceding equation can then be interpreted as the distance
between the positive and negative hyperplane, which is the so-called margin that we
want to maximize.

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Chapter 3

Now the objective function of the SVM becomes the maximization of this margin
2

by maximizing w under the constraint that the samples are classified correctly,
which can be written as follows:

w0 + w T x (i ) 1 if y (i ) = 1
w0 + w T x (i ) < 1 if y (i ) = 1
These two equations basically say that all negative samples should fall on one side
of the negative hyperplane, whereas all the positive samples should fall behind the
positive hyperplane. This can also be written more compactly as follows:

y (i ) w0 + w T x (i ) 1 i
1

w , which can be
In practice, though, it is easier to minimize the reciprocal term
2
solved by quadratic programming. However, a detailed discussion about quadratic
programming is beyond the scope of this book, but if you are interested, you can
learn more about Support Vector Machines (SVM) in Vladimir Vapnik's The Nature
of Statistical Learning Theory, Springer Science & Business Media, or Chris J.C. Burges'
excellent explanation in A Tutorial on Support Vector Machines for Pattern Recognition
(Data mining and knowledge discovery, 2(2):121167, 1998).

Dealing with the nonlinearly separable case

using slack variables
Although we don't want to dive much deeper into the more involved
mathematical concepts behind the margin classification, let's briefly mention the
slack variable . It was introduced by Vladimir Vapnik in 1995 and led to the
so-called soft-margin classification. The motivation for introducing the slack variable
was that the linear constraints need to be relaxed for nonlinearly separable data to
allow convergence of the optimization in the presence of misclassifications under the
appropriate cost penalization.

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A Tour of Machine Learning Classifiers Using Scikit-learn

The positive-values slack variable is simply added to the linear constraints:

w T x (i ) 1 if y (i ) = 1 (i )
w T x (i ) < 1 if y (i ) = 1 + (i )
So the new objective to be minimized (subject to the preceding constraints) becomes:

2
w + C (i )
2
i

Using the variable C, we can then control the penalty for misclassification. Large
values of C correspond to large error penalties whereas we are less strict about
misclassification errors if we choose smaller values for C. We can then we use the
parameter C to control the width of the margin and therefore tune the bias-variance
trade-off as illustrated in the following figure:

This concept is related to regularization, which we discussed previously in the

context of regularized regression where increasing the value of C increases the bias
and lowers the variance of the model.

[ 72 ]

Chapter 3

Now that we learned the basic concepts behind the linear SVM, let's train a SVM
model to classify the different flowers in our Iris dataset:
>>> from sklearn.svm import SVC
>>> svm = SVC(kernel='linear', C=1.0, random_state=0)
>>> svm.fit(X_train_std, y_train)
>>> plot_decision_regions(X_combined_std,
...
y_combined, classifier=svm,
...
test_idx=range(105,150))
>>> plt.xlabel('petal length [standardized]')
>>> plt.ylabel('petal width [standardized]')
>>> plt.legend(loc='upper left')
>>> plt.show()

The decision regions of the SVM visualized after executing the preceding code
example are shown in the following plot:

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A Tour of Machine Learning Classifiers Using Scikit-learn

Logistic regression versus SVM

In practical classification tasks, linear logistic regression and
linear SVMs often yield very similar results. Logistic regression
tries to maximize the conditional likelihoods of the training
data, which makes it more prone to outliers than SVMs. The
SVMs mostly care about the points that are closest to the
decision boundary (support vectors). On the other hand, logistic
regression has the advantage that it is a simpler model that can
be implemented more easily. Furthermore, logistic regression
models can be easily updated, which is attractive when working
with streaming data.

Alternative implementations in scikit-learn

The Perceptron and LogisticRegression classes that we used in the previous
sections via scikit-learn make use of the LIBLINEAR library, which is a highly
optimized C/C++ library developed at the National Taiwan University (http://
www.csie.ntu.edu.tw/~cjlin/liblinear/). Similarly, the SVC class that we
used to train an SVM makes use of LIBSVM, which is an equivalent C/C++ library
specialized for SVMs (http://www.csie.ntu.edu.tw/~cjlin/libsvm/).
The advantage of using LIBLINEAR and LIBSVM over native Python
implementations is that they allow an extremely quick training of large amounts
of linear classifiers. However, sometimes our datasets are too large to fit into
computer memory. Thus, scikit-learn also offers alternative implementations via
the SGDClassifier class, which also supports online learning via the partial_fit
method. The concept behind the SGDClassifier class is similar to the stochastic
gradient algorithm that we implemented in Chapter 2, Training Machine Learning
Algorithms for Classification, for Adaline. We could initialize the stochastic gradient
descent version of the perceptron, logistic regression, and support vector machine
with default parameters as follows:
>>>
>>>
>>>
>>>

from sklearn.linear_model import SGDClassifier

ppn = SGDClassifier(loss='perceptron')
lr = SGDClassifier(loss='log')
svm = SGDClassifier(loss='hinge')

[ 74 ]

Chapter 3

Solving nonlinear problems using a

kernel SVM
Another reason why SVMs enjoy high popularity among machine learning
practitioners is that they can be easily kernelized to solve nonlinear classification
problems. Before we discuss the main concept behind kernel SVM, let's first define and
create a sample dataset to see how such a nonlinear classification problem may look.
Using the following code, we will create a simple dataset that has the form of
an XOR gate using the logical_xor function from NumPy, where 100 samples
will be assigned the class label 1 and 100 samples will be assigned the class
label -1, respectively:
>>>
>>>
>>>
>>>

np.random.seed(0)
X_xor = np.random.randn(200, 2)
y_xor = np.logical_xor(X_xor[:, 0] > 0, X_xor[:, 1] > 0)
y_xor = np.where(y_xor, 1, -1)

>>>
...
>>>
...
>>>
>>>
>>>

plt.scatter(X_xor[y_xor==1, 0], X_xor[y_xor==1, 1],

c='b', marker='x', label='1')
plt.scatter(X_xor[y_xor==-1, 0], X_xor[y_xor==-1, 1],
c='r', marker='s', label='-1')
plt.ylim(-3.0)
plt.legend()
plt.show()

After executing the code, we will have an XOR dataset with random noise,
as shown in the following figure:

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A Tour of Machine Learning Classifiers Using Scikit-learn

Obviously, we would not be able to separate samples from the positive and negative
class very well using a linear hyperplane as the decision boundary via the linear
logistic regression or linear SVM model that we discussed in earlier sections.
The basic idea behind kernel methods to deal with such linearly inseparable data
is to create nonlinear combinations of the original features to project them onto a
higher dimensional space via a mapping function ( ) where it becomes linearly
separable. As shown in the next figure, we can transform a two-dimensional dataset
onto a new three-dimensional feature space where the classes become separable via
the following projection:

( x1 , x2 ) = ( z1 , z2 , z3 ) = ( x1 , x2 , x12 + x22 )
This allows us to separate the two classes shown in the plot via a linear hyperplane
that becomes a nonlinear decision boundary if we project it back onto the original
feature space:

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Chapter 3

Using the kernel trick to nd separating

hyperplanes in higher dimensional space
To solve a nonlinear problem using an SVM, we transform the training data onto
a higher dimensional feature space via a mapping function ( ) and train a linear
SVM model to classify the data in this new feature space. Then we can use the same
mapping function ( ) to transform new, unseen data to classify it using the linear
SVM model.
However, one problem with this mapping approach is that the construction of
the new features is computationally very expensive, especially if we are dealing
with high-dimensional data. This is where the so-called kernel trick comes into
play. Although we didn't go into much detail about how to solve the quadratic
programming task to train an SVM, in practice all we need is to replace the dot

product x (i )T x ( j ) by ( x (i ) ) ( x ( j ) ) . In order to save the expensive step of calculating

this dot product between two points explicitly, we define a so-called kernel function:
T

( ) ( )

k x (i ) , x ( j ) = x (i ) x ( j ) .
T

One of the most widely used kernels is the Radial Basis Function kernel
(RBF kernel) or Gaussian kernel:

(i )

k x ,x

( j)

x (i ) - x ( j )
= exp

2 2

This is often simplified to:

k x (i ) , x ( j ) = exp x (i ) - x ( j )
Here, =

1
2 2

is a free parameter that is to be optimized.

Roughly speaking, the term kernel can be interpreted as a similarity function between
a pair of samples. The minus sign inverts the distance measure into a similarity score
and, due to the exponential term, the resulting similarity score will fall into a range
between 1 (for exactly similar samples) and 0 (for very dissimilar samples).

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A Tour of Machine Learning Classifiers Using Scikit-learn

Now that we defined the big picture behind the kernel trick, let's see if we can train
a kernel SVM that is able to draw a nonlinear decision boundary that separates the
XOR data well. Here, we simply use the SVC class from scikit-learn that we imported
earlier and replace the parameter kernel='linear' with kernel='rbf':
>>>
>>>
>>>
>>>
>>>

svm = SVC(kernel='rbf', random_state=0, gamma=0.10, C=10.0)

svm.fit(X_xor, y_xor)
plot_decision_regions(X_xor, y_xor, classifier=svm)
plt.legend(loc='upper left')
plt.show()

As we can see in the resulting plot, the kernel SVM separates the XOR data
relatively well:

The parameter, which we set to gamma=0.1, can be understood as a cut-off

parameter for the Gaussian sphere. If we increase the value for , we increase the
influence or reach of the training samples, which leads to a softer decision boundary.
To get a better intuition for , let's apply RBF kernel SVM to our Iris flower dataset:
>>> svm = SVC(kernel='rbf', random_state=0, gamma=0.2, C=1.0)
>>> svm.fit(X_train_std, y_train)
>>> plot_decision_regions(X_combined_std,

[ 78 ]

Chapter 3
...
...
>>>
>>>
>>>
>>>

y_combined, classifier=svm,
test_idx=range(105,150))
plt.xlabel('petal length [standardized]')
plt.ylabel('petal width [standardized]')
plt.legend(loc='upper left')
plt.show()

Since we chose a relatively small value for , the resulting decision boundary of the
RBF kernel SVM model will be relatively soft, as shown in the following figure:

Now let's increase the value of and observe the effect on the decision boundary:
>>>
>>>
>>>
...
...
>>>
>>>
>>>
>>>

svm = SVC(kernel='rbf', random_state=0, gamma=100.0, C=1.0)

svm.fit(X_train_std, y_train)
plot_decision_regions(X_combined_std,
y_combined, classifier=svm,
test_idx=range(105,150))
plt.xlabel('petal length [standardized]')
plt.ylabel('petal width [standardized]')
plt.legend(loc='upper left')
plt.show()

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A Tour of Machine Learning Classifiers Using Scikit-learn

In the resulting plot, we can now see that the decision boundary around the classes 0
and 1 is much tighter using a relatively large value of :

Although the model fits the training dataset very well, such a classifier will
likely have a high generalization error on unseen data, which illustrates that the
optimization of also plays an important role in controlling overfitting.

Decision tree learning

Decision tree classifiers are attractive models if we care about interpretability.
Like the name decision tree suggests, we can think of this model as breaking down
our data by making decisions based on asking a series of questions.

[ 80 ]

Chapter 3

Let's consider the following example where we use a decision tree to decide upon an
activity on a particular day:
Work to do?
Yes

No

Stay in

Outlook?

Sunny

Go to beach

Overcast
Go running

Rainy

Friends busy?
Yes

Stay in

No
Go to movies

Based on the features in our training set, the decision tree model learns a series of
questions to infer the class labels of the samples. Although the preceding figure
illustrated the concept of a decision tree based on categorical variables, the same
concept applies if our features. This also works if our features are real numbers like
in the Iris dataset. For example, we could simply define a cut-off value along the
sepal width feature axis and ask a binary question "sepal width 2.8 cm?"
Using the decision algorithm, we start at the tree root and split the data on the
feature that results in the largest information gain (IG), which will be explained in
more detail in the following section. In an iterative process, we can then repeat this
splitting procedure at each child node until the leaves are pure. This means that the
samples at each node all belong to the same class. In practice, this can result in a very
deep tree with many nodes, which can easily lead to overfitting. Thus, we typically
want to prune the tree by setting a limit for the maximal depth of the tree.

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A Tour of Machine Learning Classifiers Using Scikit-learn

Maximizing information gain getting the

most bang for the buck
In order to split the nodes at the most informative features, we need to define an
objective function that we want to optimize via the tree learning algorithm. Here,
our objective function is to maximize the information gain at each split, which we
define as follows:
m

Nj

j =1

Np

IG ( D p , f ) = I ( D p )

I ( Dj )

Here, f is the feature to perform the split, D p and D j are the dataset of the parent
and jth child node, I is our impurity measure, N p is the total number of samples at
the parent node, and N j is the number of samples in the jth child node. As we can
see, the information gain is simply the difference between the impurity of the parent
node and the sum of the child node impuritiesthe lower the impurity of the child
nodes, the larger the information gain. However, for simplicity and to reduce the
combinatorial search space, most libraries (including scikit-learn) implement binary
decision trees. This means that each parent node is split into two child nodes, Dleft
and Dright :

IG ( D p , a ) = I ( D p )

N left
Np

I ( Dleft )

N right
Np

I ( Dright )

Now, the three impurity measures or splitting criteria that are commonly used in
binary decision trees are Gini impurity ( I G ), entropy ( I H ), and the classification
error ( I E ). Let's start with the definition of entropy for all non-empty classes
p (i | t ) 0 :
c

I H ( t ) = p ( i | t ) log 2 p ( i | t )
i =1

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Chapter 3

Here, p ( i | t ) is the proportion of the samples that belongs to class c for a particular
node t. The entropy is therefore 0 if all samples at a node belong to the same class,
and the entropy is maximal if we have a uniform class distribution. For example, in
a binary class setting, the entropy is 0 if p ( i = 1| t ) = 1 or p ( i = 0 | t ) = 0 . If the classes are
distributed uniformly with p ( i = 1| t ) = 0.5 and p ( i = 0 | t ) = 0.5 , the entropy is 1. Therefore,
we can say that the entropy criterion attempts to maximize the mutual information
in the tree.
Intuitively, the Gini impurity can be understood as a criterion to minimize the
probability of misclassification:
c

i =1

i =1

I G ( t ) = p ( i | t ) (1 p ( i | t ) ) = 1 p ( i | t )

Similar to entropy, the Gini impurity is maximal if the classes are perfectly mixed,
for example, in a binary class setting ( c = 2 ):
c

1 0.52 = 0.5
i=1

However, in practice both the Gini impurity and entropy typically yield very similar
results and it is often not worth spending much time on evaluating trees using
different impurity criteria rather than experimenting with different pruning cut-offs.
Another impurity measure is the classification error:

I E = 1 max { p ( i | t )}

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A Tour of Machine Learning Classifiers Using Scikit-learn

This is a useful criterion for pruning but not recommended for growing a decision
tree, since it is less sensitive to changes in the class probabilities of the nodes. We
can illustrate this by looking at the two possible splitting scenarios shown in the
following figure:

B
(40, 40)

(30, 10)

(40, 40)

(20, 40)

(10, 30)

(20, 0)

We start with a dataset D p at the parent node D p that consists of 40 samples from
class 1 and 40 samples from class 2 that we split into two datasets Dleft and Dright ,
respectively. The information gain using the classification error as a splitting
criterion would be the same ( IGE = 0.25 ) in both scenario A and B:

I E ( D p ) = 1 0.5 = 0.5
A : I E ( Dleft ) = 1

3
= 0.25
4

A : I E ( Dright ) = 1

3
= 0.25
4

4
4
A : IGE = 0.5 0.25 0.25 = 0.25
8
8
B : I E ( Dleft ) = 1

4 1
=
6 3

B : I E ( Dright ) = 1 1 = 0
6 1
B : IGE = 0.5 0 = 0.25
8 3

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Chapter 3

However, the Gini impurity would favor the split in scenario B ( IGG = 0.16 ) over
scenario A ( IGG = 0.125 ) , which is indeed more pure:

I G ( D p ) = 1 ( 0.52 + 0.52 ) = 0.5

3 2 1 2 3
A : I G ( Dleft ) = 1 + = = 0.375
4 4 8

1 2 3 2 3
A : I G ( Dright ) = 1 + = = 0.375
4 4 8

4
4
A : I G = 0.5 0.375 0.375 = 0.125
8
8
2 2 4 2 4
B : I G ( Dleft ) = 1 + = = 0.4
6 6 9

B : I G ( Dright ) = 1 (12 + 02 ) = 0

6
B : IGG = 0.5 0.4 0 = 0.16
8
Similarly, the entropy criterion would favor scenario B ( IGH = 0.31) over
scenario A ( IGH = 0.19 ) :

I H ( D p ) = ( 0.5 log 2 ( 0.5 ) + 0.5 log 2 ( 0.5 ) ) = 1

3
3 1
1
A : I H ( Dleft ) = log 2 + log 2 = 0.81
4 4
4
4

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A Tour of Machine Learning Classifiers Using Scikit-learn

1
1 3
3
A : I H ( Dright ) = log 2 + log 2 = 0.81
4 4
4
4
4
4
A : IGH = 1 0.81 0.81 = 0.19
8
8

2
2 4
4
B : I H ( Dleft ) = log 2 + log 2 = 0.92
6 6
6
6
B : I H ( Dright ) = 0

6
B : IGH = 1 0.92 0 = 0.31
8
For a more visual comparison of the three different impurity criteria that we
discussed previously, let's plot the impurity indices for the probability range [0, 1]
for class 1. Note that we will also add in a scaled version of the entropy (entropy/2) to
observe that the Gini impurity is an intermediate measure between entropy and the
classification error. The code is as follows:
>>>
>>>
>>>
...
>>>
...
>>>
...
>>>
>>>
>>>
>>>
>>>
>>>
>>>
...
...

import matplotlib.pyplot as plt

import numpy as np
def gini(p):
return (p)*(1 - (p)) + (1 - p)*(1 - (1-p))
def entropy(p):
return - p*np.log2(p) - (1 - p)*np.log2((1 - p))
def error(p):
return 1 - np.max([p, 1 - p])
x = np.arange(0.0, 1.0, 0.01)
ent = [entropy(p) if p != 0 else None for p in x]
sc_ent = [e*0.5 if e else None for e in ent]
err = [error(i) for i in x]
fig = plt.figure()
ax = plt.subplot(111)
for i, lab, ls, c, in zip([ent, sc_ent, gini(x), err],
['Entropy', 'Entropy (scaled)',
'Gini Impurity',

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Chapter 3
...
...
...
...
...
...
>>>
...
>>>
>>>
>>>
>>>
>>>
>>>

'Misclassification Error'],
['-', '-', '--', '-.'],
['black', 'lightgray',
'red', 'green', 'cyan']):
line = ax.plot(x, i, label=lab,
linestyle=ls, lw=2, color=c)
ax.legend(loc='upper center', bbox_to_anchor=(0.5, 1.15),
ncol=3, fancybox=True, shadow=False)
ax.axhline(y=0.5, linewidth=1, color='k', linestyle='--')
ax.axhline(y=1.0, linewidth=1, color='k', linestyle='--')
plt.ylim([0, 1.1])
plt.xlabel('p(i=1)')
plt.ylabel('Impurity Index')
plt.show()

The plot produced by the preceding code example is as follows:

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A Tour of Machine Learning Classifiers Using Scikit-learn

Building a decision tree

Decision trees can build complex decision boundaries by dividing the feature
space into rectangles. However, we have to be careful since the deeper the decision
tree, the more complex the decision boundary becomes, which can easily result in
overfitting. Using scikit-learn, we will now train a decision tree with a maximum
depth of 3 using entropy as a criterion for impurity. Although feature scaling may be
desired for visualization purposes, note that feature scaling is not a requirement for
decision tree algorithms. The code is as follows:
>>> from sklearn.tree import DecisionTreeClassifier
>>> tree = DecisionTreeClassifier(criterion='entropy',
...
max_depth=3, random_state=0)
>>> tree.fit(X_train, y_train)
>>> X_combined = np.vstack((X_train, X_test))
>>> y_combined = np.hstack((y_train, y_test))
>>> plot_decision_regions(X_combined, y_combined,
...
classifier=tree, test_idx=range(105,150))
>>>plt.xlabel('petal length [cm]')
>>>plt.ylabel('petal width [cm]')
>>> plt.legend(loc='upper left')
>>> plt.show()

After executing the preceding code example, we get the typical axis-parallel decision
boundaries of the decision tree:

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Chapter 3

A nice feature in scikit-learn is that it allows us to export the decision tree as a

.dot file after training, which we can visualize using the GraphViz program. This
program is freely available at http://www.graphviz.org and supported by Linux,
Windows, and Mac OS X.
First, we create the .dot file via scikit-learn using the export_graphviz function
from the tree submodule, as follows:
>>> from sklearn.tree import export_graphviz
>>> export_graphviz(tree,
...
out_file='tree.dot',
...
feature_names=['petal length', 'petal width'])

After we have installed GraphViz on our computer, we can convert the tree.dot file
into a PNG file by executing the following command from the command line in the
location where we saved the tree.dot file:
> dot -Tpng tree.dot -o tree.png

Looking at the decision tree figure that we created via GraphViz, we can now nicely
trace back the splits that the decision tree determined from our training dataset.
We started with 105 samples at the root and split it into two child nodes with 34
and 71 samples each using the petal width cut-off 0.75 cm. After the first split,
we can see that the left child node is already pure and only contains samples from
the Iris-Setosa class (entropy = 0). The further splits on the right are then used to
separate the samples from the Iris-Versicolor and Iris-Virginica classes.
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Combining weak to strong learners via

random forests
Random forests have gained huge popularity in applications of machine learning
during the last decade due to their good classification performance, scalability, and
ease of use. Intuitively, a random forest can be considered as an ensemble of decision
trees. The idea behind ensemble learning is to combine weak learners to build a
more robust model, a strong learner, that has a better generalization error and is less
susceptible to overfitting. The random forest algorithm can be summarized in four
simple steps:
1. Draw a random bootstrap sample of size n (randomly choose n samples from
the training set with replacement).
2. Grow a decision tree from the bootstrap sample. At each node:
1. Randomly select d features without replacement.
2. Split the node using the feature that provides the best split
according to the objective function, for instance, by maximizing
the information gain.
3. Repeat the steps 1 to 2 k times.
4. Aggregate the prediction by each tree to assign the class label by majority
vote. Majority voting will be discussed in more detail in Chapter 7, Combining
Different Models for Ensemble Learning.
There is a slight modification in step 2 when we are training the individual decision
trees: instead of evaluating all features to determine the best split at each node, we
only consider a random subset of those.
Although random forests don't offer the same level of interpretability as decision
trees, a big advantage of random forests is that we don't have to worry so much
about choosing good hyperparameter values. We typically don't need to prune the
random forest since the ensemble model is quite robust to noise from the individual
decision trees. The only parameter that we really need to care about in practice is the
number of trees k (step 3) that we choose for the random forest. Typically, the larger
the number of trees, the better the performance of the random forest classifier at the
expense of an increased computational cost.

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Chapter 3

Although it is less common in practice, other hyperparameters of the random

forest classifier that can be optimizedusing techniques we will discuss in
Chapter 5, Compressing Data via Dimensionality Reductionare the size n
of the bootstrap sample (step 1) and the number of features d that is randomly
chosen for each split (step 2.1), respectively. Via the sample size n of the bootstrap
sample, we control the bias-variance tradeoff of the random forest. By choosing
a larger value for n, we decrease the randomness and thus the forest is more
likely to overfit. On the other hand, we can reduce the degree of overfitting by
choosing smaller values for n at the expense of the model performance. In most
implementations, including the RandomForestClassifier implementation in
scikit-learn, the sample size of the bootstrap sample is chosen to be equal to the
number of samples in the original training set, which usually provides a good
bias-variance tradeoff. For the number of features d at each split, we want to choose
a value that is smaller than the total number of features in the training set. A
reasonable default that is used in scikit-learn and other implementations is d = m ,
where m is the number of features in the training set.
Conveniently, we don't have to construct the random forest classifier from individual
decision trees by ourselves; there is already an implementation in scikit-learn that
we can use:
>>>
>>>
...
...
...
>>>
>>>
...
>>>
>>>
>>>
>>>

from sklearn.ensemble import RandomForestClassifier

forest = RandomForestClassifier(criterion='entropy',
n_estimators=10,
random_state=1,
n_jobs=2)
forest.fit(X_train, y_train)
plot_decision_regions(X_combined, y_combined,
classifier=forest, test_idx=range(105,150))
plt.xlabel('petal length')
plt.ylabel('petal width')
plt.legend(loc='upper left')
plt.show()

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A Tour of Machine Learning Classifiers Using Scikit-learn

After executing the preceding code, we should see the decision regions formed by
the ensemble of trees in the random forest, as shown in the following figure:

Using the preceding code, we trained a random forest from 10 decision trees via the
n_estimators parameter and used the entropy criterion as an impurity measure to
split the nodes. Although we are growing a very small random forest from a very
small training dataset, we used the n_jobs parameter for demonstration purposes,
which allows us to parallelize the model training using multiple cores of our
computer (here, two).

K-nearest neighbors a lazy learning

algorithm
The last supervised learning algorithm that we want to discuss in this chapter is the
k-nearest neighbor classifier (KNN), which is particularly interesting because it is
fundamentally different from the learning algorithms that we have discussed so far.
KNN is a typical example of a lazy learner. It is called lazy not because of its
apparent simplicity, but because it doesn't learn a discriminative function from
the training data but memorizes the training dataset instead.

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Chapter 3

Parametric versus nonparametric models

Machine learning algorithms can be grouped into parametric and
nonparametric models. Using parametric models, we estimate
parameters from the training dataset to learn a function that can
classify new data points without requiring the original training dataset
anymore. Typical examples of parametric models are the perceptron,
logistic regression, and the linear SVM. In contrast, nonparametric
models can't be characterized by a fixed set of parameters, and the
number of parameters grows with the training data. Two examples of
nonparametric models that we have seen so far are the decision tree
classifier/random forest and the kernel SVM.
KNN belongs to a subcategory of nonparametric models that is
described as instance-based learning. Models based on instance-based
learning are characterized by memorizing the training dataset, and lazy
learning is a special case of instance-based learning that is associated
with no (zero) cost during the learning process.

The KNN algorithm itself is fairly straightforward and can be summarized by the
following steps:
1. Choose the number of k and a distance metric.
2. Find the k nearest neighbors of the sample that we want to classify.
3. Assign the class label by majority vote.
The following figure illustrates how a new data point (?) is assigned the triangle class
label based on majority voting among its five nearest neighbors.

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A Tour of Machine Learning Classifiers Using Scikit-learn

Based on the chosen distance metric, the KNN algorithm finds the k samples in the
training dataset that are closest (most similar) to the point that we want to classify.
The class label of the new data point is then determined by a majority vote among
its k nearest neighbors.
The main advantage of such a memory-based approach is that the classifier
immediately adapts as we collect new training data. However, the downside is that
the computational complexity for classifying new samples grows linearly with the
number of samples in the training dataset in the worst-case scenariounless the
dataset has very few dimensions (features) and the algorithm has been implemented
using efficient data structures such as KD-trees. J. H. Friedman, J. L. Bentley, and R.
A. Finkel. An algorithm for finding best matches in logarithmic expected time. ACM
Transactions on Mathematical Software (TOMS), 3(3):209226, 1977. Furthermore, we
can't discard training samples since no training step is involved. Thus, storage space
can become a challenge if we are working with large datasets.
By executing the following code, we will now implement a KNN model in
scikit-learn using an Euclidean distance metric:
>>>
>>>
...
>>>
>>>
...
>>>
>>>
>>>

from sklearn.neighbors import KNeighborsClassifier

knn = KNeighborsClassifier(n_neighbors=5, p=2,
metric='minkowski')
knn.fit(X_train_std, y_train)
plot_decision_regions(X_combined_std, y_combined,
classifier=knn, test_idx=range(105,150))
plt.xlabel('petal length [standardized]')
plt.ylabel('petal width [standardized]')
plt.show()

By specifying five neighbors in the KNN model for this dataset, we obtain a
relatively smooth decision boundary, as shown in the following figure:

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Chapter 3

In the case of a tie, the scikit-learn implementation of the KNN

algorithm will prefer the neighbors with a closer distance to the
sample. If the neighbors have a similar distance, the algorithm will
choose the class label that comes first in the training dataset.

The right choice of k is crucial to find a good balance between over- and underfitting.
We also have to make sure that we choose a distance metric that is appropriate for
the features in the dataset. Often, a simple Euclidean distance measure is used for
real-valued samples, for example, the flowers in our Iris dataset, which have features
measured in centimeters. However, if we are using a Euclidean distance measure, it
is also important to standardize the data so that each feature contributes equally to
the distance. The 'minkowski' distance that we used in the previous code is just a
generalization of the Euclidean and Manhattan distance that can be written as follows:

) x( ) x( )

d x (i ) , x (i ) =

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A Tour of Machine Learning Classifiers Using Scikit-learn

It becomes the Euclidean distance if we set the parameter p=2 or the Manhatten
distance at p=1, respectively. Many other distance metrics are available in scikit-learn
and can be provided to the metric parameter. They are listed at http://scikitlearn.org/stable/modules/generated/sklearn.neighbors.DistanceMetric.
html.

The curse of dimensionality

It is important to mention that KNN is very susceptible to
overfitting due to the curse of dimensionality. The curse of
dimensionality describes the phenomenon where the feature
space becomes increasingly sparse for an increasing number
of dimensions of a fixed-size training dataset. Intuitively, we
can think of even the closest neighbors being too far away in a
high-dimensional space to give a good estimate.
We have discussed the concept of regularization in the section
about logistic regression as one way to avoid overfitting. However,
in models where regularization is not applicable such as decision
trees and KNN, we can use feature selection and dimensionality
reduction techniques to help us avoid the curse of dimensionality.
This will be discussed in more detail in the next chapter.

Summary
In this chapter, you learned about many different machine algorithms that are
used to tackle linear and nonlinear problems. We have seen that decision trees are
particularly attractive if we care about interpretability. Logistic regression is not only
a useful model for online learning via stochastic gradient descent, but also allows us
to predict the probability of a particular event. Although support vector machines
are powerful linear models that can be extended to nonlinear problems via the
kernel trick, they have many parameters that have to be tuned in order to make good
predictions. In contrast, ensemble methods such as random forests don't require
much parameter tuning and don't overfit so easily as decision trees, which makes
it an attractive model for many practical problem domains. The K-nearest neighbor
classifier offers an alternative approach to classification via lazy learning that allows
us to make predictions without any model training but with a more computationally
expensive prediction step.

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Chapter 3

However, even more important than the choice of an appropriate learning algorithm
is the available data in our training dataset. No algorithm will be able to make good
predictions without informative and discriminatory features.
In the next chapter, we will discuss important topics regarding the preprocessing
of data, feature selection, and dimensionality reduction, which we will need to
build powerful machine learning models. Later in Chapter 6, Learning Best Practices
for Model Evaluation and Hyperparameter Tuning, we will see how we can evaluate
and compare the performance of our models and learn useful tricks to fine-tune the
different algorithms.

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Get more information Python Machine Learning

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