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Data Science from Scratch
“Joel

Data Science from Scratch

Data science libraries, frameworks, modules, and toolkits are great for takes you on a
doing data science, but they’re also a good way to dive into the discipline
journey from being
without actually understanding data science. In this book, you’ll learn how
many of the most fundamental data science tools and algorithms work by data-curious to getting a
implementing them from scratch. thorough understanding
If you have an aptitude for mathematics and some programming skills, of the bread-and-butter
author Joel Grus will help you get comfortable with the math and statistics algorithms that every data
at the core of data science, and with hacking skills you need to get started
as a data scientist. Today’s messy glut of data holds answers to questions
scientist should know.
—Rohit Sivaprasad
”
no one’s even thought to ask. This book provides you with the know-how Data Science, Soylent
to dig those answers out. datatau.com

■■ Get a crash course in Python

■■ Learn the basics of linear algebra, statistics, and probability—
and understand how and when they're used in data science
■■ Collect, explore, clean, munge, and manipulate data
■■ Dive into the fundamentals of machine learning
■■ Implement models such as k-nearest neighbors, Naive Bayes,

Data Science
linear and logistic regression, decision trees, neural networks,
and clustering
■■ Explore recommender systems, natural language processing,
network analysis, MapReduce, and databases

from Scratch
Joel Grus is a software engineer at Google. Before that, he worked as a data
scientist at multiple startups. He lives in Seattle, where he regularly attends data
science happy hours. He blogs infrequently at joelgrus.com and tweets all day
long at @joelgrus.

FIRST PRINCIPLES WITH PYTHON

Grus
DATA /DATA SCIENCE
Twitter: @oreillymedia
facebook.com/oreilly
US $39.99 CAN $45.99
ISBN: 978-1-491-90142-7

Joel Grus
Data Science from Scratch
“Joel

Data Science from Scratch

Data science libraries, frameworks, modules, and toolkits are great for takes you on a
doing data science, but they’re also a good way to dive into the discipline
journey from being
without actually understanding data science. In this book, you’ll learn how
many of the most fundamental data science tools and algorithms work by data-curious to getting a
implementing them from scratch. thorough understanding
If you have an aptitude for mathematics and some programming skills, of the bread-and-butter
author Joel Grus will help you get comfortable with the math and statistics algorithms that every data
at the core of data science, and with hacking skills you need to get started
as a data scientist. Today’s messy glut of data holds answers to questions
scientist should know.
—Rohit Sivaprasad
”
no one’s even thought to ask. This book provides you with the know-how Data Science, Soylent
to dig those answers out. datatau.com

■■ Get a crash course in Python

■■ Learn the basics of linear algebra, statistics, and probability—
and understand how and when they're used in data science
■■ Collect, explore, clean, munge, and manipulate data
■■ Dive into the fundamentals of machine learning
■■ Implement models such as k-nearest neighbors, Naive Bayes,

Data Science
linear and logistic regression, decision trees, neural networks,
and clustering
■■ Explore recommender systems, natural language processing,
network analysis, MapReduce, and databases

from Scratch
Joel Grus is a software engineer at Google. Before that, he worked as a data
scientist at multiple startups. He lives in Seattle, where he regularly attends data
science happy hours. He blogs infrequently at joelgrus.com and tweets all day
long at @joelgrus.

FIRST PRINCIPLES WITH PYTHON

Grus
DATA /DATA SCIENCE
Twitter: @oreillymedia
facebook.com/oreilly
US $39.99 CAN $45.99
ISBN: 978-1-491-90142-7

Joel Grus
Data Science from Scratch

Joel Grus
Data Science from Scratch
by Joel Grus
Copyright © 2015 O’Reilly Media. All rights reserved.
Printed in the United States of America.
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The O’Reilly logo is a registered trademark of O’Reilly Media, Inc. Data Science from Scratch, the cover
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thereof complies with such licenses and/or rights.

978-1-491-90142-7
[LSI]
 Table of Contents

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
The Ascendance of Data 1
What Is Data Science? 1
Motivating Hypothetical: DataSciencester 2
Finding Key Connectors 3
Data Scientists You May Know 6
Salaries and Experience 8
Paid Accounts 11
Topics of Interest 11
Onward 13

2. A Crash Course in Python. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

The Basics 15
Getting Python 15
The Zen of Python 16
Whitespace Formatting 16
Modules 17
Arithmetic 18
Functions 18
Strings 19
Exceptions 19
Lists 20
Tuples 21
Dictionaries 21
Sets 24
Control Flow 25

iii
 Truthiness 25
The Not-So-Basics 26
Sorting 27
List Comprehensions 27
Generators and Iterators 28
Randomness 29
Regular Expressions 30
Object-Oriented Programming 30
Functional Tools 31
enumerate 32
zip and Argument Unpacking 33
args and kwargs 34
Welcome to DataSciencester! 35
For Further Exploration 35

3. Visualizing Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
matplotlib 37
Bar Charts 39
Line Charts 43
Scatterplots 44
For Further Exploration 47

4. Linear Algebra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Vectors 49
Matrices 53
For Further Exploration 55

5. Statistics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Describing a Single Set of Data 57
Central Tendencies 59
Dispersion 61
Correlation 62
Simpson’s Paradox 65
Some Other Correlational Caveats 66
Correlation and Causation 67
For Further Exploration 68

6. Probability. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Dependence and Independence 69
Conditional Probability 70
Bayes’s Theorem 72
Random Variables 73

iv | Table of Contents
 Continuous Distributions 74
The Normal Distribution 75
The Central Limit Theorem 78
For Further Exploration 80

7. Hypothesis and Inference. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Statistical Hypothesis Testing 81
Example: Flipping a Coin 81
Confidence Intervals 85
P-hacking 86
Example: Running an A/B Test 87
Bayesian Inference 88
For Further Exploration 92

8. Gradient Descent. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
The Idea Behind Gradient Descent 93
Estimating the Gradient 94
Using the Gradient 97
Choosing the Right Step Size 97
Putting It All Together 98
Stochastic Gradient Descent 99
For Further Exploration 100

9. Getting Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

stdin and stdout 103
Reading Files 105
The Basics of Text Files 105
Delimited Files 106
Scraping the Web 108
HTML and the Parsing Thereof 108
Example: O’Reilly Books About Data 110
Using APIs 114
JSON (and XML) 114
Using an Unauthenticated API 115
Finding APIs 116
Example: Using the Twitter APIs 117
Getting Credentials 117
For Further Exploration 120

10. Working with Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

Exploring Your Data 121
Exploring One-Dimensional Data 121

Table of Contents | v
 Two Dimensions 123
Many Dimensions 125
Cleaning and Munging 127
Manipulating Data 129
Rescaling 132
Dimensionality Reduction 134
For Further Exploration 139

11. Machine Learning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

Modeling 141
What Is Machine Learning? 142
Overfitting and Underfitting 142
Correctness 145
The Bias-Variance Trade-off 147
Feature Extraction and Selection 148
For Further Exploration 150

12. k-Nearest Neighbors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

The Model 151
Example: Favorite Languages 153
The Curse of Dimensionality 156
For Further Exploration 163

13. Naive Bayes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165

A Really Dumb Spam Filter 165
A More Sophisticated Spam Filter 166
Implementation 168
Testing Our Model 169
For Further Exploration 172

14. Simple Linear Regression. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173

The Model 173
Using Gradient Descent 176
Maximum Likelihood Estimation 177
For Further Exploration 177

15. Multiple Regression. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179

The Model 179
Further Assumptions of the Least Squares Model 180
Fitting the Model 181
Interpreting the Model 182
Goodness of Fit 183

vi | Table of Contents
 Digression: The Bootstrap 183
Standard Errors of Regression Coefficients 184
Regularization 186
For Further Exploration 188

16. Logistic Regression. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

The Problem 189
The Logistic Function 192
Applying the Model 194
Goodness of Fit 195
Support Vector Machines 196
For Further Investigation 200

17. Decision Trees. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201

What Is a Decision Tree? 201
Entropy 203
The Entropy of a Partition 205
Creating a Decision Tree 206
Putting It All Together 208
Random Forests 211
For Further Exploration 212

18. Neural Networks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213

Perceptrons 213
Feed-Forward Neural Networks 215
Backpropagation 218
Example: Defeating a CAPTCHA 219
For Further Exploration 224

19. Clustering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

The Idea 225
The Model 226
Example: Meetups 227
Choosing k 230
Example: Clustering Colors 231
Bottom-up Hierarchical Clustering 233
For Further Exploration 238

20. Natural Language Processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239

Word Clouds 239
n-gram Models 241
Grammars 244

Table of Contents | vii

 An Aside: Gibbs Sampling 246
Topic Modeling 247
For Further Exploration 253

21. Network Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255

Betweenness Centrality 255
Eigenvector Centrality 260
Matrix Multiplication 260
Centrality 262
Directed Graphs and PageRank 264
For Further Exploration 266

22. Recommender Systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

Manual Curation 268
Recommending What’s Popular 268
User-Based Collaborative Filtering 269
Item-Based Collaborative Filtering 272
For Further Exploration 274

23. Databases and SQL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275

CREATE TABLE and INSERT 275
UPDATE 277
DELETE 278
SELECT 278
GROUP BY 280
ORDER BY 282
JOIN 283
Subqueries 285
Indexes 285
Query Optimization 286
NoSQL 287
For Further Exploration 287

24. MapReduce. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289

Example: Word Count 289
Why MapReduce? 291
MapReduce More Generally 292
Example: Analyzing Status Updates 293
Example: Matrix Multiplication 294
An Aside: Combiners 296
For Further Exploration 296

viii | Table of Contents

25. Go Forth and Do Data Science. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
IPython 299
Mathematics 300
Not from Scratch 300
NumPy 301
pandas 301
scikit-learn 301
Visualization 301
R 302
Find Data 302
Do Data Science 303
Hacker News 303
Fire Trucks 303
T-shirts 303
And You? 304

Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305

Table of Contents | ix
 Preface

Data Science
Data scientist has been called “the sexiest job of the 21st century,” presumably by
someone who has never visited a fire station. Nonetheless, data science is a hot and
growing field, and it doesn’t take a great deal of sleuthing to find analysts breathlessly
prognosticating that over the next 10 years, we’ll need billions and billions more data
scientists than we currently have.
But what is data science? After all, we can’t produce data scientists if we don’t know
what data science is. According to a Venn diagram that is somewhat famous in the
industry, data science lies at the intersection of:

• Hacking skills
• Math and statistics knowledge
• Substantive expertise

Although I originally intended to write a book covering all three, I quickly realized
that a thorough treatment of “substantive expertise” would require tens of thousands
of pages. At that point, I decided to focus on the first two. My goal is to help you
develop the hacking skills that you’ll need to get started doing data science. And my
goal is to help you get comfortable with the mathematics and statistics that are at the
core of data science.
This is a somewhat heavy aspiration for a book. The best way to learn hacking skills is
by hacking on things. By reading this book, you will get a good understanding of the
way I hack on things, which may not necessarily be the best way for you to hack on
things. You will get a good understanding of some of the tools I use, which will not
necessarily be the best tools for you to use. You will get a good understanding of the
way I approach data problems, which may not necessarily be the best way for you to
approach data problems. The intent (and the hope) is that my examples will inspire

xi
you try things your own way. All the code and data from the book is available on
GitHub to get you started.
Similarly, the best way to learn mathematics is by doing mathematics. This is emphat‐
ically not a math book, and for the most part, we won’t be “doing mathematics.” How‐
ever, you can’t really do data science without some understanding of probability and
statistics and linear algebra. This means that, where appropriate, we will dive into
mathematical equations, mathematical intuition, mathematical axioms, and cartoon
versions of big mathematical ideas. I hope that you won’t be afraid to dive in with me.
Throughout it all, I also hope to give you a sense that playing with data is fun,
because, well, playing with data is fun! (Especially compared to some of the alterna‐
tives, like tax preparation or coal mining.)

From Scratch
There are lots and lots of data science libraries, frameworks, modules, and toolkits
that efficiently implement the most common (as well as the least common) data sci‐
ence algorithms and techniques. If you become a data scientist, you will become inti‐
mately familiar with NumPy, with scikit-learn, with pandas, and with a panoply of
other libraries. They are great for doing data science. But they are also a good way to
start doing data science without actually understanding data science.
In this book, we will be approaching data science from scratch. That means we’ll be
building tools and implementing algorithms by hand in order to better understand
them. I put a lot of thought into creating implementations and examples that are
clear, well-commented, and readable. In most cases, the tools we build will be illumi‐
nating but impractical. They will work well on small toy data sets but fall over on
“web scale” ones.
Throughout the book, I will point you to libraries you might use to apply these tech‐
niques to larger data sets. But we won’t be using them here.
There is a healthy debate raging over the best language for learning data science.
Many people believe it’s the statistical programming language R. (We call those peo‐
ple wrong.) A few people suggest Java or Scala. However, in my opinion, Python is the
obvious choice.
Python has several features that make it well suited for learning (and doing) data sci‐
ence:

• It’s free.
• It’s relatively simple to code in (and, in particular, to understand).
• It has lots of useful data science–related libraries.

xii | Preface
I am hesitant to call Python my favorite programming language. There are other lan‐
guages I find more pleasant, better-designed, or just more fun to code in. And yet
pretty much every time I start a new data science project, I end up using Python.
Every time I need to quickly prototype something that just works, I end up using
Python. And every time I want to demonstrate data science concepts in a clear, easy-
to-understand way, I end up using Python. Accordingly, this book uses Python.
The goal of this book is not to teach you Python. (Although it is nearly certain that by
reading this book you will learn some Python.) I’ll take you through a chapter-long
crash course that highlights the features that are most important for our purposes,
but if you know nothing about programming in Python (or about programming at
all) then you might want to supplement this book with some sort of “Python for
Beginners” tutorial.
The remainder of our introduction to data science will take this same approach —
going into detail where going into detail seems crucial or illuminating, at other times
leaving details for you to figure out yourself (or look up on Wikipedia).
Over the years, I’ve trained a number of data scientists. While not all of them have
gone on to become world-changing data ninja rockstars, I’ve left them all better data
scientists than I found them. And I’ve grown to believe that anyone who has some
amount of mathematical aptitude and some amount of programming skill has the
necessary raw materials to do data science. All she needs is an inquisitive mind, a
willingness to work hard, and this book. Hence this book.

Conventions Used in This Book

The following typographical conventions are used in this book:
Italic
Indicates new terms, URLs, email addresses, filenames, and file extensions.
Constant width
Used for program listings, as well as within paragraphs to refer to program ele‐
ments such as variable or function names, databases, data types, environment
variables, statements, and keywords.
Constant width bold
Shows commands or other text that should be typed literally by the user.
Constant width italic
Shows text that should be replaced with user-supplied values or by values deter‐
mined by context.

Preface | xiii
 This element signifies a tip or suggestion.

This element signifies a general note.

This element indicates a warning or caution.

Using Code Examples

Supplemental material (code examples, exercises, etc.) is available for download at
https://github.com/joelgrus/data-science-from-scratch.
This book is here to help you get your job done. In general, if example code is offered
with this book, you may use it in your programs and documentation. You do not
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We appreciate, but do not require, attribution. An attribution usually includes the
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Grus (O’Reilly). Copyright 2015 Joel Grus, 978-1-4919-0142-7.”
If you feel your use of code examples falls outside fair use or the permission given
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Acknowledgments
First, I would like to thank Mike Loukides for accepting my proposal for this book
(and for insisting that I pare it down to a reasonable size). It would have been very
easy for him to say, “Who’s this person who keeps emailing me sample chapters, and

Preface | xv
how do I get him to go away?” I’m grateful he didn’t. I’d also like to thank my editor,
Marie Beaugureau, for guiding me through the publishing process and getting the
book in a much better state than I ever would have gotten it on my own.
I couldn’t have written this book if I’d never learned data science, and I probably
wouldn’t have learned data science if not for the influence of Dave Hsu, Igor Tatari‐
nov, John Rauser, and the rest of the Farecast gang. (So long ago that it wasn’t even
called data science at the time!) The good folks at Coursera deserve a lot of credit,
too.
I am also grateful to my beta readers and reviewers. Jay Fundling found a ton of mis‐
takes and pointed out many unclear explanations, and the book is much better (and
much more correct) thanks to him. Debashis Ghosh is a hero for sanity-checking all
of my statistics. Andrew Musselman suggested toning down the “people who prefer R
to Python are moral reprobates” aspect of the book, which I think ended up being
pretty good advice. Trey Causey, Ryan Matthew Balfanz, Loris Mularoni, Núria Pujol,
Rob Jefferson, Mary Pat Campbell, Zach Geary, and Wendy Grus also provided
invaluable feedback. Any errors remaining are of course my responsibility.
I owe a lot to the Twitter #datascience commmunity, for exposing me to a ton of new
concepts, introducing me to a lot of great people, and making me feel like enough of
an underachiever that I went out and wrote a book to compensate. Special thanks to
Trey Causey (again), for (inadvertently) reminding me to include a chapter on linear
algebra, and to Sean J. Taylor, for (inadvertently) pointing out a couple of huge gaps
in the “Working with Data” chapter.
Above all, I owe immense thanks to Ganga and Madeline. The only thing harder than
writing a book is living with someone who’s writing a book, and I couldn’t have pulled
it off without their support.

xvi | Preface
 CHAPTER 1
Introduction

“Data! Data! Data!” he cried impatiently. “I can’t make bricks without clay.”
—Arthur Conan Doyle

The Ascendance of Data

We live in a world that’s drowning in data. Websites track every user’s every click.
Your smartphone is building up a record of your location and speed every second of
every day. “Quantified selfers” wear pedometers-on-steroids that are ever recording
their heart rates, movement habits, diet, and sleep patterns. Smart cars collect driving
habits, smart homes collect living habits, and smart marketers collect purchasing
habits. The Internet itself represents a huge graph of knowledge that contains (among
other things) an enormous cross-referenced encyclopedia; domain-specific databases
about movies, music, sports results, pinball machines, memes, and cocktails; and too
many government statistics (some of them nearly true!) from too many governments
to wrap your head around.
Buried in these data are answers to countless questions that no one’s ever thought to
ask. In this book, we’ll learn how to find them.

What Is Data Science?

There’s a joke that says a data scientist is someone who knows more statistics than a
computer scientist and more computer science than a statistician. (I didn’t say it was a
good joke.) In fact, some data scientists are—for all practical purposes—statisticians,
while others are pretty much indistinguishable from software engineers. Some are
machine-learning experts, while others couldn’t machine-learn their way out of kin‐
dergarten. Some are PhDs with impressive publication records, while others have
never read an academic paper (shame on them, though). In short, pretty much no

1
matter how you define data science, you’ll find practitioners for whom the definition
is totally, absolutely wrong.
Nonetheless, we won’t let that stop us from trying. We’ll say that a data scientist is
someone who extracts insights from messy data. Today’s world is full of people trying
to turn data into insight.
For instance, the dating site OkCupid asks its members to answer thousands of ques‐
tions in order to find the most appropriate matches for them. But it also analyzes
these results to figure out innocuous-sounding questions you can ask someone to
find out how likely someone is to sleep with you on the first date.
Facebook asks you to list your hometown and your current location, ostensibly to
make it easier for your friends to find and connect with you. But it also analyzes these
locations to identify global migration patterns and where the fanbases of different
football teams live.
As a large retailer, Target tracks your purchases and interactions, both online and in-
store. And it uses the data to predictively model which of its customers are pregnant,
to better market baby-related purchases to them.
In 2012, the Obama campaign employed dozens of data scientists who data-mined
and experimented their way to identifying voters who needed extra attention, choos‐
ing optimal donor-specific fundraising appeals and programs, and focusing get-out-
the-vote efforts where they were most likely to be useful. It is generally agreed that
these efforts played an important role in the president’s re-election, which means it is
a safe bet that political campaigns of the future will become more and more data-
driven, resulting in a never-ending arms race of data science and data collection.
Now, before you start feeling too jaded: some data scientists also occasionally use
their skills for good—using data to make government more effective, to help the
homeless, and to improve public health. But it certainly won’t hurt your career if you
like figuring out the best way to get people to click on advertisements.

Motivating Hypothetical: DataSciencester

Congratulations! You’ve just been hired to lead the data science efforts at DataScien‐
cester, the social network for data scientists.
Despite being for data scientists, DataSciencester has never actually invested in build‐
ing its own data science practice. (In fairness, DataSciencester has never really inves‐
ted in building its product either.) That will be your job! Throughout the book, we’ll
be learning about data science concepts by solving problems that you encounter at
work. Sometimes we’ll look at data explicitly supplied by users, sometimes we’ll look
at data generated through their interactions with the site, and sometimes we’ll even
look at data from experiments that we’ll design.

2 | Chapter 1: Introduction
And because DataSciencester has a strong “not-invented-here” mentality, we’ll be
building our own tools from scratch. At the end, you’ll have a pretty solid under‐
standing of the fundamentals of data science. And you’ll be ready to apply your skills
at a company with a less shaky premise, or to any other problems that happen to
interest you.
Welcome aboard, and good luck! (You’re allowed to wear jeans on Fridays, and the
bathroom is down the hall on the right.)

Finding Key Connectors

It’s your first day on the job at DataSciencester, and the VP of Networking is full of
questions about your users. Until now he’s had no one to ask, so he’s very excited to
have you aboard.
In particular, he wants you to identify who the “key connectors” are among data sci‐
entists. To this end, he gives you a dump of the entire DataSciencester network. (In
real life, people don’t typically hand you the data you need. Chapter 9 is devoted to
getting data.)
What does this data dump look like? It consists of a list of users, each represented by a
dict that contains for each user his or her id (which is a number) and name (which,
in one of the great cosmic coincidences, rhymes with the user’s id):
users = [
{ "id": 0, "name": "Hero" },
{ "id": 1, "name": "Dunn" },
{ "id": 2, "name": "Sue" },
{ "id": 3, "name": "Chi" },
{ "id": 4, "name": "Thor" },
{ "id": 5, "name": "Clive" },
{ "id": 6, "name": "Hicks" },
{ "id": 7, "name": "Devin" },
{ "id": 8, "name": "Kate" },
{ "id": 9, "name": "Klein" }
]
He also gives you the “friendship” data, represented as a list of pairs of IDs:
friendships = [(0, 1), (0, 2), (1, 2), (1, 3), (2, 3), (3, 4),
(4, 5), (5, 6), (5, 7), (6, 8), (7, 8), (8, 9)]

For example, the tuple (0, 1) indicates that the data scientist with id 0 (Hero) and
the data scientist with id 1 (Dunn) are friends. The network is illustrated in
Figure 1-1.

Motivating Hypothetical: DataSciencester | 3

Figure 1-1. The DataSciencester network

Since we represented our users as dicts, it’s easy to augment them with extra data.

Don’t get too hung up on the details of the code right now. In
Chapter 2, we’ll take you through a crash course in Python. For
now just try to get the general flavor of what we’re doing.

For example, we might want to add a list of friends to each user. First we set each
user’s friends property to an empty list:
for user in users:
user["friends"] = []

And then we populate the lists using the friendships data:

for i, j in friendships:
# this works because users[i] is the user whose id is i
users[i]["friends"].append(users[j]) # add i as a friend of j
users[j]["friends"].append(users[i]) # add j as a friend of i

Once each user dict contains a list of friends, we can easily ask questions of our
graph, like “what’s the average number of connections?”
First we find the total number of connections, by summing up the lengths of all the
friends lists:
def number_of_friends(user):
"""how many friends does _user_ have?"""
return len(user["friends"]) # length of friend_ids list

total_connections = sum(number_of_friends(user)
for user in users) # 24
And then we just divide by the number of users:

4 | Chapter 1: Introduction
 from __future__ import division # integer division is lame
num_users = len(users) # length of the users list
avg_connections = total_connections / num_users # 2.4
It’s also easy to find the most connected people—they’re the people who have the larg‐
est number of friends.
Since there aren’t very many users, we can sort them from “most friends” to “least
friends”:
# create a list (user_id, number_of_friends)
num_friends_by_id = [(user["id"], number_of_friends(user))
for user in users]

sorted(num_friends_by_id, # get it sorted

key=lambda (user_id, num_friends): num_friends, # by num_friends
reverse=True) # largest to smallest

# each pair is (user_id, num_friends)

# [(1, 3), (2, 3), (3, 3), (5, 3), (8, 3),
# (0, 2), (4, 2), (6, 2), (7, 2), (9, 1)]
One way to think of what we’ve done is as a way of identifying people who are some‐
how central to the network. In fact, what we’ve just computed is the network metric
degree centrality (Figure 1-2).

Figure 1-2. The DataSciencester network sized by degree

This has the virtue of being pretty easy to calculate, but it doesn’t always give the
results you’d want or expect. For example, in the DataSciencester network Thor (id 4)
only has two connections while Dunn (id 1) has three. Yet looking at the network it
intuitively seems like Thor should be more central. In Chapter 21, we’ll investigate
networks in more detail, and we’ll look at more complex notions of centrality that
may or may not accord better with our intuition.

Motivating Hypothetical: DataSciencester | 5

Data Scientists You May Know
While you’re still filling out new-hire paperwork, the VP of Fraternization comes by
your desk. She wants to encourage more connections among your members, and she
asks you to design a “Data Scientists You May Know” suggester.
Your first instinct is to suggest that a user might know the friends of friends. These
are easy to compute: for each of a user’s friends, iterate over that person’s friends, and
collect all the results:
def friends_of_friend_ids_bad(user):
# "foaf" is short for "friend of a friend"
return [foaf["id"]
for friend in user["friends"] # for each of user's friends
for foaf in friend["friends"]] # get each of _their_ friends

When we call this on users[0] (Hero), it produces:

[0, 2, 3, 0, 1, 3]
It includes user 0 (twice), since Hero is indeed friends with both of his friends. It
includes users 1 and 2, although they are both friends with Hero already. And it
includes user 3 twice, as Chi is reachable through two different friends:
print [friend["id"] for friend in users[0]["friends"]] # [1, 2]
print [friend["id"] for friend in users[1]["friends"]] # [0, 2, 3]
print [friend["id"] for friend in users[2]["friends"]] # [0, 1, 3]
Knowing that people are friends-of-friends in multiple ways seems like interesting
information, so maybe instead we should produce a count of mutual friends. And we
definitely should use a helper function to exclude people already known to the user:
from collections import Counter # not loaded by default

def not_the_same(user, other_user):

"""two users are not the same if they have different ids"""
return user["id"] != other_user["id"]

def not_friends(user, other_user):

"""other_user is not a friend if he's not in user["friends"];
that is, if he's not_the_same as all the people in user["friends"]"""
return all(not_the_same(friend, other_user)
for friend in user["friends"])

def friends_of_friend_ids(user):
return Counter(foaf["id"]
for friend in user["friends"] # for each of my friends
for foaf in friend["friends"] # count *their* friends
if not_the_same(user, foaf) # who aren't me
and not_friends(user, foaf)) # and aren't my friends

print friends_of_friend_ids(users[3]) # Counter({0: 2, 5: 1})

6 | Chapter 1: Introduction
This correctly tells Chi (id 3) that she has two mutual friends with Hero (id 0) but
only one mutual friend with Clive (id 5).
As a data scientist, you know that you also might enjoy meeting users with similar
interests. (This is a good example of the “substantive expertise” aspect of data sci‐
ence.) After asking around, you manage to get your hands on this data, as a list of
pairs (user_id, interest):
interests = [
(0, "Hadoop"), (0, "Big Data"), (0, "HBase"), (0, "Java"),
(0, "Spark"), (0, "Storm"), (0, "Cassandra"),
(1, "NoSQL"), (1, "MongoDB"), (1, "Cassandra"), (1, "HBase"),
(1, "Postgres"), (2, "Python"), (2, "scikit-learn"), (2, "scipy"),
(2, "numpy"), (2, "statsmodels"), (2, "pandas"), (3, "R"), (3, "Python"),
(3, "statistics"), (3, "regression"), (3, "probability"),
(4, "machine learning"), (4, "regression"), (4, "decision trees"),
(4, "libsvm"), (5, "Python"), (5, "R"), (5, "Java"), (5, "C++"),
(5, "Haskell"), (5, "programming languages"), (6, "statistics"),
(6, "probability"), (6, "mathematics"), (6, "theory"),
(7, "machine learning"), (7, "scikit-learn"), (7, "Mahout"),
(7, "neural networks"), (8, "neural networks"), (8, "deep learning"),
(8, "Big Data"), (8, "artificial intelligence"), (9, "Hadoop"),
(9, "Java"), (9, "MapReduce"), (9, "Big Data")
]

For example, Thor (id 4) has no friends in common with Devin (id 7), but they share
an interest in machine learning.
It’s easy to build a function that finds users with a certain interest:
def data_scientists_who_like(target_interest):
return [user_id
for user_id, user_interest in interests
if user_interest == target_interest]
This works, but it has to examine the whole list of interests for every search. If we
have a lot of users and interests (or if we just want to do a lot of searches), we’re prob‐
ably better off building an index from interests to users:
from collections import defaultdict

# keys are interests, values are lists of user_ids with that interest
user_ids_by_interest = defaultdict(list)

for user_id, interest in interests:

user_ids_by_interest[interest].append(user_id)
And another from users to interests:
# keys are user_ids, values are lists of interests for that user_id
interests_by_user_id = defaultdict(list)

Motivating Hypothetical: DataSciencester | 7

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