Data Mining and Analysis Fundamental Concepts and Algorithms 1st Edition by Mohammed Zaki PDF Download
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Mohammed J. Zaki
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The fundamental algorithms in data mining and analysis form the basis
for the emerging field of data science, which includes automated meth-
ods to analyze patterns and models for all kinds of data, with applications
ranging from scientific discovery to business intelligence and analytics.
This textbook for senior undergraduate and graduate data mining courses
provides a broad yet in-depth overview of data mining, integrating related
concepts from machine learning and statistics. The main parts of the book
include exploratory data analysis, pattern mining, clustering, and classifi-
cation. The book lays the basic foundations of these tasks, and also covers
cutting-edge topics such as kernel methods, high-dimensional data analy-
sis, and complex graphs and networks. With its comprehensive coverage,
algorithmic perspective, and wealth of examples, this book offers solid
guidance in data mining for students, researchers, and practitioners alike.
Key Features:
www.cambridge.org
Information on this title: www.cambridge.org/9780521766333
c Mohammed J. Zaki and Wagner Meira, Jr. 2014
A catalog record for this publication is available from the British Library.
Preface page ix
2 Numeric Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.1 Univariate Analysis 33
2.2 Bivariate Analysis 42
2.3 Multivariate Analysis 48
2.4 Data Normalization 52
2.5 Normal Distribution 54
2.6 Further Reading 60
2.7 Exercises 60
3 Categorical Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.1 Univariate Analysis 63
3.2 Bivariate Analysis 72
3.3 Multivariate Analysis 82
3.4 Distance and Angle 87
3.5 Discretization 89
3.6 Further Reading 91
3.7 Exercises 91
4 Graph Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
4.1 Graph Concepts 93
4.2 Topological Attributes 97
v
vi Contents
Index 583
Preface
This book is an outgrowth of data mining courses at RPI and UFMG; the RPI course
has been offered every Fall since 1998, whereas the UFMG course has been offered
since 2002. Although there are several good books on data mining and related topics,
we felt that many of them are either too high-level or too advanced. Our goal was to
write an introductory text that focuses on the fundamental algorithms in data mining
and analysis. It lays the mathematical foundations for the core data mining methods,
with key concepts explained when first encountered; the book also tries to build the
intuition behind the formulas to aid understanding.
The main parts of the book include exploratory data analysis, frequent pattern
mining, clustering, and classification. The book lays the basic foundations of these
tasks, and it also covers cutting edge topics such as kernel methods, high dimensional
data analysis, and complex graphs and networks. It integrates concepts from related
disciplines such as machine learning and statistics, and is also ideal for a course on data
analysis. Most of the prerequisite material is covered in the text, especially on linear
algebra, and probability and statistics.
The book includes many examples to illustrate the main technical concepts. It also
has end of chapter exercises, which have been used in class. All of the algorithms in the
book have been implemented by the authors. We suggest that readers use their favorite
data analysis and mining software to work through our examples, and to implement the
algorithms we describe in text; we recommend the R software, or the Python language
with its NumPy package. The datasets used and other supplementary material such as
project ideas, slides, and so on, are available online at the book’s companion site and
its mirrors at RPI and UFMG:
• http://dataminingbook.info
• http://www.cs.rpi.edu/ zaki/dataminingbook
• http://www.dcc.ufmg.br/dataminingbook
Having understood the basic principles and algorithms in data mining and data
analysis, readers will be well equipped to develop their own methods or use more
advanced techniques.
ix
x Preface
2 3
14 6 7 15 5 4 19 18 8
13 16 20 21 11 9 10
17 22 12
Figure 1. Chapter dependencies
Suggested Roadmaps
The chapter dependency graph is shown in Figure 0.1. We suggest some typical
roadmaps for courses and readings based on this book. For an undergraduate level
course, we suggest the following chapters: 1–3, 8, 10, 12–15, 17–19, and 21–22. For an
undergraduate course without exploratory data analysis, we recommend Chapters 1,
8–15, 17–19, and 21–22. For a graduate course, one possibility is to quickly go over the
material in Part I, or to assume it as background reading and to directly cover Chapters
9–23; the other parts of the book, namely frequent pattern mining (Part II), clustering
(Part III), and classification (Part IV), can be covered in any order. For a course on
data analysis the chapters must include 1–7, 13–14, 15 (Section 2), and 20. Finally, for
a course with an emphasis on graphs and kernels we suggest Chapters 4, 5, 7 (Sections
1–3), 11–12, 13 (Sections 1–2), 16–17, and 20–22.
Acknowledgments
Initial drafts of this book have been used in many data mining courses. We received
many valuable comments and corrections from both the faculty and students. Our
thanks go to
We would like to thank all the students enrolled in our data mining courses at RPI
and UFMG, and also the anonymous reviewers who provided technical comments on
various chapters. We appreciate the collegial and supportive environment within the
computer science departments at RPI and UFMG. In addition, we thank NSF, CNPq,
CAPES, FAPEMIG, Inweb – the National Institute of Science and Technology for
the Web, and Brazil’s Science without Borders program for their support. We thank
NSF Lauren Cowles, our editor at Cambridge University Press, for her guidance and
patience in realizing this book.
Finally, on a more personal front, MJZ dedicates the book to his wife, Amina,
for her love, patience and support over all these years, and to his children, Abrar and
Afsah, and his parents, and WMJ gratefully dedicates the book to his wife Patricia, to
his children, Gabriel and Marina, and to his parents, Wagner and Marlene, for their
love, encouragement and inspiration.
CHAPTER 1 Data Mining and Analysis
Data mining is the process of discovering insightful, interesting, and novel patterns, as
well as descriptive, understandable, and predictive models from large-scale data. We
begin this chapter by looking at basic properties of data modeled as a data matrix. We
emphasize the geometric and algebraic views, as well as the probabilistic interpreta-
tion of data. We then discuss the main data mining tasks, which span exploratory data
analysis, frequent pattern mining, clustering, and classification, laying out the roadmap
for the book.
Data can often be represented or abstracted as an n × d data matrix, with n rows and
d columns, where rows correspond to entities in the dataset, and columns represent
attributes or properties of interest. Each row in the data matrix records the observed
attribute values for a given entity. The n × d data matrix is given as
X1 X2 · · · Xd
x x 11 x 12 · · · x 1d
1
D =.
x2 x 21 x 22 · · · x 2d
. .. .. .. ..
. . . . .
xn x n1 x n2 · · · x nd
xi = (x i1 , x i2 , . . . , x id )
X j = (x 1 j , x 2 j , . . . , x nj )
Darling Mother,
I have gone with Philip by the eight train to London. We
shall be married as soon as possible. I shall stay with
Rachel until then. You know that things could not go on as
they were.
Will you understand, dear Mother, that if I did not love you
so deeply I would not have done this? But because you
would not let Phil go I have had to choose. If only you will
understand that I do not love you less for this, but that it is
for Phil’s sake that I do it, you will love me as before. And
you know that I will love you always.
Your devoted daughter,
Katherine.
The others come in. George Trenchard entered, rubbing his hands
and laughing. He seemed, every week, redder in the face and
stouter all over; in physical reality he added but little to his girth. It
was the stoutness of moral self-satisfaction and cheerful
complaisance. His doctrine of pleasant aloofness from contact with
other human beings had acted so admirably; he would like to have
recommended it to everyone had not such recommendation been
too great a trouble.
He was never, after this evening, to be aloof again, but he did not
know that.
“Well, well,” he cried. “Punctual for once, Henry. Very nice, indeed.
Dear me, Mother, why this gaudiness? People coming to dinner?”
She looked down at her brooch.
“No, dear.... No one. I just thought I’d put it on. I haven’t worn it for
quite a time. Not for a year at least.”
“Very pretty, very pretty,” he cried. “Dear me, what a day I’ve had!
So busy, scarcely able to breathe!”
“What have you been doing, Father?” asked Henry.
“One thing and another. One thing and another,” said George airily.
“Day simply flown.”
He stood there in front of the fire, his legs spread, his huge chest
flung out, his face flaming like the sun.
“Yes, it’s been a very pleasant day,” said Mrs. Trenchard, “very
pleasant.”
“Where’s Katie?” asked her father. “She’s generally down before
anyone.”
Henry, who, in the contemplation of his mother, had forgotten, for
the moment, his sister’s strange behaviour, said:
“Oh! she’ll be late, I expect. I saw her go out about seven. Had to
see Penhaligan about something important, she told me. Went out
into all that storm.”
As he spoke eight o’clock struck.
Mrs. Trenchard looked up.
“Went out to see Penhaligan?” she asked.
“Yes, Mother. She didn’t tell me why.”
Aunt Betty came in. Her little body, her cheerful smile, her air as of
one who was ready to be pleased with anything, might lead a
careless observer into the error of supposing that she was a quite
ordinary old maid with a fancy for knitting, the Church of England,
and hot water with her meals. He would be wrong in his judgment;
her sharp little eyes, the corners of her mouth betrayed a sense of
humour that, although it had never been encouraged by the family,
provided much wise penetration and knowledge. Any casual
acquaintance in half an hour’s talk would have discovered in Aunt
Betty wisdom and judgment to which her own family would, until the
day of its decent and honourable death, be entirely blind.
Just now she had lost her spectacles.
“My spectacles,” she said. “Hum-hum—Very odd. I had them just
before tea. I was working over in that corner—I never moved from
there except once when—when—Oh! there they are! No, they are
not. And I played ‘Patience’ there, too, in the same corner. Very
odd.”
“Perhaps, dear,” said Mrs. Trenchard, “you left them in your
bedroom.”
“No, Harriet, I looked there. Hum-hum-hum. Very odd it is, because
—”
Millie came in and then Aunt Aggie.
“Is Father coming down to-night?” said George.
“Yes,” said Mrs. Trenchard. “He said that he felt better. Thought it
would be nice to come down. Yes, that it would be rather nice....
Aggie, dear, that’s your sewing, isn’t it? You left it here this morning.
Rocket put it between the pages of my novel to mark the place. I
knew it was yours—”
“Yes, it’s mine,” said Aunt Aggie, shortly.
Meanwhile Henry, looking at the door, waited for Katherine. A
strange premonition was growing in him that all was not well.
Katherine and Philip, they had not appeared—Katherine and Philip....
As he thought of it, it occurred to him that he had not heard Philip
moving as he dressed. Philip’s room was next to Henry’s, and the
division was thin; you could always hear coughs, steps, the pouring
of water, the opening and shutting of drawers.
There had been no sounds to-night. Henry’s heart began to beat
very fast. He listened to the wind that, now that the storm had
swung away, was creeping around the house, trying the doors and
windows, rattling something here, tugging at something there, all
the pipes gurgled and spluttered with the waters of the storm.
“Ah! there they are!” cried Aunt Betty.
Henry started, thinking that she must herald the entry of Katherine
and Philip; but no, it was only the gold-rimmed spectacles lying
miraculously beneath the sofa.
“Now, how,” cried Aunt Betty, “did they get there? Very odd, because
I remember distinctly that I never moved from my corner.”
“Well,” said George Trenchard, who, now that his back was warmed
by the fire, wanted his front warmed too, “how much longer are we
to wait for dinner? Katie and Philip. Playing about upstairs, I
suppose.”
Quarter-past eight struck, and Rocket, opening the door, announced
that dinner was ready.
“Suppose you just go up and see what Katie’s doing, Millie dear,”
said Mrs. Trenchard.
Millie left them and ran quickly upstairs. She pushed back Katie’s
door, then, stepping inside, the darkness and silence and a strange
murmurous chill caught her, as though someone had leapt, out of
the dusk, at her throat. She knew then instantly what had occurred.
She only said once, very softly, “Katie!” then gently closed the door
behind her, as though she did not want anyone else to see the room.
She stayed there; there, beside the door, for quite a long time. The
room was very dark, but the looking-glass glimmered like a white,
flickering shadow blown by the wet wind that came in through the
open window. Something flapped monotonously.
Millie, standing quite motionless by the door, thought to herself
“Katherine and Philip! They’ve done it!... at last, they’ve done it!” At
first, because she was very young and still believed in freedom and
adventure as the things best worth having in life, she felt nothing
but a glad, triumphant excitement; an excitement springing not only
from her pleasure in any brave movement, but also from her
reassurance in her beloved sister, her knowledge that after all
Katherine did believe in Love beyond every other power, was ready
to venture all for it. Her own impulse was to run after them, as fast
as she could, and declare her fidelity to them.
At last she moved away from the door to the dressing-table and lit a
candle. Its soft white flame for a moment blinded her. She had an
instant of hesitation; perhaps after all she had flown too rapidly to
her desired conclusions, the two of them were waiting now in the
drawing-room for her.... Then she saw Katherine’s note propped
against the looking-glass.
She took it up, saw that it was addressed to her mother, and
realised, for the first time, what this would mean to them all. She
saw then—THE OLD ONES—Grandfather, Mother, Father, Aunt Sarah,
Aunt Aggie, Aunt Betty. She was sorry for them, but she knew, as
she stood there, that she did not care, really, whether they were
hurt or no. She felt her own freedom descend upon her, there in
Katie’s room, like a golden, flaming cloud. This was the moment for
which, all her life, she had been waiting. The Old Ones had tried to
keep them and tie them down, but the day of the Old Ones was
past, their power was broken. It was the New Generation that
mattered—Katherine and Philip, Millie and Henry, and all their kind;
it was their world and their dominion—
She suddenly, alone there, with the note in her hand, danced a little
dance, the candle-flame flickering in the breeze and Katherine’s
white, neat bed so cold and tidy.
She was not hard, she was not cruel—her own time would come
when she would cry for sympathy and would not find it, and must
set her teeth because her day was past ... now was her day—She
seized it fiercely.
Very quietly she went downstairs....
She opened the drawing-room door: as she entered all their eyes
met her and she knew at once, as she saw Henry’s, that he was
expecting her announcement.
She looked across at her mother.
“Katherine’s room’s empty,” she said. “There’s no one there at all.”
She hesitated a moment, then added: “There was this note for you,
Mother, on her dressing-table.”
She went across the room and gave it to her mother. Her mother
took it; no one spoke.
Mrs. Trenchard read it; for a dreadful moment she thought that she
was going to give way before them all, was going to cry out, to
scream, to rush wildly into the road to stop the fugitives, or slap
Aunt Aggie’s face. For a dreadful moment the battle of her whole life
to obtain the mastery of herself was almost defeated—then, blindly,
obeying some impulse with which she could not reason, of which
she was scarcely conscious, some strong call from a far country, she
won a triumphant victory.
“It’s from Katherine!” she said. “The child’s mad. She’s gone up to
London.”
“London!” George Trenchard cried.
“London!” cried Aunt Aggie.
“Yes. With Philip. They have caught the eight train. They are to be
married to-morrow. ‘Because I would not let Philip go,’ she says. But
she’s mad—”
For an instant she gripped the mantelpiece behind her. She could
hear them, only from a distance, as though their voices were
muffled by the roar of sea or wind, their exclamations.
Her husband was, of course, useless. She despised him. He cried:
“They must be stopped! They must be stopped. This is impossible!
That fellow Mark—one might have guessed! They must be stopped.
At once! At once!”
“They can’t be.” She heard her voice far away with the others. “They
can’t be stopped. The train left at eight o’clock, nearly half an hour
ago. There’s nothing to be done.”
“But, of course,” cried George, “there’s something to be done. They
must be stopped at once. I’ll go up by the next train.”
“There’s no train until six to-morrow morning—and what good would
you do? They’re engaged. You gave your permission. Katherine’s of
age. It is her own affair.”
They all cried out together. Their voices sounded to Mrs. Trenchard
like the screams of children.
Through the confusion there came the sound of an opening door.
They all turned, and saw that it was old Mr. Trenchard, assisted by
Rocket.
“Why don’t you come in to dinner?” he said, in his clear, thin voice.
“I went straight into the dining-room because I was late, and here
you all are, and it’s nearly half-past eight.”
The same thought instantly struck them all. Grandfather must know
nothing about it; a very slight shock, they were all aware, would kill
Grandfather, and there could not possibly be any shock to him like
this amazing revolt of Katherine’s. Therefore he must know nothing.
Like bathers asserting themselves after the first quiver of an icy
plunge, they fought their way to the surface.
Until Grandfather was safely once more alone in his room the
situation must be suspended. After all, there was nothing to be
done! He, because he was feeling well that evening, was intent upon
his dinner.
“What! Waiting for Katherine?” he said.
“Katherine isn’t coming down to dinner, Father,” Mrs. Trenchard said.
“What, my dear?”
“Katherine isn’t coming down to dinner.”
“Not ill, I hope.”
“No—a little tired.”
George Trenchard was the only one who did not support his part.
When the old man had passed through the door, George caught his
wife’s arm.
“But, I say,” he whispered, “something—”
She turned for an instant, looking at him with scorn.
“Nothing!” she said. “It’s too late.”
They went in to dinner.
It was fortunate that Grandfather was hungry; he did not, it seems,
notice Philip’s absence.
“Very nice to see you down, Father,” Mrs. Trenchard said pleasantly.
“Very nice for us all.”
“Thank ye, my dear. Very agreeable—very agreeable. Quite myself
this evening. That rheumatism passed away, so I said to Rocket,
‘Well, ’pon my word, Rocket, I think I’ll come down to-night’ Livelier
for us all to be together. Hope Katie isn’t ill, though?”
“No—no—nothing at all.”
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