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Data Science and Machine Learning
Mathematical and Statistical Methods
Chapman & Hall/CRC Machine Learning & Pattern
Recognition
Bayesian Programming
Pierre Bessiere, Emmanuel Mazer, Juan Manuel Ahuactzin, Kamel
Mekhnacha
Dirk P. Kroese
Zdravko I. Botev
Thomas Taimre
Radislav Vaisman
Front cover image reproduced with permission from J. A. Kroese.
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
This book contains information obtained from authentic and highly regarded sources.
Reasonable efforts have been made to publish reliable data and information, but the author
and publisher cannot assume responsibility for the validity of all materials or the
consequences of their use. The authors and publishers have attempted to trace the copyright
holders of all material reproduced in this publication and apologize to copyright holders if
permission to publish in this form has not been obtained. If any copyright material has not
been acknowledged please write and let us know so we may rectify in any future reprint.
Except as permitted under U.S. Copyright Law, no part of this book may be reprinted,
reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other
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payment has been arranged.
To Valerie
— RV
CONTENTS
Preface
Notation
2 Statistical Learning
2.1 Introduction
2.2 Supervised and Unsupervised Learning
2.3 Training and Test Loss
2.4 Tradeoffs in Statistical Learning
2.5 Estimating Risk
2.5.1 In-Sample Risk
2.5.2 Cross-Validation
2.6 Modeling Data
2.7 Multivariate Normal Models
2.8 Normal Linear Models
2.9 Bayesian Learning
Exercises
4 Unsupervised Learning
4.1 Introduction
4.2 Risk and Loss in Unsupervised Learning
4.3 Expectation–Maximization (EM) Algorithm
4.4 Empirical Distribution and Density Estimation
4.5 Clustering via Mixture Models
4.5.1 Mixture Models
4.5.2 EM Algorithm for Mixture Models
4.6 Clustering via Vector Quantization
4.6.1 K-Means
4.6.2 Clustering via Continuous Multiextremal Optimization
4.7 Hierarchical Clustering
4.8 Principal Component Analysis (PCA)
4.8.1 Motivation: Principal Axes of an Ellipsoid
4.8.2 PCA and Singular Value Decomposition (SVD)
Exercises
5 Regression
5.1 Introduction
5.2 Linear Regression
5.3 Analysis via Linear Models
5.3.1 Parameter Estimation
5.3.2 Model Selection and Prediction
5.3.3 Cross-Validation and Predictive Residual Sum of Squares
5.3.4 In-Sample Risk and Akaike Information Criterion
5.3.5 Categorical Features
5.3.6 Nested Models
5.3.7 Coefficient of Determination
5.4 Inference for Normal Linear Models
5.4.1 Comparing Two Normal Linear Models
5.4.2 Confidence and Prediction Intervals
5.5 Nonlinear Regression Models
5.6 Linear Models in Python
5.6.1 Modeling
5.6.2 Analysis
5.6.3 Analysis of Variance (ANOVA)
5.6.4 Confidence and Prediction Intervals
5.6.5 Model Validation
5.6.6 Variable Selection
5.7 Generalized Linear Models
Exercises
7 Classification
7.1 Introduction
7.2 Classification Metrics
7.3 Classification via Bayes’ Rule
7.4 Linear and Quadratic Discriminant Analysis
7.5 Logistic Regression and Softmax Classification
7.6 K-Nearest Neighbors Classification
7.7 Support Vector Machine
7.8 Classification with Scikit-Learn
Exercises
9 Deep Learning
9.1 Introduction
9.2 Feed-Forward Neural Networks
9.3 Back-Propagation
9.4 Methods for Training
9.4.1 Steepest Descent
9.4.2 Levenberg–Marquardt Method
9.4.3 Limited-Memory BFGS Method
9.4.4 Adaptive Gradient Methods
9.5 Examples in Python
9.5.1 Simple Polynomial Regression
9.5.2 Image Classification
Exercises
D Python Primer
D.1 Getting Started
D.2 Python Objects
D.3 Types and Operators
D.4 Functions and Methods
D.5 Modules
D.6 Flow Control
D.7 Iteration
D.8 Classes
D.9 Files
D.10 NumPy
D.10.1 Creating and Shaping Arrays
D.10.2 Slicing
D.10.3 Array Operations
D.10.4 Random Numbers
D.11 Matplotlib
D.11.1 Creating a Basic Plot
D.12 Pandas
D.12.1 Series and DataFrame
D.12.2 Manipulating Data Frames
D.12.3 Extracting Information
D.12.4 Plotting
D.13 Scikit-learn
D.13.1 Partitioning the Data
D.13.2 Standardization
D.13.3 Fitting and Prediction
D.13.4 Testing the Model
D.14 System Calls, URL Access, and Speed-Up
Bibliography
Index
PREFACE
Python code and data sets for each chapter can be downloaded from the
GitHub site: https://github.com/DSML-book
Acknowledgments
Some of the Python code for Chapters 1 and 5 was adapted from [73]. We
thank Benoit Liquet for making this available, and Lauren Jones for
translating the R code into Python.
We thank all who through their comments, feedback, and suggestions
have contributed to this book, including Qibin Duan, Luke Taylor, Rémi
Mouzayek, Harry Goodman, Bryce Stansfield, Ryan Tongs, Dillon Steyl,
Bill Rudd, Nan Ye, Christian Hirsch, Chris van der Heide, Sarat Moka,
Aapeli Vuorinen, Joshua Ross, Giang Nguyen, and the anonymous referees.
David Grubbs deserves a special accollade for his professionalism and
attention to detail in his role as Editor for this book.
The book was test-run during the 2019 Summer School of the Australian
Mathematical Sciences Institute. More than 80 bright upper-undergraduate
(Honours) students used the book for the course Mathematical Methods for
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now to explore a rich
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Machine Learning, taught by Zdravko Botev. We are grateful for the
valuable feedback that they provided.
Our special thanks go out to Robert Salomone, Liam Berry, Robin
Carrick, and Sam Daley, who commented in great detail on earlier versions
of the entire book and wrote and improved our Python code. Their
enthusiasm, perceptiveness, and kind assistance have been invaluable.
Of course, none of this work would have been possible without the loving
support, patience, and encouragement from our families, and we thank them
with all our hearts.
This book was financially supported by the Australian Research Council
Centre of Excellence for Mathematical & Statistical Frontiers, under grant
number CE140100049.
• Random variables are generally specified with upper case roman letters
X, Y, Z and their outcomes with lower case letters x, y, z. Random
vectors are thus denoted in upper case slanted bold font: X = [X1,…,
X ]⊤.
n
• Sets of vectors are generally written in calligraphic font, such as χ, but
the set of real numbers uses the common blackboard bold font ℝ.
Expectation and probability also use the latter font.
• Probability distributions use a sans serif font, such as Bin and Gamma.
Exceptions to this rule are the “standard” notations N and U for the
normal and uniform distributions.
∇f gradient of f
∇ 2f Hessian of f
f ∈ Cp f has continuous derivatives of order p
≈ is approximately
≃ is asymptotically
≪ is much smaller than
⊕ direct sum
⊙ elementwise product
∩ intersection
∪ union
≔,=: is defined as
a.s.
converges almost surely to
−
→
d
converges in distribution to
→
P
converges in probability to
→
Lp
converges in Lp-norm to
→
Matrix/vector notation
A⊤,x⊤ transpose of matrix A or vector x
A-1 inverse of matrix A
A+ pseudo-inverse of matrix A
A-⊤ inverse of matrix A⊤ or transpose of A-1
A≻0 matrix A is positive definite
A ≥ 0 matrix A is positive semidefinite
dim( x) dimension of vector x
det(A) determinant of matrix A
|A| absolute value of the determinant of matrix A
tr(A) trace of matrix A
It might have been, and should have been, apparent to the several
members of the Baron household that Bonnie May had been giving
an admirable exhibition of self-repression from the moment she had
entered the house.
A change came at last—when Mrs. Baron disturbed the reading of
the play and announced, at nine o’clock, that it was “high time for a
little girl to be in bed.”
Mrs. Baron couldn’t possibly have realized how Bonnie May had
been accustomed to divide her hours between sleeping and waking.
The guest had spent her life among player people, whose active
hours begin at noon or later, and who do not deem the day ended
until after midnight—sometimes far later than midnight. Nor had it
been found convenient—or needful—by Bonnie May’s fellow workers
to make any exception to the rule on her behalf. She had been one
of them, and she had fared well and pleasantly.
Thus it was that when Mrs. Baron appeared, somewhat like a bolt
out of a clear sky, the child gave way to overwhelming rebellion.
“I’m not used to going to bed at this hour,” she declared bluntly. She
arose and stood by her chair, like a soldier by his guns, as the saying
is. And taking in the inexorable expression in Mrs. Baron’s eyes, she
turned appealingly to Baron. She was relying upon him to help her.
“Couldn’t she—” began Baron weakly, and added, quite without
conviction: “You know it’s Saturday night, mother!” He was glad he
had thought of its being Saturday, though he couldn’t see why that
should make very much difference. He really believed his mother’s
position was strong enough, if she had only gone about the matter
more tactfully.
“Saturday night doesn’t make any difference,” declared Bonnie May,
her rebellion now including Baron in its scope. “It just isn’t a
reasonable bedtime.”
Baron felt ready to surrender. “Anyway, it won’t be so bad just for
one night,” he ventured.
“Never mind, Victor,” said Mrs. Baron pointedly. She addressed
herself to Bonnie May. “What you’ve been accustomed to may not be
quite so important as what you ought to become accustomed to,”
she said. “Come!”
The child sauntered thoughtfully from the room. She had been
impressed by the fact that even Baron had not seemed surprised by
the suggestion that she ought to go to bed. She was trying to
comprehend the situation. After all, people who were not of the
profession had ways of their own, she realized. If they had all
decided to go to bed, she wouldn’t have minded so much. But they
were laying down a special law for her.
Rebellion triumphed again. In Mrs. Baron’s room she halted. “Where
am I to sleep?” she inquired.
“I think you heard me tell Mrs. Shepard to prepare a room.”
“In the attic? Yes. But I’m not going to sleep there.”
“Indeed, you are.”
“I beg your pardon! Not under any circumstances!”
Mrs. Baron lifted her fingers to her lips and coughed—a very inexpert
cough. “You’ll have to do as I tell you, you know.” She resumed a
resolute march toward the hall, her hand pressed firmly against
Bonnie May’s back.
The child jerked away with a sense of outrage. She had never been
treated so before.
“Truly, you’ll have to obey me,” repeated Mrs. Baron.
Bonnie May was alarmed; she quite lost control of herself. “Stop your
kiddin’!” she said with a catch in her voice. She tried to say it
playfully, but her self-possession was gone. Her remark had
sounded simply offensive, indelicate.
“And I can’t permit you to use such language, either!” declared Mrs.
Baron.
The dismayed guest pressed her hands to her eyes as if she were
trying to think clearly.
Then she made a rush for the stairway!
Mrs. Baron put dignity aside long enough to pursue her, to seize her
by the arm. She was becoming outraged, greatly indignant. “What do
you mean to do?” she demanded, her voice trembling slightly.
“I’m quitting.”
“You’re——”
“I won’t stay here!”
The distressed old gentlewoman tried to calm herself. “Where do you
think of going?” she asked.
“Anywhere—to the theatres. Any company in town will be glad to
have me. They will know who I am. They—they are the kind of
people who will appreciate me!” The words were spoken in a tone of
heart-break, of despair.
Mrs. Baron afterward confessed to members of her family that for the
first time in her life she felt completely helpless. She was, in truth, a
somewhat childish person in many ways, and she was not
accustomed to any unpleasantnesses save those which she created
for others.
At any rate, she swallowed with difficulty—and surrendered. “It’s a
very small point, after all,” she said ungraciously. “Go into my room.
Flora will look after you.” She spoke coldly, all her interest seemingly
withdrawn.
And just as the guest disappeared into Mrs. Baron’s sitting-room,
Flora came almost stealthily up the stairs.
“I wish you’d put that little limb of Satan to bed,” she said. Flora saw
that her mother’s hand, on the balustrade, trembled.
“Where shall I put her?” she inquired.
“Anywhere! just so you get her covered up for the night.”
Flora paused, her eyes uneasily seeking her mother’s.
“I’m afraid you’re angry with me, mother,” she said humbly.
“With you? Certainly not.”
Flora was puzzled. Her mother had long ago declared that Mr. Addis
must not be accepted as a visitor. Did she know that he had just
gone? She was about to enter her mother’s sitting-room when
something prompted her to turn.
“You knew Mr. Addis called, didn’t you?” she asked.
Mrs. Baron’s face flamed again. “Knew it? Certainly, I didn’t know it!
I’ve told Mrs. Shepard—I don’t intend that he shall annoy you!”
“Oh, mother! He doesn’t! And I think Mrs. Shepard didn’t know, this
time. Bonnie May went to the door and let him in. She called me
down-stairs without telling me who it was.” Flora surveyed her
mother yearningly, yet with a kind of gentle courage. “I don’t believe
in hiding things from you, mother. But I was glad to see him.”
Mrs. Baron looked grimly toward her own door. “She let him in! Very
well. Put her to bed!”
She descended the stairs with dignity. She must have been thinking
of future victories rather than of past defeats.
When Flora entered the sitting-room she found Bonnie May standing
in uneasy contemplation.
“Mother says I’m to put you to bed,” said Miss Baron.
“Why didn’t she go ahead and put me to bed herself?”
Flora perceived that the question was not wanting in sincerity. She
decided to answer quite honestly.
“I think,” she ventured gently, “you must have said something to vex
her.”
“Not at all. She tried to vex me. I behaved very properly.”
Flora sighed and shook her head slowly; but she was smiling, too.
She was wondering what it really was that had gone wrong.
“Possibly you didn’t want to obey her?” she ventured.
The child’s brow puckered. “But why should I want to obey her?”
“Why—because she’s going to be good to you, I’m sure.”
“Well, I mean to be good to her, too—if she’ll let me. And I don’t ask
her to obey me.”
“But it’s different. She’s an old lady.”
“Well, I’ve got no patience with old people. It’s all right, just as a part,
but there’s no use putting it on all the time.”
“But, dear,” implored Flora, drawing the child within the curve of her
arm, “don’t say that! I know you mean to be nice and kind, but truly
you don’t understand. We must all grow old some time—even you
will get to be old.”
The guest gave deliberate thought to this; then her expression
became resolute. “Well, if they ever hang any gray hairs on me
they’ll have to catch me when I’m asleep—I’ll tell you that right now.”
Miss Baron was not encouraged to argue the point any further. She
resumed the subject of going to bed.
“You know I’m to have his room—your brother’s?” the guest insisted.
“Mother said you might sleep where you liked.”
“Did she say that?”
“Almost exactly.”
“Well, where is that attic room?”
“It’s up one more flight of stairs—under the roof.”
The child looked quite wistful and earnest, and then her words came
with conviction. “I just couldn’t sleep up there. Attics are where
misers sleep, and poor children. It’s where people die of hunger and
cold. It’s never the right kind of people. Come, let’s go to his room.”
And so they did.
“You won’t mind my helping you?” pleaded Flora.
“Helping me?”
“To undress, you know—and to be tucked in!”
The guest looked at her unresponsively. “But I’ve been used to doing
that for myself,” she said.
Flora quickly stooped and took her into her arms impulsively. “Dear
child,” she cried, her voice tremulous, “let me do it to-night! I think
you’ll love it—and I’ll love it, too.” She drew the perplexed face
almost roughly against her own.
She did not wait to be refused. She hurried into the bathroom and
busied herself; she was singing a little crooning song. There was
also the noise of water splashing into the tub.
She reappeared presently. “The water is ready—for your bath, you
know, and I’ve left one of my nighties there for you.” She smiled
happily. “Of course it will be too big. I’ll make you some little ones
soon.”
The seeming perversion of the child asserted itself again. “I usually
take my bath in the morning,” she said a little stiffly; but she saw how
the glad light in Miss Baron’s eyes wavered, and she added quickly,
“but it will be all right.” And she went out into the bathroom.
When she reappeared after a rather long time she was smiling
radiantly. She had on Flora’s nightgown, soft and white, with pink
ribbons. She held it daintily up before her feet, and glanced back at
the train that dragged behind. “Isn’t it lovely!” she said.
“It is, dear,” said Flora.
She had turned the white coverlet and the sheet down. Now she
watched the child scramble up into the bed. She wanted to help, but
she refrained.
“Would you like me to tell you a story?” asked Flora.
Bonnie May looked at her swiftly, incredulously. “No!” she said. She
burst out into riotous laughter. “I’m not an infant,” she explained.
Flora flushed. “Very well,” she said gently. Yet she lingered in the
room a little while. She put some of Victor’s masculine decorations
out of sight. She adjusted the blind. She was about to extinguish the
light when she looked again at the strange guest.
The child’s eyes were fixed upon her widely, wonderingly.
“You lovely thing!” said Bonnie May.
“Good night, dear!” said Flora. And then she knew that the child
wished to speak to her, and she went over and bent above the bed.
“What is it, Bonnie May?” she asked.
The child stared before her in silence for a moment and then the
words came. “I wished so much that she would love me!” she said. “I
tried so hard....”
Flora slipped her hand under the guest’s head. “I’ll tell you a secret,”
she whispered. “If she hadn’t cared for you, she would have been
quite polite; she would have been wonderfully gracious. She was
ungracious and unkind because—because she loved you, dear. It
seems absurd, doesn’t it? But I know.”
The Barons were the kind of family that have just one morning
newspaper left at their door on Sunday, and who believe that it
contains everything that ought to concern them in any way—that
whatever is published in any other newspaper is to be regarded with
scepticism, or lightly discredited.
Yet on this particular Sunday morning Victor Baron arose early and
intercepted the paper-carrier, and amazed that industrious youth by
buying a copy of every journal he carried.
With this not inconsiderable burden under his arm he betook himself
to the library and began an eager search for certain information.
He scanned all the advertising columns systematically, and then
turned to the news departments.
A great heap of discarded “sections” grew about him as he
progressed, and little by little a look of troubled anticipation vanished
from his eyes. The last section of the last paper was cast away with
an air of triumph.
He hadn’t been able to find a single word about any child who was
lost, or who had strayed, or who had been stolen!
“Good!” he exclaimed, and he looked with great relief at the heap of
papers about him, their splotches of color and assertive head-lines
having no further interest for him. He smiled complacently.
In the meantime, in the sunny sitting-room up-stairs, Flora had
broken the news to Mrs. Baron—the news touching Bonnie May and
the new dress.
It had been a very difficult thing to do, because Mrs. Baron was
always at her worst on Sunday mornings.
It was on Sunday mornings that she felt most keenly the lapse of the
neighborhood from former glories to a condition of sordid griminess.
It was on these mornings that she fared forth to the old church, only
three blocks away, in which the best people in town had formerly
worshipped, but which had been deserted by nearly all the old
parishioners.
It was Mrs. Baron’s contention that it was indelicate, to say the least,
for people to desert a church. There were things in the church life,
she maintained, which could not be transplanted, and which
constituted the very warp and woof of the domestic as well as the
social foundations. She had come to regard herself as a kind of
standard-bearer in this relationship, and she attended services
somewhat ostentatiously, with the belief that she was not only
lending her influence, but administering a rebuke as well. Ignoring
the protests of her family, she had even consented to play the organ
for the Sunday-school services. As a young lady she had learned to
read music, as a matter of course, and though she possessed no
musical intelligence, and had found it impossible to regain the old
manual skill she had once possessed, she played the simple hymns
with a kind of proud rigor, because she believed her participation in
the services in this direction must impart an authority to the
proceedings which the abler playing of some obscure individual
could not have imparted.
Indeed, Mrs. Baron was a personage on Sunday mornings; a gallant
general leading a forlorn hope proudly and firmly.
When Flora confessed to her that the dress had been rejected, she
was too greatly amazed to say a great deal. She had also entered
upon her stoic mood—her Sunday-morning mood.
“You see, she is simply determined not to get along,” she declared
with finality. She took the dress into her own hands and regarded it
critically. “Do you see how carefully the feather-stitching is done?”
she demanded.
“Yes,” agreed Flora, “the—the feather-stitching is beautiful. But
really, I don’t believe she is simply perverse. If you could have seen
the dismay in her eyes—” Flora smiled at the recollection.
“I’ve seen women like that,” Mrs. Baron continued, “women who like
to make difficulties; who go into hysterics over little things. It’s always
just a lack of sense—that’s all it is.”
“Yes—or temperament. I expect there’s a good deal in what people
call temperament. I didn’t know children had it so much, but Bonnie
May isn’t like other children. Maybe she has a good deal of
temperament.”
They examined the dress together without any very definite purpose.
“She ought to know she can’t go on wearing that silly thing she came
here in,” was Mrs. Baron’s next comment.
“She must realize that,” agreed Flora. She added casually: “I think
something soft, with a little color in it, might please her. You might let
me try next time.”
This was the wrong note again. “As if I weren’t capable of making a
child’s dress!” protested Mrs. Baron.
“I only meant it would be fair to divide the work,” Flora explained
gently. “I didn’t mean I could do it better.”
As if her anger had been effectually checked in that direction, Mrs.
Baron hit upon another possible grievance. “And she’s going to
Sunday-school to-day,” she affirmed in a tone which seemed to take
account of difficulties. “We’ve done our best to dress her decently.
And I don’t intend to humor a little pagan as long as she’s in a
Christian household.”
“But in that—that peculiar dress?” faltered Flora. She had a vision of
Bonnie May in her fantastic old frock associating with the prim
children of poverty who were now the mainstay of the Sunday-
school.
“She may walk with Mrs. Shepard. People may believe she belongs
to her, if they want to.”
“Oh, mother!” There was something almost despairing in Flora’s
tone.
“It’s the best we can do. I mean to do my duty—and I’m not willing to
look ridiculous.”
Again Miss Baron perceived breakers ahead. If the child conceived
the idea that she was being commanded to go anywhere she would
very probably develop new methods of resistance. If she were
politely invited to accompany other members of the household to
church, she might decide to be altogether gracious.
She entertained a lingering regret that the guest could not be
persuaded to wear the new dress—in which, certainly, she would be
conspicuous enough, but not quite in a flaunting fashion. She even
thought of Victor, and wondered if he might not be able to prevail
upon the child to accede to the wishes of her elders. But upon
second thought she decided not to involve her brother in a phase of
the problem which did not touch him. She suspected there would be
other phases, more in his line, in due time.