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Numerical and Statistical Methods for Bioengineering
Applications in MATLAB 1st Edition Michael R. King
Digital Instant Download
Author(s): Michael R. King, Nipa A. Mody
ISBN(s): 9780521871587, 0521871581
Edition: 1
File Details: PDF, 4.17 MB
Year: 2010
Language: english
This page intentionally left blank
Numerical and Statistical Methods for Bioengineering

This is the first MATLAB-based numerical methods textbook for bioengineers that
uniquely integrates modeling concepts with statistical analysis, while maintaining a
focus on enabling the user to report the error or uncertainty in their result.
Between traditional numerical method topics of linear modeling concepts, non-
linear root finding, and numerical integration, chapters on hypothesis testing, data
regression, and probability are interweaved. A unique feature of the book is the
inclusion of examples from clinical trials and bioinformatics, which are not found
in other numerical methods textbooks for engineers. With a wealth of biomedical
engineering examples, case studies on topical biomedical research, and the inclu-
sion of end of chapter problems, this is a perfect core text for a one-semester
undergraduate course.

Michael R. King is an Associate Professor of Biomedical Engineering at Cornell

University. He is an expert on the receptor-mediated adhesion of circulating cells,
and has developed new computational and in vitro models to study the function
of leukocytes, platelets, stem, and cancer cells under flow. He has co-authored two
books and received numerous awards, including the 2008 ICNMM Outstanding
Researcher Award from the American Society of Mechanical Engineers, and
received the 2009 Outstanding Contribution for a Publication in the International
Journal Clinical Chemistry.
Nipa A. Mody is currently a postdoctoral research associate at Cornell University
in the Department of Biomedical Engineering. She received her Ph.D. in Chemical
Engineering from the University of Rochester in 2008 and has received a number of
awards including a Ruth L. Kirschstein National Research Service Award (NRSA)
from the NIH in 2005 and the Edward Peck Curtis Award for Excellence in Teaching
from University of Rochester in 2004.
CAMBRIDGE TEXTS IN BIOMEDICAL ENGINEERING

Series Editors
W. MARK SALTZMAN, Yale University
SHU CHIEN, University of California, San Diego

Series Advisors
WILLIAM HENDEE, Medical College of Wisconsin
ROGER KAMM, Massachusetts Institute of Technology
R O B E R T M A L K I N , Duke University
A L I S O N N O B L E , Oxford University
B E R N H A R D P A L S S O N , University of California, San Diego
N I C H O L A S P E P P A S , University of Texas at Austin
M I C H A E L S E F T O N , University of Toronto
G E O R G E T R U S K E Y , Duke University
C H E N G Z H U , Georgia Institute of Technology

Cambridge Texts in Biomedical Engineering provides a forum for high-quality accessible

textbooks targeted at undergraduate and graduate courses in biomedical engineering. It
covers a broad range of biomedical engineering topics from introductory texts to advanced
topics including, but not limited to, biomechanics, physiology, biomedical instrumentation,
imaging, signals and systems, cell engineering, and bioinformatics. The series blends theory
and practice, aimed primarily at biomedical engineering students, it also suits broader courses
in engineering, the life sciences and medicine.
Numerical and
Statistical Methods
for Bioengineering
Applications in MATLAB

Michael R. King and Nipa A. Mody

Cornell University
CAMBRIDGE UNIVERSITY PRESS
Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore,
São Paulo, Delhi, Dubai, Tokyo

Cambridge University Press

The Edinburgh Building, Cambridge CB2 8RU, UK

Published in the United States of America by Cambridge University Press, New York

www.cambridge.org
Information on this title: www.cambridge.org/9780521871587

© M. King and N. Mody 2010

This publication is in copyright. Subject to statutory exception and to the

provision of relevant collective licensing agreements, no reproduction of any part
may take place without the written permission of Cambridge University Press.
First published in print format 2010

ISBN-13 978-0-511-90833-0 eBook (EBL)

ISBN-13 978-0-521-87158-7 Hardback

Cambridge University Press has no responsibility for the persistence or accuracy

of urls for external or third-party internet websites referred to in this publication,
and does not guarantee that any content on such websites is, or will remain,
accurate or appropriate.
Contents

Preface page ix

1 Types and sources of numerical error 1

1.1 Introduction 1
1.2 Representation of floating-point numbers 4
1.2.1 How computers store numbers 7
1.2.2 Binary to decimal system 7
1.2.3 Decimal to binary system 9
1.2.4 Binary representation of floating-point numbers 10
1.3 Methods used to measure error 16
1.4 Significant digits 18
1.5 Round-off errors generated by floating-point operations 20
1.6 Taylor series and truncation error 26
1.6.1 Order of magnitude estimation of truncation error 28
1.6.2 Convergence of a series 32
1.6.3 Finite difference formulas for numerical differentiation 33
1.7 Criteria for convergence 39
1.8 End of Chapter 1: key points to consider 40
1.9 Problems 40
References 46

2 Systems of linear equations 47

2.1 Introduction 47
2.2 Fundamentals of linear algebra 53
2.2.1 Vectors and matrices 53
2.2.2 Matrix operations 56
2.2.3 Vector and matrix norms 64
2.2.4 Linear combinations of vectors 66
2.2.5 Vector spaces and basis vectors 69
2.2.6 Rank, determinant, and inverse of matrices 71
2.3 Matrix representation of a system of linear equations 75
2.4 Gaussian elimination with backward substitution 76
2.4.1 Gaussian elimination without pivoting 76
2.4.2 Gaussian elimination with pivoting 84
2.5 LU factorization 87
2.5.1 LU factorization without pivoting 88
2.5.2 LU factorization with pivoting 93
2.5.3 The MATLAB lu function 95
2.6 The MATLAB backslash (\) operator 96
2.7 III-conditioned problems and the condition number 97
2.8 Linear regression 101
vi Contents

2.9 Curve fitting using linear least-squares approximation 107

2.9.1 The normal equations 109
2.9.2 Coefficient of determination and quality of fit 115
2.10 Linear least-squares approximation of transformed equations 118
2.11 Multivariable linear least-squares regression 123
2.12 The MATLAB function polyfit 124
2.13 End of Chapter 2: key points to consider 125
2.14 Problems 127
References 139

3 Probability and statistics 141

3.1 Introduction 141
3.2 Characterizing a population: descriptive statistics 144
3.2.1 Measures of central tendency 145
3.2.2 Measures of dispersion 146
3.3 Concepts from probability 147
3.3.1 Random sampling and probability 149
3.3.2 Combinatorics: permutations and combinations 154
3.4 Discrete probability distributions 157
3.4.1 Binomial distribution 159
3.4.2 Poisson distribution 163
3.5 Normal distribution 166
3.5.1 Continuous probability distributions 167
3.5.2 Normal probability density 169
3.5.3 Expectations of sample-derived statistics 171
3.5.4 Standard normal distribution and the z statistic 175
3.5.5 Confidence intervals using the z statistic and the t statistic 177
3.5.6 Non-normal samples and the central-limit theorem 183
3.6 Propagation of error 186
3.6.1 Addition/subtraction of random variables 187
3.6.2 Multiplication/division of random variables 188
3.6.3 General functional relationship between two random
variables 190
3.7 Linear regression error 191
3.7.1 Error in model parameters 193
3.7.2 Error in model predictions 196
3.8 End of Chapter 3: key points to consider 199
3.9 Problems 202
References 208

4 Hypothesis testing 209

4.1 Introduction 209
4.2 Formulating a hypothesis 210
4.2.1 Designing a scientific study 211
4.2.2 Null and alternate hypotheses 217
4.3 Testing a hypothesis 219
4.3.1 The p value and assessing statistical significance 220
4.3.2 Type I and type II errors 226
4.3.3 Types of variables 228
4.3.4 Choosing a hypothesis test 230
vii Contents

4.4 Parametric tests and assessing normality 231

4.5 The z test 235
4.5.1 One-sample z test 235
4.5.2 Two-sample z test 241
4.6 The t test 244
4.6.1 One-sample and paired sample t tests 244
4.6.2 Independent two-sample t test 249
4.7 Hypothesis testing for population proportions 251
4.7.1 Hypothesis testing for a single population proportion 256
4.7.2 Hypothesis testing for two population proportions 257
4.8 One-way ANOVA 260
4.9 Chi-square tests for nominal scale data 274
4.9.1 Goodness-of-fit test 276
4.9.2 Test of independence 281
4.9.3 Test of homogeneity 285
4.10 More on non-parametric (distribution-free) tests 288
4.10.1 Sign test 289
4.10.2 Wilcoxon signed-rank test 292
4.10.3 Wilcoxon rank-sum test 296
4.11 End of Chapter 4: key points to consider 299
4.12 Problems 299
References 308

5 Root-finding techniques for nonlinear equations 310

5.1 Introduction 310
5.2 Bisection method 312
5.3 Regula-falsi method 319
5.4 Fixed-point iteration 320
5.5 Newton’s method 327
5.5.1 Convergence issues 329
5.6 Secant method 336
5.7 Solving systems of nonlinear equations 338
5.8 MATLAB function fzero 346
5.9 End of Chapter 5: key points to consider 348
5.10 Problems 349
References 353

6 Numerical quadrature 354

6.1 Introduction 354
6.2 Polynomial interpolation 361
6.3 Newton–Cotes formulas 371
6.3.1 Trapezoidal rule 372
6.3.2 Simpson’s 1/3 rule 380
6.3.3 Simpson’s 3/8 rule 384
6.4 Richardson’s extrapolation and Romberg integration 387
6.5 Gaussian quadrature 391
6.6 End of Chapter 6: key points to consider 402
6.7 Problems 403
References 408
viii Contents

7 Numerical integration of ordinary differential equations 409

7.1 Introduction 409
7.2 Euler’s methods 416
7.2.1 Euler’s forward method 417
7.2.2 Euler’s backward method 428
7.2.3 Modified Euler’s method 431
7.3 Runge–Kutta (RK) methods 434
7.3.1 Second-order RK methods 434
7.3.2 Fourth-order RK methods 438
7.4 Adaptive step size methods 440
7.5 Multistep ODE solvers 451
7.5.1 Adams methods 452
7.5.2 Predictor–corrector methods 454
7.6 Stability and stiff equations 456
7.7 Shooting method for boundary-value problems 461
7.7.1 Linear ODEs 463
7.7.2 Nonlinear ODEs 464
7.8 End of Chapter 7: key points to consider 472
7.9 Problems 473
References 478

8 Nonlinear model regression and optimization 480

8.1 Introduction 480
8.2 Unconstrained single-variable optimization 487
8.2.1 Newton’s method 488
8.2.2 Successive parabolic interpolation 492
8.2.3 Golden section search method 495
8.3 Unconstrained multivariable optimization 500
8.3.1 Steepest descent or gradient method 502
8.3.2 Multidimensional Newton’s method 509
8.3.3 Simplex method 513
8.4 Constrained nonlinear optimization 523
8.5 Nonlinear error analysis 530
8.6 End of Chapter 8: key points to consider 533
8.7 Problems 534
References 538

9 Basic algorithms of bioinformatics 539

9.1 Introduction 539
9.2 Sequence alignment and database searches 540
9.3 Phylogenetic trees using distance-based methods 554
9.4 End of Chapter 9: key points to consider 557
9.5 Problems 558
References 558

Appendix A Introduction to MATLAB 560

Appendix B Location of nodes for Gauss–Legendre quadrature 576
Index for MATLAB commands 578
Index 579
Preface

Biomedical engineering programs have exploded in popularity and number over

the past 20 years. In many programs, the fundamentals of engineering science are
taught from textbooks borrowed from other, more traditional, engineering fields:
statics, transport phenomena, circuits. Other courses in the biomedical engineering
curriculum are so multidisciplinary (think of tissue engineering, Introduction to
BME) that this approach does not apply; fortunately, excellent new textbooks have
recently emerged on these topics. On the surface, numerical and statistical methods
would seem to fall into this first category, and likely explains why biomedical
engineers have not yet contributed textbooks on this subject. I mean . . . math is
math, right? Well, not exactly.
There exist some unique aspects of biomedical engineering relevant to numerical
analysis. Graduate research in biomedical engineering is more often hypothesis
driven, compared to research in other engineering disciplines. Similarly, biomedical
engineers in industry design, test, and produce medical devices, instruments, and
drugs, and thus must concern themselves with human clinical trials and gaining
approval from regulatory agencies such as the US Food & Drug Administration. As
a result, statistics and hypothesis testing play a bigger role in biomedical engineering
and must be taught at the curricular level. This increased emphasis on statistical
analysis is reflected in special “program criteria” established for biomedical engi-
neering degree programs by the Accreditation Board for Engineering and
Technology (ABET) in the USA.
There are many general textbooks on numerical methods available for under-
graduate and graduate students in engineering; some of these use MATLAB as the
teaching platform. A good undergraduate text along these lines is Numerical
Methods with Matlab by G. Recktenwald, and a good graduate-level reference
on numerical methods is the well-known Numerical Recipes by W. H. Press et al.
These texts do a good job of covering topics such as programming basics,
nonlinear root finding, systems of linear equations, least-squares curve fitting,
and numerical integration, but tend not to devote much space to statistics and
hypothesis testing. Certainly, topics such as genomic data and design of clinical
trails are not covered. But beyond the basic numerical algorithms that may be
common to engineering and the physical sciences, one thing an instructor learns is
that biomedical engineering students want to work on biomedical problems! This
requires a biomedical engineering instructor to supplement a general numerical
methods textbook with a gathering of relevant lecture examples, homework, and
exam problems, a labor-intensive task to be sure and one that may leave students
confused and unsatisfied with their textbook investment. This book is designed to
fill an unmet need, by providing a complete numerical and statistical methods
textbook, tailored to the unique requirements of the modern BME curriculum
and implemented in MATLAB, which is inundated with examples drawn from
across the spectrum of biomedical science.
x Preface

This book is designed to serve as the primary textbook for a one-semester

course in numerical and statistical methods for biomedical engineering students.
The level of the book is appropriate for sophomore year through first year of
graduate studies, depending on the pace of the course and the number of
advanced, optional topics that are covered. A course based on this book, together
with later opportunities for implementation in a laboratory course or senior
design project, is intended to fulfil the statistics and hypothesis testing require-
ments of the program criteria established by ABET, and served this purpose at
the University of Rochester. The material within this book formed the basis for
the required junior-level course “Biomedical computation,” offered at the
University of Rochester from 2002 to 2008. As of Fall 2009, an accelerated version
of the “Biomedical computation” course is now offered at the masters level
at Cornell University. It is recommended that students have previously taken
calculus and an introductory programming course; a semester of linear algebra
is helpful but not required. It is our hope that this book will also serve as a
valuable reference for bioengineering practitioners and other researchers working
in quantitative branches of the life sciences such as biophysics and physiology.

Format
As with most textbooks, the chapters have been organized so that concepts are
progressively built upon as the reader advances from one chapter to the next.
Chapters 1 and 2 develop basic concepts, such as types of errors, linear algebra
concepts, linear problems, and linear regression, that are referred to in later
chapters. Chapters 3 (Probability and statistics) and 5 (Nonlinear root-finding
techniques) draw upon the material covered in Chapters 1 and 2. Chapter 4
(Hypothesis testing) exclusively draws upon the material covered in Chapter 3,
and can be covered at any point after Chapter 3 (Sections 3.1 to 3.5) is completed.
The material on linear regression error in Chapter 3 should precede the coverage
of Chapter 8 (Nonlinear model regression and optimization). The following chap-
ter order is strongly recommended to provide a seamless transition from one topic
to the next:

Chapter 1 → Chapter 2 → Chapter 3 → Chapter 5 → Chapter 6 → Chapter 8.

Chapter 4 can be covered at any time once the first three chapters are completed,
while Chapter 7 can be covered at any time after working through Chapters 1, 2, 3,
and 5. Chapter 9 covers an elective topic that can be taken up at any time during
a course of study.
The examples provided in each chapter are of two types: Examples and Boxes.
The problems presented in the Examples are more straightforward and the equa-
tions simpler. Examples either illustrate concepts already introduced in earlier
sections or are used to present new concepts. They are relatively quick to work
through compared to the Boxes since little additional background information is
needed to understand the example problems. The Boxes discuss biomedical
research, clinical, or industrial problems and include an explanation of relevant
biology or engineering concepts to present the nature of the problem. In a majority
of the Boxes, the equations to be solved numerically are derived from first
principles to provide a more complete understanding of the problem. The pro-
blems covered in Boxes can be more challenging and require more involvement by
xi Preface

the reader. While the Examples are critical in mastering the text material, the
choice of which boxed problems to focus on is left to the instructor or reader.
As a recurring theme of this book, we illustrate the implementation of numerical
methods through programming with the technical software package MATLAB.
Previous experience with MATLAB is not necessary to follow and understand this
book, although some prior programming knowledge is recommended. The best
way to learn how to program in a new language is to jump right into coding when
a need presents itself. Sophistication of the code is increased gradually in succes-
sive chapters. New commands and programming concepts are introduced on a
need-to-know basis. Readers who are unfamiliar with MATLAB should first study
Appendix A, Introduction to MATLAB, to orient themselves with the MATLAB
programming environment and to learn the basic commands and programming
terminology. Examples and Boxed problems are accompanied by the MATLAB
code containing the numerical algorithm to solve the numerical or statistical
problem. The MATLAB programs presented throughout the book illustrate
code writing practice. We show two ways to use MATLAB as a tool for solving
numerical problems: (1) by developing a program (m-file) that contains the numer-
ical algorithm, and (2) using built-in functions supplied by MATLAB to solve a
problem numerically. While self-written numerical algorithms coded in MATLAB
are instructive for teaching, MATLAB built-in functions that compute the numer-
ical solution can be more efficient and robust for use in practice. The reader is
taught to integrate MATLAB functions into their written code to solve a specific
problem (e.g. the backslash operator).
The book has its own website hosted by Cambridge University Press at www.
cambridge.org/kingmody. All of the m-files and numerical data sets within this book
can be found at this website, along with additional MATLAB programs relevant to
the topics and problems covered in the text.

Acknowledgements
First and foremost, M. R. K. owes a debt of gratitude to Professor David Leighton
at the University of Notre Dame. The “Biomedical computation” course that led
to this book was closely inspired by Leighton’s “Computer methods for chemical
engineers” course at Notre Dame. I (Michael King) had the good fortune of
serving as a teaching assistant and later as a graduate instructor for that course,
and it shaped the format and style of my own teaching on this subject. I would also
like to thank former students, teaching assistants, and faculty colleagues at the
University of Rochester and Cornell University; over the years, their valuable
input has helped continually to improve the material that comprises this book.
I thank my wife and colleague Cindy Reinhart-King for her constant support.
Finally, I thank my co-author, friend, and former student Nipa Mody: without her
tireless efforts this book would not exist.
N.A.M. would like to acknowledge the timely and helpful advice on creating
bioengineering examples from the following business and medical professionals:
Khyati Desai, Shimoni Shah, Shital Modi, and Pinky Shah. I (Nipa Mody) also
thank Banu Sankaran and Ajay Sadrangani for their general feedback on parts of
the book. I am indebted to the support provided by the following faculty and
staff members of the Biomedical Engineering Department of the University of
Rochester: Professor Richard E. Waugh, Donna Porcelli, Nancy Gronski, Mary
xii Preface

Gilmore, and Gayle Hurlbutt, in this endeavor. I very much appreciate the valiant
support of my husband, Anand Mody, while I embarked on the formidable task
of book writing.
We thank those people who have critically read versions of this manuscript, in
particular, Ayotunde Oluwakorede Ositelu, Aram Chung, and Bryce Allio, and also
to our reviewers for their excellent recommendations. We express many thanks
to Michelle Carey, Sarah Matthews, Christopher Miller, and Irene Pizzie at
Cambridge University Press for their help in the planning and execution of this
book project and for their patience.
If readers wish to suggest additional topics or comments, please write to us.
We welcome all comments and criticisms as this book (and the field of biomedical
engineering) continue to evolve.
1 Types and sources of numerical error

1.1 Introduction
The job of a biomedical engineer often involves the task of formulating and solving
mathematical equations that define, for example, the design criteria of biomedical
equipment or a prosthetic organ or physiological/pathological processes occurring
in the human body. Mathematics and engineering are inextricably linked. The types
of equations that one may come across in various fields of engineering vary widely,
but can be broadly categorized as: linear equations in one variable, linear equations
with respect to multiple variables, nonlinear equations in one or more variables,
linear and nonlinear ordinary differential equations, higher order differential equa-
tions of nth order, and integral equations. Not all mathematical equations are
amenable to an analytical solution, i.e. a solution that gives an exact answer either
as a number or as some function of the variables that define the problem. For
example, the analytical solution for
(1) x2 þ 2x þ 1 ¼ 0 is x ¼ 1, and
(2) dy=dx þ 3x ¼ 5, with initial conditions x ¼ 0; y ¼ 0, is y ¼ 5x  3x2 =2.
Sometimes the analytical solution to a system of equations may be exceedingly
difficult and time-consuming to obtain, or once obtained may be too complicated
to provide insight.
The need to obtain a solution to these otherwise unsolvable problems in a
reasonable amount of time and with the resources at hand has led to the develop-
ment of numerical methods. Such methods are used to determine an approximation
to the actual solution within some tolerable degree of error. A numerical method
is an iterative mathematical procedure that can be applied to only certain types
or forms of a mathematical equation, and under usual circumstances allows the
solution to converge to a final value with a pre-determined level of accuracy or
tolerance. Numerical methods can often provide exceedingly accurate solutions for
the problem under consideration. However, keep in mind that the solutions are
rarely ever exact. A closely related branch of mathematics is numerical analysis,
which goes hand-in-hand with the development and application of numerical meth-
ods. This related field of study is concerned with analyzing the performance
characteristics of established numerical methods, i.e. how quickly the numerical
technique converges to the final solution and accuracy limitations. It is important
to have, at the least, basic knowledge of numerical analysis so that you can make an
informed decision when choosing a technique for solving a numerical problem. The
accuracy and precision of the numerical solution obtained is dependent on a number
of factors, which include the choice of the numerical technique and the implementa-
tion of the technique chosen.
Errors can creep into any mathematical solution or statistical analysis in several
ways. Human mistakes include, for example, (1) entering incorrect data into
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