Showing posts with label statistics. Show all posts
Showing posts with label statistics. Show all posts

10/13/2012

Game Theory and Strategy (Mathematical Association of America Textbooks) Review

Game Theory and Strategy (Mathematical Association of America Textbooks)
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I found this book to be a very enjoyable read, covering the most interesting ideas in game theory and how they have impacted on other sciences from biology to sociology.
Almost no mathematical knowledge is required, because the text focuses on the ideas not the math.
Even if you want to learn about Game Theory including the mathematical foundation, I recommend to read this book first. It will wet your appetite for Game Theory and show the breath of ideas and applications.

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This book pays careful attention to applications of game theory in a wide variety of disciplines. The applications are treated in considerable depth. The book assumes only high school algebra, yet gently builds to mathematical thinking of some sophistication. Game Theory and Strategy might serve as an introduction to both axiomatic mathematical thinking and the fundamental process of mathematical modelling. It gives insight into both the nature of pure mathematics, and the way in which mathematics can be applied to real problems.

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10/12/2012

Bayes and Empirical Bayes Methods for Data Analysis, Second Edition Review

Bayes and Empirical Bayes Methods for Data Analysis, Second Edition
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This book features a deep and focused lesson on Bayes and Empirical Bayes Methods. It goes through the key topics as conjugate priors, MCMC methods (non iteratives and iteratives as the well known Gibbs samplining and metropolitis hastings algorithms), model selection methods (as bayes factor) and issues related as model robusteness.
The Approach is increasingly formal and deeply complex, allowing for getting the basics or diving into more complex knowledge according to your former background. You need at least a good understanding of Frequentist statistic to be able to follow the reasonings. Each chapter allow you to stop at some point without losing the thread. Last part of the book is in fact deep knowledge demanding.
The most interesting point of this book according to my very limited statistics background is that it makes good comparations with the frequentist approach (classical approaches as confidence intervals and point estimators), checking performance of either method. Even, it features some combination of both approaches getting some bayessian intervals.
As a negative point, I would say that examples are hard to follow for someone with limited bakground and too much complex. They really do not clear me up enough.
All in all, is a very profitable book for jumping into bayesian methods.

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In recent years, Bayes and empirical Bayes (EB) methods have continued to increase in popularity and impact. Building on the first edition of their popular text, Carlin and Louis introduce these methods, demonstrate their usefulness in challenging applied settings, and show how they can be implemented using modern Markov chain Monte Carlo (MCMC) methods. Their presentation is accessible to those new to Bayes and empirical Bayes methods, while providing in-depth coverage valuable to seasoned practitioners.With its broad appeal as a text for those in biomedical science, education, social science, agriculture, and engineering, this second edition offers a relatively gentle and comprehensive introduction for students and practitioners already familiar with more traditional frequentist statistical methods. Focusing on practical tools for data analysis, the book shows how properly structured Bayes and EB procedures typically have good frequentist and Bayesian performance, both in theory and in practice.

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10/09/2012

Dynamic Models in Biology Review

Dynamic Models in Biology
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This is an excellent book for students or faculty interested in learning more about the current state of the art in modeling of biological systems. The authors make a great effort to keep the mathematical sophistication at a level that students (or faculty) who primarily have a biological background will still be able to follow in some detail. They are also able to suggest some of the exciting current areas of research and new areas for the future. All in all, well worth reading if you are interested in the topic of modeling of biological systems.

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9/27/2012

Computational Cell Biology Review

Computational Cell Biology
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As a field of applied mathematics, computational biology has exploded in the last decade, and shows every sign of increasing in the next. This book overviews a few of the topics in the computational modeling of cells. I only read chapters 12 and 13 on molecular motors, and so my review will be confined to these.
Nanotechnology could be described as an up-and-coming field, but in the natural world one can find examples of this technology that surpass greatly what has been accomplished by human engineers. The authors begin their articles with a few examples of natural molecular machines, including the "rotary motors" DNA helicase and bacteriophage, and the "linear motor" kinesin, the latter they refer to as a "walking enzyme". Important in the modeling of all these is the theory of stochastic processes in the guise of Brownian motion, which the authors hold is the key to understanding the mechanics of proteins. In chapter 12 they give a detailed overview of the mathematical modeling of protein dynamics, followed in chapter 13 by an illustration of the mathematical formalism in the bacterial flagellar motor, a polymerization ratchet, and a motor governing ATP synthase.
To the authors a molecular motor is an entity that converts chemical energy into mechanical force. The production of mechanical force though may involve intermediate steps of energy transduction, all these involving the release of free energy during binding events. But due to their size, molecular motors are subjected to thermal fluctuations, and thus to model their motion accurately requires the theory of stochastic processes. Thus the authors begin a study of stochastic processes, restricting their attention to ones that satisfy the Markov property. Starting with a discrete model of protein motion as a simple random walk, the authors show that the variance of the motion grows linearly with time, which is a sign of diffusive motion. The partial differential equation satisfied by the probability distribution function, in the continuous limit where the space and time scales are large enough, is left to the reader to derive as an exercise.
The authors then consider polymer growth as another example of a stochastic process, a kind of hybrid one in that it involves both discrete and continuous random variables, the position of the polymer being continuous, while the number of monomers in the polymer is discrete. The authors derive an ordinary differential equation for the probability of there being exactly n polymers at a particular time. From this they show how to obtain sample paths for polymer growth and give a brief discussion on the statistics of polymer growth.
Attention is then turned to the modeling of molecular motions, with the first example being the Brownian motion of proteins in aqueous solutions. The (stochastic) Langevin equation is given for the motion of the protein, both with and without an external force acting on the protein. To find a numerical solution of this equation is straightforward, as the authors show. But they caution however that simulation of this solution on a computer is liable to introduce spurious results, and so they derive the Smoluchowski model, a somewhat different way of looking at random motion via the evolution of ensembles of paths. In this formulation the Brownian force is replaced by a diffusion term, and the external force is modeled by a drift term.
The authors then consider the modeling of chemical reactions, which supply the energy to the molecular motors. Because of the time scales involved in these reactions, a correct treatment of them would involve quantum mechanics, but the authors use the Smoluchowski model. The simple reaction model they consider involves a positive ion binding to negatively charged amino acid, and using as reaction coordinate the distance between the ion and the amino acid, study the free energy change as a function of the reaction coordinate.
The numerical simulation of the protein motion is then considered in much greater detail, using an algorithm that preserves detailed balance. This involves converting the problem to a Markov chain and a consideration of the boundary conditions, which the authors do for the case of periodic, reflecting, and absorbing. Euler's method is used to solve the resulting equations for the Markov chain, and after dealing with issues of stability and accuracy, the Crank-Nicolson method is used. The last few sections of the chapter are devoted to the physics of these solutions and the authors give some intuitive feel for the entropic factors and energy balance on a protein motor.
In the last chapter of the book, the considerations in chapter 12 are applied to concrete molecular motors. The first one examined is a model for switching in a bacterial flagellar motor, which involves the protein CheY as a signaling pathway. The binding of CheY to the motor is modeled as a two-state process, with the binding site being either empty or occupied. The resulting set of coupled differential equations for the probabilities is solved for when the concentration of CheY is constant. An expression for the change in free energy is obtained, and the authors give a discussion of the physics in the light of what was done in the last chapter. The switching rate is computed, along with the mean first passage time.
Some other examples of molecular motors are also discussed, including the flashing racket, the polymerization ratchet, and a simplified model of the ion-driven F0 motor of ATP synthase. This latter motor is fascinating, since it describes the electrochemical energy involved in mitochondria for the production of ATP. The authors do a nice job of showing how the techniques of chapter 12 are used to solve this model, and also give an analytical solution for a certain limiting case.

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This textbook provides an introduction to dynamic modeling in molecular cell biology, taking a computational and intuitive approach. Detailed illustrations, examples, and exercises are included throughout the text. Appendices containing mathematical and computational techniques are provided as a reference tool.

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9/24/2012

R Through Excel: A Spreadsheet Interface for Statistics, Data Analysis, and Graphics (Use R) Review

R Through Excel: A Spreadsheet Interface for Statistics, Data Analysis, and Graphics (Use R)
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Skip this paragraph if you know about R and Excel.... R is a powerful programming language that is useful for generating scientific graphics (both simple and extremely complex) and for statistical work. Unfortunately it has a steep learning curve and many say the help files are not particularly helpful for novices. Excel has a user friendly system for entering data and doing basic graphics but has relatively very limited tools for statistics or complex scientific graphics. Combining the strengths of the two is the goal of this book and the free software that goes with it.
With the tools described in this book the user can point and click their way to common analyses and graphics inside of Excel without having to learn to write code in the R programming language. Both the software and book are good but not great because they do not add much to the existing tools for R.
Years ago, John Fox wrote a point-and-click code-generating add-on package for R called R Commander that revolutionized the usability of R. Inside of the R programming environment you can download the Rcmdr package and type library(Rcmdr) and get practically all the same functionality as the tools provided here. What the authors of this book do is bring the functionality of Rcmdr into a Excel as an add-on to the Excel 2003 menus or 2007 ribbon. The implementation is surprisingly smooth (including adding nice right-click menu items) and bug free.
The book itself is mostly nicely rendered color pictures. Think of it as a very well annotated PowerPoint presentation. You will be able to quickly page through it and it is well indexed. The less than 10 page appendix which explains how to install the R packages and required services (or how to install from scratch) is probably the most useful part of the book. The authors do not focus much on the "behind the scenes" strengths of their work which allow you to recalculate and pass information into and out of R "on the fly." However, they do include a few worksheets that demonstrate the ability to pass information into R and return graphics effortlessly. Think of this as the ability to add sliders and push buttons to Excel and have instantly updated high quality graphics. Unfortunately, they only give one example where they use there new RApply function to return a calculated value from R into Excel. There clearly is a lot of functionality but the book does not explain it.
If you are just starting with R this book will probably be a HUGE help to you because it saves you from memorizing a lot of code and it will help you learn how to write code by showing you the commands that were used to generate analyses and graphics. However, if you have experience with R and Rcmdr you probably want to save your money.

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In this book, the authors build on RExcel, a free add-in for Excel that can be downloaded from the R distribution network. RExcel seamlessly integrates the entire set of R's statistical and graphical methods into Excel, allowing students to focus on statistical methods and concepts and minimizing the distraction of learning a new programming language.

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9/23/2012

Bayesian Methods for Measures of Agreement (Chapman & Hall/CRC Biostatistics Series) Review

Bayesian Methods for Measures of Agreement (Chapman and Hall/CRC Biostatistics Series)
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This is the scond book of Lyle Broemeling that I am reviewing for Amazon. I met him at the Joint Statistical Meetings a few years ago when he was just retiring from M.D. Anderson. in recent years M. D. Anderson has become a leader in designing Bayesian adaptive designs of clinical trials. This is mainly due to the leadership of Don Berry who came to head up the biostatistics group at M. D. Anderson several years ago when he was attracted away from Duke. Broemeling benefitted from the arrival of Berry because he was establishe there as a Bayesian and had written a book on Bayesian analysis many years earlier.
Now that he is retired from M. D. Anderson he is writing applied biostatistics texts applying Bayesian methods to specialized topics. The first one which I reviewed earlier on amazon was on diagnostic testing and this one is to analyze measures of agreement among judges. The two books are both scholarly written and authoritative and clear. They both also provide many real examples based on Lyle's vast experience at M. D. Anderson.
A few years ago I was supporting the company BioImaging in the development of their protocols for medical imaging data from patients in oncology clinical trials. I learned that an important aspect of determining the efficacy of a drug against a particular cancer tumor. This performance is usually measured by individual ranking from radiologist who read the scans over time and assess growth or shrinkage of the tumor after being treated by a drug. Typically there are two or three readers and the rating of progression or remission depends on a concensus of the radiologists assessments.
This is exactly the problem Broemeling faced at at M. D. Anderson and he has a wealth of applications in the setting of oncology trials. Broemeling details the history of the develop of methods used to reach a conclusion. He provides a wealth of examples and also includes interesting examples from sports including an analysis of a famous boxing match between Lennox Lewis and Evander Holyfield. He deals methodically with the case of two raters (where an adjudicator general resolve the conflicting cases) and then three or more raters where things get more complicated.
Modern Bayesian approaches are demonstrated using the winBugs software. Broemeling provides the code in the winBugs language to handle various examples. This approach involves Markov Chain Monte Carlo methods. Examples are explained in detail and illustrated very carefully.
Broemeling also provides a history of the various statistics used to measure agrrement between readers or judges. Another example that struck me as very interesting is a forgery case where a signature was forged to produce a fake will. Usually in forgery cases the methods are used to find differences in the signature that are large enough to assert that they came from different people. However in this example the forged signature was traced from the original persons sample signature. So in the case the objective was to show that the cases are too similar not to have been forged. We are able to do this because we can show repeated signatures from the same hand will have more variability than the traced signature. So in this case the hired statisticians showed that the two signatures are much too similar for the second one to be real and independent of each other.
Bayesian sample size estimation is also covered in the text. It is a great reference book for anyone who does oncology trials and appreciates the advantages of the Bayesian approach. The Kappa measure is the one that is given the most attention in the book.

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Using WinBUGS to implement Bayesian inferences of estimation and testing hypotheses, Bayesian Methods for Measures of Agreement presents useful methods for the design and analysis of agreement studies. It focuses on agreement among the various players in the diagnostic process.The author employs a Bayesian approach to provide statistical inferences based on various models of intra- and interrater agreement. He presents many examples that illustrate the Bayesian mode of reasoning and explains elements of a Bayesian application, including prior information, experimental information, the likelihood function, posterior distribution, and predictive distribution. The appendices provide the necessary theoretical foundation to understand Bayesian methods as well as introduce the fundamentals of programming and executing the WinBUGS software.Taking a Bayesian approach to inference, this hands-on book explores numerous measures of agreement, including the Kappa coefficient, the G coefficient, and intraclass correlation. With examples throughout and end-of-chapter exercises, it discusses how to successfully design and analyze an agreement study.

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9/12/2012

R in a Nutshell: A Desktop Quick Reference Review

R in a Nutshell: A Desktop Quick Reference
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'R in a Nutshell' is the essential introductory book on R. Do not try to learn R without it.
I made two attempts to learn R before purchasing this book. In both previous attempts, I had to abort and use another tool to solve my problem because it was taking me too long to accomplish very simple things in R.
The reason R is hard to learn is that its documentation is organized for statisticians that already know R, but have forgotten a detail or two. There are a few other books on learning R, but they are setup like a college course - complete the entire book and THEN you can actually accomplish something.
R in a Nutshell allows you to get working immediately. Simply lookup what you need to do. The firsts thing I did was load a file and make a histogram. I found that stuff in the section on "Loading Data" and the section on charts. In no time I was making stacked area charts for cohorts. Now R is an essential tool for me - and I haven't even taken the time to learn it well! With this book, I don't have to. I can learn as I go. So I actually use R.
Do not R without it.

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What people are saying about R in a Nutshell

"I am excited about this book. R in a Nutshell is a great introduction to R, as well as a comprehensive reference for using R in data analytics and visualization. Adler provides 'real world' examples, practical advice, and scripts, making it accessible to anyone working with data, not just professional statisticians." --Martin Schultz, Arthur K. Watson Professor of Computer Science, Yale University

"R in a Nutshell is an ideal book for getting started with R. Newcomers will find the fundamentals for performing statistical analysis and graphics, all illustrated with practical examples. This book is an invaluable reference for anyone who wants to learn what R is and what is can do, even for longtime R users looking for new tips and tricks." --David M. Smith, Editor of the "Revolutions" blog at REvolution Computing

Why learn R? Because it's rapidly becoming the standard for developing statistical software. R in a Nutshell provides a quick and practical way to learn this increasingly popular open source language and environment. You'll not only learn how to program in R, but also how to find the right user-contributed R packages for statistical modeling, visualization, and bioinformatics.

The author introduces you to the R environment, including the R graphical user interface and console, and takes you through the fundamentals of the object-oriented R language. Then, through a variety of practical examples from medicine, business, and sports, you'll learn how you can use this remarkable tool to solve your own data analysis problems.

Understand the basics of the language, including the nature of R objects
Learn how to write R functions and build your own packages
Work with data through visualization, statistical analysis, and other methods
Explore the wealth of packages contributed by the R community
Become familiar with the lattice graphics package for high-level data visualization
Learn about bioinformatics packages provided by Bioconductor


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9/11/2012

Utility-Based Learning from Data (Chapman & Hall/CRC Machine Learning & Pattern Recognition) Review

Utility-Based Learning from Data (Chapman and Hall/CRC Machine Learning and Pattern Recognition)
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This book is just as great inside the cover as
the elegant cover leads you to expect.
A very ambitious book with a very broad scope.
As a Professor of Applied Mathematics and
of mathematical finance, I very much look
forward to presenting parts of this material
in the future.
Concerning the contents, citing from the introduction of
the book:"Our point of view is motivated by the notion that probabilistic models are
usually not learned for their own sake-rather, they are used to make decisions"
and "finance and decision theory provide a language in which it is
natural to express these assumptions-namely, utility theory-and formulate,
from first principals, model performance measures and the notion of optimal
and robust model performance"
and the books purpose is : " to provide a pedagogical and self-contained discussion of a select set of
methods for estimating probability distributions that can be approached
coherently from a decision-theoretic point of view"
The last sentence is extremely telling. Friedman and Sandow indeed
demonstrate in this book that, in struggling to quantify
default risk, in their daytime jobs at Standard and Poor's,
they carefully put into place their own approach, and painstakingly
tested it on read data, throughout many different economic
cycles (as far back as 2001, when I worked in Friedman's group).
In addition, after Friedman presented some of this material at
New York University's Courant Institute, Friedman and Sandow saw fit to
include a through introduction to topics which are of interest
to all economic students, such as utility theory and
minimum relative theory. And they do so in a crisp, clear and no-nonsense
manner that is rarely seen in books on economics.
A key aspect of the point of view taken in this book, is to relate
betting odds, such as in a horse race, to expected
growth of wealth.
Readers should race to the bookstore to get a
hold of this book!

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Utility-Based Learning from Data provides a pedagogical, self-contained discussion of probability estimation methods via a coherent approach from the viewpoint of a decision maker who acts in an uncertain environment. This approach is motivated by the idea that probabilistic models are usually not learned for their own sake; rather, they are used to make decisions. Specifically, the authors adopt the point of view of a decision maker who(i) operates in an uncertain environment where the consequences of possible outcomes are explicitly monetized,(ii) bases his decisions on a probabilistic model, and(iii) builds and assesses his models accordingly.These assumptions are naturally expressed in the language of utility theory, which is well known from finance and decision theory. By taking this point of view, the book sheds light on and generalizes some popular statistical learning approaches, connecting ideas from information theory, statistics, and finance. It strikes a balance between rigor and intuition, conveying the main ideas to as wide an audience as possible.

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9/10/2012

Hidden Markov Models in Finance (International Series in Operations Research & Management Science) Review

Hidden Markov Models in Finance (International Series in Operations Research and Management Science)
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Hidden Markov Models have come into vogue in recent years in various fields. Notably automatic speech recognition. An HMM is useful in a Bayesian context, where you have to work back from some observations to discern an underlying probability model that is supposedly generating those observations. Often in the presence of noise. Well, it turns out that this general description can also be applied to financial models, which is the book's subject.
Various specific models are tackled. Including the seminal Black-Scholes, where the security market is modelled as a Markov modulated Brownian. Typically, the maths in the book uses sophisticated probabilistic analysis and often assuming Markov processes. As an aside, if your field is electrical engineering or information theory, where you might have used Markov processes, then your background should suffice if you want to migrate to finance. It's not that different, at a certain conceptual level.
The book could be improved by the addition of an index.

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A number of methodologies have been employed to provide decision making solutions globalized markets. Hidden Markov Models in Finance offers the first systematic application of these methods to specialized financial problems: option pricing, credit risk modeling, volatility estimation and more. The book provides tools for sorting through turbulence, volatility, emotion, chaotic events - the random "noise" of financial markets - to analyze core components.

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9/04/2012

Numerical Geometry of Non-Rigid Shapes (Monographs in Computer Science) Review

Numerical Geometry of Non-Rigid Shapes (Monographs in Computer Science)
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Numerical geometry of non-rigid shapes is the first attempt to present a focused and broad study of topics in non-rigid shape analysis. The book presents theoretical foundations, methods, algorithms and applications involving non-rigid shapes in different fields including computer vision, pattern recognition, and computer graphics. A special focus is made on practical value of the book - it is accompanied with code examples and references to commercial and public-domain software. Recommended as a textbook for computer vision and pattern recognition courses, reference for students and experts in the field.

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Deformable objects are ubiquitous in the world surrounding us, on all levels from micro to macro. The need to study such shapes and model their behavior arises in a wide spectrum of applications, ranging from medicine to security. In recent years, non-rigid shapes have attracted growing interest, which has led to rapid development of the field, where state-of-the-art results from very different sciences - theoretical and numerical geometry, optimization, linear algebra, graph theory, machine learning and computer graphics, to mention several - are applied to find solutions.This book gives an overview of the current state of science in analysis and synthesis of non-rigid shapes. Everyday examples are used to explain concepts and to illustrate different techniques. The presentation unfolds systematically and numerous figures enrich the engaging exposition. Practice problems follow at the end of each chapter, with detailed solutions to selected problems in the appendix. A gallery of colored images enhances the text.This book will be of interest to graduate students, researchers and professionals in different fields of mathematics, computer science and engineering. It may be used for courses in computer vision, numerical geometry and geometric modeling and computer graphics or for self-study.

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8/26/2012

Metaheuristics: From Design to Implementation (Wiley Series on Parallel and Distributed Computing) Review

Metaheuristics: From Design to Implementation (Wiley Series on Parallel and Distributed Computing)
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The book is a good and detailed description of what metaheuristics involves. This is applied to solving hard computational problems. There are summaries of many methods developed over the last 50 years. The simplex method. Metropolis Monte Carlo. Simulated annealing. Genetic algorithms. And others. There is deliberately not enough information about most of these for you to use them given only the book as a starting point. Space considerations.
But mostly the book explains at a higher level, how methods can be understood. Some are for exploiting; ie. intensively looking in a given region of the objective space around a starting point. Simulated annealing is a good example of such a method.
Other methods are for exploring. A broader search in the objective or solution space. Genetic algorithms, with their mutations and crossover recombinations are very strong here, using ideas borrowed from biological evolution.
More importantly, the book shows how many hard problems have to be tackled by a combination of exploring and exploiting. The combining of algorithms is what gives metaheuristics its name.
One caveat is that even at a summary level, the description of tabu search was a bit unclear, compared to the excellent synopses of simulated annealing and genetic algorithms.

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A unified view of metaheuristics
This book provides a complete background on metaheuristics and shows readers how to design and implement efficient algorithms to solve complex optimization problems across a diverse range of applications, from networking and bioinformatics to engineering design, routing, and scheduling. It presents the main design questions for all families of metaheuristics and clearly illustrates how to implement the algorithms under a software framework to reuse both the design and code.
Throughout the book, the key search components of metaheuristics are considered as a toolbox for:

Designing efficient metaheuristics (e.g. local search, tabu search, simulated annealing, evolutionary algorithms, particle swarm optimization, scatter search, ant colonies, bee colonies, artificial immune systems) for optimization problems

Designing efficient metaheuristics for multi-objective optimization problems

Designing hybrid, parallel, and distributed metaheuristics

Implementing metaheuristics on sequential and parallel machines

Using many case studies and treating design and implementation independently, this book gives readers the skills necessary to solve large-scale optimization problems quickly and efficiently. It is a valuable reference for practicing engineers and researchers from diverse areas dealing with optimization or machine learning; and graduate students in computer science, operations research, control, engineering, business and management, and applied mathematics.

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8/17/2012

R Cookbook (O'Reilly Cookbooks) Review

R Cookbook (O'Reilly Cookbooks)
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I'd give this book ten stars if I could. I bought one copy for the office and one for my house. This guy has the ability to write simply and with the mind set of people who are busy and want to get results right away. Of course we'd all love to be leisurely scholars and plow through theory and practice but most of us just need to get things done. A good example is the way he treats ARIMA. He warns you about using auto.arima but does not hide it from you because it is "dangerous." The book is full of tips, well organized and is oriented towards beginners, though it gets into depth. So many of the R books I've read absolutely pound you with up front details, some of which relate to obscure concerns, rather than starting with a task. For example, on page 199 he writes "Problem -- you want to count the relative frequency of certain observations in your sample" Next is "Solution" -- and he explains just the minimum needed to do that job. Some of the tips are just simple time savers, such as the function head(dataframe) to show a few of the dataframe rows at the start and tail(dataframe) to show a few at the end. Finally .... I don't know this writer personally, but I hope he keeps on writing because it is a craft he has thoroughly absorbed somewhere along the line.Bill Yarberry, Houston, TX


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With more than 200 practical recipes, this book helps you perform data analysis with R quickly and efficiently. The R language provides everything you need to do statistical work, but its structure can be difficult to master. This collection of concise, task-oriented recipes makes you productive with R immediately, with solutions ranging from basic tasks to input and output, general statistics, graphics, and linear regression.

Each recipe addresses a specific problem, with a discussion that explains the solution and offers insight into how it works. If you're a beginner, R Cookbook will help get you started. If you're an experienced data programmer, it will jog your memory and expand your horizons. You'll get the job done faster and learn more about R in the process.

Create vectors, handle variables, and perform other basic functions
Input and output data
Tackle data structures such as matrices, lists, factors, and data frames
Work with probability, probability distributions, and random variables
Calculate statistics and confidence intervals, and perform statistical tests
Create a variety of graphic displays
Build statistical models with linear regressions and analysis of variance (ANOVA)
Explore advanced statistical techniques, such as finding clusters in your data

"Wonderfully readable, R Cookbook serves not only as a solutions manual of sorts, but as a truly enjoyable way to explore the R language—one practical example at a time." —Jeffrey Ryan, software consultant and R package author


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8/14/2012

Visualizing Data Review

Visualizing Data
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This book was recommended highly to me by a former university professor (and now consultant). It exceeds my expectations. The figures and acompanying explanations are very clear, as is the language throughout. Visualizing Data discusses several tools with which I was not familiar, and clarifies tools that I thought I understood (including box plots). I have taken several university statistics classes, but I believe this book would help anyone involved in displaying or interpreting data. A picture may be worth a thousand words, but when your business depends on it, a well-defined plot or graph can be worth much more. Visualizing Data enables you to produce well-defined plots and graphs with confidence.

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Visualizing Data is about visualizationtools that provide deep insight into thestructure of data. There are graphicaltools such as coplots, multiway dot plots,and the equal count algorithm. There arefitting tools such as loess and bisquarethat fit equations, nonparametric curves,and nonparametric surfaces to data.But the book is much more than just acompendium of useful tools. It conveys astrategy for data analysis that stressesthe use of visualization to thoroughlystudy the structure of data and to checkthe validity of statistical models fittedto data. The result of the tools and thestrategy is a vast increase in what you canlearn from your data. The book demonstratesthis by reanalyzing many data sets from thescientific literature, revealing missedeffects and inappropriate models fitted to data.

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Interaction And Non-Linear Effects In Structural Equation Review

Interaction And Non-Linear Effects In Structural Equation
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This is an excellent reference book for applied researchers who use advanced structural equation modeling (SEM) in social, psychological, and biomedical studies. The authors are well-known experienced experts in SEM, and the contents of this book are practical. Researcher who use different software in SEM can find their practical examples and related theoretical bases.

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This volume provides a comprehensive presentation of the various procedures currently available for testing interaction and nonlinear effects in structural equation modeling. By focusing on various software applications, the reader should quickly be able to incorporate one of the procedures into testing interaction or nonlinear effects in their own model. Although every attempt is made to keep mathematical details to a minimum, it is assumed that the reader has mastered the equivalent of a graduate-level multivariate statistics course which includes adequate coverage of structural equation modeling. This book will be of interest to researchers and practitioners in education and the social sciences.

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8/11/2012

Econometric Analysis of Count Data Review

Econometric Analysis of Count Data
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excellent. the book provides good examples and helps the readers to relate the huge literature and how one paper is related to another one.

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The book provides an up-to-date survey of statistical and econometric techniques for the analysis of count data, with a focus on conditional distribution models. The book starts with a presentation of the benchmark Poisson regression model. Alternative models address unobserved heterogeneity, state dependence, selectivity, endogeneity, underreporting, and clustered sampling. Testing and estimation is discussed. Finally, applications are reviewed in various fields.

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Bayesian Methods for Data Analysis, Third Edition (Chapman & Hall/CRC Texts in Statistical Science) Review

Bayesian Methods for Data Analysis, Third Edition (Chapman and Hall/CRC Texts in Statistical Science)
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I like this book a lot. It's not the book that I would've written, and that's a good thing. Buying Carlin and Louis along with our book will give you two perspectives on applied Bayesian statistics as it is practiced in the 21st century. Compared to our book, Carlin and Louis offer the following:
- Discussion of the debates over Bayesianism within the statistical community, culminating in chapter 5, which covers the links between Bayes, empirical Bayes, and frequentist methods of evaluating statistical procedures.
- A crisp presentation of Bayesian computation (chapter 5), which offers a different perspective than ours.
- A chapter on experimental design including several biomedical examples. This chapter should be useful to a lot of people, I think.
- Near the end of the book, discussion of several classes of models--longitudinal analysis, survival analysis, spatial models, clinical trials, and others--where I often think, "What's would a Bayesian do here?"
I don't think Carlin and Louis have made our own Bayesian Data Analysis obsolete but I do think their book is a great complement to ours, with a slightly different perspective, strong coverage of the theoretical issues of point and interval estimation, and a bunch of compelling biomedical examples.

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Broadening its scope to nonstatisticians, Bayesian Methods for Data Analysis, Third Edition provides an accessible introduction to the foundations and applications of Bayesian analysis. Along with a complete reorganization of the material, this edition concentrates more on hierarchical Bayesian modeling as implemented via Markov chain Monte Carlo (MCMC) methods and related data analytic techniques. New to the Third Edition New data examples, corresponding R and WinBUGS code, and homework problems Explicit descriptions and illustrations of hierarchical modeling-now commonplace in Bayesian data analysisA new chapter on Bayesian design that emphasizes Bayesian clinical trialsA completely revised and expanded section on ranking and histogram estimationA new case study on infectious disease modeling and the 1918 flu epidemicA solutions manual for qualifying instructors that contains solutions, computer code, and associated output for every homework problem-available both electronically and in printIdeal for Anyone Performing Statistical Analyses Focusing on applications from biostatistics, epidemiology, and medicine, this text builds on the popularity of its predecessors by making it suitable for even more practitioners and students.

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8/09/2012

Nonlinear System Identification: From Classical Approaches to Neural Networks and Fuzzy Models Review

Nonlinear System Identification: From Classical Approaches to Neural Networks and Fuzzy Models
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This book is excellent compehensive overwiev over many relevant topics that are useful in the wide spectrum of data analysis:
Starting with least squares - regression and its variants it comes to nonlinear local and global optimization techniques and even advanced neurofuzzy models.
This book is so precious because it explains and compares nearly all useful approaches, their advantages and disadvantages, including numerical and stastical arguments.
You can understand it without being a mathematician. But you should be familiar with the following expressions:
Gradient, Hessian, Inverse, Covariance Matrix, Estimator
Lots of useful details condensed into just one book!
Excellent!

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Written from an engineering point of view, this book covers the most common and important approaches for the identification of nonlinear static and dynamic systems. The book also provides the reader with the necessary background on optimization techniques, making it fully self-contained. The new editionincludes exercises.

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