*with Applications in Systems Biology*

Author: Radhakrishnan Nagarajan,Marco Scutari,Sophie Lèbre

Publisher: Springer Science & Business Media

ISBN: 1461464463

Category: Computers

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### Bayesian Networks in R

Bayesian Networks in R with Applications in Systems Biology is unique as it introduces the reader to the essential concepts in Bayesian network modeling and inference in conjunction with examples in the open-source statistical environment R. The level of sophistication is also gradually increased across the chapters with exercises and solutions for enhanced understanding for hands-on experimentation of the theory and concepts. The application focuses on systems biology with emphasis on modeling pathways and signaling mechanisms from high-throughput molecular data. Bayesian networks have proven to be especially useful abstractions in this regard. Their usefulness is especially exemplified by their ability to discover new associations in addition to validating known ones across the molecules of interest. It is also expected that the prevalence of publicly available high-throughput biological data sets may encourage the audience to explore investigating novel paradigms using the approaches presented in the book.

### Bayesian Networks

Understand the Foundations of Bayesian Networks—Core Properties and Definitions Explained Bayesian Networks: With Examples in R introduces Bayesian networks using a hands-on approach. Simple yet meaningful examples in R illustrate each step of the modeling process. The examples start from the simplest notions and gradually increase in complexity. The authors also distinguish the probabilistic models from their estimation with data sets. The first three chapters explain the whole process of Bayesian network modeling, from structure learning to parameter learning to inference. These chapters cover discrete Bayesian, Gaussian Bayesian, and hybrid networks, including arbitrary random variables. The book then gives a concise but rigorous treatment of the fundamentals of Bayesian networks and offers an introduction to causal Bayesian networks. It also presents an overview of R and other software packages appropriate for Bayesian networks. The final chapter evaluates two real-world examples: a landmark causal protein signaling network paper and graphical modeling approaches for predicting the composition of different body parts. Suitable for graduate students and non-statisticians, this text provides an introductory overview of Bayesian networks. It gives readers a clear, practical understanding of the general approach and steps involved.

### Graphical Models with R

Graphical models in their modern form have been around since the late 1970s and appear today in many areas of the sciences. Along with the ongoing developments of graphical models, a number of different graphical modeling software programs have been written over the years. In recent years many of these software developments have taken place within the R community, either in the form of new packages or by providing an R interface to existing software. This book attempts to give the reader a gentle introduction to graphical modeling using R and the main features of some of these packages. In addition, the book provides examples of how more advanced aspects of graphical modeling can be represented and handled within R. Topics covered in the seven chapters include graphical models for contingency tables, Gaussian and mixed graphical models, Bayesian networks and modeling high dimensional data.

### Learning Probabilistic Graphical Models in R

Familiarize yourself with probabilistic graphical models through real-world problems and illustrative code examples in R About This Book Predict and use a probabilistic graphical models (PGM) as an expert system Comprehend how your computer can learn Bayesian modeling to solve real-world problems Know how to prepare data and feed the models by using the appropriate algorithms from the appropriate R package Who This Book Is For This book is for anyone who has to deal with lots of data and draw conclusions from it, especially when the data is noisy or uncertain. Data scientists, machine learning enthusiasts, engineers, and those who curious about the latest advances in machine learning will find PGM interesting. What You Will Learn Understand the concepts of PGM and which type of PGM to use for which problem Tune the model's parameters and explore new models automatically Understand the basic principles of Bayesian models, from simple to advanced Transform the old linear regression model into a powerful probabilistic model Use standard industry models but with the power of PGM Understand the advanced models used throughout today's industry See how to compute posterior distribution with exact and approximate inference algorithms In Detail Probabilistic graphical models (PGM, also known as graphical models) are a marriage between probability theory and graph theory. Generally, PGMs use a graph-based representation. Two branches of graphical representations of distributions are commonly used, namely Bayesian networks and Markov networks. R has many packages to implement graphical models. We'll start by showing you how to transform a classical statistical model into a modern PGM and then look at how to do exact inference in graphical models. Proceeding, we'll introduce you to many modern R packages that will help you to perform inference on the models. We will then run a Bayesian linear regression and you'll see the advantage of going probabilistic when you want to do prediction. Next, you'll master using R packages and implementing its techniques. Finally, you'll be presented with machine learning applications that have a direct impact in many fields. Here, we'll cover clustering and the discovery of hidden information in big data, as well as two important methods, PCA and ICA, to reduce the size of big problems. Style and approach This book gives you a detailed and step-by-step explanation of each mathematical concept, which will help you build and analyze your own machine learning models and apply them to real-world problems. The mathematics is kept simple and each formula is explained thoroughly.

### Bayesian Networks and Decision Graphs

This is a brand new edition of an essential work on Bayesian networks and decision graphs. It is an introduction to probabilistic graphical models including Bayesian networks and influence diagrams. The reader is guided through the two types of frameworks with examples and exercises, which also give instruction on how to build these models. Structured in two parts, the first section focuses on probabilistic graphical models, while the second part deals with decision graphs, and in addition to the frameworks described in the previous edition, it also introduces Markov decision process and partially ordered decision problems.

### Building Probabilistic Graphical Models with Python

This is a short, practical guide that allows data scientists to understand the concepts of Graphical models and enables them to try them out using small Python code snippets, without being too mathematically complicated. If you are a data scientist who knows about machine learning and want to enhance your knowledge of graphical models, such as Bayes network, in order to use them to solve real-world problems using Python libraries, this book is for you.This book is intended for those who have some Python and machine learning experience, or are exploring the machine learning field.

### Risk Assessment and Decision Analysis with Bayesian Networks, Second Edition

Since the first edition of this book published, Bayesian networks have become even more important for applications in a vast array of fields. This second edition includes new material on influence diagrams, learning from data, value of information, cybersecurity, debunking bad statistics, and much more. Focusing on practical real-world problem-solving and model building, as opposed to algorithms and theory, it explains how to incorporate knowledge with data to develop and use (Bayesian) causal models of risk that provide more powerful insights and better decision making than is possible from purely data-driven solutions. Features Provides all tools necessary to build and run realistic Bayesian network models Supplies extensive example models based on real risk assessment problems in a wide range of application domains provided; for example, finance, safety, systems reliability, law, forensics, cybersecurity and more Introduces all necessary mathematics, probability, and statistics as needed Establishes the basics of probability, risk, and building and using Bayesian network models, before going into the detailed applications A dedicated website contains exercises and worked solutions for all chapters along with numerous other resources. The AgenaRisk software contains a model library with executable versions of all of the models in the book. Lecture slides are freely available to accredited academic teachers adopting the book on their course.

### Bayesian Networks

Bayesian Networks: An Introduction provides a self-contained introduction to the theory and applications of Bayesian networks, a topic of interest and importance for statisticians, computer scientists and those involved in modelling complex data sets. The material has been extensively tested in classroom teaching and assumes a basic knowledge of probability, statistics and mathematics. All notions are carefully explained and feature exercises throughout. Features include: An introduction to Dirichlet Distribution, Exponential Families and their applications. A detailed description of learning algorithms and Conditional Gaussian Distributions using Junction Tree methods. A discussion of Pearl's intervention calculus, with an introduction to the notion of see and do conditioning. All concepts are clearly defined and illustrated with examples and exercises. Solutions are provided online. This book will prove a valuable resource for postgraduate students of statistics, computer engineering, mathematics, data mining, artificial intelligence, and biology. Researchers and users of comparable modelling or statistical techniques such as neural networks will also find this book of interest.

### Learning Bayesian Networks

For courses in Bayesian Networks or Advanced Networking focusing on Bayesian networks found in departments of Computer Science, Computer Engineering and Electrical Engineering. Also appropriate as a supplementary text in courses on Expert Systems, Machine Learning, and Artificial Intelligence where the topic of Bayesian Networks is covered. This book provides an accessible and unified discussion of Bayesian networks. It includes discussions of topics related to the areas of artificial intelligence, expert systems and decision analysis, the fields in which Bayesian networks are frequently applied. The author discusses both methods for doing inference in Bayesian networks and influence diagrams. The book also covers the Bayesian method for learning the values of discrete and continuous parameters. Both the Bayesian and constraint-based methods for learning structure are discussed in detail.

### Learning Bayesian Models with R

Become an expert in Bayesian Machine Learning methods using R and apply them to solve real-world big data problems About This Book Understand the principles of Bayesian Inference with less mathematical equations Learn state-of-the art Machine Learning methods Familiarize yourself with the recent advances in Deep Learning and Big Data frameworks with this step-by-step guide Who This Book Is For This book is for statisticians, analysts, and data scientists who want to build a Bayes-based system with R and implement it in their day-to-day models and projects. It is mainly intended for Data Scientists and Software Engineers who are involved in the development of Advanced Analytics applications. To understand this book, it would be useful if you have basic knowledge of probability theory and analytics and some familiarity with the programming language R. What You Will Learn Set up the R environment Create a classification model to predict and explore discrete variables Get acquainted with Probability Theory to analyze random events Build Linear Regression models Use Bayesian networks to infer the probability distribution of decision variables in a problem Model a problem using Bayesian Linear Regression approach with the R package BLR Use Bayesian Logistic Regression model to classify numerical data Perform Bayesian Inference on massively large data sets using the MapReduce programs in R and Cloud computing In Detail Bayesian Inference provides a unified framework to deal with all sorts of uncertainties when learning patterns form data using machine learning models and use it for predicting future observations. However, learning and implementing Bayesian models is not easy for data science practitioners due to the level of mathematical treatment involved. Also, applying Bayesian methods to real-world problems requires high computational resources. With the recent advances in computation and several open sources packages available in R, Bayesian modeling has become more feasible to use for practical applications today. Therefore, it would be advantageous for all data scientists and engineers to understand Bayesian methods and apply them in their projects to achieve better results. Learning Bayesian Models with R starts by giving you a comprehensive coverage of the Bayesian Machine Learning models and the R packages that implement them. It begins with an introduction to the fundamentals of probability theory and R programming for those who are new to the subject. Then the book covers some of the important machine learning methods, both supervised and unsupervised learning, implemented using Bayesian Inference and R. Every chapter begins with a theoretical description of the method explained in a very simple manner. Then, relevant R packages are discussed and some illustrations using data sets from the UCI Machine Learning repository are given. Each chapter ends with some simple exercises for you to get hands-on experience of the concepts and R packages discussed in the chapter. The last chapters are devoted to the latest development in the field, specifically Deep Learning, which uses a class of Neural Network models that are currently at the frontier of Artificial Intelligence. The book concludes with the application of Bayesian methods on Big Data using the Hadoop and Spark frameworks. Style and approach The book first gives you a theoretical description of the Bayesian models in simple language, followed by details of its implementation in the R package. Each chapter has illustrations for the use of Bayesian model and the corresponding R package, using data sets from the UCI Machine Learning repository. Each chapter also contains sufficient exercises for you to get more hands-on practice.

### Bayesian Artificial Intelligence, Second Edition

Updated and expanded, Bayesian Artificial Intelligence, Second Edition provides a practical and accessible introduction to the main concepts, foundation, and applications of Bayesian networks. It focuses on both the causal discovery of networks and Bayesian inference procedures. Adopting a causal interpretation of Bayesian networks, the authors discuss the use of Bayesian networks for causal modeling. They also draw on their own applied research to illustrate various applications of the technology. New to the Second Edition New chapter on Bayesian network classifiers New section on object-oriented Bayesian networks New section that addresses foundational problems with causal discovery and Markov blanket discovery New section that covers methods of evaluating causal discovery programs Discussions of many common modeling errors New applications and case studies More coverage on the uses of causal interventions to understand and reason with causal Bayesian networks Illustrated with real case studies, the second edition of this bestseller continues to cover the groundwork of Bayesian networks. It presents the elements of Bayesian network technology, automated causal discovery, and learning probabilities from data and shows how to employ these technologies to develop probabilistic expert systems. Web Resource The book’s website at www.csse.monash.edu.au/bai/book/book.html offers a variety of supplemental materials, including example Bayesian networks and data sets. Instructors can email the authors for sample solutions to many of the problems in the text.

### Bayesian Networks in Educational Assessment

Bayesian inference networks, a synthesis of statistics and expert systems, have advanced reasoning under uncertainty in medicine, business, and social sciences. This innovative volume is the first comprehensive treatment exploring how they can be applied to design and analyze innovative educational assessments. Part I develops Bayes nets’ foundations in assessment, statistics, and graph theory, and works through the real-time updating algorithm. Part II addresses parametric forms for use with assessment, model-checking techniques, and estimation with the EM algorithm and Markov chain Monte Carlo (MCMC). A unique feature is the volume’s grounding in Evidence-Centered Design (ECD) framework for assessment design. This “design forward” approach enables designers to take full advantage of Bayes nets’ modularity and ability to model complex evidentiary relationships that arise from performance in interactive, technology-rich assessments such as simulations. Part III describes ECD, situates Bayes nets as an integral component of a principled design process, and illustrates the ideas with an in-depth look at the BioMass project: An interactive, standards-based, web-delivered demonstration assessment of science inquiry in genetics. This book is both a resource for professionals interested in assessment and advanced students. Its clear exposition, worked-through numerical examples, and demonstrations from real and didactic applications provide invaluable illustrations of how to use Bayes nets in educational assessment. Exercises follow each chapter, and the online companion site provides a glossary, data sets and problem setups, and links to computational resources.

### Bayesian Networks

Bayesian Networks, the result of the convergence of artificial intelligence with statistics, are growing in popularity. Their versatility and modelling power is now employed across a variety of fields for the purposes of analysis, simulation, prediction and diagnosis. This book provides a general introduction to Bayesian networks, defining and illustrating the basic concepts with pedagogical examples and twenty real-life case studies drawn from a range of fields including medicine, computing, natural sciences and engineering. Designed to help analysts, engineers, scientists and professionals taking part in complex decision processes to successfully implement Bayesian networks, this book equips readers with proven methods to generate, calibrate, evaluate and validate Bayesian networks. The book: Provides the tools to overcome common practical challenges such as the treatment of missing input data, interaction with experts and decision makers, determination of the optimal granularity and size of the model. Highlights the strengths of Bayesian networks whilst also presenting a discussion of their limitations. Compares Bayesian networks with other modelling techniques such as neural networks, fuzzy logic and fault trees. Describes, for ease of comparison, the main features of the major Bayesian network software packages: Netica, Hugin, Elvira and Discoverer, from the point of view of the user. Offers a historical perspective on the subject and analyses future directions for research. Written by leading experts with practical experience of applying Bayesian networks in finance, banking, medicine, robotics, civil engineering, geology, geography, genetics, forensic science, ecology, and industry, the book has much to offer both practitioners and researchers involved in statistical analysis or modelling in any of these fields.

### Bayesian Networks and Influence Diagrams: A Guide to Construction and Analysis

Bayesian Networks and Influence Diagrams: A Guide to Construction and Analysis, Second Edition, provides a comprehensive guide for practitioners who wish to understand, construct, and analyze intelligent systems for decision support based on probabilistic networks. This new edition contains six new sections, in addition to fully-updated examples, tables, figures, and a revised appendix. Intended primarily for practitioners, this book does not require sophisticated mathematical skills or deep understanding of the underlying theory and methods nor does it discuss alternative technologies for reasoning under uncertainty. The theory and methods presented are illustrated through more than 140 examples, and exercises are included for the reader to check his or her level of understanding. The techniques and methods presented for knowledge elicitation, model construction and verification, modeling techniques and tricks, learning models from data, and analyses of models have all been developed and refined on the basis of numerous courses that the authors have held for practitioners worldwide.

### Introduction to Bayesian Networks

Disk contains: Tool for building Bayesian networks -- Library of examples -- Library of proposed solutions to some exercises.

### Bayesian Essentials with R

This Bayesian modeling book provides a self-contained entry to computational Bayesian statistics. Focusing on the most standard statistical models and backed up by real datasets and an all-inclusive R (CRAN) package called bayess, the book provides an operational methodology for conducting Bayesian inference, rather than focusing on its theoretical and philosophical justifications. Readers are empowered to participate in the real-life data analysis situations depicted here from the beginning. Special attention is paid to the derivation of prior distributions in each case and specific reference solutions are given for each of the models. Similarly, computational details are worked out to lead the reader towards an effective programming of the methods given in the book. In particular, all R codes are discussed with enough detail to make them readily understandable and expandable. Bayesian Essentials with R can be used as a textbook at both undergraduate and graduate levels. It is particularly useful with students in professional degree programs and scientists to analyze data the Bayesian way. The text will also enhance introductory courses on Bayesian statistics. Prerequisites for the book are an undergraduate background in probability and statistics, if not in Bayesian statistics.

### Bayesian Cost-Effectiveness Analysis with the R package BCEA

The book provides a description of the process of health economic evaluation and modelling for cost-effectiveness analysis, particularly from the perspective of a Bayesian statistical approach. Some relevant theory and introductory concepts are presented using practical examples and two running case studies. The book also describes in detail how to perform health economic evaluations using the R package BCEA (Bayesian Cost-Effectiveness Analysis). BCEA can be used to post-process the results of a Bayesian cost-effectiveness model and perform advanced analyses producing standardised and highly customisable outputs. It presents all the features of the package, including its many functions and their practical application, as well as its user-friendly web interface. The book is a valuable resource for statisticians and practitioners working in the field of health economics wanting to simplify and standardise their workflow, for example in the preparation of dossiers in support of marketing authorisation, or academic and scientific publications.

### Statistical Analysis of Network Data with R

Networks have permeated everyday life through everyday realities like the Internet, social networks, and viral marketing. As such, network analysis is an important growth area in the quantitative sciences, with roots in social network analysis going back to the 1930s and graph theory going back centuries. Measurement and analysis are integral components of network research. As a result, statistical methods play a critical role in network analysis. This book is the first of its kind in network research. It can be used as a stand-alone resource in which multiple R packages are used to illustrate how to conduct a wide range of network analyses, from basic manipulation and visualization, to summary and characterization, to modeling of network data. The central package is igraph, which provides extensive capabilities for studying network graphs in R. This text builds on Eric D. Kolaczyk’s book Statistical Analysis of Network Data (Springer, 2009).

### Bayesian Learning for Neural Networks

Artificial "neural networks" are widely used as flexible models for classification and regression applications, but questions remain about how the power of these models can be safely exploited when training data is limited. This book demonstrates how Bayesian methods allow complex neural network models to be used without fear of the "overfitting" that can occur with traditional training methods. Insight into the nature of these complex Bayesian models is provided by a theoretical investigation of the priors over functions that underlie them. A practical implementation of Bayesian neural network learning using Markov chain Monte Carlo methods is also described, and software for it is freely available over the Internet. Presupposing only basic knowledge of probability and statistics, this book should be of interest to researchers in statistics, engineering, and artificial intelligence.

### Modeling and Reasoning with Bayesian Networks

This book provides a thorough introduction to the formal foundations and practical applications of Bayesian networks. It provides an extensive discussion of techniques for building Bayesian networks that model real-world situations, including techniques for synthesizing models from design, learning models from data, and debugging models using sensitivity analysis. It also treats exact and approximate inference algorithms at both theoretical and practical levels. The author assumes very little background on the covered subjects, supplying in-depth discussions for theoretically inclined readers and enough practical details to provide an algorithmic cookbook for the system developer.

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*with Applications in Systems Biology*

Author: Radhakrishnan Nagarajan,Marco Scutari,Sophie Lèbre

Publisher: Springer Science & Business Media

ISBN: 1461464463

Category: Computers

Page: 157

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