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.
with Applications in Systems Biology
Author: Radhakrishnan Nagarajan,Marco Scutari,Sophie Lèbre
Publisher: Springer Science & Business Media
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.
With Examples in R
Author: Marco Scutari,Jean-Baptiste Denis
Publisher: CRC Press
praktische Werkzeuge und Techniken für das maschinelle Lernen
Author: Ian H. Witten,Eibe Frank
"This book should have a place on the bookshelf of every forensic scientist who cares about the science of evidence interpretation" Dr. Ian Evett, Principal Forensic Services Ltd, London, UK Continuing developments in science and technology mean that the amounts of information forensic scientists are able to provide for criminal investigations is ever increasing. The commensurate increase in complexity creates difficulties for scientists and lawyers with regard to evaluation and interpretation, notably with respect to issues of inference and decision. Probability theory, implemented through graphical methods, and specifically Bayesian networks, provides powerful methods to deal with this complexity. Extensions of these methods to elements of decision theory provide further support and assistance to the judicial system. Bayesian Networks for Probabilistic Inference and Decision Analysis in Forensic Science provides a unique and comprehensive introduction to the use of Bayesian decision networks for the evaluation and interpretation of scientific findings in forensic science, and for the support of decision-makers in their scientific and legal tasks. • Includes self-contained introductions to probability and decision theory. • Develops the characteristics of Bayesian networks, object-oriented Bayesian networks and their extension to decision models. • Features implementation of the methodology with reference to commercial and academically available software. • Presents standard networks and their extensions that can be easily implemented and that can assist in the reader’s own analysis of real cases. • Provides a technique for structuring problems and organizing data based on methods and principles of scientific reasoning. • Contains a method for the construction of coherent and defensible arguments for the analysis and evaluation of scientific findings and for decisions based on them. • Is written in a lucid style, suitable for forensic scientists and lawyers with minimal mathematical background. • Includes a foreword by Ian Evett. The clear and accessible style of this second edition makes this book ideal for all forensic scientists, applied statisticians and graduate students wishing to evaluate forensic findings from the perspective of probability and decision analysis. It will also appeal to lawyers and other scientists and professionals interested in the evaluation and interpretation of forensic findings, including decision making based on scientific information.
Author: Franco Taroni,Alex Biedermann,Silvia Bozza,Paolo Garbolino,Colin Aitken
Publisher: John Wiley & Sons
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.
Author: David Bellot
Publisher: Packt Publishing Ltd
Wozu sollte man R lernen? Da gibt es viele Gründe: Weil man damit natürlich ganz andere Möglichkeiten hat als mit einer Tabellenkalkulation wie Excel, aber auch mehr Spielraum als mit gängiger Statistiksoftware wie SPSS und SAS. Anders als bei diesen Programmen hat man nämlich direkten Zugriff auf dieselbe, vollwertige Programmiersprache, mit der die fertigen Analyse- und Visualisierungsmethoden realisiert sind – so lassen sich nahtlos eigene Algorithmen integrieren und komplexe Arbeitsabläufe realisieren. Und nicht zuletzt, weil R offen gegenüber beliebigen Datenquellen ist, von der einfachen Textdatei über binäre Fremdformate bis hin zu den ganz großen relationalen Datenbanken. Zudem ist R Open Source und erobert momentan von der universitären Welt aus die professionelle Statistik. R kann viel. Und Sie können viel mit R machen – wenn Sie wissen, wie es geht. Willkommen in der R-Welt: Installieren Sie R und stöbern Sie in Ihrem gut bestückten Werkzeugkasten: Sie haben eine Konsole und eine grafische Benutzeroberfläche, unzählige vordefinierte Analyse- und Visualisierungsoperationen – und Pakete, Pakete, Pakete. Für quasi jeden statistischen Anwendungsbereich können Sie sich aus dem reichen Schatz der R-Community bedienen. Sprechen Sie R! Sie müssen Syntax und Grammatik von R nicht lernen – wie im Auslandsurlaub kommen Sie auch hier gut mit ein paar aufgeschnappten Brocken aus. Aber es lohnt sich: Wenn Sie wissen, was es mit R-Objekten auf sich hat, wie Sie eigene Funktionen schreiben und Ihre eigenen Pakete schnüren, sind Sie bei der Analyse Ihrer Daten noch flexibler und effektiver. Datenanalyse und Statistik in der Praxis: Anhand unzähliger Beispiele aus Medizin, Wirtschaft, Sport und Bioinformatik lernen Sie, wie Sie Daten aufbereiten, mithilfe der Grafikfunktionen des lattice-Pakets darstellen, statistische Tests durchführen und Modelle anpassen. Danach werden Ihnen Ihre Daten nichts mehr verheimlichen.
Author: Joseph Adler
Publisher: O'Reilly Germany
Wenn Sie programmieren können, beherrschen Sie bereits Techniken, um aus Daten Wissen zu extrahieren. Diese kompakte Einführung in die Statistik zeigt Ihnen, wie Sie rechnergestützt, anstatt auf mathematischem Weg Datenanalysen mit Python durchführen können. Praktischer Programmier-Workshop statt grauer Theorie: Das Buch führt Sie anhand eines durchgängigen Fallbeispiels durch eine vollständige Datenanalyse -- von der Datensammlung über die Berechnung statistischer Kennwerte und Identifikation von Mustern bis hin zum Testen statistischer Hypothesen. Gleichzeitig werden Sie mit statistischen Verteilungen, den Regeln der Wahrscheinlichkeitsrechnung, Visualisierungsmöglichkeiten und vielen anderen Arbeitstechniken und Konzepten vertraut gemacht. Statistik-Konzepte zum Ausprobieren: Entwickeln Sie über das Schreiben und Testen von Code ein Verständnis für die Grundlagen von Wahrscheinlichkeitsrechnung und Statistik: Überprüfen Sie das Verhalten statistischer Merkmale durch Zufallsexperimente, zum Beispiel indem Sie Stichproben aus unterschiedlichen Verteilungen ziehen. Nutzen Sie Simulationen, um Konzepte zu verstehen, die auf mathematischem Weg nur schwer zugänglich sind. Lernen Sie etwas über Themen, die in Einführungen üblicherweise nicht vermittelt werden, beispielsweise über die Bayessche Schätzung. Nutzen Sie Python zur Bereinigung und Aufbereitung von Rohdaten aus nahezu beliebigen Quellen. Beantworten Sie mit den Mitteln der Inferenzstatistik Fragestellungen zu realen Daten.
Author: Allen B. Downey
Publisher: O'Reilly Germany
These four volumes (CCIS 297, 298, 299, 300) constitute the proceedings of the 14th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems, IPMU 2012, held in Catania, Italy, in July 2012. The 258 revised full papers presented together with six invited talks were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections on fuzzy machine learning and on-line modeling; computing with words and decision making; soft computing in computer vision; rough sets and complex data analysis: theory and applications; intelligent databases and information system; information fusion systems; philosophical and methodological aspects of soft computing; basic issues in rough sets; 40th anniversary of the measures of fuziness; SPS11 uncertainty in profiling systems and applications; handling uncertainty with copulas; formal methods to deal with uncertainty of many-valued events; linguistic summarization and description of data; fuzzy implications: theory and applications; sensing and data mining for teaching and learning; theory and applications of intuitionistic fuzzy sets; approximate aspects of data mining and database analytics; fuzzy numbers and their applications; information processing and management of uncertainty in knowledge-based systems; aggregation functions; imprecise probabilities; probabilistic graphical models with imprecision: theory and applications; belief function theory: basics and/or applications; fuzzy uncertainty in economics and business; new trends in De Finetti's approach; fuzzy measures and integrals; multicriteria decision making; uncertainty in privacy and security; uncertainty in the spirit of Pietro Benvenuti; coopetition; game theory; probabilistic approach.
14th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems, IPMU 2012, Catania, Italy, July 9 - 13, 2012. Proceedings
Author: Salvatore Greco,Bernadette Bouchon-Meunier,Giulianella Coletti,Mario Fedrizzi,Benedetto Matarazzo,Ronald R. Yager
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.
Author: Adnan Darwiche
Publisher: Cambridge University Press
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.
Author: Søren Højsgaard,David Edwards,Steffen Lauritzen
Publisher: Springer Science & Business Media
R is open source statistical computing software. Since the R core group was formed in 1997, R has been extended by a very large number of packages with extensive documentation along with examples freely available on the internet. It offers a large number of statistical and numerical methods and graphical tools and visualization of extraordinarily high quality. R was recently ranked in 14th place by the Transparent Language Popularity Index and 6th as a scripting language, after PHP, Python, and Perl. The book is designed so that it can be used right away by novices while appealing to experienced users as well. Each article begins with a data example that can be downloaded directly from the R website. Data analysis questions are articulated following the presentation of the data. The necessary R commands are spelled out and executed and the output is presented and discussed. Other examples of data sets with a different flavor and different set of commands but following the theme of the article are presented as well. Each chapter predents a hands-on-experience. R has superb graphical outlays and the book brings out the essentials in this arena. The end user can benefit immensely by applying the graphics to enhance research findings. The core statistical methodologies such as regression, survival analysis, and discrete data are all covered. Addresses data examples that can be downloaded directly from the R website No other source is needed to gain practical experience Focus on the essentials in graphical outlays
Computational Statistics with R
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.
Author: Russell G. Almond,Robert J. Mislevy,Linda Steinberg,Duanli Yan,David Williamson
Category: Social Science
Mechatronics is a synergic discipline integrating precise mechanics, electrotechnics, electronics and IT technologies. The main goal of mechatronical approach to design of complex products is to achieve new quality of their utility value at reasonable price. Successful accomplishment of this task would not be possible without application of advanced software and hardware tools for simulation of design, technologies and production control and also for simulation of behavior of these products in order to provide the highest possible level of spatial and functional integration of the final product. This book brings a review of the current state of the art in mechatronics, as presented at the 8th International Conference Mechatronics 2009, organized by the Brno Technical University, Faculty of Mechanical Engineering, Czech Republic. The specific topics of the conference are Modelling and Simulation, Metrology & Diagnostics, Sensorics & Photonics, Control & Robotics, MEMS Design & Mechatronic Products, Production Machines and Biomechanics. The selected contributions provide an insight into the current development of these scientific disciplines, present the new results of research and development and indicate the trends of development in the interdisciplinary field of mechatronic systems. Therefore, the book provides the latest and helpful information both for the R&D specialists and for the designers working in mechatronics and related fields.
2008 - 2009
Author: Tomas Brezina,Ryszard Jablonski
Publisher: Springer Science & Business Media
Category: Technology & Engineering
This book constitutes the refereed proceedings of the joint conference on Machine Learning and Knowledge Discovery in Databases: ECML PKDD 2008, held in Antwerp, Belgium, in September 2008. The 100 papers presented in two volumes, together with 5 invited talks, were carefully reviewed and selected from 521 submissions. In addition to the regular papers the volume contains 14 abstracts of papers appearing in full version in the Machine Learning Journal and the Knowledge Discovery and Databases Journal of Springer. The conference intends to provide an international forum for the discussion of the latest high quality research results in all areas related to machine learning and knowledge discovery in databases. The topics addressed are application of machine learning and data mining methods to real-world problems, particularly exploratory research that describes novel learning and mining tasks and applications requiring non-standard techniques.
European Conference, Antwerp, Belgium, September 15-19, 2008, Proceedings
Author: Walter Daelemans
Publisher: Springer Science & Business Media
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.
Author: Richard E. Neapolitan
Publisher: Prentice Hall
Third Mexican International Conference on Artificial Intelligence, Mexico City, Mexico, April 26-30, 2004, Proceedings
Author: Raúl Monroy,Gustavo Arroyo-Figueroa,Luis Enrique Sucar,Humberto Sossa
Publisher: Springer Science & Business Media