Bayesian Networks in R

with Applications in Systems Biology

Author: Radhakrishnan Nagarajan,Marco Scutari,Sophie Lèbre

Publisher: Springer Science & Business Media

ISBN: 1461464463

Category: Computers

Page: 157

View: 1860

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

With Examples in R

Author: Marco Scutari,Jean-Baptiste Denis

Publisher: CRC Press

ISBN: 1482225581

Category: Computers

Page: 241

View: 5154

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.

Data mining

praktische Werkzeuge und Techniken für das maschinelle Lernen

Author: Ian H. Witten,Eibe Frank

Publisher: N.A

ISBN: 9783446215337

Category:

Page: 386

View: 5050


Graphical Models with R

Author: Søren Højsgaard,David Edwards,Steffen Lauritzen

Publisher: Springer Science & Business Media

ISBN: 146142299X

Category: Mathematics

Page: 182

View: 1651

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.

R in a Nutshell

Author: Joseph Adler

Publisher: O'Reilly Germany

ISBN: 3897216507

Category: Computers

Page: 768

View: 5551

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.

Bayesian Networks for Probabilistic Inference and Decision Analysis in Forensic Science

Author: Franco Taroni,Alex Biedermann,Silvia Bozza,Paolo Garbolino,Colin Aitken

Publisher: John Wiley & Sons

ISBN: 1118914740

Category: Mathematics

Page: 472

View: 9036

"This book should have a place on the bookshelf of everyforensic scientist who cares about the science of evidenceinterpretation" Dr. Ian Evett, Principal Forensic Services Ltd, London, UK Continuing developments in science and technology mean that theamounts of information forensic scientists are able to provide forcriminal investigations is ever increasing. The commensurate increase in complexity creates difficulties forscientists and lawyers with regard to evaluation andinterpretation, notably with respect to issues of inference anddecision. Probability theory, implemented through graphical methods, andspecifically Bayesian networks, provides powerful methods to dealwith this complexity. Extensions of these methods to elements of decision theory provide further support and assistance to thejudicial system. Bayesian Networks for Probabilistic Inference and DecisionAnalysis in Forensic Science provides a unique and comprehensiveintroduction to the use of Bayesian decision networks for theevaluation and interpretation of scientific findings in forensicscience, and for the support of decision-makers in their scientificand legal tasks. • Includes self-contained introductions to probabilityand decision theory. • Develops the characteristics of Bayesian networks,object-oriented Bayesian networks and their extension to decisionmodels. • Features implementation of the methodology withreference to commercial and academically available software. • Presents standard networks and their extensions thatcan be easily implemented and that can assist in the reader’sown analysis of real cases. • Provides a technique for structuring problems andorganizing data based on methods and principles of scientificreasoning. • Contains a method for the construction of coherent anddefensible arguments for the analysis and evaluation of scientificfindings and for decisions based on them. • Is written in a lucid style, suitable for forensicscientists and lawyers with minimal mathematical background. • Includes a foreword by Ian Evett. The clear and accessible style of this second edition makes thisbook ideal for all forensic scientists, applied statisticians andgraduate students wishing to evaluate forensic findings from theperspective of probability and decision analysis. It will alsoappeal to lawyers and other scientists and professionals interestedin the evaluation and interpretation of forensic findings,including decision making based on scientific information.

Learning Probabilistic Graphical Models in R

Author: David Bellot

Publisher: Packt Publishing Ltd

ISBN: 1784397415

Category: Computers

Page: 250

View: 5717

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.

Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics

Author: Raphaël Mourad

Publisher: OUP Oxford

ISBN: 0191019208

Category: Mathematics

Page: 464

View: 1448

Nowadays bioinformaticians and geneticists are faced with myriad high-throughput data usually presenting the characteristics of uncertainty, high dimensionality and large complexity. These data will only allow insights into this wealth of so-called 'omics' data if represented by flexible and scalable models, prior to any further analysis. At the interface between statistics and machine learning, probabilistic graphical models (PGMs) represent a powerful formalism to discover complex networks of relations. These models are also amenable to incorporating a priori biological information. Network reconstruction from gene expression data represents perhaps the most emblematic area of research where PGMs have been successfully applied. However these models have also created renewed interest in genetics in the broad sense, in particular regarding association genetics, causality discovery, prediction of outcomes, detection of copy number variations, and epigenetics. This book provides an overview of the applications of PGMs to genetics, genomics and postgenomics to meet this increased interest. A salient feature of bioinformatics, interdisciplinarity, reaches its limit when an intricate cooperation between domain specialists is requested. Currently, few people are specialists in the design of advanced methods using probabilistic graphical models for postgenomics or genetics. This book deciphers such models so that their perceived difficulty no longer hinders their use and focuses on fifteen illustrations showing the mechanisms behind the models. Probabilistic Graphical Models for Genetics, Genomics and Postgenomics covers six main themes: (1) Gene network inference (2) Causality discovery (3) Association genetics (4) Epigenetics (5) Detection of copy number variations (6) Prediction of outcomes from high-dimensional genomic data. Written by leading international experts, this is a collection of the most advanced work at the crossroads of probabilistic graphical models and genetics, genomics, and postgenomics. The self-contained chapters provide an enlightened account of the pros and cons of applying these powerful techniques.

Statistik-Workshop für Programmierer

Author: Allen B. Downey

Publisher: O'Reilly Germany

ISBN: 3868993436

Category: Computers

Page: 160

View: 3682

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.

Advances in Computational Intelligence, Part III

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

Publisher: Springer

ISBN: 3642317189

Category: Computers

Page: 628

View: 5607

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.

Modeling and Reasoning with Bayesian Networks

Author: Adnan Darwiche

Publisher: Cambridge University Press

ISBN: 0521884381

Category: Computers

Page: 548

View: 664

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.

Programmieren lernen mit Python

Author: Allen B. Downey

Publisher: O'Reilly Germany

ISBN: 3868999477

Category: Computers

Page: 312

View: 3985

Python ist eine moderne, interpretierte, interaktive und objektorientierte Skriptsprache, vielseitig einsetzbar und sehr beliebt. Mit mathematischen Vorkenntnissen ist Python leicht erlernbar und daher die ideale Sprache für den Einstieg in die Welt des Programmierens. Das Buch führt Sie Schritt für Schritt durch die Sprache, beginnend mit grundlegenden Programmierkonzepten, über Funktionen, Syntax und Semantik, Rekursion und Datenstrukturen bis hin zum objektorientierten Design. Jenseits reiner Theorie: Jedes Kapitel enthält passende Übungen und Fallstudien, kurze Verständnistests und kleinere Projekte, an denen Sie die neu erlernten Programmierkonzepte gleich ausprobieren und festigen können. Auf diese Weise können Sie das Gelernte direkt anwenden und die jeweiligen Programmierkonzepte nachvollziehen. Lernen Sie Debugging-Techniken kennen: Am Ende jedes Kapitels finden Sie einen Abschnitt zum Thema Debugging, der Techniken zum Aufspüren und Vermeiden von Bugs sowie Warnungen vor entsprechenden Stolpersteinen in Python enthält. Starten Sie durch: Beginnen Sie mit den Grundlagen der Programmierung und den verschiedenen Programmierkonzepten, und lernen Sie, wie ein Informatiker zu programmieren.

Learning Bayesian Models with R

Author: Dr. Hari M. Koduvely

Publisher: Packt Publishing Ltd

ISBN: 1783987618

Category: Computers

Page: 168

View: 3467

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.

Mustererkennung 2000

22. DAGM-Symposium. Kiel, 13.–15. September 2000

Author: Gerald Sommer,Norbert Krüger,Christian Perwass

Publisher: Springer-Verlag

ISBN: 3642598021

Category: Computers

Page: 490

View: 5131

Die Deutsche Arbeitsgemeinschaft für Mustererkennung veranstaltet seit 1978 jährlich an verschiedenen Orten ein wissenschaftliches Symposium mit dem Ziel, Aufgabenstellungen, Denkweisen und Forschungsergebnisse aus den Gebieten der Mustererkennung vorzustellen, den Erfahrungs- und Ideenaustausch zwischen den Fachleuten anzuregen und den Nachwuchs zu fördern. In dem dieses Jahr erstmals durchgeführten Kontaktforum unter dem Titel "Forum Industrie und Wissenschaft" findet der Austausch von Industrie und Wirtschaft besondere Beachtung.

Handbook of Statistics

Computational Statistics with R

Author: N.A

Publisher: Elsevier

ISBN: 044463441X

Category: Mathematics

Page: 412

View: 9811

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

Bayesian Networks in Educational Assessment

Author: Russell G. Almond,Robert J. Mislevy,Linda S. Steinberg,Duanli Yan,David M. Williamson

Publisher: Springer

ISBN: 1493921258

Category: Social Science

Page: 662

View: 476

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 and Influence Diagrams: A Guide to Construction and Analysis

Author: Uffe B. Kjærulff,Anders L. Madsen

Publisher: Springer Science & Business Media

ISBN: 9780387741017

Category: Computers

Page: 318

View: 6924

Probabilistic networks, also known as Bayesian networks and influence diagrams, have become one of the most promising technologies in the area of applied artificial intelligence. This book provides a comprehensive guide for practitioners who wish to understand, construct, and analyze intelligent systems for decision support based on probabilistic networks. Intended primarily for practitioners, this book does not require sophisticated mathematical skills. The theory and methods presented are illustrated through more than 140 examples, and exercises are included for the reader to check his/her level of understanding.