Download or read book Random Forests with R written by Robin Genuer and published by Springer Nature. This book was released on 2020-09-10 with total page 107 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers an application-oriented guide to random forests: a statistical learning method extensively used in many fields of application, thanks to its excellent predictive performance, but also to its flexibility, which places few restrictions on the nature of the data used. Indeed, random forests can be adapted to both supervised classification problems and regression problems. In addition, they allow us to consider qualitative and quantitative explanatory variables together, without pre-processing. Moreover, they can be used to process standard data for which the number of observations is higher than the number of variables, while also performing very well in the high dimensional case, where the number of variables is quite large in comparison to the number of observations. Consequently, they are now among the preferred methods in the toolbox of statisticians and data scientists. The book is primarily intended for students in academic fields such as statistical education, but also for practitioners in statistics and machine learning. A scientific undergraduate degree is quite sufficient to take full advantage of the concepts, methods, and tools discussed. In terms of computer science skills, little background knowledge is required, though an introduction to the R language is recommended. Random forests are part of the family of tree-based methods; accordingly, after an introductory chapter, Chapter 2 presents CART trees. The next three chapters are devoted to random forests. They focus on their presentation (Chapter 3), on the variable importance tool (Chapter 4), and on the variable selection problem (Chapter 5), respectively. After discussing the concepts and methods, we illustrate their implementation on a running example. Then, various complements are provided before examining additional examples. Throughout the book, each result is given together with the code (in R) that can be used to reproduce it. Thus, the book offers readers essential information and concepts, together with examples and the software tools needed to analyse data using random forests.

Download or read book Hands On Machine Learning with R written by Brad Boehmke and published by CRC Press. This book was released on 2019-11-07 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hands-on Machine Learning with R provides a practical and applied approach to learning and developing intuition into today’s most popular machine learning methods. This book serves as a practitioner’s guide to the machine learning process and is meant to help the reader learn to apply the machine learning stack within R, which includes using various R packages such as glmnet, h2o, ranger, xgboost, keras, and others to effectively model and gain insight from their data. The book favors a hands-on approach, providing an intuitive understanding of machine learning concepts through concrete examples and just a little bit of theory. Throughout this book, the reader will be exposed to the entire machine learning process including feature engineering, resampling, hyperparameter tuning, model evaluation, and interpretation. The reader will be exposed to powerful algorithms such as regularized regression, random forests, gradient boosting machines, deep learning, generalized low rank models, and more! By favoring a hands-on approach and using real word data, the reader will gain an intuitive understanding of the architectures and engines that drive these algorithms and packages, understand when and how to tune the various hyperparameters, and be able to interpret model results. By the end of this book, the reader should have a firm grasp of R’s machine learning stack and be able to implement a systematic approach for producing high quality modeling results. Features: · Offers a practical and applied introduction to the most popular machine learning methods. · Topics covered include feature engineering, resampling, deep learning and more. · Uses a hands-on approach and real world data.

Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Download or read book Geocomputation with R written by Robin Lovelace and published by CRC Press. This book was released on 2019-03-22 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Geocomputation with R is for people who want to analyze, visualize and model geographic data with open source software. It is based on R, a statistical programming language that has powerful data processing, visualization, and geospatial capabilities. The book equips you with the knowledge and skills to tackle a wide range of issues manifested in geographic data, including those with scientific, societal, and environmental implications. This book will interest people from many backgrounds, especially Geographic Information Systems (GIS) users interested in applying their domain-specific knowledge in a powerful open source language for data science, and R users interested in extending their skills to handle spatial data. The book is divided into three parts: (I) Foundations, aimed at getting you up-to-speed with geographic data in R, (II) extensions, which covers advanced techniques, and (III) applications to real-world problems. The chapters cover progressively more advanced topics, with early chapters providing strong foundations on which the later chapters build. Part I describes the nature of spatial datasets in R and methods for manipulating them. It also covers geographic data import/export and transforming coordinate reference systems. Part II represents methods that build on these foundations. It covers advanced map making (including web mapping), "bridges" to GIS, sharing reproducible code, and how to do cross-validation in the presence of spatial autocorrelation. Part III applies the knowledge gained to tackle real-world problems, including representing and modeling transport systems, finding optimal locations for stores or services, and ecological modeling. Exercises at the end of each chapter give you the skills needed to tackle a range of geospatial problems. Solutions for each chapter and supplementary materials providing extended examples are available at https://geocompr.github.io/geocompkg/articles/.

Download or read book Ensemble Machine Learning written by Cha Zhang and published by Springer Science & Business Media. This book was released on 2012-02-17 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is common wisdom that gathering a variety of views and inputs improves the process of decision making, and, indeed, underpins a democratic society. Dubbed “ensemble learning” by researchers in computational intelligence and machine learning, it is known to improve a decision system’s robustness and accuracy. Now, fresh developments are allowing researchers to unleash the power of ensemble learning in an increasing range of real-world applications. Ensemble learning algorithms such as “boosting” and “random forest” facilitate solutions to key computational issues such as face recognition and are now being applied in areas as diverse as object tracking and bioinformatics. Responding to a shortage of literature dedicated to the topic, this volume offers comprehensive coverage of state-of-the-art ensemble learning techniques, including the random forest skeleton tracking algorithm in the Xbox Kinect sensor, which bypasses the need for game controllers. At once a solid theoretical study and a practical guide, the volume is a windfall for researchers and practitioners alike.

Download or read book Applied Predictive Modeling written by Max Kuhn and published by Springer Science & Business Media. This book was released on 2013-05-17 with total page 595 pages. Available in PDF, EPUB and Kindle. Book excerpt: Applied Predictive Modeling covers the overall predictive modeling process, beginning with the crucial steps of data preprocessing, data splitting and foundations of model tuning. The text then provides intuitive explanations of numerous common and modern regression and classification techniques, always with an emphasis on illustrating and solving real data problems. The text illustrates all parts of the modeling process through many hands-on, real-life examples, and every chapter contains extensive R code for each step of the process. This multi-purpose text can be used as an introduction to predictive models and the overall modeling process, a practitioner’s reference handbook, or as a text for advanced undergraduate or graduate level predictive modeling courses. To that end, each chapter contains problem sets to help solidify the covered concepts and uses data available in the book’s R package. This text is intended for a broad audience as both an introduction to predictive models as well as a guide to applying them. Non-mathematical readers will appreciate the intuitive explanations of the techniques while an emphasis on problem-solving with real data across a wide variety of applications will aid practitioners who wish to extend their expertise. Readers should have knowledge of basic statistical ideas, such as correlation and linear regression analysis. While the text is biased against complex equations, a mathematical background is needed for advanced topics.

Download or read book Practical Propensity Score Methods Using R written by Walter Leite and published by SAGE Publications. This book was released on 2016-10-28 with total page 225 pages. Available in PDF, EPUB and Kindle. Book excerpt: Practical Propensity Score Methods Using R by Walter Leite is a practical book that uses a step-by-step analysis of realistic examples to help students understand the theory and code for implementing propensity score analysis with the R statistical language. With a comparison of both well-established and cutting-edge propensity score methods, the text highlights where solid guidelines exist to support best practices and where there is scarcity of research. Readers will find that this scaffolded approach to R and the book’s free online resources help them apply the text’s concepts to the analysis of their own data.

Download or read book Small Sample Size Solutions written by Rens van de Schoot and published by Routledge. This book was released on 2020-02-13 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Researchers often have difficulties collecting enough data to test their hypotheses, either because target groups are small or hard to access, or because data collection entails prohibitive costs. Such obstacles may result in data sets that are too small for the complexity of the statistical model needed to answer the research question. This unique book provides guidelines and tools for implementing solutions to issues that arise in small sample research. Each chapter illustrates statistical methods that allow researchers to apply the optimal statistical model for their research question when the sample is too small. This essential book will enable social and behavioral science researchers to test their hypotheses even when the statistical model required for answering their research question is too complex for the sample sizes they can collect. The statistical models in the book range from the estimation of a population mean to models with latent variables and nested observations, and solutions include both classical and Bayesian methods. All proposed solutions are described in steps researchers can implement with their own data and are accompanied with annotated syntax in R. The methods described in this book will be useful for researchers across the social and behavioral sciences, ranging from medical sciences and epidemiology to psychology, marketing, and economics.

Download or read book Machine Learning for Ecology and Sustainable Natural Resource Management written by Grant Humphries and published by Springer. This book was released on 2018-11-05 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ecologists and natural resource managers are charged with making complex management decisions in the face of a rapidly changing environment resulting from climate change, energy development, urban sprawl, invasive species and globalization. Advances in Geographic Information System (GIS) technology, digitization, online data availability, historic legacy datasets, remote sensors and the ability to collect data on animal movements via satellite and GPS have given rise to large, highly complex datasets. These datasets could be utilized for making critical management decisions, but are often “messy” and difficult to interpret. Basic artificial intelligence algorithms (i.e., machine learning) are powerful tools that are shaping the world and must be taken advantage of in the life sciences. In ecology, machine learning algorithms are critical to helping resource managers synthesize information to better understand complex ecological systems. Machine Learning has a wide variety of powerful applications, with three general uses that are of particular interest to ecologists: (1) data exploration to gain system knowledge and generate new hypotheses, (2) predicting ecological patterns in space and time, and (3) pattern recognition for ecological sampling. Machine learning can be used to make predictive assessments even when relationships between variables are poorly understood. When traditional techniques fail to capture the relationship between variables, effective use of machine learning can unearth and capture previously unattainable insights into an ecosystem's complexity. Currently, many ecologists do not utilize machine learning as a part of the scientific process. This volume highlights how machine learning techniques can complement the traditional methodologies currently applied in this field.

Download or read book Classification and Regression Trees written by Leo Breiman and published by Routledge. This book was released on 2017-10-19 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

Download or read book Decision Forests written by Antonio Criminisi and published by Foundations and Trends(r) in C. This book was released on 2012-03 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents a unified, efficient model of random decision forests which can be used in a number of applications such as scene recognition from photographs, object recognition in images, automatic diagnosis from radiological scans and document analysis.

Download or read book The Elements of Statistical Learning written by Trevor Hastie and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 545 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the past decade there has been an explosion in computation and information technology. With it have come vast amounts of data in a variety of fields such as medicine, biology, finance, and marketing. The challenge of understanding these data has led to the development of new tools in the field of statistics, and spawned new areas such as data mining, machine learning, and bioinformatics. Many of these tools have common underpinnings but are often expressed with different terminology. This book describes the important ideas in these areas in a common conceptual framework. While the approach is statistical, the emphasis is on concepts rather than mathematics. Many examples are given, with a liberal use of color graphics. It should be a valuable resource for statisticians and anyone interested in data mining in science or industry. The book’s coverage is broad, from supervised learning (prediction) to unsupervised learning. The many topics include neural networks, support vector machines, classification trees and boosting---the first comprehensive treatment of this topic in any book. This major new edition features many topics not covered in the original, including graphical models, random forests, ensemble methods, least angle regression & path algorithms for the lasso, non-negative matrix factorization, and spectral clustering. There is also a chapter on methods for “wide” data (p bigger than n), including multiple testing and false discovery rates. Trevor Hastie, Robert Tibshirani, and Jerome Friedman are professors of statistics at Stanford University. They are prominent researchers in this area: Hastie and Tibshirani developed generalized additive models and wrote a popular book of that title. Hastie co-developed much of the statistical modeling software and environment in R/S-PLUS and invented principal curves and surfaces. Tibshirani proposed the lasso and is co-author of the very successful An Introduction to the Bootstrap. Friedman is the co-inventor of many data-mining tools including CART, MARS, projection pursuit and gradient boosting.

Download or read book Interpretable Machine Learning written by Christoph Molnar and published by Lulu.com. This book was released on 2020 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is about making machine learning models and their decisions interpretable. After exploring the concepts of interpretability, you will learn about simple, interpretable models such as decision trees, decision rules and linear regression. Later chapters focus on general model-agnostic methods for interpreting black box models like feature importance and accumulated local effects and explaining individual predictions with Shapley values and LIME. All interpretation methods are explained in depth and discussed critically. How do they work under the hood? What are their strengths and weaknesses? How can their outputs be interpreted? This book will enable you to select and correctly apply the interpretation method that is most suitable for your machine learning project.

Download or read book Machine Learning written by Kevin P. Murphy and published by MIT Press. This book was released on 2012-08-24 with total page 1102 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive introduction to machine learning that uses probabilistic models and inference as a unifying approach. Today's Web-enabled deluge of electronic data calls for automated methods of data analysis. Machine learning provides these, developing methods that can automatically detect patterns in data and then use the uncovered patterns to predict future data. This textbook offers a comprehensive and self-contained introduction to the field of machine learning, based on a unified, probabilistic approach. The coverage combines breadth and depth, offering necessary background material on such topics as probability, optimization, and linear algebra as well as discussion of recent developments in the field, including conditional random fields, L1 regularization, and deep learning. The book is written in an informal, accessible style, complete with pseudo-code for the most important algorithms. All topics are copiously illustrated with color images and worked examples drawn from such application domains as biology, text processing, computer vision, and robotics. Rather than providing a cookbook of different heuristic methods, the book stresses a principled model-based approach, often using the language of graphical models to specify models in a concise and intuitive way. Almost all the models described have been implemented in a MATLAB software package—PMTK (probabilistic modeling toolkit)—that is freely available online. The book is suitable for upper-level undergraduates with an introductory-level college math background and beginning graduate students.

Download or read book Machine Learning Essentials written by Alboukadel Kassambara and published by STHDA. This book was released on 2018-03-10 with total page 211 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discovering knowledge from big multivariate data, recorded every days, requires specialized machine learning techniques. This book presents an easy to use practical guide in R to compute the most popular machine learning methods for exploring real word data sets, as well as, for building predictive models. The main parts of the book include: A) Unsupervised learning methods, to explore and discover knowledge from a large multivariate data set using clustering and principal component methods. You will learn hierarchical clustering, k-means, principal component analysis and correspondence analysis methods. B) Regression analysis, to predict a quantitative outcome value using linear regression and non-linear regression strategies. C) Classification techniques, to predict a qualitative outcome value using logistic regression, discriminant analysis, naive bayes classifier and support vector machines. D) Advanced machine learning methods, to build robust regression and classification models using k-nearest neighbors methods, decision tree models, ensemble methods (bagging, random forest and boosting). E) Model selection methods, to select automatically the best combination of predictor variables for building an optimal predictive model. These include, best subsets selection methods, stepwise regression and penalized regression (ridge, lasso and elastic net regression models). We also present principal component-based regression methods, which are useful when the data contain multiple correlated predictor variables. F) Model validation and evaluation techniques for measuring the performance of a predictive model. G) Model diagnostics for detecting and fixing a potential problems in a predictive model. The book presents the basic principles of these tasks and provide many examples in R. This book offers solid guidance in data mining for students and researchers. Key features: - Covers machine learning algorithm and implementation - Key mathematical concepts are presented - Short, self-contained chapters with practical examples.

Download or read book Analyzing Categorical Data written by Jeffrey S. Simonoff and published by Springer Science & Business Media. This book was released on 2013-06-05 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt: Categorical data arise often in many fields, including biometrics, economics, management, manufacturing, marketing, psychology, and sociology. This book provides an introduction to the analysis of such data. The coverage is broad, using the loglinear Poisson regression model and logistic binomial regression models as the primary engines for methodology. Topics covered include count regression models, such as Poisson, negative binomial, zero-inflated, and zero-truncated models; loglinear models for two-dimensional and multidimensional contingency tables, including for square tables and tables with ordered categories; and regression models for two-category (binary) and multiple-category target variables, such as logistic and proportional odds models. All methods are illustrated with analyses of real data examples, many from recent subject area journal articles. These analyses are highlighted in the text, and are more detailed than is typical, providing discussion of the context and background of the problem, model checking, and scientific implications. More than 200 exercises are provided, many also based on recent subject area literature. Data sets and computer code are available at a web site devoted to the text. Adopters of this book may request a solutions manual from: [email protected]. From the reviews: "Jeff Simonoff's book is at the top of the heap of categorical data analysis textbooks...The examples are superb. Student reactions in a class I taught from this text were uniformly positive, particularly because of the examples and exercises. Additional materials related to the book, particularly code for S-Plus, SAS, and R, useful for analysis of examples, can be found at the author's Web site at New York University. I liked this book for this reason, and recommend it to you for pedagogical purposes." (Stanley Wasserman, The American Statistician, August 2006, Vol. 60, No. 3) "The book has various noteworthy features. The examples used are from a variety of topics, including medicine, economics, sports, mining, weather, as well as social aspects like needle-exchange programs. The examples motivate the theory and also illustrate nuances of data analytical procedures. The book also incorporates several newer methods for analyzing categorical data, including zero-inflated Poisson models, robust analysis of binomial and poisson models, sandwich estimators, multinomial smoothing, ordinal agreement tables...this is definitely a good reference book for any researcher working with categorical data." Technometrics, May 2004 "This guide provides a practical approach to the appropriate analysis of categorical data and would be a suitable purchase for individuals with varying levels of statistical understanding." Paediatric and Perinatal Epidemiology, 2004, 18 "This book gives a fresh approach to the topic of categorical data analysis. The presentation of the statistical methods exploits the connection to regression modeling with a focus on practical features rather than formal theory...There is much to learn from this book. Aside from the ordinary materials such as association diagrams, Mantel-Haenszel estimators, or overdispersion, the reader will also find some less-often presented but interesting and stimulating topics...[T]his is an excellent book, giving an up-to-date introduction to the wide field of analyzing categorical data." Biometrics, September 2004 "...It is of great help to data analysts, practitioners and researchers who deal with categorical data and need to get a necessary insight into the methods of analysis as well as practical guidelines for solving problems." International Journal of General Systems, August 2004 "The author has succeeded in writing a useful and readable textbook combining most of general theory and practice of count data." Kwantitatieve Methoden "The book especially stresses how to analyze and interpret data...In fact, the highly detailed multi-page descriptions of analysis and interpretation make the book stand out." Mathematical Geology, February 2005 "Overall, this is a competent and detailed text that I would recommend to anyone dealing with the analysis of categorical data." Journal of the Royal Statistical Society "This important work allows for clear analogies between the well-known linear models for Gaussian data and categorical data problems. ... Jeffrey Simonoff’s Analyzing Categorical Data provides an introduction to many of the important ideas and methods for understanding counted data and tables of counts. ... Some readers will find Simonoff’s style very much to their liking due to reliance on extended real data examples to illuminate ideas. ... I think the extensive examples will appeal to most students." (Sanford Weisberg, SIAM Review, Vol. 47 (4), 2005) "It is clear that the focus of Simonoff’s book is different from other books on categorical data analysis. ... As an introductory textbook, the book is comprehensive enough since all basic topics in categorical data analysis are discussed. ... I think Simonoff’s book is a valuable addition to the literature because it discusses important models for counts ... ." (Jeroen K. Vermunt, Statistics in Medicine, Vol. 24, 2005) "The author based this book on his notes for a class with a very diverse pool of students. The material is presented in such a way that a very heterogeneous group of students could grasp it. All methods are illustrated with analyses of real data examples. The author provides a detailed discussion of the context and background of the problem. ... The book is very interesting and can be warmly recommended to people working with categorical data." (EMS - European Mathematical Society Newsletter, December, 2004) "Categorical data arise often in many fields ... . This book provides an introduction to the analysis of such data. ... All methods are illustrated with analyses of real data examples, many from recent subject-area journal articles. These analyses are highlighted in the text and are more detailed than is typical ... . More than 200 exercises are provided, including many based on recent subject-area literature. Data sets and computer code are available at a Web site devoted to this text." (T. Postelnicu, Zentralblatt MATH, Vol. 1028, 2003) "This book grew out of notes prepared by the author for classes in categorical data analysis. The presentation is fresh and compelling to read. Regression ideas are used to motivate the modelling presented. The book focuses on applying methods to real problems; many of these will be novel to readers of statistics texts ... . All chapters end with a section providing references to books or articles for the inquiring reader." (C.M. O’Brien, Short Book Reviews, Vol. 23 (3), 2003)

Download or read book Multivariate Statistical Machine Learning Methods for Genomic Prediction written by Osval Antonio Montesinos López and published by Springer Nature. This book was released on 2022-02-14 with total page 707 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is open access under a CC BY 4.0 license This open access book brings together the latest genome base prediction models currently being used by statisticians, breeders and data scientists. It provides an accessible way to understand the theory behind each statistical learning tool, the required pre-processing, the basics of model building, how to train statistical learning methods, the basic R scripts needed to implement each statistical learning tool, and the output of each tool. To do so, for each tool the book provides background theory, some elements of the R statistical software for its implementation, the conceptual underpinnings, and at least two illustrative examples with data from real-world genomic selection experiments. Lastly, worked-out examples help readers check their own comprehension.The book will greatly appeal to readers in plant (and animal) breeding, geneticists and statisticians, as it provides in a very accessible way the necessary theory, the appropriate R code, and illustrative examples for a complete understanding of each statistical learning tool. In addition, it weighs the advantages and disadvantages of each tool.