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People are often interested in predicting a new or future observation. In clinical prediction, the uptake of Electronic Health Records (EHRs) has generated massive health datasets that are big in volume and diverse in variety. The outcomes can be of different types, e.g., continuous, binary, time-to-event, etc., and covariates can be either time-fixed or longitudinal. These datasets can provide rich and diverse information for modeling and prediction but also pose challenges to fast and accurate prediction of outcomes of interest. One challenge of predicting is that when the data are heterogeneous in the relationship between the covariates and the outcome. In this case, it is quite possible that localizing a subset of data in an informative manner to aid in making predictions will lead to better performance than including all information. Chapter 3 deals with a continuous outcome, and I have developed methodology that gives an interpretable and meaningful definition of similarity, and an algorithm to uncover the similarity structure to improve the prediction accuracy by making similarity-based predictions. In Chapter 4, the similarity-based prediction is extended to a survival outcome, with possible independent or dependent censoring. The algorithm is developed under the random forest framework, and I showed through both simulations and a real data example that incorporating the similarity structure indeed improves prediction accuracy in these cases. Another challenge in prediction arises when longitudinal covariates are present, and that there are scenarios when one needs to make an early prediction as soon as practical and thus cannot monitor the full trajectory of longitudinal covariates (before the prediction is required). In Chapter 5, I address this concern by quantifying the relationship between the earliness of prediction and the prediction accuracy. A penalization approach with a graphical method is introduced to select a monitoring window length given specific prediction accuracy. Comprehensive simulations are conducted to investigate the performance of the algorithm in selecting the length of the monitoring window in different scenarios.
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.
The past decades have transformed the world of statistical data analysis, with new methods, new types of data, and new computational tools. Modern Statistics with R introduces you to key parts of this modern statistical toolkit. It teaches you: Data wrangling - importing, formatting, reshaping, merging, and filtering data in R. Exploratory data analysis - using visualisations and multivariate techniques to explore datasets. Statistical inference - modern methods for testing hypotheses and computing confidence intervals. Predictive modelling - regression models and machine learning methods for prediction, classification, and forecasting. Simulation - using simulation techniques for sample size computations and evaluations of statistical methods. Ethics in statistics - ethical issues and good statistical practice. R programming - writing code that is fast, readable, and (hopefully!) free from bugs. No prior programming experience is necessary. Clear explanations and examples are provided to accommodate readers at all levels of familiarity with statistical principles and coding practices. A basic understanding of probability theory can enhance comprehension of certain concepts discussed within this book. In addition to plenty of examples, the book includes more than 200 exercises, with fully worked solutions available at: www.modernstatisticswithr.com.
This open access book comprehensively covers the fundamentals of clinical data science, focusing on data collection, modelling and clinical applications. Topics covered in the first section on data collection include: data sources, data at scale (big data), data stewardship (FAIR data) and related privacy concerns. Aspects of predictive modelling using techniques such as classification, regression or clustering, and prediction model validation will be covered in the second section. The third section covers aspects of (mobile) clinical decision support systems, operational excellence and value-based healthcare. Fundamentals of Clinical Data Science is an essential resource for healthcare professionals and IT consultants intending to develop and refine their skills in personalized medicine, using solutions based on large datasets from electronic health records or telemonitoring programmes. The book’s promise is “no math, no code”and will explain the topics in a style that is optimized for a healthcare audience.
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.
From a review of the first edition: "Modern Data Science with R... is rich with examples and is guided by a strong narrative voice. What’s more, it presents an organizing framework that makes a convincing argument that data science is a course distinct from applied statistics" (The American Statistician). Modern Data Science with R is a comprehensive data science textbook for undergraduates that incorporates statistical and computational thinking to solve real-world data problems. Rather than focus exclusively on case studies or programming syntax, this book illustrates how statistical programming in the state-of-the-art R/RStudio computing environment can be leveraged to extract meaningful information from a variety of data in the service of addressing compelling questions. The second edition is updated to reflect the growing influence of the tidyverse set of packages. All code in the book has been revised and styled to be more readable and easier to understand. New functionality from packages like sf, purrr, tidymodels, and tidytext is now integrated into the text. All chapters have been revised, and several have been split, re-organized, or re-imagined to meet the shifting landscape of best practice.
Produce a fully functioning Intelligent System that leverages machine learning and data from user interactions to improve over time and achieve success. This book teaches you how to build an Intelligent System from end to end and leverage machine learning in practice. You will understand how to apply your existing skills in software engineering, data science, machine learning, management, and program management to produce working systems. Building Intelligent Systems is based on more than a decade of experience building Internet-scale Intelligent Systems that have hundreds of millions of user interactions per day in some of the largest and most important software systems in the world. What You’ll Learn Understand the concept of an Intelligent System: What it is good for, when you need one, and how to set it up for success Design an intelligent user experience: Produce data to help make the Intelligent System better over time Implement an Intelligent System: Execute, manage, and measure Intelligent Systems in practice Create intelligence: Use different approaches, including machine learning Orchestrate an Intelligent System: Bring the parts together throughout its life cycle and achieve the impact you want Who This Book Is For Software engineers, machine learning practitioners, and technical managers who want to build effective intelligent systems
Data Mining Applications with R is a great resource for researchers and professionals to understand the wide use of R, a free software environment for statistical computing and graphics, in solving different problems in industry. R is widely used in leveraging data mining techniques across many different industries, including government, finance, insurance, medicine, scientific research and more. This book presents 15 different real-world case studies illustrating various techniques in rapidly growing areas. It is an ideal companion for data mining researchers in academia and industry looking for ways to turn this versatile software into a powerful analytic tool. R code, Data and color figures for the book are provided at the RDataMining.com website. Helps data miners to learn to use R in their specific area of work and see how R can apply in different industries Presents various case studies in real-world applications, which will help readers to apply the techniques in their work Provides code examples and sample data for readers to easily learn the techniques by running the code by themselves
Now fully updated, this uniquely accessible book will help you use predictive analytics to solve real business problems and drive real competitive advantage. If you're new to the discipline, it will give you the strong foundation you need to get accurate, actionable results. If you're already a modeler, programmer, or manager, it will teach you crucial skills you don't yet have. This guide illuminates the discipline through realistic vignettes and intuitive data visualizations-not complex math. Thomas W. Miller, leader of Northwestern University's pioneering program in predictive analytics, guides you through defining problems, identifying data, crafting and optimizing models, writing effective R code, interpreting results, and more. Every chapter focuses on one of today's key applications for predictive analytics, delivering skills and knowledge to put models to work-and maximize their value. Reflecting extensive student and instructor feedback, this edition adds five classroom-tested case studies, updates all code for new versions of R, explains code behavior more clearly and completely, and covers modern data science methods even more effectively.
Edited by world-famous pioneers in chemoinformatics, this is a clearly structured and applications-oriented approach to the topic, providing up-to-date and focused information on the wide range of applications in this exciting field. The authors explain methods and software tools, such that the reader will not only learn the basics but also how to use the different software packages available. Experts describe applications in such different fields as structure-spectra correlations, virtual screening, prediction of active sites, library design, the prediction of the properties of chemicals, the development of new cosmetics products, quality control in food, the design of new materials with improved properties, toxicity modeling, assessment of the risk of chemicals, and the control of chemical processes. The book is aimed at advanced students as well as lectures but also at scientists that want to learn how chemoinformatics could assist them in solving their daily scientific tasks. Together with the corresponding textbook Chemoinformatics - Basic Concepts and Methods (ISBN 9783527331093) on the fundamentals of chemoinformatics readers will have a comprehensive overview of the field.