Mcmc From Scratch

This textbook explains the fundamentals of Markov Chain Monte Carlo (MCMC) without assuming advanced knowledge of mathematics and programming. MCMC is a powerful technique that can be used to integrate complicated functions or to handle complicated probability distributions. MCMC is frequently used in diverse fields where statistical methods are important – e.g. Bayesian statistics, quantum physics, machine learning, computer science, computational biology, and mathematical economics. This book aims to equip readers with a sound understanding of MCMC and enable them to write simulation codes by themselves. The content consists of six chapters. Following Chap. 2, which introduces readers to the Monte Carlo algorithm and highlights the advantages of MCMC, Chap. 3 presents the general aspects of MCMC. Chap. 4 illustrates the essence of MCMC through the simple example of the Metropolis algorithm. In turn, Chap. 5 explains the HMC algorithm, Gibbs sampling algorithm and Metropolis-Hastings algorithm, discussing their pros, cons and pitfalls. Lastly, Chap. 6 presents several applications of MCMC. Including a wealth of examples and exercises with solutions, as well as sample codes and further math topics in the Appendix, this book offers a valuable asset for students and beginners in various fields.

Bridging the gap between research and application, Markov Chain Monte Carlo: Stochastic Simulation for Bayesian Inference provides a concise, and integrated account of Markov chain Monte Carlo (MCMC) for performing Bayesian inference. This volume, which was developed from a short course taught by the author at a meeting of Brazilian statisticians and probabilists, retains the didactic character of the original course text. The self-contained text units make MCMC accessible to scientists in other disciplines as well as statisticians. It describes each component of the theory in detail and outlines related software, which is of particular benefit to applied scientists.

Praise for Bayes Rules!: An Introduction to Applied Bayesian Modeling “A thoughtful and entertaining book, and a great way to get started with Bayesian analysis.” Andrew Gelman, Columbia University “The examples are modern, and even many frequentist intro books ignore important topics (like the great p-value debate) that the authors address. The focus on simulation for understanding is excellent.” Amy Herring, Duke University “I sincerely believe that a generation of students will cite this book as inspiration for their use of – and love for – Bayesian statistics. The narrative holds the reader’s attention and flows naturally – almost conversationally. Put simply, this is perhaps the most engaging introductory statistics textbook I have ever read. [It] is a natural choice for an introductory undergraduate course in applied Bayesian statistics." Yue Jiang, Duke University “This is by far the best book I’ve seen on how to (and how to teach students to) do Bayesian modeling and understand the underlying mathematics and computation. The authors build intuition and scaffold ideas expertly, using interesting real case studies, insightful graphics, and clear explanations. The scope of this book is vast – from basic building blocks to hierarchical modeling, but the authors’ thoughtful organization allows the reader to navigate this journey smoothly. And impressively, by the end of the book, one can run sophisticated Bayesian models and actually understand the whys, whats, and hows.” Paul Roback, St. Olaf College “The authors provide a compelling, integrated, accessible, and non-religious introduction to statistical modeling using a Bayesian approach. They outline a principled approach that features computational implementations and model assessment with ethical implications interwoven throughout. Students and instructors will find the conceptual and computational exercises to be fresh and engaging.” Nicholas Horton, Amherst College An engaging, sophisticated, and fun introduction to the field of Bayesian statistics, Bayes Rules!: An Introduction to Applied Bayesian Modeling brings the power of modern Bayesian thinking, modeling, and computing to a broad audience. In particular, the book is an ideal resource for advanced undergraduate statistics students and practitioners with comparable experience. Bayes Rules! empowers readers to weave Bayesian approaches into their everyday practice. Discussions and applications are data driven. A natural progression from fundamental to multivariable, hierarchical models emphasizes a practical and generalizable model building process. The evaluation of these Bayesian models reflects the fact that a data analysis does not exist in a vacuum. Features • Utilizes data-driven examples and exercises. • Emphasizes the iterative model building and evaluation process. • Surveys an interconnected range of multivariable regression and classification models. • Presents fundamental Markov chain Monte Carlo simulation. • Integrates R code, including RStan modeling tools and the bayesrules package. • Encourages readers to tap into their intuition and learn by doing. • Provides a friendly and inclusive introduction to technical Bayesian concepts. • Supports Bayesian applications with foundational Bayesian theory.

As the first book of a three-part series, this book is offered as a tribute to pioneers in vision, such as Béla Julesz, David Marr, King-Sun Fu, Ulf Grenander, and David Mumford. The authors hope to provide foundation and, perhaps more importantly, further inspiration for continued research in vision. This book covers David Marr's paradigm and various underlying statistical models for vision. The mathematical framework herein integrates three regimes of models (low-, mid-, and high-entropy regimes) and provides foundation for research in visual coding, recognition, and cognition. Concepts are first explained for understanding and then supported by findings in psychology and neuroscience, after which they are established by statistical models and associated learning and inference algorithms. A reader will gain a unified, cross-disciplinary view of research in vision and will accrue knowledge spanning from psychology to neuroscience to statistics.

In a family study of breast cancer, epidemiologists in Southern California increase the power for detecting a gene-environment interaction. In Gambia, a study helps a vaccination program reduce the incidence of Hepatitis B carriage. Archaeologists in Austria place a Bronze Age site in its true temporal location on the calendar scale. And in France,

Researchers across the natural and social sciences find themselves navigating tremendous amounts of new data. Making sense of this flood of information requires more than the rote application of formulaic statistical methods. The premise of Statistical Thinking from Scratch is that students who want to become confident data analysts are better served by a deep introduction to a single statistical method than by a cursory overview of many methods. In particular, this book focuses on simple linear regression-a method with close connections to the most important tools in applied statistics-using it as a detailed case study for teaching resampling-based, likelihood-based, and Bayesian approaches to statistical inference. Considering simple linear regression in depth imparts an idea of how statistical procedures are designed, a flavour for the philosophical positions one assumes when applying statistics, and tools to probe the strengths of one's statistical approach. Key to the book's novel approach is its mathematical level, which is gentler than most texts for statisticians but more rigorous than most introductory texts for non-statisticians. Statistical Thinking from Scratch is suitable for senior undergraduate and beginning graduate students, professional researchers, and practitioners seeking to improve their understanding of statistical methods across the natural and social sciences, medicine, psychology, public health, business, and other fields.

This new graduate textbook adopts a pedagogical approach to contemporary cosmology that enables readers to build an intuitive understanding of theory and data, and of how they interact, which is where the greatest advances in the field are currently being made. Using analogies, intuitive explanations of complex topics, worked examples and computational problems, the book begins with the physics of the early universe, and goes on to cover key concepts such as inflation, dark matter and dark energy, large‐scale structure, and cosmic microwave background. Computational and data analysis techniques, and statistics, are integrated throughout the text, particularly in the chapters on late-universe cosmology, while another chapter is entirely devoted to the basics of statistical methods. A solutions manual for end-of-chapter problems is available to instructors, and suggested syllabi, based on different course lengths and emphasis, can be found in the Preface. Online computer code and datasets enhance the student learning experience.

Harness the power of randomness (and Python code) to solve real-world problems in fun, hands-on experiments—from simulating evolution to encrypting messages to making machine-learning algorithms! The Art of Randomness is a hands-on guide to mastering the many ways you can use randomized algorithms to solve real programming and scientific problems. You’ll learn how to use randomness to run simulations, hide information, design experiments, and even create art and music. All you need is some Python, basic high school math, and a roll of the dice. Author Ronald T. Kneusel focuses on helping you build your intuition so that you’ll know when and how to use random processes to get things done. You’ll develop a randomness engine (a Python class that supplies random values from your chosen source), then explore how to leverage randomness to: Simulate Darwinian evolution and optimize with swarm-based search algorithms Design scientific experiments to produce more meaningful results by making them truly random Implement machine learning algorithms like neural networks and random forests Use Markov Chain Monte Carlo methods to sample from complex distributions Hide information in audio files and images, generate art, and create music Reconstruct original signals and images from only randomly sampled data Scientific anecdotes and code examples throughout illustrate how randomness plays into areas like optimization, machine learning, and audio signals. End-of-chapter exercises encourage further exploration. Whether you’re a programmer, scientist, engineer, mathematician, or artist, you’ll find The Art of Randomness to be your ticket to discovering the hidden power of applied randomness and the ways it can transform your approach to solving problems, from the technical to the artistic.