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Microarray Image Analysis

Author: Karl Fraser
Publisher: CRC Press
ISBN: 9781420091540
Size: 55.32 MB
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To harness the high-throughput potential of DNA microarray technology, it is crucial that the analysis stages of the process are decoupled from the requirements of operator assistance. Microarray Image Analysis: An Algorithmic Approach presents an automatic system for microarray image processing to make this decoupling a reality. The proposed system integrates and extends traditional analytical-based methods and custom-designed novel algorithms. The book first explores a new technique that takes advantage of a multiview approach to image analysis and addresses the challenges of applying powerful traditional techniques, such as clustering, to full-scale microarray experiments. It then presents an effective feature identification approach, an innovative technique that renders highly detailed surface models, a new approach to subgrid detection, a novel technique for the background removal process, and a useful technique for removing "noise." The authors also develop an expectation–maximization (EM) algorithm for modeling gene regulatory networks from gene expression time series data. The final chapter describes the overall benefits of these techniques in the biological and computer sciences and reviews future research topics. This book systematically brings together the fields of image processing, data analysis, and molecular biology to advance the state of the art in this important area. Although the text focuses on improving the processes involved in the analysis of microarray image data, the methods discussed can be applied to a broad range of medical and computer vision analysis areas.

Music Data Analysis

Author: Claus Weihs
Publisher: CRC Press
ISBN: 1315353830
Size: 74.48 MB
Format: PDF
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This book provides a comprehensive overview of music data analysis, from introductory material to advanced concepts. It covers various applications including transcription and segmentation as well as chord and harmony, instrument and tempo recognition. It also discusses the implementation aspects of music data analysis such as architecture, user interface and hardware. It is ideal for use in university classes with an interest in music data analysis. It also could be used in computer science and statistics as well as musicology.

Exploratory Data Analysis With Matlab Third Edition

Author: Wendy L. Martinez
Publisher: CRC Press
ISBN: 1315349841
Size: 61.73 MB
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Praise for the Second Edition: "The authors present an intuitive and easy-to-read book. ... accompanied by many examples, proposed exercises, good references, and comprehensive appendices that initiate the reader unfamiliar with MATLAB." —Adolfo Alvarez Pinto, International Statistical Review "Practitioners of EDA who use MATLAB will want a copy of this book. ... The authors have done a great service by bringing together so many EDA routines, but their main accomplishment in this dynamic text is providing the understanding and tools to do EDA. —David A Huckaby, MAA Reviews Exploratory Data Analysis (EDA) is an important part of the data analysis process. The methods presented in this text are ones that should be in the toolkit of every data scientist. As computational sophistication has increased and data sets have grown in size and complexity, EDA has become an even more important process for visualizing and summarizing data before making assumptions to generate hypotheses and models. Exploratory Data Analysis with MATLAB, Third Edition presents EDA methods from a computational perspective and uses numerous examples and applications to show how the methods are used in practice. The authors use MATLAB code, pseudo-code, and algorithm descriptions to illustrate the concepts. The MATLAB code for examples, data sets, and the EDA Toolbox are available for download on the book’s website. New to the Third Edition Random projections and estimating local intrinsic dimensionality Deep learning autoencoders and stochastic neighbor embedding Minimum spanning tree and additional cluster validity indices Kernel density estimation Plots for visualizing data distributions, such as beanplots and violin plots A chapter on visualizing categorical data

Data Science Foundations

Author: Fionn Murtagh
Publisher: CRC Press
ISBN: 1315350491
Size: 44.92 MB
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"Data Science Foundations?is most welcome and, indeed, a piece of literature that the field is very much in need of...quite different from most data analytics texts which largely ignore foundational concepts and simply present a cookbook of methods...a very useful text and I would certainly use it in my teaching." - Mark Girolami, Warwick University Data Science encompasses the traditional disciplines of mathematics, statistics, data analysis, machine learning, and pattern recognition. This book is designed to provide a new framework for Data Science, based on a solid foundation in mathematics and computational science. It is written in an accessible style, for readers who are engaged with the subject but not necessarily experts in all aspects. It includes a wide range of case studies from diverse fields, and seeks to inspire and motivate the reader with respect to data, associated information, and derived knowledge.

Exploratory Multivariate Analysis By Example Using R Second Edition

Author: Francois Husson
Publisher: CRC Press
ISBN: 1315301865
Size: 45.39 MB
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Full of real-world case studies and practical advice, Exploratory Multivariate Analysis by Example Using R, Second Edition focuses on four fundamental methods of multivariate exploratory data analysis that are most suitable for applications. It covers principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, and hierarchical cluster analysis. The authors take a geometric point of view that provides a unified vision for exploring multivariate data tables. Within this framework, they present the principles, indicators, and ways of representing and visualising objects that are common to the exploratory methods. The authors show how to use categorical variables in a PCA context in which variables are quantitative, how to handle more than two categorical variables in a CA context in which there are originally two variables, and how to add quantitative variables in an MCA context in which variables are categorical. They also illustrate the methods using examples from various fields, with related R code accessible in the FactoMineR package developed by the authors. The book has been written using minimal mathematics so as to appeal to applied statisticians, as well as researchers from various disciplines, including medical research and the social sciences. Readers can use the theory, examples, and software presented in this book in order to be fully equipped to tackle real-life multivariate data.

Foundations Of Statistical Algorithms

Author: Claus Weihs
Publisher: CRC Press
ISBN: 1439878870
Size: 34.71 MB
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A new and refreshingly different approach to presenting the foundations of statistical algorithms, Foundations of Statistical Algorithms: With References to R Packages reviews the historical development of basic algorithms to illuminate the evolution of today’s more powerful statistical algorithms. It emphasizes recurring themes in all statistical algorithms, including computation, assessment and verification, iteration, intuition, randomness, repetition and parallelization, and scalability. Unique in scope, the book reviews the upcoming challenge of scaling many of the established techniques to very large data sets and delves into systematic verification by demonstrating how to derive general classes of worst case inputs and emphasizing the importance of testing over a large number of different inputs. Broadly accessible, the book offers examples, exercises, and selected solutions in each chapter as well as access to a supplementary website. After working through the material covered in the book, readers should not only understand current algorithms but also gain a deeper understanding of how algorithms are constructed, how to evaluate new algorithms, which recurring principles are used to tackle some of the tough problems statistical programmers face, and how to take an idea for a new method and turn it into something practically useful.

Clustering

Author: Boris Mirkin
Publisher: CRC Press
ISBN: 1439838429
Size: 25.42 MB
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Often considered more of an art than a science, books on clustering have been dominated by learning through example with techniques chosen almost through trial and error. Even the two most popular, and most related, clustering methods—K-Means for partitioning and Ward's method for hierarchical clustering—have lacked the theoretical underpinning required to establish a firm relationship between the two methods and relevant interpretation aids. Other approaches, such as spectral clustering or consensus clustering, are considered absolutely unrelated to each other or to the two above mentioned methods. Clustering: A Data Recovery Approach, Second Edition presents a unified modeling approach for the most popular clustering methods: the K-Means and hierarchical techniques, especially for divisive clustering. It significantly expands coverage of the mathematics of data recovery, and includes a new chapter covering more recent popular network clustering approaches—spectral, modularity and uniform, additive, and consensus—treated within the same data recovery approach. Another added chapter covers cluster validation and interpretation, including recent developments for ontology-driven interpretation of clusters. Altogether, the insertions added a hundred pages to the book, even in spite of the fact that fragments unrelated to the main topics were removed. Illustrated using a set of small real-world datasets and more than a hundred examples, the book is oriented towards students, practitioners, and theoreticians of cluster analysis. Covering topics that are beyond the scope of most texts, the author’s explanations of data recovery methods, theory-based advice, pre- and post-processing issues and his clear, practical instructions for real-world data mining make this book ideally suited for teaching, self-study, and professional reference.

Statistical Analysis Of Gene Expression Microarray Data

Author: Terry Speed
Publisher: CRC Press
ISBN: 9780203011232
Size: 51.50 MB
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Although less than a decade old, the field of microarray data analysis is now thriving and growing at a remarkable pace. Biologists, geneticists, and computer scientists as well as statisticians all need an accessible, systematic treatment of the techniques used for analyzing the vast amounts of data generated by large-scale gene expression studies. And there is arguably no group better qualified to do so than the authors of this book. Statistical Analysis of Gene Expression Microarray Data promises to become the definitive basic reference in the field. Under the editorship of Terry Speed, some of the world's most pre-eminent authorities have joined forces to present the tools, features, and problems associated with the analysis of genetic microarray data. These include:: Model-based analysis of oligonucleotide arrays, including expression index computation, outlier detection, and standard error applications Design and analysis of comparative experiments involving microarrays, with focus on \ two-color cDNA or long oligonucleotide arrays on glass slides Classification issues, including the statistical foundations of classification and an overview of different classifiers Clustering, partitioning, and hierarchical methods of analysis, including techniques related to principal components and singular value decomposition Although the technologies used in large-scale, high throughput assays will continue to evolve, statistical analysis will remain a cornerstone of their success and future development. Statistical Analysis of Gene Expression Microarray Data will help you meet the challenges of large, complex datasets and contribute to new methodological and computational advances.

Structural Bioinformatics

Author: Forbes J. Burkowski
Publisher: CRC Press
ISBN: 1420011790
Size: 23.57 MB
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The Beauty of Protein Structures and the Mathematics behind Structural Bioinformatics Providing the framework for a one-semester undergraduate course, Structural Bioinformatics: An Algorithmic Approach shows how to apply key algorithms to solve problems related to macromolecular structure. Helps Students Go Further in Their Study of Structural Biology Following some introductory material in the first few chapters, the text solves the longest common subsequence problem using dynamic programming and explains the science models for the Nussinov and MFOLD algorithms. It then reviews sequence alignment, along with the basic mathematical calculations needed for measuring the geometric properties of macromolecules. After looking at how coordinate transformations facilitate the translation and rotation of molecules in a 3D space, the author introduces structural comparison techniques, superposition algorithms, and algorithms that compare relationships within a protein. The final chapter explores how regression and classification are becoming more useful in protein analysis and drug design. At the Crossroads of Biology, Mathematics, and Computer Science Connecting biology, mathematics, and computer science, this practical text presents various bioinformatics topics and problems within a scientific methodology that emphasizes nature (the source of empirical observations), science (the mathematical modeling of the natural process), and computation (the science of calculating predictions and mathematical objects based on mathematical models).

Statistics And Data Analysis For Microarrays Using R And Bioconductor Second Edition

Author: Sorin Drăghici
Publisher: CRC Press
ISBN: 1439809763
Size: 57.90 MB
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Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on, example-based approach that teaches students the basics of R and microarray technology as well as how to choose and apply the proper data analysis tool to specific problems. New to the Second Edition Completely updated and double the size of its predecessor, this timely second edition replaces the commercial software with the open source R and Bioconductor environments. Fourteen new chapters cover such topics as the basic mechanisms of the cell, reliability and reproducibility issues in DNA microarrays, basic statistics and linear models in R, experiment design, multiple comparisons, quality control, data pre-processing and normalization, Gene Ontology analysis, pathway analysis, and machine learning techniques. Methods are illustrated with toy examples and real data and the R code for all routines is available on an accompanying CD-ROM. With all the necessary prerequisites included, this best-selling book guides students from very basic notions to advanced analysis techniques in R and Bioconductor. The first half of the text presents an overview of microarrays and the statistical elements that form the building blocks of any data analysis. The second half introduces the techniques most commonly used in the analysis of microarray data.