Download or read book Model based Classification with Applications to Hyigh dimensional Data in Bioinformatics written by Muting Wan and published by . This book was released on 2015 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, sparse classification problems have emerged in many fields of study. Finite mixture models have been developed to facilitate Bayesian inference where parameter sparsity is substantial. Shrinkage estimation allows strength borrowing across features in light of the parallel nature of multiple hypothesis tests. Important examples that incorporate shrinkage estimation and finite mixture model for sparse classification include the hierarchical model in Smyth (2004) and the explicit mixture model in Bar et al. (2010) for Bayesian microarray analysis. Classification with finite mixture models is based on the posterior expectation of latent indicator variables. These quantities are typically estimated using the expectation-maximization (EM) algorithm in an empirical Bayes approach or Markov chain Monte Carlo (MCMC) in a fully Bayesian approach. MCMC is limited in applicability where high-dimensional data are involved because its sampling-based nature leads to slow computations and hard-to-monitor convergence. In a fully Bayesian framework, we investigate the feasibility and performance of variational Bayes (VB) approximation and apply the VB approach to fully Bayesian versions of several finite mixture models that have been proposed in bioinformatics. We find that it achieves desirable speed and accuracy in sparse classification with hierarchical mixture models for high-dimensional data. Another example of sparse classification in bioinformatics solvable via model-based approaches is expression quantitative trait loci (eQTL) detection, in which determining whether association between a gene and any given single nucleotide polymorphism (SNP) is significant is regarded as classifying genes as null or non-null with respect to the given SNP. High-dimensionality of the data not only causes difficulties in computations, but also renders the confounding impact of unwanted variation in the data irrefutable. Model-based approaches that account for unwanted variation by incorporating a factor analysis term representing hidden factors and their effects have been adopted in applications such as differential analysis and eQTL detection. HEFT (Gao et al., 2014) is a fast approach for model-based eQTL identification while simultaneously learning hidden effects. We develop a hierarchical mixture model-based empirical Bayes approach for sparse classification while simultaneously accounting for unwanted variation, as well as a family of model-based approaches that are its simplifications with the aim of attractive computational efficiency. We investigate feasibility and performance of these model-based approaches in comparison with HEFT using several real data examples in bioinformatics.

Download or read book High Dimensional Data Analysis in Cancer Research written by Xiaochun Li and published by Springer Science & Business Media. This book was released on 2008-12-19 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt: Multivariate analysis is a mainstay of statistical tools in the analysis of biomedical data. It concerns with associating data matrices of n rows by p columns, with rows representing samples (or patients) and columns attributes of samples, to some response variables, e.g., patients outcome. Classically, the sample size n is much larger than p, the number of variables. The properties of statistical models have been mostly discussed under the assumption of fixed p and infinite n. The advance of biological sciences and technologies has revolutionized the process of investigations of cancer. The biomedical data collection has become more automatic and more extensive. We are in the era of p as a large fraction of n, and even much larger than n. Take proteomics as an example. Although proteomic techniques have been researched and developed for many decades to identify proteins or peptides uniquely associated with a given disease state, until recently this has been mostly a laborious process, carried out one protein at a time. The advent of high throughput proteome-wide technologies such as liquid chromatography-tandem mass spectroscopy make it possible to generate proteomic signatures that facilitate rapid development of new strategies for proteomics-based detection of disease. This poses new challenges and calls for scalable solutions to the analysis of such high dimensional data. In this volume, we will present the systematic and analytical approaches and strategies from both biostatistics and bioinformatics to the analysis of correlated and high-dimensional data.

Download or read book Clustering Classification and Function Estimation for High Dimensional Data Arising from Bioinformatics and Related Domains written by Samiran Ghosh and published by . This book was released on 2006 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Statistical Analysis for High Dimensional Data written by Arnoldo Frigessi and published by Springer. This book was released on 2016-02-16 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book features research contributions from The Abel Symposium on Statistical Analysis for High Dimensional Data, held in Nyvågar, Lofoten, Norway, in May 2014. The focus of the symposium was on statistical and machine learning methodologies specifically developed for inference in “big data” situations, with particular reference to genomic applications. The contributors, who are among the most prominent researchers on the theory of statistics for high dimensional inference, present new theories and methods, as well as challenging applications and computational solutions. Specific themes include, among others, variable selection and screening, penalised regression, sparsity, thresholding, low dimensional structures, computational challenges, non-convex situations, learning graphical models, sparse covariance and precision matrices, semi- and non-parametric formulations, multiple testing, classification, factor models, clustering, and preselection. Highlighting cutting-edge research and casting light on future research directions, the contributions will benefit graduate students and researchers in computational biology, statistics and the machine learning community.

Download or read book Model Based Clustering and Classification for Data Science written by Charles Bouveyron and published by Cambridge University Press. This book was released on 2019-07-25 with total page 447 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cluster analysis finds groups in data automatically. Most methods have been heuristic and leave open such central questions as: how many clusters are there? Which method should I use? How should I handle outliers? Classification assigns new observations to groups given previously classified observations, and also has open questions about parameter tuning, robustness and uncertainty assessment. This book frames cluster analysis and classification in terms of statistical models, thus yielding principled estimation, testing and prediction methods, and sound answers to the central questions. It builds the basic ideas in an accessible but rigorous way, with extensive data examples and R code; describes modern approaches to high-dimensional data and networks; and explains such recent advances as Bayesian regularization, non-Gaussian model-based clustering, cluster merging, variable selection, semi-supervised and robust classification, clustering of functional data, text and images, and co-clustering. Written for advanced undergraduates in data science, as well as researchers and practitioners, it assumes basic knowledge of multivariate calculus, linear algebra, probability and statistics.

Download or read book Feature Selection for High Dimensional Data written by Verónica Bolón-Canedo and published by Springer. This book was released on 2015-10-05 with total page 163 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers a coherent and comprehensive approach to feature subset selection in the scope of classification problems, explaining the foundations, real application problems and the challenges of feature selection for high-dimensional data. The authors first focus on the analysis and synthesis of feature selection algorithms, presenting a comprehensive review of basic concepts and experimental results of the most well-known algorithms. They then address different real scenarios with high-dimensional data, showing the use of feature selection algorithms in different contexts with different requirements and information: microarray data, intrusion detection, tear film lipid layer classification and cost-based features. The book then delves into the scenario of big dimension, paying attention to important problems under high-dimensional spaces, such as scalability, distributed processing and real-time processing, scenarios that open up new and interesting challenges for researchers. The book is useful for practitioners, researchers and graduate students in the areas of machine learning and data mining.

Download or read book Handbook of Mixture Analysis written by Sylvia Fruhwirth-Schnatter and published by CRC Press. This book was released on 2019-01-04 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mixture models have been around for over 150 years, and they are found in many branches of statistical modelling, as a versatile and multifaceted tool. They can be applied to a wide range of data: univariate or multivariate, continuous or categorical, cross-sectional, time series, networks, and much more. Mixture analysis is a very active research topic in statistics and machine learning, with new developments in methodology and applications taking place all the time. The Handbook of Mixture Analysis is a very timely publication, presenting a broad overview of the methods and applications of this important field of research. It covers a wide array of topics, including the EM algorithm, Bayesian mixture models, model-based clustering, high-dimensional data, hidden Markov models, and applications in finance, genomics, and astronomy. Features: Provides a comprehensive overview of the methods and applications of mixture modelling and analysis Divided into three parts: Foundations and Methods; Mixture Modelling and Extensions; and Selected Applications Contains many worked examples using real data, together with computational implementation, to illustrate the methods described Includes contributions from the leading researchers in the field The Handbook of Mixture Analysis is targeted at graduate students and young researchers new to the field. It will also be an important reference for anyone working in this field, whether they are developing new methodology, or applying the models to real scientific problems.

Download or read book Computational Intelligence and Healthcare Informatics written by Om Prakash Jena and published by John Wiley & Sons. This book was released on 2021-10-19 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: COMPUTATIONAL INTELLIGENCE and HEALTHCARE INFORMATICS The book provides the state-of-the-art innovation, research, design, and implements methodological and algorithmic solutions to data processing problems, designing and analysing evolving trends in health informatics, intelligent disease prediction, and computer-aided diagnosis. Computational intelligence (CI) refers to the ability of computers to accomplish tasks that are normally completed by intelligent beings such as humans and animals. With the rapid advance of technology, artificial intelligence (AI) techniques are being effectively used in the fields of health to improve the efficiency of treatments, avoid the risk of false diagnoses, make therapeutic decisions, and predict the outcome in many clinical scenarios. Modern health treatments are faced with the challenge of acquiring, analyzing and applying the large amount of knowledge necessary to solve complex problems. Computational intelligence in healthcare mainly uses computer techniques to perform clinical diagnoses and suggest treatments. In the present scenario of computing, CI tools present adaptive mechanisms that permit the understanding of data in difficult and changing environments. The desired results of CI technologies profit medical fields by assembling patients with the same types of diseases or fitness problems so that healthcare facilities can provide effectual treatments. This book starts with the fundamentals of computer intelligence and the techniques and procedures associated with it. Contained in this book are state-of-the-art methods of computational intelligence and other allied techniques used in the healthcare system, as well as advances in different CI methods that will confront the problem of effective data analysis and storage faced by healthcare institutions. The objective of this book is to provide researchers with a platform encompassing state-of-the-art innovations; research and design; implementation of methodological and algorithmic solutions to data processing problems; and the design and analysis of evolving trends in health informatics, intelligent disease prediction and computer-aided diagnosis. Audience The book is of interest to artificial intelligence and biomedical scientists, researchers, engineers and students in various settings such as pharmaceutical & biotechnology companies, virtual assistants developing companies, medical imaging & diagnostics centers, wearable device designers, healthcare assistance robot manufacturers, precision medicine testers, hospital management, and researchers working in healthcare system.

Download or read book Mixture Model Based Classification written by Paul D. McNicholas and published by CRC Press. This book was released on 2016-10-04 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This is a great overview of the field of model-based clustering and classification by one of its leading developers. McNicholas provides a resource that I am certain will be used by researchers in statistics and related disciplines for quite some time. The discussion of mixtures with heavy tails and asymmetric distributions will place this text as the authoritative, modern reference in the mixture modeling literature." (Douglas Steinley, University of Missouri) Mixture Model-Based Classification is the first monograph devoted to mixture model-based approaches to clustering and classification. This is both a book for established researchers and newcomers to the field. A history of mixture models as a tool for classification is provided and Gaussian mixtures are considered extensively, including mixtures of factor analyzers and other approaches for high-dimensional data. Non-Gaussian mixtures are considered, from mixtures with components that parameterize skewness and/or concentration, right up to mixtures of multiple scaled distributions. Several other important topics are considered, including mixture approaches for clustering and classification of longitudinal data as well as discussion about how to define a cluster Paul D. McNicholas is the Canada Research Chair in Computational Statistics at McMaster University, where he is a Professor in the Department of Mathematics and Statistics. His research focuses on the use of mixture model-based approaches for classification, with particular attention to clustering applications, and he has published extensively within the field. He is an associate editor for several journals and has served as a guest editor for a number of special issues on mixture models.

Download or read book Interactive Knowledge Discovery and Data Mining in Biomedical Informatics written by Andreas Holzinger and published by Springer. This book was released on 2014-06-17 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the grand challenges in our digital world are the large, complex and often weakly structured data sets, and massive amounts of unstructured information. This “big data” challenge is most evident in biomedical informatics: the trend towards precision medicine has resulted in an explosion in the amount of generated biomedical data sets. Despite the fact that human experts are very good at pattern recognition in dimensions of = 3; most of the data is high-dimensional, which makes manual analysis often impossible and neither the medical doctor nor the biomedical researcher can memorize all these facts. A synergistic combination of methodologies and approaches of two fields offer ideal conditions towards unraveling these problems: Human–Computer Interaction (HCI) and Knowledge Discovery/Data Mining (KDD), with the goal of supporting human capabilities with machine learning./ppThis state-of-the-art survey is an output of the HCI-KDD expert network and features 19 carefully selected and reviewed papers related to seven hot and promising research areas: Area 1: Data Integration, Data Pre-processing and Data Mapping; Area 2: Data Mining Algorithms; Area 3: Graph-based Data Mining; Area 4: Entropy-Based Data Mining; Area 5: Topological Data Mining; Area 6 Data Visualization and Area 7: Privacy, Data Protection, Safety and Security.

Download or read book Data Mining for Bioinformatics written by Sumeet Dua and published by CRC Press. This book was released on 2012-11-06 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering theory, algorithms, and methodologies, as well as data mining technologies, Data Mining for Bioinformatics provides a comprehensive discussion of data-intensive computations used in data mining with applications in bioinformatics. It supplies a broad, yet in-depth, overview of the application domains of data mining for bioinformatics to help readers from both biology and computer science backgrounds gain an enhanced understanding of this cross-disciplinary field. The book offers authoritative coverage of data mining techniques, technologies, and frameworks used for storing, analyzing, and extracting knowledge from large databases in the bioinformatics domains, including genomics and proteomics. It begins by describing the evolution of bioinformatics and highlighting the challenges that can be addressed using data mining techniques. Introducing the various data mining techniques that can be employed in biological databases, the text is organized into four sections: Supplies a complete overview of the evolution of the field and its intersection with computational learning Describes the role of data mining in analyzing large biological databases—explaining the breath of the various feature selection and feature extraction techniques that data mining has to offer Focuses on concepts of unsupervised learning using clustering techniques and its application to large biological data Covers supervised learning using classification techniques most commonly used in bioinformatics—addressing the need for validation and benchmarking of inferences derived using either clustering or classification The book describes the various biological databases prominently referred to in bioinformatics and includes a detailed list of the applications of advanced clustering algorithms used in bioinformatics. Highlighting the challenges encountered during the application of classification on biological databases, it considers systems of both single and ensemble classifiers and shares effort-saving tips for model selection and performance estimation strategies.

Download or read book Handbook of Statistical Bioinformatics written by Henry Horng-Shing Lu and published by Springer Science & Business Media. This book was released on 2011-05-17 with total page 621 pages. Available in PDF, EPUB and Kindle. Book excerpt: Numerous fascinating breakthroughs in biotechnology have generated large volumes and diverse types of high throughput data that demand the development of efficient and appropriate tools in computational statistics integrated with biological knowledge and computational algorithms. This volume collects contributed chapters from leading researchers to survey the many active research topics and promote the visibility of this research area. This volume is intended to provide an introductory and reference book for students and researchers who are interested in the recent developments of computational statistics in computational biology.

Download or read book Case Studies in Biometry written by Nicholas Lange and published by Wiley-Interscience. This book was released on 1994-09-02 with total page 532 pages. Available in PDF, EPUB and Kindle. Book excerpt: Features 21 case studies that illustrate commonly used approaches to answer scientific questions in such areas as biology, toxicology, clinical medicine, environmental hazards, agriculture, forestry and wildlife. Examples of statistical methods used in these case studies include linear regression, survival analysis, principle components, design of experiments, resampling and bootstrap. A disk containing the collective data sets will accompany the book.

Download or read book High Dimensional Classification and Variable Selection written by and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in biotechnology and other disciplines have led to the generation of many high-dimensional data, which raises challenges to develop new statistical methodologies to handle them. This dissertation focuses on two aspects of high-dimensional data inference: (1) classification based on high-dimensional covariates; (2) variable selection of high-dimensional linear regression model. Both aspects have great importance in high-dimensional data inference and are related with each other. Variable selection plays a critical rule to reduce the dimension of data. It usually boosts the signal to noise ratio and results in a simpler model that becomes much easier to interpret. Classification has many important applications in practice, such as face detection, hand-writing recognition, etc. For the high-dimensional classification problem, I have developed a new Sparse Quadratic Discriminant Analysis (SQDA) approach, which extends the application of traditional low-dimensional Quadratic Discriminant Analysis. The theoretical properties of the new SQDA approach is thoroughly addressed. Simulation studies have been conducted to compare SQDA with many other well-known classifiers in the literature. This new approach has also been applied to analyze one dataset from a colon cancer study. For the variable selection problem, a Regularized LASSO approach has been proposed, which alleviates the strong conditions for the classical LASSO method to perform well. It has been found that the new Regularized LASSO approach includes many other well-known variable selection methods as its special cases, which makes it a very general approach. The asymptotic properties of Regularized LASSO is thoroughly studied. It has been shown that the Regularized LASSO asymptotically identifies the correct model under mild assumptions. The new method has also been investigated through simulation studies, where it outperforms many other variable selection methods.

Download or read book Data Mining written by Sushmita Mitra and published by John Wiley & Sons. This book was released on 2005-01-21 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: First title to ever present soft computing approaches and their application in data mining, along with the traditional hard-computing approaches Addresses the principles of multimedia data compression techniques (for image, video, text) and their role in data mining Discusses principles and classical algorithms on string matching and their role in data mining

Download or read book Advanced AI Techniques and Applications in Bioinformatics written by Loveleen Gaur and published by CRC Press. This book was released on 2021-10-17 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advanced AI techniques are essential for resolving various problematic aspects emerging in the field of bioinformatics. This book covers the recent approaches in artificial intelligence and machine learning methods and their applications in Genome and Gene editing, cancer drug discovery classification, and the protein folding algorithms among others. Deep learning, which is widely used in image processing, is also applicable in bioinformatics as one of the most popular artificial intelligence approaches. The wide range of applications discussed in this book are an indispensable resource for computer scientists, engineers, biologists, mathematicians, physicians, and medical informaticists. Features: Focusses on the cross-disciplinary relation between computer science and biology and the role of machine learning methods in resolving complex problems in bioinformatics Provides a comprehensive and balanced blend of topics and applications using various advanced algorithms Presents cutting-edge research methodologies in the area of AI methods when applied to bioinformatics and innovative solutions Discusses the AI/ML techniques, their use, and their potential for use in common and future bioinformatics applications Includes recent achievements in AI and bioinformatics contributed by a global team of researchers

Download or read book Clinical Technologies Concepts Methodologies Tools and Applications written by Management Association, Information Resources and published by IGI Global. This book was released on 2011-05-31 with total page 2366 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This multi-volume book delves into the many applications of information technology ranging from digitizing patient records to high-performance computing, to medical imaging and diagnostic technologies, and much more"--