Edward R. Dougherty - Böcker

Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathematical definitions and propositions for the main elements of GSP and by paying attention to the validity of models relative to the data. Ilya Shmulevich and Edward Dougherty cover real-world situations and explain their mathematical modeling in relation to systems biology and systems medicine.Genomic Signal Processing makes a major contribution to computational biology, systems biology, and translational genomics by providing a self-contained explanation of the fundamental mathematical issues facing researchers in four areas: classification, clustering, network modeling, and network intervention.

"This book gives readers an intuitive appreciation for random functions, plus theory and processes necessary for sophisticated applications. It covers probability theory, random processes, canonical representation, optimal filtering, and random models. Second in the SPIE/IEEE Series on Imaging Science & Engineering. It also presents theory along with applications, to help readers intuitively appreciate random functions. Included are special cases in which probabilistic insight is more readily achievable. When provided, proofs are in the main body of the text and clearly delineated; sometimes they are either not provided or outlines of conceptual arguments are given. The intent is to state theorems carefully and to draw clear distinctions between rigorous mathematical arguments and heuristic explanations. When a proof can be given at a mathematical level commensurate with the text and when it enhances conceptual understanding, it is usually provided; in other cases, the effort is to explain subtleties of the definitions and properties concerning random functions, and to state conditions under which a proposition applies. Attention is drawn to the differences between deterministic concepts and their random counterparts, for instance, in the mean-square calculus, orthonormal representation, and linear filtering. Such differences are sometimes glossed over in method books; however, lack of differentiation between random and deterministic analysis can lead to misinterpretation of experimental results and misuse of techniques. The author's motivation for the book comes from his experience in teaching graduate-level image processing and having to end up teaching random processes. Even students who have taken a course on random processes have often done so in the context of linear operators on signals. This approach is inadequate for image processing. Nonlinear operators play a widening role in image processing, and the spatial nature of imaging makes it significantly different from one-dimensional signal processing. Moreover, students who have some background in stochastic processes often lack a unified view in terms of canonical representation and orthogonal projections in inner product spaces."

"This text covers key mathematical principles and algorithms for nonlinear filters used in image processing. Readers will gain an in-depth understanding of the underlying mathematical and filter design methodologies needed to construct and use nonlinear filters in a variety of applications. The 11 chapters explore topics of contemporary interest as well as fundamentals drawn from nonlinear filtering's historical roots in mathematical morphology and digital signal processing. This book examines various filter options and the types of applications for which they are best suited. The presentation is rigorous, yet accessible to engineers with a solid background in mathematics."

This text deals with a fast growing research area. The development of the subject springs from two factors: the great expansion of nonlinear methods applied to problems in imaging and vision, and the degree to which nonlinear approaches are both using and fostering new developments in diverse areas of mathematics. It should be of interest to people working in areas of applied mathematics, as well as researchers in computer vision. It is an edited volume of original research, and has been published as a special issue of "The Journal of Mathematical Imaging and Vision" (Vol 2, Issue 2/3)

Probability theory; random processes; canonical representation; optimal filtering; random models.

This unique reference presents in-depth coverage of the latest methods and applications of digital image processing describing various computer architectures ideal for satisfying specific image processing demands.

Studying large sets of genes and their collective function requires tools that can easily handle huge amounts of information. Recent research indicates that engineering approaches for prediction, signal processing, and control are well suited for studying multivariate interactions. A tutorial guide to the current engineering research in genomics, Introduction to Genomic Signal Processing with Control provides a state-of-the-art account of the use of control theory to obtain intervention strategies for gene regulatory networks.The book builds up the necessary molecular biology background with a basic review of organic chemistry and an introduction of DNA, RNA, and proteins, followed by a description of the processes of transcription and translation and the genetic code that is used to carry out the latter. It discusses control of gene expression, introduces genetic engineering tools such as microarrays and PCR, and covers cell cycle control and tissue renewal in multi-cellular organisms.The authors then delineate how the engineering approaches of classification and clustering are appropriate for carrying out gene-based disease classification. This leads naturally to expression prediction, which in turn leads to genetic regulatory networks. The book concludes with a discussion of control approaches that can be used to alter the behavior of such networks in the hope that this alteration will move the network from a diseased state to a disease-free state.Written by recognized leaders in this emerging field, the book provides the exact amount of molecular biology required to understand the engineering applications. It is a self-contained resource that spans the diverse disciplines of molecular biology and electrical engineering.

This book is the first of its kind to discuss error estimation with a model-based approach. From the basics of classifiers and error estimators to distributional and Bayesian theory, it covers important topics and essential issues pertaining to the scientific validity of pattern classification.Error Estimation for Pattern Recognition focuses on error estimation, which is a broad and poorly understood topic that reaches all research areas using pattern classification. It includes model-based approaches and discussions of newer error estimators such as bolstered and Bayesian estimators. This book was motivated by the application of pattern recognition to high-throughput data with limited replicates, which is a basic problem now appearing in many areas. The first two chapters cover basic issues in classification error estimation, such as definitions, test-set error estimation, and training-set error estimation. The remaining chapters in this book cover results on the performance and representation of training-set error estimators for various pattern classifiers.Additional features of the book include:• The latest results on the accuracy of error estimation• Performance analysis of re-substitution, cross-validation, and bootstrap error estimators using analytical and simulation approaches• Highly interactive computer-based exercises and end-of-chapter problemsThis is the first book exclusively about error estimation for pattern recognition.Ulisses M. Braga Neto is an Associate Professor in the Department of Electrical and Computer Engineering at Texas A&M University, USA. He received his PhD in Electrical and Computer Engineering from The Johns Hopkins University. Dr. Braga Neto received an NSF CAREER Award for his work on error estimation for pattern recognition with applications in genomic signal processing. He is an IEEE Senior Member.Edward R. Dougherty is a Distinguished Professor, Robert F. Kennedy ’26 Chair, and Scientific Director at the Center for Bioinformatics and Genomic Systems Engineering at Texas A&M University, USA. He is a fellow of both the IEEE and SPIE, and he has received the SPIE Presidents Award. Dr. Dougherty has authored several books including Epistemology of the Cell: A Systems Perspective on Biological Knowledge and Random Processes for Image and Signal Processing (Wiley-IEEE Press).