An unprecedented wealth of data is being generated by genome sequencing projects and other experimental efforts to determine the structure and function of biological molecules. The demands and opportunities for interpreting these data are expanding more than ever. Biotechnology, pharmacology, and medicine will be particularly affected by the new results and the increased understanding of life at the molecular level. Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments. It has emerged as a strategic frontier between biology and computer science. Machine learning approaches (e.g., neural networks, hidden Markov models, and belief networks) are ideally suited for areas where there is a lot of data but little theory—and this is exactly the situation in molecular biology. As with its predecessor, statistical model fitting, the goal in machine learning is to extract useful information from a body of data by building good probabilistic models. The particular twist behind machine learning, however, is to automate the process as much as possible. In this book, Pierre Baldi and Soren Brunak present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological data. The book is aimed at two types of researchers and students. First are the biologists and biochemists who need to understand new data-driven algorithms, such as neural networks and hidden Markov models, in the context of biological sequences and their molecular structure and function. Second are those with a primary background in physics, mathematics, statistics, or computer science who need to know more about specific applications in molecular biology.

This book covers a wide range of subjects in applying machine learning approaches for bioinformatics projects. The book succeeds on two key unique features. First, it introduces the most widely used machine learning approaches in bioinformatics and discusses, with evaluations from real case studies, how they are used in individual bioinformatics projects. Second, it introduces state-of-the-art bioinformatics research methods. The theoretical parts and the practical parts are well integrated for readers to follow the existing procedures in individual research. Unlike most of the bioinformatics books on the market, the content coverage is not limited to just one subject. A broad spectrum of relevant topics in bioinformatics including systematic data mining and computational systems biology researches are brought together in this book, thereby offering an efficient and convenient platform for teaching purposes. An essential reference for both final year undergraduates and graduate students in universities, as well as a comprehensive handbook for new researchers, this book will also serve as a practical guide for software development in relevant bioinformatics projects.

An introduction to machine learning methods and their applications to problems in bioinformatics Machine learning techniques are increasingly being used to address problems in computational biology and bioinformatics. Novel computational techniques to analyze high throughput data in the form of sequences, gene and protein expressions, pathways, and images are becoming vital for understanding diseases and future drug discovery. Machine learning techniques such as Markov models, support vector machines, neural networks, and graphical models have been successful in analyzing life science data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. From an internationally recognized panel of prominent researchers in the field, Machine Learning in Bioinformatics compiles recent approaches in machine learning methods and their applications in addressing contemporary problems in bioinformatics. Coverage includes: feature selection for genomic and proteomic data mining; comparing variable selection methods in gene selection and classification of microarray data; fuzzy gene mining; sequence-based prediction of residue-level properties in proteins; probabilistic methods for long-range features in biosequences; and much more. Machine Learning in Bioinformatics is an indispensable resource for computer scientists, engineers, biologists, mathematicians, researchers, clinicians, physicians, and medical informaticists. It is also a valuable reference text for computer science, engineering, and biology courses at the upper undergraduate and graduate levels.

This book covers a wide range of subjects in applying machine learning approaches for bioinformatics projects. The book succeeds on two key unique features. First, it introduces the most widely used machine learning approaches in bioinformatics and discusses, with evaluations from real case studies, how they are used in individual bioinformatics projects. Second, it introduces state-of-the-art bioinformatics research methods. The theoretical parts and the practical parts are well integrated for readers to follow the existing procedures in individual research.Unlike most of the bioinformatics books on the market, the content coverage is not limited to just one subject. A broad spectrum of relevant topics in bioinformatics including systematic data mining and computational systems biology researches are brought together in this book, thereby offering an efficient and convenient platform for teaching purposes.An essential reference for both final year undergraduates and graduate students in universities, as well as a comprehensive handbook for new researchers, this book will also serve as a practical guide for software development in relevant bioinformatics projects.

Machine learning techniques are increasingly being used to address problems in computational biology and bioinformatics. Novel machine learning computational techniques to analyze high throughput data in the form of sequences, gene and protein expressions, pathways, and images are becoming vital for understanding diseases and future drug discovery. Machine learning techniques such as Markov models, support vector machines, neural networks, and graphical models have been successful in analyzing life science data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. Machine Learning in Bioinformatics compiles recent approaches in machine learning methods and their applications in addressing contemporary problems in bioinformatics approximating classification and prediction of disease, feature selection, dimensionality reduction, gene selection and classification of microarray data and many more.

A guide to machine learning approaches and their application to the analysis of biological data. An unprecedented wealth of data is being generated by genome sequencing projects and other experimental efforts to determine the structure and function of biological molecules. The demands and opportunities for interpreting these data are expanding rapidly. Bioinformatics is the development and application of computer methods for management, analysis, interpretation, and prediction, as well as for the design of experiments. Machine learning approaches (e.g., neural networks, hidden Markov models, and belief networks) are ideally suited for areas where there is a lot of data but little theory, which is the situation in molecular biology. The goal in machine learning is to extract useful information from a body of data by building good probabilistic models—and to automate the process as much as possible. In this book Pierre Baldi and Søren Brunak present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological data. The book is aimed both at biologists and biochemists who need to understand new data-driven algorithms and at those with a primary background in physics, mathematics, statistics, or computer science who need to know more about applications in molecular biology. This new second edition contains expanded coverage of probabilistic graphical models and of the applications of neural networks, as well as a new chapter on microarrays and gene expression. The entire text has been extensively revised.

Data fusion problems arise frequently in many different fields. This book provides a specific introduction to data fusion problems using support vector machines. In the first part, this book begins with a brief survey of additive models and Rayleigh quotient objectives in machine learning, and then introduces kernel fusion as the additive expansion of support vector machines in the dual problem. The second part presents several novel kernel fusion algorithms and some real applications in supervised and unsupervised learning. The last part of the book substantiates the value of the proposed theories and algorithms in MerKator, an open software to identify disease relevant genes based on the integration of heterogeneous genomic data sources in multiple species. The topics presented in this book are meant for researchers or students who use support vector machines. Several topics addressed in the book may also be interesting to computational biologists who want to tackle data fusion challenges in real applications. The background required of the reader is a good knowledge of data mining, machine learning and linear algebra.