Machine Learning in Bioinformatics

Steganography is the art of communicating a secret message, hiding the very existence of a secret message. This is typically done by hiding the message within a non-sensitive document. Steganalysis is the art and science of detecting such hidden messages. The task in steganalysis is to take an object (communication) and classify it as either a steganogram or a clean document. Most recent solutions apply classification algorithms from machine learning and pattern recognition, which tackle problems too complex for analytical solution by teaching computers to learn from empirical data. Part 1of the book is an introduction to steganalysis as part of the wider trend of multimedia forensics, as well as a practical tutorial on machine learning in this context. Part 2 is a survey of a wide range of feature vectors proposed for steganalysis with performance tests and comparisons. Part 3 is an in-depth study of machine learning techniques and classifier algorithms, and presents a critical assessment of the experimental methodology and applications in steganalysis. Key features: Serves as a tutorial on the topic of steganalysis with brief introductions to much of the basic theory provided, and also presents a survey of the latest research. Develops and formalises the application of machine learning in steganalysis; with much of the understanding of machine learning to be gained from this book adaptable for future study of machine learning in other applications. Contains Python programs and algorithms to allow the reader to modify and reproduce outcomes discussed in the book. Includes companion software available from the author’s website.

ALGORITHMS IN BIOINFORMATICS Explore a comprehensive and insightful treatment of the practical application of bioinformatic algorithms in a variety of fields Algorithms in Bioinformatics: Theory and Implementation delivers a fulsome treatment of some of the main algorithms used to explain biological functions and relationships. It introduces readers to the art of algorithms in a practical manner which is linked with biological theory and interpretation. The book covers many key areas of bioinformatics, including global and local sequence alignment, forced alignment , detection of motifs, Sequence logos, Markov chains or information entropy. Other novel approaches are also described, such as Self-Sequence alignment, Objective Digital Stains (ODSs) or Spectral Forecast and the Discrete Probability Detector (DPD) algorithm. The text incorporates graphical illustrations to highlight and emphasize the technical details of computational algorithms found within, to further the reader’s understanding and retention of the material. Throughout, the book is written in an accessible and practical manner, showing how algorithms can be implemented and used in JavaScript on Internet Browsers. The author has included more than 120 open-source implementations of the material, as well as 33 ready-to-use presentations. The book contains original material that has been class-tested by the author and numerous cases are examined in a biological and medical context. Readers will also benefit from the inclusion of: A thorough introduction to biological evolution, including the emergence of life, classifications and some known theories and molecular mechanismsA detailed presentation of new methods, such as Self-sequence alignment, Objective Digital Stains and Spectral Forecast A treatment of sequence alignment, including local sequence alignment, global sequence alignment and forced sequence alignment with full implementationsDiscussions of position-specific weight matrices, including the count, weight, relative frequencies, and log-likelihoods matricesA detailed presentation of the methods related to Markov Chains as well as a description of their implementation in Bioinformatics and adjacent fieldsAn examination of information and entropy, including sequence logos and explanations related to their meaningAn exploration of the current state of bioinformatics, including what is known and what issues are usually avoided in the fieldA chapter on philosophical transactions that allows the reader a broader view of the prediction processNative computer implementations in the context of the field of BioinformaticsExtensive worked examples with detailed case studies that point out the meaning of different results Perfect for professionals and researchers in biology, medicine, engineering, and information technology, as well as upper level undergraduate students in these fields, Algorithms in Bioinformatics: Theory and Implementation will also earn a place in the libraries of software engineers who wish to understand how to implement bioinformatic algorithms in their products.

Get to know the ‘why’ and ‘how’ of machine learning and big data in quantitative investment Big Data and Machine Learning in Quantitative Investment is not just about demonstrating the maths or the coding. Instead, it’s a book by practitioners for practitioners, covering the questions of why and how of applying machine learning and big data to quantitative finance. The book is split into 13 chapters, each of which is written by a different author on a specific case. The chapters are ordered according to the level of complexity; beginning with the big picture and taxonomy, moving onto practical applications of machine learning and finally finishing with innovative approaches using deep learning. • Gain a solid reason to use machine learning • Frame your question using financial markets laws • Know your data • Understand how machine learning is becoming ever more sophisticated Machine learning and big data are not a magical solution, but appropriately applied, they are extremely effective tools for quantitative investment – and this book shows you how.

Multiblock Data Fusion in Statistics and Machine Learning Explore the advantages and shortcomings of various forms of multiblock analysis, and the relationships between them, with this expert guide Arising out of fusion problems that exist in a variety of fields in the natural and life sciences, the methods available to fuse multiple data sets have expanded dramatically in recent years. Older methods, rooted in psychometrics and chemometrics, also exist. Multiblock Data Fusion in Statistics and Machine Learning: Applications in the Natural and Life Sciences is a detailed overview of all relevant multiblock data analysis methods for fusing multiple data sets. It focuses on methods based on components and latent variables, including both well-known and lesser-known methods with potential applications in different types of problems. Many of the included methods are illustrated by practical examples and are accompanied by a freely available R-package. The distinguished authors have created an accessible and useful guide to help readers fuse data, develop new data fusion models, discover how the involved algorithms and models work, and understand the advantages and shortcomings of various approaches. This book includes: A thorough introduction to the different options available for the fusion of multiple data sets, including methods originating in psychometrics and chemometrics Practical discussions of well-known and lesser-known methods with applications in a wide variety of data problems Included, functional R-code for the application of many of the discussed methods Perfect for graduate students studying data analysis in the context of the natural and life sciences, including bioinformatics, sensometrics, and chemometrics, Multiblock Data Fusion in Statistics and Machine Learning: Applications in the Natural and Life Sciences is also an indispensable resource for developers and users of the results of multiblock methods.

Combining biology, computer science, mathematics, and statistics, the field of bioinformatics has become a hot new discipline with profound impacts on all aspects of biology and industrial application. Now, Computational Intelligence in Bioinformatics offers an introduction to the topic, covering the most relevant and popular CI methods, while also encouraging the implementation of these methods to readers' research.

Machine learning and optimization techniques are revolutionizing our world. Other types of information technology have not progressed as rapidly in recent years, in terms of real impact. The aim of this book is to present some of the innovative techniques in the field of optimization and machine learning, and to demonstrate how to apply them in the fields of engineering.

Optimization and Machine Learning presents modern advances in the selection, configuration and engineering of algorithms that rely on machine learning and optimization. The first part of the book is dedicated to applications where optimization plays a major role, and the second part describes and implements several applications that are mainly based on machine learning techniques. The methods addressed in these chapters are compared against their competitors, and their effectiveness in their chosen field of application is illustrated.

The purpose of this edited book is to bring together the ideas and findings of data mining researchers and bioinformaticians by discussing cutting-edge research topics such as, gene expressions, protein/RNA structure prediction, phylogenetics, sequence and structural motifs, genomics and proteomics, gene findings, drug design, RNAi and microRNA analysis, text mining in bioinformatics, modelling of biochemical pathways, biomedical ontologies, system biology and pathways, and biological database management.

Informatics and Machine Learning Discover a thorough exploration of how to use computational, algorithmic, statistical, and informatics methods to analyze digital data Informatics and Machine Learning: From Martingales to Metaheuristics delivers an interdisciplinary presentation on how analyze any data captured in digital form. The book describes how readers can conduct analyses of text, general sequential data, experimental observations over time, stock market and econometric histories, or symbolic data, like genomes. It contains large amounts of sample code to demonstrate the concepts contained within and assist with various levels of project work. The book offers a complete presentation of the mathematical underpinnings of a wide variety of forms of data analysis and provides extensive examples of programming implementations. It is based on two decades worth of the distinguished author’s teaching and industry experience. A thorough introduction to probabilistic reasoning and bioinformatics, including Python shell scripting to obtain data counts, frequencies, probabilities, and anomalous statistics, or use with Bayes’ rule An exploration of information entropy and statistical measures, including Shannon entropy, relative entropy, maximum entropy (maxent), and mutual information A practical discussion of ad hoc, ab initio , and bootstrap signal acquisition methods, with examples from genome analytics and signal analytics Perfect for undergraduate and graduate students in machine learning and data analytics programs, Informatics and Machine Learning: From Martingales to Metaheuristics will also earn a place in the libraries of mathematicians, engineers, computer scientists, and life scientists with an interest in those subjects.

The book begins with a chapter on traditional methods of supervised learning, covering recursive least squares learning, mean square error methods, and stochastic approximation. Chapter 2 covers single agent reinforcement learning. Topics include learning value functions, Markov games, and TD learning with eligibility traces. Chapter 3 discusses two player games including two player matrix games with both pure and mixed strategies. Numerous algorithms and examples are presented. Chapter 4 covers learning in multi-player games, stochastic games, and Markov games, focusing on learning multi-player grid games—two player grid games, Q-learning, and Nash Q-learning. Chapter 5 discusses differential games, including multi player differential games, actor critique structure, adaptive fuzzy control and fuzzy interference systems, the evader pursuit game, and the defending a territory games. Chapter 6 discusses new ideas on learning within robotic swarms and the innovative idea of the evolution of personality traits. • Framework for understanding a variety of methods and approaches in multi-agent machine learning. • Discusses methods of reinforcement learning such as a number of forms of multi-agent Q-learning • Applicable to research professors and graduate students studying electrical and computer engineering, computer science, and mechanical and aerospace engineering

Clustering techniques are increasingly being put to use in the analysis of high-throughput biological datasets. Novel computational techniques to analyse 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. This book details the complete pathway of cluster analysis, from the basics of molecular biology to the generation of biological knowledge. The book also presents the latest clustering methods and clustering validation, thereby offering the reader a comprehensive review of clustering analysis in bioinformatics from the fundamentals through to state-of-the-art techniques and applications. Key Features: Offers a contemporary review of clustering methods and applications in the field of bioinformatics, with particular emphasis on gene expression analysis Provides an excellent introduction to molecular biology with computer scientists and information engineering researchers in mind, laying out the basic biological knowledge behind the application of clustering analysis techniques in bioinformatics Explains the structure and properties of many types of high-throughput datasets commonly found in biological studies Discusses how clustering methods and their possible successors would be used to enhance the pace of biological discoveries in the future Includes a companion website hosting a selected collection of codes and links to publicly available datasets