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Introduces biological concepts and biotechnologies producing the data, graph and network theory, cluster analysis and machine learning, using real-world biological and medical examples.
Deep learning has already achieved remarkable results in many fields. Now it’s making waves throughout the sciences broadly and the life sciences in particular. This practical book teaches developers and scientists how to use deep learning for genomics, chemistry, biophysics, microscopy, medical analysis, and other fields. Ideal for practicing developers and scientists ready to apply their skills to scientific applications such as biology, genetics, and drug discovery, this book introduces several deep network primitives. You’ll follow a case study on the problem of designing new therapeutics that ties together physics, chemistry, biology, and medicine—an example that represents one of science’s greatest challenges. Learn the basics of performing machine learning on molecular data Understand why deep learning is a powerful tool for genetics and genomics Apply deep learning to understand biophysical systems Get a brief introduction to machine learning with DeepChem Use deep learning to analyze microscopic images Analyze medical scans using deep learning techniques Learn about variational autoencoders and generative adversarial networks Interpret what your model is doing and how it’s working
Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource. - Presents recent advances in biological network analysis, combining Graph Theory, Graph Analysis, and various network models - Discusses three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN) and Human Brain Connectomes - Includes a discussion of various graph theoretic and data analytics approaches
Biology, medicine and biochemistry have become data-centric fields for which Deep Learning methods are delivering groundbreaking results. Addressing high impact challenges, Deep Learning in Biology and Medicine provides an accessible and organic collection of Deep Learning essays on bioinformatics and medicine. It caters for a wide readership, ranging from machine learning practitioners and data scientists seeking methodological knowledge to address biomedical applications, to life science specialists in search of a gentle reference for advanced data analytics.With contributions from internationally renowned experts, the book covers foundational methodologies in a wide spectrum of life sciences applications, including electronic health record processing, diagnostic imaging, text processing, as well as omics-data processing. This survey of consolidated problems is complemented by a selection of advanced applications, including cheminformatics and biomedical interaction network analysis. A modern and mindful approach to the use of data-driven methodologies in the life sciences also requires careful consideration of the associated societal, ethical, legal and transparency challenges, which are covered in the concluding chapters of this book.
Graph-structured data is ubiquitous throughout the natural and social sciences, from telecommunication networks to quantum chemistry. Building relational inductive biases into deep learning architectures is crucial for creating systems that can learn, reason, and generalize from this kind of data. Recent years have seen a surge in research on graph representation learning, including techniques for deep graph embeddings, generalizations of convolutional neural networks to graph-structured data, and neural message-passing approaches inspired by belief propagation. These advances in graph representation learning have led to new state-of-the-art results in numerous domains, including chemical synthesis, 3D vision, recommender systems, question answering, and social network analysis. This book provides a synthesis and overview of graph representation learning. It begins with a discussion of the goals of graph representation learning as well as key methodological foundations in graph theory and network analysis. Following this, the book introduces and reviews methods for learning node embeddings, including random-walk-based methods and applications to knowledge graphs. It then provides a technical synthesis and introduction to the highly successful graph neural network (GNN) formalism, which has become a dominant and fast-growing paradigm for deep learning with graph data. The book concludes with a synthesis of recent advancements in deep generative models for graphs—a nascent but quickly growing subset of graph representation learning.
This book deals with network representation learning. It deals with embedding nodes, edges, subgraphs and graphs. There is a growing interest in understanding complex systems in different domains including health, education, agriculture and transportation. Such complex systems are analyzed by modeling, using networks that are aptly called complex networks. Networks are becoming ubiquitous as they can represent many real-world relational data, for instance, information networks, molecular structures, telecommunication networks and protein–protein interaction networks. Analysis of these networks provides advantages in many fields such as recommendation (recommending friends in a social network), biological field (deducing connections between proteins for treating new diseases) and community detection (grouping users of a social network according to their interests) by leveraging the latent information of networks. An active and important area of current interest is to come out with algorithms that learn features by embedding nodes or (sub)graphs into a vector space. These tasks come under the broad umbrella of representation learning. A representation learning model learns a mapping function that transforms the graphs' structure information to a low-/high-dimension vector space maintaining all the relevant properties.
This is the first book to describe modern methods for analyzing complex networks arising from a wide range of disciplines.
This book reviews recent advances in the emerging field of computational network biology with special emphasis on comparative network analysis and network module detection. The chapters in this volume are contributed by leading international researchers in computational network biology and offer in-depth insight on the latest techniques in network alignment, network clustering, and network module detection. Chapters discuss the advantages of the respective techniques and present the current challenges and open problems in the field. Recent Advances in Biological Network Analysis: Comparative Network Analysis and Network Module Detection will serve as a great resource for graduate students, academics, and researchers who are currently working in areas relevant to computational network biology or wish to learn more about the field. Data scientists whose work involves the analysis of graphs, networks, and other types of data with topological structure or relations can also benefit from the book's insights.
Rigorous treatment of the theory of deep learning from first principles, with applications to beautiful problems in the natural sciences.