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Molecular Representations For Machine Learning
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Book Synopsis Molecular Representations for Machine Learning by : Grier M. Jones
Download or read book Molecular Representations for Machine Learning written by Grier M. Jones and published by American Chemical Society. This book was released on 2023-05-19 with total page 177 pages. Available in PDF, EPUB and Kindle. Book excerpt: This primer helps the reader understand the basic categories of molecular representations and provides computational tools to generate molecular descriptors in each of these categories. After reading this primer, you will be able to use various methods to generate machine and/or human interpretable representations of molecular systems for inputs to machine learning models or for general chemical data science applications.
Book Synopsis Deep Learning for the Life Sciences by : Bharath Ramsundar
Download or read book Deep Learning for the Life Sciences written by Bharath Ramsundar and published by O'Reilly Media. This book was released on 2019-04-10 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis De novo Molecular Design by : Gisbert Schneider
Download or read book De novo Molecular Design written by Gisbert Schneider and published by Wiley-VCH. This book was released on 2013-12-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systematically examining current methods and strategies, this ready reference covers a wide range of molecular structures, from organic-chemical drugs to peptides, Proteins and nucleic acids, in line with emerging new drug classes derived from biomacromolecules. A leader in the field and one of the pioneers of this young discipline has assembled here the most prominent experts from across the world to provide first-hand knowledge. While most of their methods and examples come from the area of pharmaceutical discovery and development, the approaches are equally applicable for chemical probes and diagnostics, pesticides, and any other molecule designed to interact with a biological system. Numerous images and screenshots illustrate the many examples and method descriptions. With its broad and balanced coverage, this will be the firststop resource not only for medicinal chemists, biochemists and biotechnologists, but equally for bioinformaticians and molecular designers for many years to come. From the content: * Reaction-driven de novo design * Adaptive methods in molecular design * Design of ligands against multitarget profiles * Free energy methods in ligand design * Fragment-based de novo design * Automated design of focused and target family-oriented compound libraries * Molecular de novo design by nature-inspired computing * 3D QSAR approaches to de novo drug design * Bioisosteres in de novo design * De novo design of peptides, proteins and nucleic acid structures, including RNA aptamers and many more.
Book Synopsis Machine Learning in Chemistry by : Jon Paul Janet
Download or read book Machine Learning in Chemistry written by Jon Paul Janet and published by American Chemical Society. This book was released on 2020-05-28 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in machine learning or artificial intelligence for vision and natural language processing that have enabled the development of new technologies such as personal assistants or self-driving cars have brought machine learning and artificial intelligence to the forefront of popular culture. The accumulation of these algorithmic advances along with the increasing availability of large data sets and readily available high performance computing has played an important role in bringing machine learning applications to such a wide range of disciplines. Given the emphasis in the chemical sciences on the relationship between structure and function, whether in biochemistry or in materials chemistry, adoption of machine learning by chemistsderivations where they are important
Download or read book Chemoinformatics written by Thomas Engel and published by John Wiley & Sons. This book was released on 2018-12-10 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: Von den Grundlagen zu Methoden - dieses Fachbuch, übersichtlich und didaktisch klar gegliedert, ist eine maßgebliche Handreichung mit allem Wissenswerten und Erläuterungen der Tools in diesem Fachgebiet.
Book Synopsis Handbook of Deep Learning Applications by : Valentina Emilia Balas
Download or read book Handbook of Deep Learning Applications written by Valentina Emilia Balas and published by Springer. This book was released on 2019-02-25 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a broad range of deep-learning applications related to vision, natural language processing, gene expression, arbitrary object recognition, driverless cars, semantic image segmentation, deep visual residual abstraction, brain–computer interfaces, big data processing, hierarchical deep learning networks as game-playing artefacts using regret matching, and building GPU-accelerated deep learning frameworks. Deep learning, an advanced level of machine learning technique that combines class of learning algorithms with the use of many layers of nonlinear units, has gained considerable attention in recent times. Unlike other books on the market, this volume addresses the challenges of deep learning implementation, computation time, and the complexity of reasoning and modeling different type of data. As such, it is a valuable and comprehensive resource for engineers, researchers, graduate students and Ph.D. scholars.
Book Synopsis Artificial Intelligence in Drug Design by : Alexander Heifetz
Download or read book Artificial Intelligence in Drug Design written by Alexander Heifetz and published by . This book was released on 2021 with total page 529 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume looks at applications of artificial intelligence (AI), machine learning (ML), and deep learning (DL) in drug design. The chapters in this book describe how AI/ML/DL approaches can be applied to accelerate and revolutionize traditional drug design approaches such as: structure- and ligand-based, augmented and multi-objective de novo drug design, SAR and big data analysis, prediction of binding/activity, ADMET, pharmacokinetics and drug-target residence time, precision medicine and selection of favorable chemical synthetic routes. How broadly are these approaches applied and where do they maximally impact productivity today and potentially in the near future. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary software and tools, step-by-step, readily reproducible modeling protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and unique, Artificial Intelligence in Drug Design is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists and drug designers.
Book Synopsis Graph Representation Learning by : William L. William L. Hamilton
Download or read book Graph Representation Learning written by William L. William L. Hamilton and published by Springer Nature. This book was released on 2022-06-01 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Quantum Chemistry in the Age of Machine Learning by : Pavlo O. Dral
Download or read book Quantum Chemistry in the Age of Machine Learning written by Pavlo O. Dral and published by Elsevier. This book was released on 2022-09-16 with total page 702 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantum chemistry is simulating atomistic systems according to the laws of quantum mechanics, and such simulations are essential for our understanding of the world and for technological progress. Machine learning revolutionizes quantum chemistry by increasing simulation speed and accuracy and obtaining new insights. However, for nonspecialists, learning about this vast field is a formidable challenge. Quantum Chemistry in the Age of Machine Learning covers this exciting field in detail, ranging from basic concepts to comprehensive methodological details to providing detailed codes and hands-on tutorials. Such an approach helps readers get a quick overview of existing techniques and provides an opportunity to learn the intricacies and inner workings of state-of-the-art methods. The book describes the underlying concepts of machine learning and quantum chemistry, machine learning potentials and learning of other quantum chemical properties, machine learning-improved quantum chemical methods, analysis of Big Data from simulations, and materials design with machine learning. Drawing on the expertise of a team of specialist contributors, this book serves as a valuable guide for both aspiring beginners and specialists in this exciting field. Compiles advances of machine learning in quantum chemistry across different areas into a single resource Provides insights into the underlying concepts of machine learning techniques that are relevant to quantum chemistry Describes, in detail, the current state-of-the-art machine learning-based methods in quantum chemistry
Book Synopsis An Introduction to Chemoinformatics by : Andrew R. Leach
Download or read book An Introduction to Chemoinformatics written by Andrew R. Leach and published by Springer. This book was released on 2007-09-04 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book aims to provide an introduction to the major techniques of chemoinformatics. It is the first text written specifically for this field. The first part of the book deals with the representation of 2D and 3D molecular structures, the calculation of molecular descriptors and the construction of mathematical models. The second part describes other important topics including molecular similarity and diversity, the analysis of large data sets, virtual screening, and library design. Simple illustrative examples are used throughout to illustrate key concepts, supplemented with case studies from the literature.
Book Synopsis Reviews in Computational Chemistry by : Abby L. Parrill
Download or read book Reviews in Computational Chemistry written by Abby L. Parrill and published by John Wiley & Sons. This book was released on 2017-03-16 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered on molecular modeling. • Provides background and theory, strategies for using the methods correctly, pitfalls to avoid, applications, and references • Contains updated and comprehensive compendiums of molecular modeling software that list hundreds of programs, services, suppliers and other information that every chemist will find useful • Includes detailed indices on each volume help the reader to quickly discover particular topics • Uses a tutorial manner and non-mathematical style, allowing students and researchers to access computational methods outside their immediate area of expertise
Book Synopsis Machine Learning Meets Quantum Physics by : Kristof T. Schütt
Download or read book Machine Learning Meets Quantum Physics written by Kristof T. Schütt and published by Springer Nature. This book was released on 2020-06-03 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.
Book Synopsis Multiple Representations in Chemical Education by : John K. Gilbert
Download or read book Multiple Representations in Chemical Education written by John K. Gilbert and published by Springer Science & Business Media. This book was released on 2009-02-28 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemistry seeks to provide qualitative and quantitative explanations for the observed behaviour of elements and their compounds. Doing so involves making use of three types of representation: the macro (the empirical properties of substances); the sub-micro (the natures of the entities giving rise to those properties); and the symbolic (the number of entities involved in any changes that take place). Although understanding this triplet relationship is a key aspect of chemical education, there is considerable evidence that students find great difficulty in achieving mastery of the ideas involved. In bringing together the work of leading chemistry educators who are researching the triplet relationship at the secondary and university levels, the book discusses the learning involved, the problems that students encounter, and successful approaches to teaching. Based on the reported research, the editors argue for a coherent model for understanding the triplet relationship in chemical education.
Book Synopsis Artificial Intelligence in Drug Discovery by : Nathan Brown
Download or read book Artificial Intelligence in Drug Discovery written by Nathan Brown and published by Royal Society of Chemistry. This book was released on 2020-11-04 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: Following significant advances in deep learning and related areas interest in artificial intelligence (AI) has rapidly grown. In particular, the application of AI in drug discovery provides an opportunity to tackle challenges that previously have been difficult to solve, such as predicting properties, designing molecules and optimising synthetic routes. Artificial Intelligence in Drug Discovery aims to introduce the reader to AI and machine learning tools and techniques, and to outline specific challenges including designing new molecular structures, synthesis planning and simulation. Providing a wealth of information from leading experts in the field this book is ideal for students, postgraduates and established researchers in both industry and academia.
Book Synopsis Molecular Descriptors for Chemoinformatics by : Roberto Todeschini
Download or read book Molecular Descriptors for Chemoinformatics written by Roberto Todeschini and published by John Wiley & Sons. This book was released on 2009-10-30 with total page 1257 pages. Available in PDF, EPUB and Kindle. Book excerpt: The number-one reference on the topic now contains a wealth of new data: The entire relevant literature over the past six years has been painstakingly surveyed, resulting in hundreds of new descriptors being added to the list, and some 3,000 new references in the bibliography section. Volume 1 contains an alphabetical listing of more than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties, while the second volume lists over 6,000 references selected from 450 journals. To make the data even more accessible, the introductory section has been completely re-written and now contains several "walk-through" reading lists of selected keywords for novice users.
Book Synopsis Machine Learning Methodologies To Study Molecular Interactions by : Elif Ozkirimli
Download or read book Machine Learning Methodologies To Study Molecular Interactions written by Elif Ozkirimli and published by Frontiers Media SA. This book was released on 2022-01-21 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dr. Elif Ozkirimli is a full time employee of F. Hoffmann-La Roche AG, Switzerland and Dr. Artur Yakimovich is a full time employee of Roche Products Limited, UK. All other Topic Editors declare no competing interests with regards to the Research Topic.
Download or read book Nanoinformatics written by Isao Tanaka and published by Springer. This book was released on 2018-01-15 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book brings out the state of the art on how informatics-based tools are used and expected to be used in nanomaterials research. There has been great progress in the area in which “big-data” generated by experiments or computations are fully utilized to accelerate discovery of new materials, key factors, and design rules. Data-intensive approaches play indispensable roles in advanced materials characterization. "Materials informatics" is the central paradigm in the new trend. "Nanoinformatics" is its essential subset, which focuses on nanostructures of materials such as surfaces, interfaces, dopants, and point defects, playing a critical role in determining materials properties. There have been significant advances in experimental and computational techniques to characterize individual atoms in nanostructures and to gain quantitative information. The collaboration of researchers in materials science and information science is growing actively and is creating a new trend in materials science and engineering.
