Data Driven Computational Neuroscience

Trains researchers and graduate students in state-of-the-art statistical and machine learning methods to build models with real-world data.

This book is intended for use in advanced graduate courses in statistics / machine learning, as well as for all experimental neuroscientists seeking to understand statistical methods at a deeper level, and theoretical neuroscientists with a limited background in statistics. It reviews almost all areas of applied statistics, from basic statistical estimation and test theory, linear and nonlinear approaches for regression and classification, to model selection and methods for dimensionality reduction, density estimation and unsupervised clustering. Its focus, however, is linear and nonlinear time series analysis from a dynamical systems perspective, based on which it aims to convey an understanding also of the dynamical mechanisms that could have generated observed time series. Further, it integrates computational modeling of behavioral and neural dynamics with statistical estimation and hypothesis testing. This way computational models in neuroscience are not only explanatory frameworks, but become powerful, quantitative data-analytical tools in themselves that enable researchers to look beyond the data surface and unravel underlying mechanisms. Interactive examples of most methods are provided through a package of MatLab routines, encouraging a playful approach to the subject, and providing readers with a better feel for the practical aspects of the methods covered. "Computational neuroscience is essential for integrating and providing a basis for understanding the myriads of remarkable laboratory data on nervous system functions. Daniel Durstewitz has excellently covered the breadth of computational neuroscience from statistical interpretations of data to biophysically based modeling of the neurobiological sources of those data. His presentation is clear, pedagogically sound, and readily useable by experts and beginners alike. It is a pleasure to recommend this very well crafted discussion to experimental neuroscientists as well as mathematically well versed Physicists. The book acts as a window to the issues, to the questions, and to the tools for finding the answers to interesting inquiries about brains and how they function." Henry D. I. Abarbanel Physics and Scripps Institution of Oceanography, University of California, San Diego “This book delivers a clear and thorough introduction to sophisticated analysis approaches useful in computational neuroscience. The models described and the examples provided will help readers develop critical intuitions into what the methods reveal about data. The overall approach of the book reflects the extensive experience Prof. Durstewitz has developed as a leading practitioner of computational neuroscience. “ Bruno B. Averbeck

The International Conference on Computational Science (ICCS 2004) held in Krak ́ ow, Poland, June 6–9, 2004, was a follow-up to the highly successful ICCS 2003 held at two locations, in Melbourne, Australia and St. Petersburg, Russia; ICCS 2002 in Amsterdam, The Netherlands; and ICCS 2001 in San Francisco, USA. As computational science is still evolving in its quest for subjects of inves- gation and e?cient methods, ICCS 2004 was devised as a forum for scientists from mathematics and computer science, as the basic computing disciplines and application areas, interested in advanced computational methods for physics, chemistry, life sciences, engineering, arts and humanities, as well as computer system vendors and software developers. The main objective of this conference was to discuss problems and solutions in all areas, to identify new issues, to shape future directions of research, and to help users apply various advanced computational techniques. The event harvested recent developments in com- tationalgridsandnextgenerationcomputingsystems,tools,advancednumerical methods, data-driven systems, and novel application ?elds, such as complex - stems, ?nance, econo-physics and population evolution.

Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information

Computational and Data-Driven Chemistry Using Artificial Intelligence: Volume 1: Fundamentals, Methods and Applications highlights fundamental knowledge and current developments in the field, giving readers insight into how these tools can be harnessed to enhance their own work. Offering the ability to process large or complex data-sets, compare molecular characteristics and behaviors, and help researchers design or identify new structures, Artificial Intelligence (AI) holds huge potential to revolutionize the future of chemistry. Volume 1 explores the fundamental knowledge and current methods being used to apply AI across a whole host of chemistry applications. Drawing on the knowledge of its expert team of global contributors, the book offers fascinating insight into this rapidly developing field and serves as a great resource for all those interested in exploring the opportunities afforded by the intersection of chemistry and AI in their own work. Part 1 provides foundational information on AI in chemistry, with an introduction to the field and guidance on database usage and statistical analysis to help support newcomers to the field. Part 2 then goes on to discuss approaches currently used to address problems in broad areas such as computational and theoretical chemistry; materials, synthetic and medicinal chemistry; crystallography, analytical chemistry, and spectroscopy. Finally, potential future trends in the field are discussed. Provides an accessible introduction to the current state and future possibilities for AI in chemistry Explores how computational chemistry methods and approaches can both enhance and be enhanced by AI Highlights the interdisciplinary and broad applicability of AI tools across a wide range of chemistry fields

A guide to computational modeling methods in neuroscience, covering a range of modeling scales from molecular reactions to large neural networks. This book offers an introduction to current methods in computational modeling in neuroscience. The book describes realistic modeling methods at levels of complexity ranging from molecular interactions to large neural networks. A “how to” book rather than an analytical account, it focuses on the presentation of methodological approaches, including the selection of the appropriate method and its potential pitfalls. It is intended for experimental neuroscientists and graduate students who have little formal training in mathematical methods, but it will also be useful for scientists with theoretical backgrounds who want to start using data-driven modeling methods. The mathematics needed are kept to an introductory level; the first chapter explains the mathematical methods the reader needs to master to understand the rest of the book. The chapters are written by scientists who have successfully integrated data-driven modeling with experimental work, so all of the material is accessible to experimentalists. The chapters offer comprehensive coverage with little overlap and extensive cross-references, moving from basic building blocks to more complex applications. Contributors Pablo Achard, Haroon Anwar, Upinder S. Bhalla, Michiel Berends, Nicolas Brunel, Ronald L. Calabrese, Brenda Claiborne, Hugo Cornelis, Erik De Schutter, Alain Destexhe, Bard Ermentrout, Kristen Harris, Sean Hill, John R. Huguenard, William R. Holmes, Gwen Jacobs, Gwendal LeMasson, Henry Markram, Reinoud Maex, Astrid A. Prinz, Imad Riachi, John Rinzel, Arnd Roth, Felix Schürmann, Werner Van Geit, Mark C. W. van Rossum, Stefan Wils

Combining scientific computing methods and algorithms with modern data analysis techniques, including basic applications of compressive sensing and machine learning, this book develops techniques that allow for the integration of the dynamics of complex systems and big data. MATLAB is used throughout for mathematical solution strategies.