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Data-driven computational neuroscience : machine learning and statistical models
\"Data-driven computational neuroscience facilitates the transformation of data into insights into the structure and functions of the brain. This introduction for researchers and graduate students is the first in-depth, comprehensive treatment of statistical and machine learning methods for neuroscience. The methods are demonstrated through case studies of real problems to empower readers to build their own solutions. The book covers a wide variety of methods, including supervised classification with non-probabilistic models (nearest-neighbors, classification trees, rule induction, artificial neural networks and support vector machines) and probabilistic models (discriminant analysis, logistic regression and Bayesian network classifiers), meta-classifiers, multi-dimensional classifiers and feature subset selection methods. Other parts of the book are devoted to association discovery with probabilistic graphical models (Bayesian networks and Markov networks) and spatial statistics with point processes (complete spatial randomness and cluster, regular and Gibbs processes). Cellular, structural, functional, medical and behavioral neuroscience levels are considered\"-- Provided by publisher.
BOOK
Signal Processing for Neuroscientists - Introduction to the Analysis of Physiological Signals
This book introduces analysis techniques primarily aimed at neuroscientists and biomedical engineering students with a reasonable but modest background in mathematics, physics, and computer programming. The focus of this text is on what can be considered the 'golden trio' in the signal processing field: averaging, Fourier analysis, and filtering. Techniques such as convolution, correlation, coherence, and wavelet analysis are considered in the context of time and frequency domain analysis. The whole spectrum of signal analysis is covered, ranging from data acquisition to data processing; and from the mathematical background of the analysis to the practical application of processing algorithms. Overall, the approach to the mathematics is informal with a focus on basic understanding of the methods and their interrelationships rather than detailed proofs or derivations.
eBook
MATLAB for neuroscientists : an introduction to scientific computing in MATLAB
This is the first comprehensive teaching resource and textbook for the teaching of Matlab in the Neurosciences and in Psychology. Matlab is unique in that it can be used to learn the entire empirical and experimental process, including stimulus generation, experimental control, data collection, data analysis and modeling. Thus a wide variety of computational problems can be addressed in a single programming environment. The idea is to empower advanced undergraduates and beginning graduate students by allowing them to design and implement their own analytical tools. As students advance in their research careers, they will have achieved the fluency required to understand and adapt more specialized tools as opposed to treating them as \"black boxes\".
eBook
Explaining the Computational Mind
A defense of the computational explanation of cognition that relies on mechanistic philosophy of science and advocates for explanatory pluralism.
In this book, Marcin Milkowski argues that the mind can be explained computationally because it is itself computational—whether it engages in mental arithmetic, parses natural language, or processes the auditory signals that allow us to experience music. Defending the computational explanation against objections to it—from John Searle and Hilary Putnam in particular—Milkowski writes that computationalism is here to stay but is not what many have taken it to be. It does not, for example, rely on a Cartesian gulf between software and hardware, or mind and brain. Milkowski's mechanistic construal of computation allows him to show that no purely computational explanation of a physical process will ever be complete. Computationalism is only plausible, he argues, if you also accept explanatory pluralism.
Milkowski sketches a mechanistic theory of implementation of computation against a background of extant conceptions, describing four dissimilar computational models of cognition. He reviews other philosophical accounts of implementation and computational explanation and defends a notion of representation that is compatible with his mechanistic account and adequate vis à vis the four models discussed earlier. Instead of arguing that there is no computation without representation, he inverts the slogan and shows that there is no representation without computation—but explains that representation goes beyond purely computational considerations. Milkowski's arguments succeed in vindicating computational explanation in a novel way by relying on mechanistic theory of science and interventionist theory of causation.
eBook
A study of problems encountered in Granger causality analysis from a neuroscience perspective
Granger causality methods were developed to analyze the flow of information between time series. These methods have become more widely applied in neuroscience. Frequency-domain causality measures, such as those of Geweke, as well as multivariate methods, have particular appeal in neuroscience due to the prevalence of oscillatory phenomena and highly multivariate experimental recordings. Despite its widespread application in many fields, there are ongoing concerns regarding the applicability of Granger causality methods in neuroscience. When are these methods appropriate? How reliably do they recover the system structure underlying the observed data? What do frequency-domain causality measures tell us about the functional properties of oscillatory neural systems? In this paper, we analyze fundamental properties of Granger–Geweke (GG) causality, both computational and conceptual. Specifically, we show that (i) GG causality estimates can be either severely biased or of high variance, both leading to spurious results; (ii) even if estimated correctly, GG causality estimates alone are not interpretable without examining the component behaviors of the system model; and (iii) GG causality ignores critical components of a system’s dynamics. Based on this analysis, we find that the notion of causality quantified is incompatible with the objectives of many neuroscience investigations, leading to highly counterintuitive and potentially misleading results. Through the analysis of these problems, we provide important conceptual clarification of GG causality, with implications for other related causality approaches and for the role of causality analyses in neuroscience as a whole.
Journal Article
Cognitive computational neuroscience
To learn how cognition is implemented in the brain, we must build computational models that can perform cognitive tasks, and test such models with brain and behavioral experiments. Cognitive science has developed computational models that decompose cognition into functional components. Computational neuroscience has modeled how interacting neurons can implement elementary components of cognition. It is time to assemble the pieces of the puzzle of brain computation and to better integrate these separate disciplines. Modern technologies enable us to measure and manipulate brain activity in unprecedentedly rich ways in animals and humans. However, experiments will yield theoretical insight only when employed to test brain-computational models. Here we review recent work in the intersection of cognitive science, computational neuroscience and artificial intelligence. Computational models that mimic brain information processing during perceptual, cognitive and control tasks are beginning to be developed and tested with brain and behavioral data.
Journal Article
The Human Connectome Project: A retrospective
The Human Connectome Project (HCP) was launched in 2010 as an ambitious effort to accelerate advances in human neuroimaging, particularly for measures of brain connectivity; apply these advances to study a large number of healthy young adults; and freely share the data and tools with the scientific community. NIH awarded grants to two consortia; this retrospective focuses on the “WU-Minn-Ox” HCP consortium centered at Washington University, the University of Minnesota, and University of Oxford. In just over 6 years, the WU-Minn-Ox consortium succeeded in its core objectives by: 1) improving MR scanner hardware, pulse sequence design, and image reconstruction methods, 2) acquiring and analyzing multimodal MRI and MEG data of unprecedented quality together with behavioral measures from more than 1100 HCP participants, and 3) freely sharing the data (via the ConnectomeDB database) and associated analysis and visualization tools. To date, more than 27 Petabytes of data have been shared, and 1538 papers acknowledging HCP data use have been published. The “HCP-style” neuroimaging paradigm has emerged as a set of best-practice strategies for optimizing data acquisition and analysis. This article reviews the history of the HCP, including comments on key events and decisions associated with major project components. We discuss several scientific advances using HCP data, including improved cortical parcellations, analyses of connectivity based on functional and diffusion MRI, and analyses of brain-behavior relationships. We also touch upon our efforts to develop and share a variety of associated data processing and analysis tools along with detailed documentation, tutorials, and an educational course to train the next generation of neuroimagers. We conclude with a look forward at opportunities and challenges facing the human neuroimaging field from the perspective of the HCP consortium.
Journal Article
Wiener–Granger Causality: A well established methodology
For decades, the main ways to study the effect of one part of the nervous system upon another have been either to stimulate or lesion the first part and investigate the outcome in the second. This article describes a fundamentally different approach to identifying causal connectivity in neuroscience: a focus on the predictability of ongoing activity in one part from that in another. This approach was made possible by a new method that comes from the pioneering work of Wiener (1956) and Granger (1969). The Wiener–Granger method, unlike stimulation and ablation, does not require direct intervention in the nervous system. Rather, it relies on the estimation of causal statistical influences between simultaneously recorded neural time series data, either in the absence of identifiable behavioral events or in the context of task performance. Causality in the Wiener–Granger sense is based on the statistical predictability of one time series that derives from knowledge of one or more others. This article defines Wiener–Granger Causality, discusses its merits and limitations in neuroscience, and outlines recent developments in its implementation.
Journal Article