Showing posts with label neuroscience. Show all posts
Showing posts with label neuroscience. Show all posts

3/16/2012

Methods in Neuronal Modeling - 2nd Edition: From Ions to Networks (Computational Neuroscience) Review

Methods in Neuronal Modeling - 2nd Edition: From Ions to Networks (Computational Neuroscience)
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Great book for the theorist and experimentalist! I used the section on Epilepsy and the Neural Code for a grant I wrote. This book is a great reference and time spent reading it is very well rewarded. I bought the 1st & 2nd editions which are very different. Both editions are worth buying if one is involved with computer modeling, computation, mathematics, and plain old fashion recording neurophysiology.

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Much research focuses on the question of how information is processed innervous systems, from the level of individual ionic channels to large-scale neuronalnetworks, and from "simple" animals such as sea slugs and flies to cats andprimates. New interdisciplinary methodologies combine a bottom-up experimentalmethodology with the more top-down-driven computational and modeling approach. Thisbook serves as a handbook of computational methods and techniques for modeling thefunctional properties of single and groups of nerve cells.The contributors highlightseveral key trends: (1) the tightening link between analytical/numerical models andthe associated experimental data, (2) the broadening of modeling methods, at boththe subcellular level and the level of large neuronal networks that incorporate realbiophysical properties of neurons as well as the statistical properties of spiketrains, and (3) the organization of the data gained by physical emulation of thenervous system components through the use of very large scale circuit integration(VLSI) technology.The field of neuroscience has grown dramatically since the firstedition of this book was published nine years ago. Half of the chapters of thesecond edition are completely new; the remaining ones have all been thoroughlyrevised. Many chapters provide an opportunity for interactive tutorials andsimulation programs. They can be accessed via Christof Koch's Website.Contributors :Larry F. Abbott, Paul R. Adams, Hagai Agmon-Snir, James M. Bower, Robert E. Burke,Erik de Schutter, Alain Destexhe, Rodney Douglas, Bard Ermentrout, FabrizioGabbiani, David Hansel, Michael Hines, Christof Koch, Misha Mahowald, Zachary F.Mainen, Eve Marder, Michael V. Mascagni, Alexander D. Protopapas, Wilfrid Rall, JohnRinzel, Idan Segev, Terrence J. Sejnowski, Shihab Shamma, Arthur S. Sherman, PaulSmolen, Haim Sompolinsky, Michael Vanier, Walter M. Yamada.

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1/18/2012

An Introduction to the Mathematics of Neurons: Modeling in the Frequency Domain (Cambridge Studies in Mathematical Biology) Review

An Introduction to the Mathematics of Neurons: Modeling in the Frequency Domain (Cambridge Studies in Mathematical Biology)
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The goal of Hoppensteadt's book is "to study the frequency and timing of neuron firing and how these can interact in networks to carry information and to control biological systems."

Hoppensteadt's book is condensed. It has 211 pages, but seven chapters and two appendixes. The readers will need other books for better and deeper understanding on the presented material. A case in point is that I have purchased this book for a long time, but I am not able to read through it until Dr. Diana Verzi and Dr. Imre Tuba, both of San Diego State University, gave me Christof Koch's "Biophysics of Computation." Biophysics of Computation has more than five hundred (500) pages. Later on, under the suggestion of Dr. Verzi, I purchased Eugene M. Izhikevich's "Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting" for better and deeper understanding the material presented on Hoppensteadt's book. Izhikevich's book has more than four hundred (400) pages.
Hoppensteadt's book is an economical introductory book on how to apply mathematics on physiological research though. Chapter one, two, and four covers the background material for the rest of the book, such as useful electrical circuits, theory of simple clock, and signal processing in phase-locked systems. Chapter three and five covers the mathematical models of neurons and neural networks. Chapter six and seven presents memory and attention. Appendix A provides the mathematical background on low pass filter and harmonic oscillator. Appendix B presents bifurcation analysis.


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This book describes signal processing aspects of neural networks, how we receive and assess information. Beginning with a presentation of the necessary background material in electronic circuits, mathematical modeling and analysis, signal processing, and neurosciences, it proceeds to applications.These applications include small networks of neurons, such as those used in control of warm-up and flight in moths and control of respiration during exercise in humans.Next, Hoppensteadt develops a theory of mnemonic surfaces and presents material on pattern formation and cellular automata. Finally, the text addresses the large networks, such as the thalamus-reticular complex circuit, that may be involved in focusing attention, and the development of connections in the visual cortex. This book will serve as an excellent text for advanced undergraduates and graduates in the physical sciences, mathematics, engineering, medicine and life sciences.

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12/16/2011

Gateway to Memory: An Introduction to Neural Network Modeling of the Hippocampus and Learning (Issues in Clinical and Cognitive Neuropsychology) Review

Gateway to Memory: An Introduction to Neural Network Modeling of the Hippocampus and Learning (Issues in Clinical and Cognitive Neuropsychology)
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To those students, mostly at the undergraduate level, that are not applied mathematic specialists and have looked for an easy to understand, well written, introduction to Neural Networks in learning processes; this is a must-have book. "Gateway..." is an excellent read, targeted to readers from a wide scope of backgrounds, from Biologists to Computer Science Majors through Medical Sciences.
Although leaning a bit too heavily on the conceptual view of the subject, the book introduces the reader gradually to what a Neural Network is, what a computer model is and how it works.
Two basic tools are of special interest to the reader. First, the beginning half of the book gives a general, yet very complete, introduction of the concepts, history and theory to be used. Second, for those with a little more interest in the mathematics there's a good number of "Math Boxes" delving into the details of the subject(s).
The effect of these tools is that, by the time you reach into the core matter of how neural networks models are constructed and worked in the field of Hippocampal memory, the reader suddenly finds his/herself well-familiarized with the theory. A comfortable, gradual, learning process has taken place without any discomfort (and in less time than you would think!).

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This book is for students and researchers who have a specific interest inlearning and memory and want to understand how computational models can beintegrated into experimental research on the hippocampus and learning. It emphasizesthe function of brain structures as they give rise to behavior, rather than themolecular or neuronal details. It also emphasizes the process of modeling, ratherthan the mathematical details of the models themselves.The book is divided into twoparts. The first part provides a tutorial introduction to topics in neuroscience,the psychology of learning and memory, and the theory of neural network models. Thesecond part, the core of the book, reviews computational models of how thehippocampus cooperates with other brain structures--including the entorhinal cortex,basal forebrain, cerebellum, and primary sensory and motor cortices--to supportlearning and memory in both animals and humans. The book assumes no prior knowledgeof computational modeling or mathematics. For those who wish to delve more deeplyinto the formal details of the models, there are optional "mathboxes" andappendices. The book also includes extensive references and suggestions for furtherreadings.

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10/07/2011

Tutorial on Neural Systems Modeling Review

Tutorial on Neural Systems Modeling
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We used this book for the upper-level undergraduate students in an interdisciplinary computational neuroscience course at a small liberal arts college. This is a fine, well-written book. One of the strengths of this book is that it starts with very basic programming in Matlab, so that the students without programming backgrounds can easily follow along. The programs in the book are well commented, and they progress slowly and logically in complexity. More advanced math topics are well separated out in Math Boxes. The examples of the neural systems are covered in enough (but not too much) details to be interesting and accessible to the readers. The book is definitely considerate of and sensitive to the wonderfully interdisciplinary nature of this field, so that the materials can be digested by people with different backgrounds. One can not contain all the topics in computational neuroscience in a single book, but this book does a great job of covering many important and interesting ideas/areas (Hebbian learning, Hopfield model, lateral inhibition, adaptation, supervised and unsupervised learning, etc.).
It works very well as an introductory textbook (or tutorial) of the field. The codes and the discussions are clear and simple (not intended as an advanced textbook), and to me, that's the strength and unique quality of this book.
By the way, most of the computer programs listed in the book work well with Octave (as well as Matlab).

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Neural systems models are elegant conceptual tools that provide satisfying insight into brain function. The goal of this new book is to make these tools accessible. It is written specifically for students in neuroscience, cognitive science, and related areas who want to learn about neural systems modeling but lack extensive background in mathematics and computer programming.The book opens with an introduction to computer programming. Each of twelve subsequent chapters presents a different modeling paradigm by describing its basic structure and showing how it can be applied in understanding brain function. The text guides the reader through short, simple computer programs printed in the book and available by download at the companion website that implement the paradigms and simulate real neural systems. Motivation for the simulations is provided in the form of a narrative that places specific aspects of neural system behavior in the context of more general brain function. The narrative integrates instruction for using the programs with description of neural system function, and readers can actively experience the fun and excitement of doing the simulations themselves. Designed as a hands-on tutorial for students, this book also serves instructors as both a teaching tool and a source of examples and exercises that provide convenient starting points for more in-depth exploration of topics of their own specific interest.The distinguishing pedagogical feature of this book is its computer programs, written in MATLAB, that help readers develop basic skill in the area of neural systems modeling. (All of the program files are available online via the book s companion website. Actual data on real neural systems is presented in the book for comparison with the results of the simulations. Also included are asides ( Math Boxes ) that present mathematical material that is relevant but not essential to running the programs. Exercises and references at the end of each chapter invite readers to explore each topic area on their own.

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9/28/2011

Exercises in Rethinking Innateness: A Handbook for Connectionist Simulations (Neural Network Modeling and Connectionism) Review

Exercises in Rethinking Innateness: A Handbook for Connectionist Simulations (Neural Network Modeling and Connectionism)
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Here's a self-contained introduction to connectionist modeling. Easy to read and straight-forward, this text provides software and excercises aimed at stepping a novice through the basics of connectionism. Designed to accompany Rethinking Innateness (1996), these examples provide a glimpse into the world of cognitive modeling. The examples can, at times, be frustrating and the text is in need of more debugging hints; yet, the simulations are rewarding and thought-provoking. While those already familiar with connectionism will find the excercises too basic, those curious about connectionism will find the book a great place to start and one that doesn't bog the reader down with technical jargon. It is accessible, enjoyable, and written by two key players in connectionism: Kim Plunkett and Jeff Elman. Well worth reading, but only if the reader is willing to work through the basic simulations and answer the excercises along the way.

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This book is the companion volume to Rethinking Innateness: AConnectionist Perspective on Development (The MIT Press, 1996), which proposed a newtheoretical framework to answer the question "What does it mean to say that abehavior is innate?" The new work provides concrete illustrations--in the form ofcomputer simulations--of properties of connectionist models that are particularlyrelevant to cognitive development. This enables the reader to pursue in depth someof the practical and empirical issues raised in the first book. The authors' largergoal is to demonstrate the usefulness of neural network modeling as a researchmethodology.The book comes with a complete software package, including demonstrationprojects, for running neural network simulations on both Macintosh and Windows 95.It also contains a series of exercises in the use of the neural network simulatorprovided with the book. The software is also available to run on a variety of UNIXplatforms.

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9/01/2011

Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems (Computational Neuroscience) Review

Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems (Computational Neuroscience)
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This book is a detailed overview of the computational modeling of nervous systems from the molecular and cellular level and from the standpoint of human psychophysics and psychology. They divide their conception of modeling into descriptive, mechanistic, and interpretive models. My sole interest was in Part 3, which covers the mathematical modeling of adaptation and learning, so my review will be confined to these chapters. The virtue of this book, and others like it, is the insistence on empirical validation of the models, and not their justification by "thought experiments" and arm-chair reasoning, as is typically done in philosophy.
Part 3 begins with a discussion of synaptic plasticity and to what degree it explains learning and memory. The goal here is to develop mathematical models to understand how experience and training modify the neuronal synapses and how these changes effect the neuronal patterns and the eventual behavior. The Hebb model of neuronal firing is ubiquitous in this area of research, and the authors discuss it as a rule that synapses change in proportion to the correlation of the activities of pre- and postsynaptic neurons. Experimental data is immediately given that illustrates long-term potentiation (LTP) and long-term depression (LTD). The authors concentrate mostly on models based on unsupervised learning in this chapter. The rules for synaptic modification are given as differential equations and describe the rate of change of the synaptic weights with respect to the pre- and postsynaptic activity. The covariance and BCM rules are discussed, the first separately requiring postsynaptic and presynaptic activity, the second requiring both simultaneously. The authors consider ocular dominance in the context of unsupervised learning and study the effect of plasticity on multiple neurons. The last section of the chapter covers supervised learning, in which a set of inputs and the desired outputs are imposed during training.
In the next chapter, the authors consider the area of reinforcement learning, beginning with a discussion of the mathematical models for classical conditioning, and introducing the temporal difference learning algorithm. The authors discuss the Rescorla-Wagner rule , which is a trial-by-trial learning rule for the weight adjustments, in terms of the reward, the prediction, and the learning rate. They then discuss more realistic policies such as static action choice, where the reward/punishment immediately follows the action taken, and sequential action choice, where rewards may be delayed. The authors discuss foraging behavior of bees as an example of static action choice, reducing it to a stochastic two-armed bandit problem. The maze task for rats is discussed as an example of sequential action choice, and the authors reduce it to the "actor-critic algorithm." A generalized reinforcement learning algorithm is then discussed, with the rat water maze problem given as an example.
Chapter 10 is an overview of what the authors call "representational learning", which, as they explain, is a study of neural representations from a computational point of view. The goal is to begin with sensory input and find out how representations are generated on the basis of these inputs. That such representations are necessary is based on for example the consideration of the visual system, since, argue the authors, what is presented at the retina is too crude for an accurate representation of the visual world. The main strategy in the chapter is to begin with a deterministic or probabilistic input and construct a recognition algorithm that gives an estimate of the input. The algorithms constructed are all based on unsupervised learning, and hence the existence and nature of the causes must be computed using heuristics and the statistics of the input data. These two requirements are met via the construction of first a generative model and then a recognition model in the chapter. The familiar 'expectation maximization' is discussed as a method of optimization between real and synthetic data in generative models. A detailed overview of expectation maximization is given in the context of 'density estimation'. The authors then move on to discuss causal models for density estimation, such as Gaussian mixtures, the K-means algorithm, factor analysis, and principal components analysis. They then discuss sparse coding, as a technique to deal with the fact that the cortical activity is not Gaussian. They illustrate an experimental sample, showing the activity follows an exponential distribution in a neuron in the inferotemporal area of the macaque brain. The reader will recognize 'sparse' probability distributions as being 'heavy-tailed', i.e. having values close to zero usually, but ones far from zero sometimes. The authors emphasize the difficulties in the computation of the recognition distribution explicitly. The Olshausen/Field model is used to give a deterministic approximate recognition model for this purpose. The authors then give a fairly detailed overview of a two-layer, nonlinear 'Helmholtz machine' with binary inputs. They illustrate how to obtain the expectation maximization in terms of the Kullback-Leibler divergence. The learning in this model takes place via stochastic sampling and occurs in two phases, the so-called "wake and sleep" algorithm. The last section of the chapter gives a general discussion of how recent interest in coding, transmitting, and decoding images has led to much more research into representational learning algorithms. They discuss multi-resolution decomposition and its relationship to the coding algorithms available.

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Theoretical neuroscience provides a quantitative basis for describingwhat nervous systems do, determining how they function, and uncovering the generalprinciples by which they operate. This text introduces the basic mathematical andcomputational methods of theoretical neuroscience and presents applications in avariety of areas including vision, sensory-motor integration, development, learning,and memory.The book is divided into three parts. Part I discusses the relationshipbetween sensory stimuli and neural responses, focusing on the representation ofinformation by the spiking activity of neurons. Part II discusses the modeling ofneurons and neural circuits on the basis of cellular and synaptic biophysics. PartIII analyzes the role of plasticity in development and learning. An appendix coversthe mathematical methods used, and exercises are available on the book's Website.

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