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2020-21 Catalog: Computation & Neural Systems (E&AS)

CNS 100

Introduction to Computation and Neural Systems

1 unit   |  first term
This course is designed to introduce undergraduate and first-year CNS graduate students to the wide variety of research being undertaken by CNS faculty. Topics from all the CNS research labs are discussed and span the range from biology to engineering. Graded pass/fail.
Instructor: Siapas
CNS/Psy/Bi 102 ab

Brains, Minds, and Society

9 units (3-0-6)   |  second, third terms
Prerequisites: Bi/CNS/NB/Psy 150 and CNS/Bi/Ph/CS/NB 187, or instructor's permission.
Introduction to the computations made by the brain during economic and social decision making and their neural substrates. Part a: Reinforcement learning. Unconscious and conscious processing. Emotion. Behavioral economics. Goal-directed and habit learning. Facial processing in social neuroscience. Part b: History and mechanisms of reinforcement. Associative learning. Mentalizing and strategic thinking. Neural basis of prosociality. Exploration-exploitation tradeoff. Functions of basal ganglia.
Instructors: O'Doherty/Adolphs, O'Doherty
Psy/CNS 105 ab

Frontiers in Neuroeconomics

5 units (1.5-0-3.5)   |  second term
The new discipline of Neuroeconomics seeks to understand the mechanisms underlying human choice behavior, born out of a confluence of approaches derived from Psychology, Neuroscience and Economics. This seminar will consider a variety of emerging themes in this new field. Some of the topics we will address include the neural bases of reward and motivation, the neural representation of utility and risk, neural systems for inter-temporal choice, goals vs habits, and strategic interactions. We will also spend time evaluating various forms of computational and theoretical models that underpin the field such as reinforcement-learning, Bayesian models and race to barrier models. Each week we will focus on key papers and/or book chapters illustrating the relevant concepts. Not offered 2020-21.
Psy/CNS 130

Introduction to Human Memory

9 units (3-0-6)   |  second term
The course offers an overview of experimental findings and theoretical issues in the study of human memory. Topics include iconic and echoic memory, working memory, spatial memory, implicit learning and memory; forgetting: facts vs. skills, memory for faces; retrieval: recall vs. recognition, context-dependent memory, semantic memory, spreading activation models and connectionist networks, memory and emotion, infantile amnesia, memory development, and amnesia. Not offered 2020-21.
CNS/Psy/Bi 131

The Psychology of Learning and Motivation

9 units (3-0-6)   |  second term
This course will serve as an introduction to basic concepts, findings, and theory from the field of behavioral psychology, covering areas such as principles of classical conditioning, blocking and conditioned inhibition, models of classical conditioning, instrumental conditioning, reinforcement schedules, punishment and avoidance learning. The course will track the development of ideas from the beginnings of behavioral psychology in the early 20th century to contemporary learning theory. Not offered 2020-21.
Instructor: O'Doherty
Psy/CNS 132

Computational Reinforcement-learning in Biological and Non-biological Systems

9 units (3-0-6)   |  third term
Reinforcement-learning concerns the computational principles by which animals and artificial agents can learn to select actions in their environment in order to maximize their future rewards. Over the past 50 years there has been a rich interplay between the development and application of reinforcement-learning models in artificial intelligence, and the investigation of reinforcement-learning in biological systems, including humans. This course will review this rich literature, covering the psychology of animal-learning, the neurobiology of reward and reinforcement, and the theoretical basis and application of reinforcement-learning models to biological and non-biological systems. Not offered 2020-21.
EE/CNS/CS 148

Selected Topics in Computational Vision

9 units (3-0-6)   |  third term
Prerequisites: undergraduate calculus, linear algebra, geometry, statistics, computer programming.
The class will focus on an advanced topic in computational vision: recognition, vision-based navigation, 3-D reconstruction. The class will include a tutorial introduction to the topic, an exploration of relevant recent literature, and a project involving the design, implementation, and testing of a vision system.
Instructor: Perona
Bi/CNS/NB/Psy 150

Introduction to Neuroscience

10 units (4-0-6)   |  third term
Prerequisites: Bi 8, 9, or instructor's permission.
General principles of the function and organization of nervous systems, providing both an overview of the subject and a foundation for advanced courses. Topics include the physical and chemical bases for action potentials, synaptic transmission, and sensory transduction; anatomy; development; sensory and motor pathways; memory and learning at the molecular, cellular, and systems level; and the neuroscience of brain diseases. Letter grades only.
Instructors: Adolphs, Lester
Bi/CNS/NB 152

Neural Circuits and Physiology of Appetite and Body Homeostasis

6 units (2-0-4)   |  third term
Prerequisites: Graduate standing or Bi/CNS/NB/Psy 150, or equivalent.
An advanced course of lectures, readings, and student presentations focusing on neural basis of appetites such as hunger and thirst. This course will cover the mechanisms that control appetites both at peripheral and central level. These include genetics, neural manipulation, and viral tracing tools with particular emphasis on the logic of how the body and the brain cooperate to maintain homeostasis. Given in alternate years; offered 2020-21.
Instructor: Oka
Bi/CNS/NB 154

Principles of Neuroscience

9 units (3-0-6)   |  first term
Prerequisites: Bi/CNS/NB/Psy 150 or equivalent.
This course aims to distill the fundamental tenets of brain science, unlike the voluminous textbook with a similar title. What are the essential facts and ways of understanding in this discipline? How does neuroscience connect to other parts of life science, physics, and mathematics? Lectures and guided reading will touch on a broad range of phenomena from evolution, development, biophysics, computation, behavior, and psychology. Students will benefit from prior exposure to at least some of these domains. Given in alternate years; offered 2020-21.
Instructor: Meister
CMS/CS/CNS/EE/IDS 155

Machine Learning & Data Mining

12 units (3-3-6)   |  second term
Prerequisites: CS/CNS/EE 156 a.
Having a sufficient background in algorithms, linear algebra, calculus, probability, and statistics, is highly recommended. This course will cover popular methods in machine learning and data mining, with an emphasis on developing a working understanding of how to apply these methods in practice. The course will focus on basic foundational concepts underpinning and motivating modern machine learning and data mining approaches. We will also discuss recent research developments.
Instructor: Pachter
CS/CNS/EE 156 ab

Learning Systems

9 units (3-1-5)   |  first, third terms
Prerequisites: Ma 2 and CS 2, or equivalent.
Introduction to the theory, algorithms, and applications of automated learning. How much information is needed to learn a task, how much computation is involved, and how it can be accomplished. Special emphasis will be given to unifying the different approaches to the subject coming from statistics, function approximation, optimization, pattern recognition, and neural networks.
Instructor: Abu-Mostafa
Bi/CNS/NB 157

Comparative Nervous Systems

9 units (2-3-4)   |  third term
Prerequisites: instructor's permission.
An introduction to the comparative study of the gross and microscopic structure of nervous systems. Emphasis on the vertebrate nervous system; also, the highly developed central nervous systems found in arthropods and cephalopods. Variation in nervous system structure with function and with behavioral and ecological specializations and the evolution of the vertebrate brain. Letter grades only. Given in alternate years; offered 2020-21.
Instructor: Allman
Bi/CNS 158

Vertebrate Evolution

9 units (3-0-6)   |  third term
Prerequisites: Bi 1, Bi 8, or instructor's permission.
An integrative approach to the study of vertebrate evolution combining comparative anatomical, behavioral, embryological, genetic, paleontological, and physiological findings. Special emphasis will be given to: (1) the modification of developmental programs in evolution; (2) homeostatic systems for temperature regulation; (3) changes in the life cycle governing longevity and death; (4) the evolution of brain and behavior. Letter grades only. Given in alternate years; not offered 2020-21.
Instructor: Allman
CS/CNS/EE/IDS 159

Advanced Topics in Machine Learning

9 units (3-0-6)   |  third term
Prerequisites: CS 155; strong background in statistics, probability theory, algorithms, and linear algebra; background in optimization is a plus as well.
This course focuses on current topics in machine learning research. This is a paper reading course, and students are expected to understand material directly from research articles. Students are also expected to present in class, and to do a final project. Not offered 2020-21.
Pl/CNS/NB/Bi 161

Consciousness

9 units (3-0-6)   |  second term
Prerequisites: None, but strongly suggest prior background in philosophy of mind and basic neurobiology (such as Bi 150).
One of the last great challenges to our understanding of the world concerns conscious experience. What exactly is it? How is it caused or constituted? And how does it connect with the rest of our science? This course will cover philosophy of mind, cognitive psychology, and cognitive neuroscience in a mixture of lectures and in-class discussion. There are no formal pre-requisites, but background in philosophy (equivalent to Pl 41, Pl 110) and in neuroscience (equivalent to BI/CNS 150) is strongly recommended and students with such background will be preferentially considered. Limited to 20.
Instructors: Adolphs, Eberhardt
Bi/CNS/NB 162

Cellular and Systems Neuroscience Laboratory

12 units (2-4-6)   |  second term
Prerequisites: Bi/CNS/NB/Psy 150 or instructor's permission.
A laboratory-based introduction to experimental methods used for electrophysiological studies of the central nervous system. Through the term, students investigate the physiological response properties of neurons in vertebrate and invertebrate brains, using extra- and intracellular recording techniques. Students are instructed in all aspects of experimental procedures, including proper surgical techniques, electrode fabrication, and data analysis. The class also includes a brain dissection and independent student projects that utilize modern digital neuroscience resources. Not offered 2020-21.
Instructor: Bremner
NB/Bi/CNS 163

The Biological Basis of Neural Disorders

6 units (3-0-3)   |  second term
Prerequisites: Bi/CNS/NB/Psy 150 or instructor's permission.
The neuroscience of psychiatric, neurological, and neurodegenerative disorders and of substance abuse, in humans and in animal models. Students master the biological principles including genetics, cell biology, biochemistry, physiology, and circuits. Topics are taught at the research level and include classical and emerging therapeutic approaches and diagnostic strategies. Given in alternate years; Not offered 2020-21.
Instructors: Lester, Lois
Bi/CNS/NB 164

Tools of Neurobiology

9 units (3-0-6)   |  first term
Prerequisites: Bi/CNS/NB/Psy 150 or equivalent.
Offers a broad survey of methods and approaches to understanding in modern neurobiology. The focus is on understanding the tools of the discipline, and their use will be illustrated with current research results. Topics include: molecular genetics, disease models, transgenic and knock-in technology, virus tools, tracing methods, gene profiling, light and electron microscopy, optogenetics, optical and electrical recording, neural coding, quantitative behavior, modeling and theory.
Instructor: Meister
CS/CNS/EE/IDS 165

Foundations of Machine Learning and Statistical Inference

12 units (3-3-6)   |  second term
Prerequisites: CMS/ACM/IDS 113, ACM/EE/IDS 116, CS 156 a, ACM/CS/IDS 157 or instructor's permission.
The course assumes students are comfortable with analysis, probability, statistics, and basic programming. This course will cover core concepts in machine learning and statistical inference. The ML concepts covered are spectral methods (matrices and tensors), non-convex optimization, probabilistic models, neural networks, representation theory, and generalization. In statistical inference, the topics covered are detection and estimation, sufficient statistics, Cramer-Rao bounds, Rao-Blackwell theory, variational inference, and multiple testing. In addition to covering the core concepts, the course encourages students to ask critical questions such as: How relevant is theory in the age of deep learning? What are the outstanding open problems? Assignments will include exploring failure modes of popular algorithms, in addition to traditional problem-solving type questions.
Instructor: Anandkumar
CS/CNS 171

Computer Graphics Laboratory

12 units (3-6-3)   |  first term
Prerequisites: Extensive programming experience and proficiency in linear algebra, starting with CS 2 and Ma 1 b.
This is a challenging course that introduces the basic ideas behind computer graphics and some of its fundamental algorithms. Topics include graphics input and output, the graphics pipeline, sampling and image manipulation, three-dimensional transformations and interactive modeling, basics of physically based modeling and animation, simple shading models and their hardware implementation, and some of the fundamental algorithms of scientific visualization. Students will be required to perform significant implementations.
Instructor: Barr
CS/CNS 174

Computer Graphics Projects

12 units (3-6-3)   |  third term
Prerequisites: Extensive programming experience, CS/CNS 171 or instructor's permission.
This laboratory class offers students an opportunity for independent work including recent computer graphics research. In coordination with the instructor, students select a computer graphics modeling, rendering, interaction, or related algorithm and implement it. Students are required to present their work in class and discuss the results of their implementation and possible improvements to the basic methods. May be repeated for credit with instructor's permission.
Instructor: Barr
CNS/Bi/Psy/NB 176

Cognition

9 units (4-0-5)   |  third term
The cornerstone of current progress in understanding the mind, the brain, and the relationship between the two is the study of human and animal cognition. This course will provide an in-depth survey and analysis of behavioral observations, theoretical accounts, computational models, patient data, electrophysiological studies, and brain-imaging results on mental capacities such as attention, memory, emotion, object representation, language, and cognitive development. Given in alternate years; Offered 2020-21.
Instructor: Shimojo
CNS 180

Research in Computation and Neural Systems

Units by arrangement with faculty
Offered to precandidacy students.
Bi/CNS/NB 184

The Primate Visual System

9 units (3-1-5)   |  third term
This class focuses on the primate visual system, investigating it from an experimental, psychophysical, and computational perspective. The course will focus on two essential problems: 3-D vision and object recognition. We will examine how a visual stimulus is represented starting in the retina, and ending in the frontal lobe, with a special emphasis placed on mechanisms for high-level vision in the parietal and temporal lobes. An important aspect of the course is the lab component in which students design and analyze their own fMRI experiment. Given in alternate years; not offered 2020-21.
Instructor: Tsao
Bi/CNS/NB 185

Large Scale Brain Networks

6 units (2-0-4)   |  third term
This class will focus on understanding what is known about the large-scale organization of the brain, focusing on the mammalian brain. What large scale brain networks exist and what are their principles of function? How is information flexibly routed from one area to another? What is the function of thalamocortical loops? We will examine large scale networks revealed by anatomical tracing, functional connectivity studies, and mRNA expression analyses, and explore the brain circuits mediating complex behaviors such as attention, memory, sleep, multisensory integration, decision making, and object vision. While each of these topics could cover an entire course in itself, our focus will be on understanding the master plan-how the components of each of these systems are put together and function as a whole. A key question we will delve into, from both a biological and a theoretical perspective, is: how is information flexibly routed from one brain area to another? We will discuss the communication through coherence hypothesis, small world networks, and sparse coding. Given in alternate years, not offered 2020-21.
Instructor: Tsao
CNS/Bi/EE/CS/NB 186

Vision: From Computational Theory to Neuronal Mechanisms

12 units (4-4-4)   |  second term
Lecture, laboratory, and project course aimed at understanding visual information processing, in both machines and the mammalian visual system. The course will emphasize an interdisciplinary approach aimed at understanding vision at several levels: computational theory, algorithms, psychophysics, and hardware (i.e., neuroanatomy and neurophysiology of the mammalian visual system). The course will focus on early vision processes, in particular motion analysis, binocular stereo, brightness, color and texture analysis, visual attention and boundary detection. Students will be required to hand in approximately three homework assignments as well as complete one project integrating aspects of mathematical analysis, modeling, physiology, psychophysics, and engineering. Given in alternate years; Not Offered 2020-21.
Instructors: Meister, Perona, Shimojo, Tsao
CNS/Bi/Ph/CS/NB 187

Neural Computation

9 units (3-0-6)   |  first term
Prerequisites: familiarity with digital circuits, probability theory, linear algebra, and differential equations.
Programming will be required. This course investigates computation by neurons. Of primary concern are models of neural computation and their neurological substrate, as well as the physics of collective computation. Thus, neurobiology is used as a motivating factor to introduce the relevant algorithms. Topics include rate-code neural networks, their differential equations, and equivalent circuits; stochastic models and their energy functions; associative memory; supervised and unsupervised learning; development; spike-based computing; single-cell computation; error and noise tolerance. Not Offered 2020-21.
Instructor: Perona
BE/CS/CNS/Bi 191 ab

Biomolecular Computation

9 units (3-0-6) second term; (2-4-3) third term   |  second, third terms
Prerequisites: none. Recommended: ChE/BE 163, CS 21, CS 129 ab, or equivalent.
This course investigates computation by molecular systems, emphasizing models of computation based on the underlying physics, chemistry, and organization of biological cells. We will explore programmability, complexity, simulation of, and reasoning about abstract models of chemical reaction networks, molecular folding, molecular self-assembly, and molecular motors, with an emphasis on universal architectures for computation, control, and construction within molecular systems. If time permits, we will also discuss biological example systems such as signal transduction, genetic regulatory networks, and the cytoskeleton.
Instructor: Winfree
Bi/CNS/NB 195

Mathematics in Biology

9 units (3-0-6)   |  first term
Prerequisites: calculus.
This course develops the mathematical methods needed for a quantitative understanding of biological phenomena, including data analysis, formulation of simple models, and the framing of quantitative questions. Topics include: probability and stochastic processes, linear algebra and transforms, dynamical systems, scientific programming.
Instructor: Thomson
Bi/CNS/NB 216

Behavior of Mammals

6 units (2-0-4)   |  first term
A course of lectures, readings, and discussions focused on the genetic, physiological, and ecological bases of behavior in mammals. A basic knowledge of neuroanatomy and neurophysiology is desirable. Given in alternate years; not offered 2020-21.
Instructor: Allman
Bi/CNS/NB 217

Central Mechanisms in Perception

6 units (2-0-4)   |  first term
Reading and discussions of behavioral and electrophysiological studies of the systems for the processing of sensory information in the brain. Given in alternate years; offered 2020-21.
Instructor: Allman
Bi/CNS/NB 220

Genetic Dissection of Neural Circuit Function

6 units (2-0-4)   |  third term
Prerequisites: Bi/CNS/NB/Psy 150 or equivalent. Open to advanced (junior or senior) undergraduates only and with instructor permission.
This advanced course will discuss the emerging science of neural "circuit breaking" through the application of molecular genetic tools. These include optogenetic and pharmacogenetic manipulations of neuronal activity, genetically based tracing of neuronal connectivity, and genetically based indicators of neuronal activity. Both viral and transgenic approaches will be covered, and examples will be drawn from both the invertebrate and vertebrate literature. Interested CNS or other graduate students who have little or no familiarity with molecular biology will be supplied with the necessary background information. Lectures and student presentations from the current literature.
Instructor: Anderson
Bi/CNS/BE/NB 230

Optogenetic and CLARITY Methods in Experimental Neuroscience

9 units (3-2-4)   |  third term
Prerequisites: Graduate standing or Bi/CNS/NB/Psy 150 or equivalent or instructor's permission.
The class covers the theoretical and practical aspects of using (1) optogenetic sensors and actuators to visualize and modulate the activity of neuronal ensembles; and (2) CLARITY approaches for anatomical mapping and phenotyping using tissue-hydrogel hybrids. The class offers weekly hands-on LAB exposure for opsin viral production and delivery to neurons, recording of light-modulated activity, and tissue clearing, imaging, and 3D reconstruction of fluorescent samples. Lecture topics include: opsin design (including natural and artificial sources), delivery (genetic targeting, viral transduction), light activation requirements (power requirements, wavelength, fiberoptics), compatible readout modalities (electrophysiology, imaging); design and use of methods for tissue clearing (tissue stabilization by polymers/hydrogels and selective extractions, such as of lipids for increased tissue transparency and macromolecule access). Class will discuss applications of these methods to neuronal circuits (case studies based on recent literature). Given in alternate years; not offered 2020-21.
Instructor: Gradinaru
CNS/Bi/NB 247

Cerebral Cortex

6 units (2-0-4)   |  second term
Prerequisites: Bi/CNS/NB/Psy 150 or equivalent.
A general survey of the structure and function of the cerebral cortex. Topics include cortical anatomy, functional localization, and newer computational approaches to understanding cortical processing operations. Motor cortex, sensory cortex (visual, auditory, and somatosensory cortex), association cortex, and limbic cortex. Emphasis is on using animal models to understand human cortical function and includes correlations between animal studies and human neuropsychological and functional imaging literature. Offered 2020-21.
Instructor: Andersen
Bi/CNS/NB 250 c

Topics in Systems Neuroscience

9 units (3-0-6)   |  third term
Prerequisites: graduate standing.
The class focuses on quantitative studies of problems in systems neuroscience. Students will study classical work such as Hodgkin and Huxley's landmark papers on the ionic basis of the action potential, and will move from the study of interacting currents within neurons to the study of systems of interacting neurons. Topics will include lateral inhibition, mechanisms of motion tuning, local learning rules and their consequences for network structure and dynamics, oscillatory dynamics and synchronization across brain circuits, and formation and computational properties of topographic neural maps. The course will combine lectures and discussions, in which students and faculty will examine papers on systems neuroscience, usually combining experimental and theoretical/modeling components.
Instructor: Siapas
CNS 251

Human Brain Mapping: Theory and Practice

9 units (2-1-6)   |  second term
A course in functional brain imaging. An overview of contemporary brain imaging techniques, usefulness of brain imaging compared to other techniques available to the modern neuroscientist. Review of what is known about the physical and biological bases of the signals being measured. Design and implementation of a brain imaging experiment and analysis of data (with a particular emphasis on fMRI). Offered 2020-21.
Instructor: O'Doherty
Psy/Bi/CNS 255

Topics in Emotion and Social Cognition

9 units (3-0-6)   |  third term
Prerequisites: Bi/CNS/NB/Psy 150 or instructor's permission.
Emotions are at the forefront of most human endeavors. Emotions aid us in decision-making (gut feelings), help us remember, torment us, yet have ultimately helped us to survive. Over the past few decades, we have begun to characterize the neural systems that extend from primitive affective response such as fight or flight to the complex emotions experienced by humans including guilt, envy, empathy and social pain. This course will begin with an in-depth examination of the neurobiological systems that underlie negative and positive emotions and move onto weekly discussions, based on assigned journal articles that highlight both rudimentary and complex emotions. The final weeks will be devoted to exploring how the neurobiological systems are disrupted in affective disorders including anxiety, aggression and psychopathy. In addition to these discussions and readings, each student will be required to write a review paper or produce a short movie on a topic related to one of the emotions discussed in these seminars and its underlying neural mechanisms.
Instructor: Mobbs
CNS/Bi/NB 256

Decision Making

6 units (2-0-4)   |  third term
This special topics course will examine the neural mechanisms of reward, decision making, and reward-based learning. The course covers the anatomy and physiology of reward and action systems. Special emphasis will be placed on the representation of reward expectation; the interplay between reward, motivation, and attention; and the selection of actions. Links between concepts in economics and the neural mechanisms of decision making will be explored. Data from animal and human studies collected using behavioral, neurophysiological, and functional magnetic resonance techniques will be reviewed. Not offered 2020-21.
Instructor: Andersen
CNS 280

Research in Computation and Neural Systems

Hours and units by arrangement
For graduate students admitted to candidacy in computation and neural systems.
SS/Psy/CNS 285

Topics in Social, Cognitive, and Decision Sciences

3 units (3-0-0)   |  second term
Select faculty will present their research background, methods, and a sampling of current questions/studies. Background readings and pdf of presentation will be provided. Not offered 2020-21.
CNS/Bi 286 abc

Special Topics in Computation and Neural Systems

Units to be arranged   |  first, second, third terms
Students may register with permission of the responsible faculty member.
Published Date: July 28, 2022