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Course 9: Brain and Cognitive Sciences |
 | | | 9.00-9.499 | | | 9.50-9.999 plus Thesis, UROP | | |  |
9.00 Introduction to Psychological Science
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Prereq: None Units: 4-0-8 
A survey of the scientific study of human nature, including how the mind works, and how the brain supports the mind. Topics include the mental and neural bases of perception, emotion, learning, memory, cognition, child development, personality, psychopathology, and social interaction. Consideration of how such knowledge relates to debates about nature and nurture, free will, consciousness, human differences, self, and society. J. D. Gabrieli 9.01 Introduction to Neuroscience
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Prereq: None Units: 4-0-8  Lecture: MW1-2.30 (46-3002) Recitation: R12 (46-1015) or R EVE (7 PM) (46-3037) or F11 (46-3037) or F1 (46-3037)
Introduction to the mammalian nervous system, with emphasis on the structure and function of the human brain. Topics include the function of nerve cells, sensory systems, control of movement, learning and memory, and diseases of the brain. M. Bear Textbooks (Fall 2025) 9.011 Systems Neuroscience Core I
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Prereq: Permission of instructor Units: 6-0-12 Lecture: MWF2-4 (46-5313) +final
Survey of brain and behavioral studies. Examines principles underlying the structure and function of the nervous system, with a focus on systems approaches. Topics include development of the nervous system and its connections, sensory systems of the brain, the motor system, higher cortical functions, and behavioral and cellular analyses of learning and memory. Preference to first-year graduate students in BCS. R. Desimone, E. K. Miller No textbook information available 9.012 Cognitive Science
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Prereq: Permission of instructor Units: 6-0-12
Intensive survey of cognitive science. Topics include visual perception, language, memory, cognitive architecture, learning, reasoning, decision-making, and cognitive development. Topics covered from behavioral, computational, and neural perspectives. E. Gibson, P. Sinha, J. Tenenbaum 9.013[J] Molecular and Cellular Neuroscience Core II
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(Same subject as 7.68[J]) Prereq: Permission of instructor Units: 3-0-9
Survey and primary literature review of major areas in molecular and cellular neurobiology. Covers genetic neurotrophin signaling, adult neurogenesis, G-protein coupled receptor signaling, glia function, epigenetics, neuronal and homeostatic plasticity, neuromodulators of circuit function, and neurological/psychiatric disease mechanisms. Includes lectures and exams, and involves presentation and discussion of primary literature. 9.015 recommended, though the core subjects can be taken in any sequence. G. Feng, L.-H. Tsai 9.014 Quantitative Methods and Computational Models in Neurosciences
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Prereq: None Units: 2-2-8 Lecture: M10-12 (46-1015) Lab: F10-12 (46-1015)
Provides theoretical background and practical skills needed to analyze and model neurobiological observations at the molecular, systems and cognitive levels. Develops an intuitive understanding of mathematical tools and computational techniques which students apply to analyze, visualize and model research data using MATLAB programming. Topics include linear systems and operations, dimensionality reduction (e.g., PCA), Bayesian approaches, descriptive and generative models, classification and clustering, and dynamical systems. Limited to 18; priority to current BCS Graduate students. M. Jazayeri, A. Rebei No textbook information available 9.015[J] Molecular and Cellular Neuroscience Core I
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(Same subject as 7.65[J]) Prereq: None Units: 3-0-9 Lecture: TR1-2.30 (46-4062)
Survey and primary literature review of selected major topic areas in molecular and cellular neurobiology. Covers nervous system development, axonal pathfinding, synapse formation and function, synaptic plasticity, ion channels and receptors, cellular neurophysiology, glial cells, sensory transduction, and relevant examples in human disease. Includes lectures and weekly paper write-ups, together with student presentations and discussion of primary literature. A final two-page research write-up is also due at the end of the term. J. T. Littleton, M. Sheng, B. Weissbourd No required or recommended textbooks 9.016[J] Introduction to Sound, Speech, and Hearing
()Not offered regularly; consult department (Same subject as HST.714[J]) Prereq: (6.3000 and 8.03) or permission of instructor Units: 4-0-8
Introduces students to the acoustics, anatomy, physiology, and mechanics related to speech and hearing. Focuses on how humans generate and perceive speech. Topics related to speech, explored through applications and challenges involving acoustics, speech recognition, and speech disorders, include acoustic theory of speech production, basic digital speech processing, control mechanisms of speech production and basic elements of speech and voice perception. Topics related to hearing include acoustics and mechanics of the outer ear, middle ear, and cochlea, how pathologies affect their function, and methods for clinical diagnosis. Surgical treatments and medical devices such as hearing aids, bone conduction devices, and implants are also covered. S. Ghosh, H. Nakajima, S. Puria 9.017 Systems Neuroscience Core II
()Not offered regularly; consult department Prereq: 18.06 or (9.011 and 9.014) Units: 2-2-8
Covers systems and computational neuroscience topics relevant to understanding how animal brains solve a wide range of cognitive tasks. Focuses on experimental approaches in systems neuroscience (behavioral design, parametric stimulus control, recording techniques) and theory-driven analyses (dynamical systems, control theory, Bayesian theory), both at the level of behavioral and neural data. Also focuses on regional organization (cortex, thalamus, basal ganglia, midbrain, and cerebellum), along with traditional divisions in systems neuroscience: sensory systems, motor systems, and associative systems. Staff 9.021[J] Cellular Neurophysiology and Computing
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(Same subject as 2.794[J], 6.4812[J], 20.470[J], HST.541[J]) (Subject meets with 2.791[J], 6.4810[J], 9.21[J], 20.370[J]) Prereq: (Physics II (GIR), 18.03, and (2.005, 6.2000, 6.3000, 10.301, or 20.110)) or permission of instructor Units: 5-2-5
Integrated overview of the biophysics of cells from prokaryotes to neurons, with a focus on mass transport and electrical signal generation across cell membrane. First third of course focuses on mass transport through membranes: diffusion, osmosis, chemically mediated, and active transport. Second third focuses on electrical properties of cells: ion transport to action potential generation and propagation in electrically excitable cells. Synaptic transmission. Electrical properties interpreted via kinetic and molecular properties of single voltage-gated ion channels. Final third focuses on biophysics of synaptic transmission and introduction to neural computing. Laboratory and computer exercises illustrate the concepts. Students taking graduate version complete different assignments. Staff 9.07 Statistics for Brain and Cognitive Science
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Prereq: 6.100B Units: 4-0-8 Lecture: MW9.30-11 (46-3310) Recitation: F10 (46-3310) +final
Provides students with the basic tools for analyzing experimental data, properly interpreting statistical reports in the literature, and reasoning under uncertain situations. Topics organized around three key theories: probability, statistical, and the linear model. Probability theory covers axioms of probability, discrete and continuous probability models, law of large numbers, and the Central Limit Theorem. Statistical theory covers estimation, likelihood theory, Bayesian methods, bootstrap and other Monte Carlo methods, as well as hypothesis testing, confidence intervals, elementary design of experiments principles and goodness-of-fit. The linear model theory covers the simple regression model and the analysis of variance. Places equal emphasis on theory, data analyses, and simulation studies. E. Brown No textbook information available 9.073[J] Statistics for Neuroscience Research
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(Same subject as HST.460[J]) Prereq: Permission of instructor Units: 3-0-9
A survey of statistical methods for neuroscience research. Core topics include introductions to the theory of point processes, the generalized linear model, Monte Carlo methods, Bayesian methods, multivariate methods, time-series analysis, spectral analysis and state-space modeling. Emphasis on developing a firm conceptual understanding of the statistical paradigm and statistical methods primarily through analyses of actual experimental data. E. N. Brown 9.09[J] Cellular and Molecular Neurobiology
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(Same subject as 7.29[J]) Prereq: 7.05 or 9.01 Units: 4-0-8
Introduction to the structure and function of the nervous system. Emphasizes the cellular properties of neurons and other excitable cells. Includes the structure and biophysical properties of excitable cells, synaptic transmission, neurochemistry, neurodevelopment, integration of information in simple systems, and detection and information coding during sensory transduction. T. Littleton, S. Prescott 9.110[J] Nonlinear Control
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(Same subject as 2.152[J]) Prereq: 2.151, 6.7100, 16.31, or permission of instructor Units: 3-0-9
Introduction to nonlinear control and estimation in physical and biological systems. Nonlinear stability theory, Lyapunov analysis, Barbalat's lemma. Feedback linearization, differential flatness, internal dynamics. Sliding surfaces. Adaptive nonlinear control and estimation. Multiresolution bases, nonlinear system identification. Contraction analysis, differential stability theory. Nonlinear observers. Asynchronous distributed computation and learning. Concurrent synchronization, polyrhythms. Monotone nonlinear systems. Emphasizes application to physical systems (robots, aircraft, spacecraft, underwater vehicles, reaction-diffusion processes, machine vision, oscillators, internet), machine learning, computational neuroscience, and systems biology. Includes term projects. Staff 9.12 Experimental Molecular Neurobiology
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Prereq: Biology (GIR) and 9.01 Units: 2-4-6
Experimental techniques in cellular and molecular neurobiology. Designed for students without previous experience in techniques of cellular and molecular biology. Experimental approaches include DNA manipulation, molecular cloning, protein biochemistry, dissection and culture of brain cells, synaptic protein analysis, immunocytochemistry, and fluorescent microscopy. One lab session plus one paper review session per week. Instruction and practice in written communication provided. Enrollment limited. Staff 9.123[J] Neurotechnology in Action
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(Same subject as 20.203[J]) Prereq: Permission of instructor Units: 3-6-3
Offers a fast-paced introduction to numerous laboratory methods at the forefront of modern neurobiology. Comprises a sequence of modules focusing on neurotechnologies that are developed and used by MIT research groups. Each module consists of a background lecture and 1-2 days of firsthand laboratory experience. Topics typically include optical imaging, optogenetics, high throughput neurobiology, MRI/fMRI, advanced electrophysiology, viral and genetic tools, and connectomics. E. Boyden, M. Jonas 9.13 The Human Brain
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Prereq: 9.00, 9.01, or permission of instructor Units: 3-0-9
Surveys the core perceptual and cognitive abilities of the human mind and asks how these are implemented in the brain. Key themes include the functional organization of the cortex, as well as the representations and computations, developmental origins, and degree of functional specificity of particular cortical regions. Emphasizes the methods available in human cognitive neuroscience, and what inferences can and cannot be drawn from each. N. Kanwisher 9.17 Systems Neuroscience Laboratory
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Prereq: 9.01 or permission of instructor Units: 2-4-6 Lecture: M3 (46-3310) Lab: F1-5 (46-1024) Recitation: T10 (46-3310)
Consists of a series of laboratories designed to give students experience with basic techniques for conducting systems neuroscience research. Includes sessions on anatomical, neurophysiological, and data acquisition and analysis techniques, and how these techniques are used to study nervous system function. Involves the use of experimental animals. Assignments include weekly preparation for lab sessions, two major lab reports and a series of basic computer programming tutorials (MATLAB). Instruction and practice in written communication provided. Enrollment limited. Frawley No required or recommended textbooks 9.175[J] Robotics
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(Same subject as 2.165[J]) Prereq: 2.151 or permission of instructor Units: 3-0-9 Lecture: TR1-2.30 (5-217)
Introduction to robotics and learning in machines. Kinematics and dynamics of rigid body systems. Adaptive control, system identification, sparse representations. Force control, adaptive visual servoing. Task planning, teleoperation, imitation learning. Navigation. Underactuated systems, approximate optimization and control. Dynamics of learning and optimization in networks. Elements of biological planning and control. Motor primitives, entrainment, active sensing, binding models. Term projects. J-J Slotine No textbook information available 9.18[J] Developmental Neurobiology
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(Same subject as 7.49[J]) (Subject meets with 7.69[J], 9.181[J]) Prereq: 7.03, 7.05, 9.01, or permission of instructor Units: 3-0-9
Considers molecular control of neural specification, formation of neuronal connections, construction of neural systems, and the contributions of experience to shaping brain structure and function. Topics include: neural induction and pattern formation, cell lineage and fate determination, neuronal migration, axon guidance, synapse formation and stabilization, activity-dependent development and critical periods, development of behavior. Students taking graduate version complete additional readings that will be addressed in their mid-term and final exams. E. Nedivi, S. Prescott 9.181[J] Developmental Neurobiology
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(Same subject as 7.69[J]) (Subject meets with 7.49[J], 9.18[J]) Prereq: 9.011 or permission of instructor Units: 3-0-9
Considers molecular control of neural specification, formation of neuronal connections, construction of neural systems, and the contributions of experience to shaping brain structure and function. Topics include: neural induction and pattern formation, cell lineage and fate determination, neuronal migration, axon guidance, synapse formation and stabilization, activity-dependent development and critical periods, development of behavior. In addition to final exam, analysis and presentation of research papers required for final grade. Students taking graduate version complete additional assignments. Students taking graduate version complete additional readings that will be addressed in their mid-term and final exams. E. Nedivi, S. Prescott 9.19 Computational Psycholinguistics
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(Subject meets with 9.190) Prereq: (6.100B and (6.3700, 9.40, or 24.900)) or permission of instructor Units: 4-0-8  Subject Cancelled
Introduces computational approaches to natural language processing and acquisition by humans and machines, combining symbolic and probabilistic modeling techniques. Covers models such as n-grams, finite state automata, and context-free and mildly context-sensitive grammars, for analyzing phonology, morphology, syntax, semantics, pragmatics, and larger document structure. Applications range from accurate document classification and sentence parsing by machine to modeling human language acquisition and real-time understanding. Covers both theory and contemporary computational tools and datasets. Students taking graduate version complete additional assignments. Staff 9.190 Computational Psycholinguistics
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(Subject meets with 9.19) Prereq: (6.100B and (6.3702, 9.40, or 24.900)) or permission of instructor Units: 4-0-8 Subject Cancelled
Introduces computational approaches to natural language processing and acquisition by humans and machines, combining symbolic and probabilistic modeling techniques. Covers models such as n-grams, finite state automata, and context-free and mildly context-sensitive grammars, for analyzing phonology, morphology, syntax, semantics, pragmatics, and larger document structure. Applications range from accurate document classification and sentence parsing by machine to modeling human language acquisition and real-time understanding. Covers both theory and contemporary computational tools and datasets. Students taking graduate version complete additional assignments. R. P. Levy 9.21[J] Cellular Neurophysiology and Computing
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(Same subject as 2.791[J], 6.4810[J], 20.370[J]) (Subject meets with 2.794[J], 6.4812[J], 9.021[J], 20.470[J], HST.541[J]) Prereq: (Physics II (GIR), 18.03, and (2.005, 6.2000, 6.3000, 10.301, or 20.110)) or permission of instructor Units: 5-2-5
Integrated overview of the biophysics of cells from prokaryotes to neurons, with a focus on mass transport and electrical signal generation across cell membrane. First third of course focuses on mass transport through membranes: diffusion, osmosis, chemically mediated, and active transport. Second third focuses on electrical properties of cells: ion transport to action potential generation and propagation in electrically excitable cells. Synaptic transmission. Electrical properties interpreted via kinetic and molecular properties of single voltage-gated ion channels. Final third focuses on biophysics of synaptic transmission and introduction to neural computing. Laboratory and computer exercises illustrate the concepts. Students taking graduate version complete different assignments. Preference to juniors and seniors. Staff 9.24 Disorders and Diseases of the Nervous System
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Prereq: (7.29 and 9.01) or permission of instructor Units: 3-0-9
Topics examined include regional functional anatomy of the CNS; brain systems and circuits; neurodevelopmental disorders including autism; neuropsychiatric disorders such as schizophrenia; neurodegenerative diseases such as Parkinson's and Alzheimer's; autoimmune disorders such as multiple sclerosis; gliomas. Emphasis on diseases for which a molecular mechanism is understood. Diagnostic criteria, clinical and pathological findings, genetics, model systems, pathophysiology, and treatment are discussed for individual disorders and diseases. Limited to 18. M. Sur 9.26[J] Principles and Applications of Genetic Engineering for Biotechnology and Neuroscience
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(Same subject as 20.205[J]) Prereq: Biology (GIR) Units: 3-0-9
Covers principles underlying current and future genetic engineering approaches, ranging from single cellular organisms to whole animals. Focuses on development and invention of technologies for engineering biological systems at the genomic level, and applications of engineered biological systems for medical and biotechnological needs, with particular emphasis on genetic manipulation of the nervous system. Design projects by students. F. Zhang 9.271[J] Pioneering Technologies for Interrogating Complex Biological Systems
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(Same subject as 10.562[J], HST.562[J]) Prereq: None Units: 3-0-9
Introduces pioneering technologies in biology and medicine and discusses their underlying biological/molecular/engineering principles. Topics include emerging sample processing technologies, advanced optical imaging modalities, and next-gen molecular phenotyping techniques. Provides practical experience with optical microscopy and 3D phenotyping techniques. Limited to 15. K. Chung 9.272[J] Topics in Neural Signal Processing
()Not offered regularly; consult department (Same subject as HST.576[J]) Prereq: Permission of instructor Units: 3-0-9
Presents signal processing and statistical methods used to study neural systems and analyze neurophysiological data. Topics include state-space modeling formulated using the Bayesian Chapman-Kolmogorov system, theory of point processes, EM algorithm, Bayesian and sequential Monte Carlo methods. Applications include dynamic analyses of neural encoding, neural spike train decoding, studies of neural receptive field plasticity, algorithms for neural prosthetic control, EEG and MEG source localization. Students should know introductory probability theory and statistics. E. N. Brown 9.285[J] Audition: Neural Mechanisms, Perception and Cognition
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(Same subject as HST.723[J]) Prereq: Permission of instructor Units: 6-0-6
Neural structures and mechanisms mediating the detection, localization and recognition of sounds. General principles are conveyed by theme discussions of auditory masking, sound localization, musical pitch, cochlear implants, cortical plasticity and auditory scene analysis. Follows Harvard FAS calendar. A. Takesian, J. McDermott, D. Polley, D. Mehta 9.300 BCS PhD Qualifying Exam
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| | | 9.00-9.499 | | | 9.50-9.999 plus Thesis, UROP | | | |
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