Mathematical Tools
Mathematical Tools for Theoretical Neuroscience (NBHV GU4359)
Spring 2023
Class Assistants:Amol Pasarkar ([email protected]), Christine Liu ([email protected]), Elom Amematsro ([email protected]), Ines Aitsahalia ([email protected]), Ching Fang ([email protected]).
Faculty contact: Prof. Ken Miller ([email protected])
Time: Tuesdays, Thursdays 12:10  1:25pm
Place: L5084
Webpage: CourseWorks (announcements, assignments, readings)
Credits: 3
Description: An introduction to mathematical concepts used in theoretical neuroscience aimed to give a minimal requisite background for NBHV G4360, Introduction to Theoretical Neuroscience. The target audience is students with limited mathematical background who are interested in rapidly acquiring the vocabulary and basic mathematical skills for studying theoretical neuroscience, or who wish to gain a deeper exposure to mathematical concepts than offered by NBHV G4360. Topics include single and multivariable calculus, linear algebra, differential equations, signals and systems, and probability. Examples and applications are drawn primarily from theoretical and computational neuroscience.
Prerequisites: Basic prior exposure to trigonometry, calculus, and vector/matrix operations at the high school level.
Registration:
 Undergraduate and graduate students: Must register** on SSOL.
(**If you’re only interested in attending a subset of lectures, register Pass/Fail and contact Dan)
Mathematical Tools for Theoretical Neuroscience (Spring 2021)
Mathematical Tools for Theoretical Neuroscience (Spring 2020)
Computational Statistics
Computational Statistics (Stat GR6104), Spring 2023
This is a Ph.D.level course in computational statistics. A link to the most recent previous iteration of this course is here.
Note: instructor permission is required to take this class for students outside of the Statistics Ph.D. program.
Time: Th 2:30  4.00 pm
Place: JLG L3079
Professor: Liam Paninski; Email: liam at stat dot columbia dot edu. Hours by appointment.
Course goals: (partially adapted from the preface of Givens' and Hoeting's book): Computation plays a central role in modern statistics and machine learning. This course aims to cover topics needed to develop a broad working knowledge of modern computational statistics. We seek to develop a practical understanding of how and why existing methods work, enabling effective use of modern statistical methods. Achieving these goals requires familiarity with diverse topics in statistical computing, computational statistics, computer science, and numerical analysis. Our choice of topics reflects our view of what is central to this evolving field, and what will be interesting and useful. A key theme is scalability to problems of high dimensionality, which are of most interest to many recent applications.
Some important topics will be omitted because highquality solutions are already available in most software. For example, the generation of pseudorandom numbers is a classic topic, but existing methods built in to standard software packages will suffice for our needs. On the other hand, we will spend a bit of time on some classical numerical linear algebra ideas, because choosing the right method for solving a linear equation (for example) can have a huge impact on the time it takes to solve a problem in practice, particularly if there is some special structure that we can exploit.
Audience: The course will be aimed at first and secondyear students in the Statistics Ph.D. program. Students from other departments or programs are welcome, space permitting; instructor permission required.
Background: The level of mathematics expected does not extend much beyond standard calculus and linear algebra. Breadth of mathematical training is more helpful than depth; we prefer to focus on the big picture of how algorithms work and to sweep under the rug some of the nittygritty numerical details. The expected level of statistics is equivalent to that obtained by a graduate student in his or her first year of study of the theory of statistics and probability. An understanding of maximum likelihood methods, Bayesian methods, elementary asymptotic theory, Markov chains, and linear models is most important.
Programming: With respect to computer programming, good students can learn as they go. We'll forgo much languagespecific examples, algorithms, or coding; I won't be teaching much programming per se, but rather will focus on the overarching ideas and techniques. For the exercises and projects, I recommend you choose a highlevel, interactive package that permits the flexible design of graphical displays and includes supporting statistics and probability functions, e.g., R, Python, or MATLAB.
Evaluation: Final grades will be based on class participation and a student project.
Topics:
Deterministic optimization
 NewtonRaphson, conjugate gradients, preconditioning, quasiNewton methods, Fisher scoring, EM and its various derivatives
 Numerical recipes for linear algebra: matrix inverse, LU, Cholesky decompositions, lowrank updates, SVD, banded matrices, Toeplitz matrices and the FFT, Kronecker products (separable matrices), sparse matrix solvers
 Convex analysis: convex functions, duality, KKT conditions, interior point methods, projected gradients, augmented Lagrangian methods, convex relaxations
 Applications: support vector machines, splines, Gaussian processes, isotonic regression, LASSO and LARS regression
Graphical models: dynamic programming, hidden Markov models, forwardbackward algorithm, Kalman filter, Markov random fields
Stochastic optimization: RobbinsMonro and KieferWolfowitz algorithms, simulated annealing, stochastic gradient methods
Deterministic integration: Gaussian quadrature, quasiMonte Carlo. Application: expectation propagation
Monte Carlo methods
 Rejection sampling, importance sampling, variance reduction methods (RaoBlackwellization, stratified sampling)
 MCMC methods: Gibbs sampling, MetropolisHastings, Langevin methods, Hamiltonian Monte Carlo, slice sampling. Implementation issues: burnin, monitoring convergence
 Sequential Monte Carlo (particle filtering)
 Variational and stochastic variational inference
References:
Givens and Hoeting (2005) Computational statistics
Robert and Casella (2004) Monte Carlo Statistical Methods
Boyd and Vandenberghe (2004), Convex Optimization.
Press et al, Numerical Recipes
Sun and Yuan (2006), Optimization theory and methods
Fletcher (2000) Practical methods of optimization
Searle (2006) Matrix Algebra Useful for Statistics
Spall (2003), Introduction to Stochastic Search and Optimization: Estimation, Simulation, and Control
Shewchuk (1994), An Introduction to the Conjugate Gradient Method Without the Agonizing Pain
Boyd et al (2011), Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers
Neuroscience and Philosophy
Neuroscience and Philosophy (GU4500), Spring 2023
Time: Thursdays, 2:104:00
Place: L5084, Jerome L Greene (Zuckerman Institute)
Professor: John Morrison, Email: [email protected], office hours
Description: This course is about the philosophical foundations of cognitive neuroscience. Cognitive neuroscientists often describe the brain as representing and inferring. It is their way of describing the overall function of the brain’s activity, an abstraction away from detailed neural recordings. But, because there are no settled definitions of representation and inference, there are often no objective grounds for these descriptions. As a result, they are often treated as casual glosses rather than as rigorous analyses. Philosophers have proposed a number of (somewhat) rigorous definitions, but they rarely say anything about the brain. The goal of this course is to survey the philosophical literature and consider which definitions, if any, might be useful to cognitive neuroscientists. I will begin each class with a description of a different definition from the philosophical literature. We will then rely on our collective expertise to assess its potential applications to the brain. This course is for graduate students in Neurobiology and Behavior. No prior background in philosophy will be assumed.
Format: Each lecture will begin with a summary of the books and articles listed below. But I don’t expect you to read any of them. Many of them are (unnecessarily!) dense and inaccessible. Plus, they total hundreds of pages. It’s my job to distill them into a few basic points. If you want to learn more, reach out and I will recommend particular chapters, papers, etc.
Evaluation: Graduate students in Neurobiology and Behavior should write a 15page term paper applying one of the philosophical definitions to a particular experiment, preferably an experiment relevant to their own research. Other students should consult with the professor to identify an alternative form of evaluation. Undergraduates will be required to write at least two papers.
January 19th: Introduction
January 26th: Representation: Information Theories
Artiga and Sebasti, “Informational theories of content and mental representation”
DeWeese and Meister, “How to Measure the information gained from one symbol”
Scarantino, “Information as a probabilistic difference maker''
Fodor, “Information and representation”
Field, “Narrow” aspects of intentionality and the informationtheoretic approach to content”
Roche and Shogenji, “Information and inaccuracy”
Usher, “A statistical referential theory of content: Using information theory to account for
Misrepresentation”
February 2nd: Representation: Causal Theories
Buras, “An argument against causal theories of mental content”
Dretske, Knowledge and the Flow of Information
Dretske, Naturalizing the Mind
Dretske, “Misrepresentation”
Eliasmith, “A new perspective on representational problems”
Fodor, A Theory of Content and Other Essays
Fodor, Psychosemantics
Rupert, “The Best Test Theory of Extension: First Principle(s)”
Ryder, “SINBAD neurosemantics: A Theory of Mental Representation”
Sober and Roche, ``Disjunction and distality”
Tye, Ten Problems of Consciousness
Tye, Consciousness, Color, and Content
February 9th: No class
February 16th: Representation: Signaling Theories
Birch, “Propositional content in signalling systems''
GodfreySmith, Complexity and the Function of Mind in Nature
Lewis, Convention
Skyrms, Signals: Evolution, Learning, and Information
Shea, GodfreySmith, Cao, “Content in simple signalling systems”
Viera, “Representation without informative signaling”
February 23rd: Representation: Isomorphism Theories
Clark, Sensory Qualities
Cummins, Meaning and Mental Representation
Cummins, Representations, Targets and Attitudes
Ismael, The Situated Self
Millikan, “Review of Cummins Representations, Targets and Attitudes”
O’Brien and Opie, “Notes Toward a Structuralist Theory of Mental Representation”
Newell, Unified Theories of Cognition
Shagrir, “Structural Representations and the Brain”
March 2nd: Representation: Selection Theories
Millikan, “Biosemantics”
Millikan, “Pushmipullyu Representations”
Millikan, Language, Thought and Other Biological Categories
Millikan, White Queen Psychology and Other Essays for Alice
Millikan, Beyond Concepts: Unicepts, Language, and Natural Information
Millikan. “Neuroscience and Teleosemantics”
Shea, On Millikan
March 9th: Representation: Selection Theories (Part II)
Green, “Psychosemantics and The Rich/Thin Debate”
Neander, A Mark of the Mental: A Defence of Informational Teleosemantics
PPR symposium on A Mark of the Mental
Neander, “Content for Cognitive Science”
Nanay, “Teleosemantics Without Etiology”
Schulte, “Perceiving the outside world”
March 23rd: Representation: Selection and Isomorphism Hybrid
Shea, Representation in Cognitive Science
PPR symposium on Representation in Cognitive Science
March 30th: Representation: Nihilists, Deflationists, Pragmatists, and Interpretationists
Cao, “Putting representations to use'”
Chomsky, “Language and nature”
Churchland, Patricia Neurophilosophy
Churchland, Paul A Neurocomputational Perspective
Dennett, The Intentional Stance
Egan, “How to think about mental content”
Egan, “The nature and function of content in computational models”
Egan, “A deflationary account of mental representation”
Horgan and Tienson, Connectionism and the Philosophy of Psychology
Ramsey, Representation Reconsidered
RudderBaker, “Instrumental intentionality”
Sprevak, “Fictionalism about Neural Representations”
Williams, “Representational scepticism”
April 6th: Representation: Spillover, my own view (“comparativism”), and optional presentations
April 13th and April 20th: Inference: Mapping, Mechanistic, and Teleological Theories
Chalmers, “A Computational Foundation for the Study of Cognition” (and replies)
Chalmers, “Does a Rock Implement Every FiniteState Automaton?”
Chalmers, “On Implementing a Computation”
GodfreySmith, “Triviality Arguments Against Functionalism”
Maley, “Medium Independence and the Failure of the Mechanistic Account of Computation”
Maudlin, “Computation and Consciousness”
Putnam, Representation and Reality
Piccinini, Physical Computation
Rescorla, “A Theory of Computational Implementation”
Shagrir, The Nature of Physical Computation
Shagrir, “In Defense of the Semantic View of Computation”
Sprevak, “Triviality arguments about computational implementation”
Sprevak, “Computation, individuation, and the received view on representation”
April 27th: Inference: Spillover, my own view (“learning aptitude”), and optional presentations
Advanced Theory
Spring 2023
Meetings: Wednesdays, 10.0011.30 am
Location: L4.078 (will eventually be L5.084, but check email announcements) Jerome L. Greene Science Center, Broadway, New York, NY
For the zoom link contact [email protected]
Registration: Please register via Courseworks, the course is also open to external guests
Schedule:
Information theory
 Jan 25 Information theory (Jeff Johnston) Material
 Feb 01 Fisher information (Jeff Johnston)
 Feb 08 Gaussian Information bottleneck (Rainer Engelken)
Learning systems
 Feb 15 Expectation Maximization (Ji Xia)
 Feb 22 Reinforcement learning I (Kaushik Lakshminarasimhan)
 Mar 01 Reinforcement learning II (Kaushik Lakshminarasimhan)
 Mar 08 No session (Cosyne)
 Mar 15 No session (Spring break)
 Mar 22 Feedforward architectures I (Samuel Muscinelli)
 29 Mar Feedforward architectures II (Samuel Muscinelli)
Neural dynamics and computations
 Apr 05 Oscillations and WilsonCowan model (Patricia Cooney)
 Apr 12 Meanfield theory and perturbative approaches (Agostina Palmigiano)
 Apr 19 Lowrank neural networks I (Manuel Beiran)
 Apr 26 Lowrank neural networks II (Manuel Beiran)
 May 3 Singleneuron computations (Salomon Muller)

May 10 Student presentations
Advanced Theory Seminar (Spring 2022)
Advanced Theory Seminar (Summer/Fall 2020)
Advanced Theory Seminar (Spring 2020) website
Advanced Theory Seminar (Spring 2019) website
Intro to Theory
Computational Neuroscience, Fall 2022
Larry Abbott, Ken Miller, Ashok Litwin Kumar, Stefano Fusi, Sean Escola
TAs: Elom Amematsro, Ho Yin Chau, David Clark, Zhenrui Liao
Meetings: Tuesdays & Thursdays 2:003:30 (JLG L5084)
Text  Theoretical Neuroscience by P. Dayan and L.F. Abbott (MIT Press)
Webpage  https://ctn.zuckermaninstitute.columbia.edu/courses
September
6 (Larry) Introduction to Course and to Computational Neuroscience
8 (Larry) Electrical Properties of Neurons, IntegrateandFire Model
13 (Larry) Numerical Methods, Filtering (Assignment 1)
15 (Larry) The HodgkinHuxley Model
20 (Larry) Types of Neuron Models and Networks (Assignment 2)
21 Assignment 1 Due
22 (Stefano) Adaptation, Synapses, Synaptic Plasticity
27 (Sean) Generalized Linear Models
28 Assignment 2 Due
29 (Ken) Linear Algebra I (Assignment 3)
October
4 (Ken) Linear Algebra II
6 (Ken) PCA and Dimensionality Reduction
11 (Ken) Rate Networks/EI networks I (Assignment 4)
12 Assignment 3 Due
13 (Ken) Rate Networks/EI networks II
18 (Ken) Unsupervised/Hebbian Learning, Developmental Models (Assignment 5)
19 Assignment 4 Due
20 (Ashok) Introduction to Probability, Encoding, Decoding
25 (Ashok) Decoding, Fisher Information I
26 Assignment 5 Due
27 (Ashok) Decoding, Fisher Information II (Assignment 6)
November
1 (Ashok) Information Theory
3 (Ashok) Optimization I (Assignment 7)
8 Holiday
9 Assignment 6 Due
10 (Ashok) Optimization II
15 (Stefano) The Perceptron (Assignment 8)
16 Assignment 7 Due
17 (Stefano) Multilayer Perceptrons and Mixed Selectivity
22 (Stefano) Deep Learning (Assignment 9)
23 Assignment 8 Due
24 Holiday
29 (Sean) Learning in Recurrent Networks
December
1 (Stefano) Continual Learning and Catastrophic Forgetting
6 (Stefano) Reinforcement Learning (Assignment 10)
7 Assignment 9 Due
8 (Larry) Course Wrap up
14 Assignment 10 Due
Introduction to Theoretical Neuroscience (Fall 2021)
Introduction to Theoretical Neuroscience (Spring 2021)
Introduction to Theoretical Neuroscience (Spring 2020)
Statistical analysis of neural data
Statistical analysis of neural data (GR8201), Fall 2021
This is a Ph.D.level topics course in statistical analysis of neural data. Students from statistics, neuroscience, and engineering are all welcome to attend. A link to the last iteration of this course is here.
Time: F 1011:30
Place: JLG L8084
Professor: Liam Paninski; Office: Zoom. Email: [email protected]. Hours by appointment.
View Schedule
Prerequisite: A good working knowledge of basic statistical concepts (likelihood, Bayes' rule, Poisson processes, Markov chains, Gaussian random vectors), including especially linearalgebraic concepts related to regression and principal components analysis, is necessary. No previous experience with neural data is required.
Evaluation: Final grades will be based on class participation and a student project. Additional informal exercises will be suggested, but not required. The project can involve either the implementation and justification of a novel analysis technique, or a standard analysis applied to a novel data set. Students can work in pairs or alone (if you work in pairs, of course, the project has to be twice as impressive). See this page for some links to available datasets; or talk to other students in the class, many of whom have collected their own datasets.
Course goals: We will introduce a number of advanced statistical techniques relevant in neuroscience. Each technique will be illustrated via application to problems in neuroscience. The focus will be on the analysis of single and multiple spike train and calcium imaging data, with a few applications to analyzing intracellular voltage and dendritic imaging data. Note that this class will not focus on MRI or EEG data. A brief list of statistical concepts and corresponding neuroscience applications is below.
Page Last Updated: 01/23/2023