Course home pages: courses.kersten.org
Instructor: Daniel Kersten, kersten@umn.edu, Office:
S212 Elliott Hall, Phone: 6252589
Office hours: Mondays 11:00 to 12:00 and by appointment.
Teaching
assistant: Brent Carpenter, carpe429@umn.edu
Office hours: Tuesdays at 9:00 11:00 am and by appointment
Course description. Introduction to large scale parallel distributed processing models in neural and cognitive science. Topics include: linear models, statistical pattern theory, Hebbian rules, selforganization, nonlinear models, information optimization, and representation of neural information. Applications to sensory processing, perception, learning, and memory.
Prerequisites: Linear algebra, multivariate calculus.
Lecture notes (see below)
Mathematica is the primary programming environment for this course. If you wish to purchase Mathematica for Students see http://www.wolfram.com/products/student/mathforstudents/index.html).
Accessing Mathematica on the CLA server wts.umn.edu::
For user help on using Mathematica, see: http://mathematica.stackexchange.com
Learning center: http://www.wolfram.com/learningcenter/
To start a notebook on the CLA server,
bring up a terminal window with: cmd,
then type: ipython notebook
Gopen, G. D., & Swan, J. A., 1990. The Science of Scientific Writing. American Scientist, 78, 550558. (pdf)
THE CENTER FOR WRITING offers free onetoone writing assistance to
undergraduate and graduate students, with appointments up to 45 minutes.
Nonnative speaker specialists are available. For more information, see http://writing.umn.edu
*Anderson, James. (1995) Introduction to Neural Networks, MIT Press.
***Bishop, C. M. (2006). Pattern recognition and machine learning. New
York: Springer.
*Dayan, P., & Abbott, L. F. (2001). Theoretical neuroscience
: computational and mathematical modeling of neural systems. Cambridge,
Mass.: MIT Press.
Freeman, J. A. (1994). Simulating Neural Networks with Mathematica . Reading,
MA: AddisonWesley Publishing Company. http://library.wolfram.com/infocenter/Books/3485/
**Gershenfeld, N. A. (1999). The nature of mathematical modeling. Cambridge
; New York: Cambridge University Press.
**Hertz, J., Krogh, A., &;Palmer, R. G. (1991). Introduction to the theory of neural computation (Santa Fe
Institute Studies in the Sciences of Complexity ed.). Reading, MA:
AddisonWesley Publishing Company.
Koch, C., & Segev, I. (Eds.). (1998). Methods in
Neuronal Modeling : From Ions to Networks (2nd ed.).
Cambridge, MA: MIT Press.
***MacKay, D. J. C. (2003). Information theory,
inference, and learning algorithms. Cambridge, UK ; New York: Cambridge University Press. http://www.inference.phy.cam.ac.uk/mackay/itila/book.html
***Murphy, K. P. (2012). Machine Learning: a Probabilistic Perspective. MIT Press.
*Neural/Cognitive Science
**Physics/Applied Math
***Statistical/machine learning
There will be programming assignments, as well as a final project. The grade weights are:
http://onestop.umn.edu/calendars/#fall2016
(NOTE: Links to revised lecture material below will be posted on
the day of the lecture.
Links to the pdfs for additional readings may require
a password.
If you want to preview similar material, check
out lectures from 2014)
Lecture notes are in Mathematica Notebook and pdf format. You can download the Mathematica notebook files below to view with Mathematica or Wolfram CDF Player (which is free).
Date 
Lecture 
Additional Readings & supplementary material 
Assignments 

1 
Sep 7 
Introduction 
Mathematica screencast 

2 
Sep 12 
The neuron (pdf file) Mathematica notebook 
HodgkinHuxley.nb 

3 
Sep 14 
Neural Models, McCullochPitt (pdf file) Mathematica notebook 
Koch, C., & Segev, I. (Eds.). (1998) (pdf) 

4 
Sep 19 
Generic neuron model (pdf file) Mathematica notebook 
Exercise 1  
5 
Sep 21 
Lateral inhibition (pdf file) Mathematica notebook 
Hartline (1972) (pdf) 

6 
Sep 26 
Matrices (pdf file) Mathematica notebook 

7 
Sep 28 
Linear
systems, learning & memory (pdf file) 

8 
Oct 3 
Linear recall, association and memory simulations (pdf file) Mathematica notebook 


9 
Oct 5 
Overview of nonlinear networks, discriminative models, Perceptron, SVMs (pdf file) , Mathematica notebook 


10 
Oct 10 
Supervised learning as regression, WidrowHoff, backprop (pdf file) Mathematica notebook 
XOR backpropagation demo. Mathematica notebook Poirazi, Brannon & Mel (2003) (pdf) Williams (1992) (pdf) 

11 
Oct 12 
Hopfield networks (pdf file) Mathematica notebook 
Hopfield
(1982) (pdf) IPython demo of Hopfield Stereo correspondence. Mathematica demo. IPython demo. 

12 
Oct 17 
Boltzmann machine (pdf file) Mathematica notebook 
Sculpting the energy function, interpolation (Mathematica notebook) Berkes, P., Orban, G., Lengyel, M., & Fiser, J. (2011). Spontaneous cortical activity reveals hallmarks of an optimal internal model of the environment. Science, 331(6013), 83. (pdf) 
Exercise 3 
13 
Oct 19 
Probability and
neural networks 
Griffiths and Yuille (2006) (pdf) Kersten D. & Yuille, A.L (2013) .Vision: Bayesian Inference and Beyond. The New Visual Neurosciences. John S. Werner and Leo M. Chalupa (Editors) MIT Press. Cambridge MA..(draft pdf) 

14 
Oct 24 
Multivariate distributions, Regression, Interpolation, perceptual completion 
Bias/Variance
notes 

15 
Oct 26 
Graphical models 
Pattern Recognition and Machine Learning, Chapter 8: Graphical Models. Christopher M. Bishop (pdf) Weiss Y. (pdf) 

16 
Oct 31 
Belief Propagation: regression and interpolation revisited (pdf ) Mathematica notebook (revised 10/31)

PROJECT GUIDELINES (pdf) SAMPLE PROJECT
IDEAS from previous years(pdf) For demonstration style projects, see the Wolfram Demonstration site How To Do Research. William T. Freeman (2013), (link) 
Correction to Problem 4: The Appendix in Lecture 15 (not 14) goes through the example using lists. 
17 
Nov 2 
Utility
& probabiilty: Bayes decision theory (pdf)

Geisler, W. S., & Kersten, D. (2002). Illusions, perception and Bayes. Nat Neurosci, 5(6), 508510. (pdf) 

18 
Nov 7

Supervised learning: neural networks in the context of machine learning 


19 
Nov 9 
More sampling 
http://pymcdevs.github.io/pymc/ Recommended pymc tutorials: http://camdavidsonpilon.github.io/ProbabilisticProgrammingandBayesianMethodsforHackers/ Lake, B. M., Salakhutdinov, R., & Tenenbaum, J. B. (2015). Humanlevel concept learning through probabilistic program induction. Science, 350(6266), 1332–1338. http://doi.org/10.1126/science.aab3050 

20 
Nov 14 
Overview of python/ipython for scientific compution/neural networks, and Bayesian computations. IPython notebook (using nbviewer) Raw notebook (needs viewer or jupyter to An older version at wakari.io:

Anaconda python installation recommended. We will use IPython, a browserbased notebook interface for python. See here for illustrations of IPython cell types, and here for a collection of sample notebooks. Look here for some good tips on installation, as well as the parent directory for excellent ipythonbased course material on scientific computing using Monte Carlo methods. For a quick start to scientific programming, see: http://nbviewer.ipython.org/gist/rpmuller/5920182 For a list of some notebooks in psychology, neuroscience, and machine learning see: For a comphrensive coverage of scientific python see:https://scipylectures.github.io And for a groundup set of tutorials on python see: http://learnpythonthehardway.org/book/ Switching from matlab to python? http://wiki.scipy.org/NumPy_for_Matlab_Users Practice: 1) TwoNeuroHopfield.py, 2) ConvolutionDemoFor5038.ipynb, which needs Zebra_running_Ngorongoro.jpg 

21 
Nov 16 
Lect_21_PyMC (raw IPython notebook) or Jupyter nbviewer PyMC2 sprinkler (raw) PyMC3 Gaussian mixtures (raw) PyMC3 spike rate transitions (raw) Scikitlearn gaussian mixtures (raw)

Carrandini, Heeger, Movshon (1996)(pdf) Supplement (pdf file) Mathematica notebook Kersten D. & Yuille, A.L. (2014) Inferential Models of the Visual Cortical Hierarchy. The New Cognitive Neurosciences, 5th Edition.(draft pdf) 
Revised to correct Question 5 
22 
Nov 21 
Architectures: Overview of visual hierarchy: Lect_22a_VisualArchitecture(Keynote pdf)


Final project title & paragraph outline due (2%) 
23 
Nov 23 
Neural networks for selforganization AdaptMaps(pdf) Mathematica notebook

Oja's rule and PCA: Sanger (2003) (pdf) Simoncelli,
E. P., & Olshausen, B. A. (2001). Natural image
statistics and neural representation. Annu Rev Neurosci, 24, 11931216.(pdf)


24 
Nov 28 
Efficient coding. Mathematica notebook (pdf)
Neural population codes(Mathematica notebook) (pdf) Probabilistic
neural representations, Poissonlike codes, and the neural integration of information. Keynote presentation

Knill & Pouget (2004) (pdf) Ma, W. J. (2012). Organizing probabilistic models of perception. Trends in Cognitive Sciences, 16(10), 511–518. (pdf) Quiroga, R. Q., Reddy, L., Kreiman,
G., Koch, C., & Fried, I. (2005).(pdf) 

25 
Nov 30 
Scientific writing and presentations (pdf) 
Gopen & Swan, 1990 (pdf) 

26 
Dec 5 
Clustering, EM, segmentation 
Expectation Maximization: Weiss Y. (pdf) Kirchner, H., & Thorpe, S. J. (2006). Ultrarapid object detection with saccadic eye movements: Visual processing speed revisited. Vision Research, 46(11), 1762–1776. doi:10.1016/j.visres.2005.10.002 (pdf) Ullman,
S., VidalNaquet, M., & Sali,
E. (2002). Visual features of intermediate complexity and their use in
classification. Nat Neurosci, 5(7), 682687. (pdf) Serre,
T., Oliva, A., & Poggio,
T. (2007). A feedforward architecture accounts for
rapid categorization. Proc Natl Acad Sci U S A, 104(15),
64246429. 
(~32 Mbytes) 
27 
Dec 7 
Bidirectional hierarchical models keynote presentation (pdf) 
Hong, H., Yamins, D. L. K., Majaj, N. J., & DiCarlo, J. J. (2016). Explicit information for categoryorthogonal object properties increases along the ventral stream. Nature Neuroscience, 1–18. http://doi.org/10.1038/nn.4247 Bullier, J. (2001). Integrated model of visual processing. Brain Res Brain Res Rev, 36(23), 96107. (pdf) Epshtein, B., Lifshitz, I., & Ullman, S. (2008). Image interpretation by a single bottomup topdown cycle. Proceedings of the National Academy of Sciences of the United States of America, 105(38), 14298. (pdf) Fang, F., Boyaci, H., Kersten, D., & Murray, S. O. (2008). Attentiondependent representation of a size illusion in human V1. Curr Biol, 18(21), 17071712 (pdf) Yuille,
A., & Kersten, D. (2006). Vision as Bayesian inference: analysis by
synthesis? Trends Cogn Sci,
10(7), 301308. (pdf) 
Complete
Draft of Final Project (5%) 

Dec 12 
Class presentations 
Peer comments on Final Project (5%)


Dec 14 Last day 
Class presentations 
Drafts returned with Instructor and peer comments December 14 

Dec 22 
End of Semester 
Submit Final Revised Draft of Project (28%) 
This course teaches you how to understand cognitive and perceptual aspects of brain processing in terms of computation. Writing a computer program encourages you to think clearly about the assumptions underlying a given theory. Getting a program to work, however, tests just one level of clear thinking. By writing about your work, you will learn to think through the broader implications of your final project, and to effectively communicate the rationale and results in words.
Your final project will involve: 1) a computer simulation and; 2) a 20003000 word final paper describing your simulation. For your computer project, you will do one of the following: 1) Devise a novel application for a neural network model studied in the course; 2) Write a program to simulate a model from the neural network literature ; 3) Design and program a method for solving some problem in perception, cognition or motor control. The results of your final project should be written up in the form of a short scientific paper, describing the motivation, methods, results, and interpretation. Your paper will be critiqued and returned for you to revise and resubmit in final form. You should write for an audience consisting of your class peers. You may elect to have your final paper published in the course's webbased electronic journal.
Completing the final paper involves 3 steps:
If you choose to write your program in Mathematica, your paper and program can be combined can be formated as a Mathematica notebook. See: Books and Tutorials on Notebooks.
Your paper will be critiqued and returned for you to revise and resubmit in final form. You should write for an audience consisting of your class peers.
Some Resources:
Student Writing Support: Center for Writing, 306b Lind Hall and satellite locations
(612.625.1893) http://writing.umn.edu.
Online Writing Center: http://writing.umn.edu/sws/visit/online/index.html
NOTE: Plagiarism, a form of scholastic dishonesty and a disciplinaryoffense, is described by the Regents as follows: Scholasticdishonesty means plagiarizing; cheating on assignments or examinations;engaging in unauthorized collaboration on academic work; taking,acquiring, or using test materials without faculty permission; submittingfalse or incomplete records of academic achievement; acting alone or incooperation with another to falsify records or to obtain dishonestlygrades, honors, awards, or professional endorsement; or altering,forging, or misusing a University academic record; or fabricating orfalsifying of data, research procedures, or data analysis.http://regents.umn.edu/sites/regents.umn.edu/files/policies/Student_Conduct_Code.pdf
NOTE: Sexual Assault and higher education: Training modules and information
The Department of Psychology supports the efforts of the University of Minnesota towards prevention of sexual assault. We encourage all students to participate in the free online training that has been established for undergraduate students and graduate students. The training highlights pertinent issues regarding sexual assault, including, but not limited to: defining healthy relationships, consent, bystander intervention, and gender roles. Haven (for undergraduate students under the age of 25) and Haven Plus (for undergraduates over 25, graduate students, and professional students) is the training available at no cost to University of Minnesota students. Additionally, to learn more about how you can help reduce sexual assault at the University of Minnesota, please visit the Aurora Center.
© 2016 Daniel Kersten, University of Minnesota