CISC 3250: Systems Neuroscience



Class times: Monday and Thursday, 10:00 – 11:15am, John Mulcahy Hall (JMH) 342
Instructor: Prof. Daniel D. Leeds (my homepage)
Office: JMH 332
E-mail:
Office hours: Monday 2 – 3pm and Thursday 3 – 4pm, and by appointment

Full syllabus is available here.
Course announcements and assignments will be posted over the course of the semester.

Course text: No good book for our course. "Fundamentals of Computational Neuroscience" (suggested); "Computational Cognitive Science" (suggested)

Matlab: We will be introduced to the Matlab computing environment in this course and use it selectively in homework assignments across the semester. You may use the copy available in the JMH 330 computer lab, but it also would be beneficial for you to download the Student license for $50 from Mathworks.

Sections below:

  1. Announcements
  2. Supplemental readings
  3. Slides
  4. Resources
  5. Assignments

Announcements:
May 7, 1:10pm: Office hours are today, 2-3pm!
May 6, 5:45pm: Our final exam is on May 10, 10am to noon Office hours Monday will be 12-1pm.
April 16, 12:15am: Office hours Monday will be 12-1pm.
April 9, 1:00am: Office hours Monday will be 12-1 and 3-4pm. Class will begin in JMH 330.
April 4, 4:00pm: Office hours tomorrow (Thursday) will be 2-3pm. I may also be free to meet earlier in the day as well if you have questions.
Also, exam 2 will be April 23.
March 29, 11:00am: As announced in class before break, Exam 2 will beeither April 19 or April 23. I will make an official determination by Tuesday, April 3.
March 1, 10:00am: As announced in class last time, I will not be holding office hours today. Please e-mail me if you have any questions.
February 14, 2:30pm: Office hours tomorrow (Thursday) are back to their regular time ... they will be 3-4pm. Sorry for the changes!
February 12, 9:35am: As announced last class, exam 1 will be March 1
February 7, 12:19am: Office hours this and next Thursday will be 2-3pm.
February 1, 11:37am: Office hours today are 2-3pm.
January 31, 11:00pm: As announced in class last time, we will begin class Feb 1 in the JMH 330 computer lab

Supplemental readings:
All readings are in Trappenberg, and they are optional.
TopicReadingEquations
Philosophy of neural modelingChapter 1: all (predominantly for perspective)
The neuron — biology and input/output behaviorChapter 2: 2.1, 2.2 (through 2.2.2);
Chapter 3: 3.1 (through 3.1.2), 3.3, 3.4.1, 3.4.5, 3.5		 3.1-3.4; 3.33, 3.35; 3.44; 3.45, 3.46
Learning in the neuronChapter 4: 4.1, 4.3 (through page 101), 4.4.3 4.3, 4.8, 4.10; 4.24, 4.27, 4.28, 4.29


Slides:
Check slides after each lecture - I sometimes update the slides with additional content based on class discussion

Lecture 1, The neuron biology and behavior.
Lecture M, Intro Matlab
Lecture 2, Learning in the neuron
Lecture M2, Matlab Lecture 2, Data for lecture
Lecture 3, Cortical organization and data formats
Lecture 4, Representations in the brain. V1 neuron responses -- check out first 3 minutes
Lecture M3, Matlab multi-dimensional matrices, we will use a MAT file Brain Anatomy and MAT file fMRI data
Lecture 5, Perception.
Lecture M4, Linear algebra and pattern comparisons, and here is related correlation data, and S11_localizer.mat
Lecture 6, Motor control - example of failed error correction with cerebllar ataxia
Lecture 7, Memory


Resources:
Matlab
spikeExample.mat
spikePlot.m

Below are exam 1 practice questions! Questions are randomly color-coded. I recommend trying to answer one set of colored questions first (for example, red questions), review the answers to those questions, and then move on to another set of colored questions (for example, green).
Note: The term "template recognition" used in one of the practice questions is synonymous with the term "prototype recognition."

Below are exam 2 practice questions

Below are final exam practice questions
  • Final Exam practice EXTRA QUESTIONS questions
  • Final Exam EXTRA QUESTIONS practice answers red
  • Final Exam EXTRA QUESTIONS practice answers blue
  • Final Exam EXTRA QUESTIONS practice answers green

    Assignments:
    Homework 1 - due February 5
    Homework 1 answers, grade assignments
    86-96 "A range"
    76-86 "B range"
    64-76 "C range"


    Homework 2 - due February 22, Correction to HW2 on pages 3 and 5 (as of Feb 15); data for homework in hw2.mat and S11_LOCbehav.mat
    Homework 2 answers
    72-80 A range
    64-72 B range
    54-64 C range


    Exam 1 answers
    72-80 A range
    64-72 B range
    56-64 C range


    Homework 3 - due March 19
    Homework 3 answers
    97-109 A range
    86-97 B range
    75-86 C range


    Homework 4 - due April 12; a few corrections made Apr 5 afternoon; additional clarifications added April 10 (makes some of the questions easier to understand)
    Homework 4 answers
    76-86 A range
    66-76 B range
    56-66 C range

    Homework 5 - due April 30
    Homework 5 answers


    Exam 2 answers
    84-94 A range
    71-84 B range
    61-71 C range