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 328A
E-mail:
Office hours: Tuesday 2 – 3pm, Thursday 12:00 – 1:00pm and by appointment

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

Course text: "Fundamentals of Computational Neuroscience" (suggested); "Computational Cognitive Science" (will be used occasionally)

SciLab: Software website, course resources

Sections below:

  1. Announcements
  2. Readings
  3. Slides
  4. Assignments

Announcements:
May 4, 2015 4:50pm Just a reminder! Our final is on Thursday, May 7, 9:30-11:30am in our regular classroom. It is closed-book, and a simple calculator is allowed.

May 3, 2015 4:10pm I will have office hours on Wednesday 1-2pm of finals week; I will not be available in my office on Tuesday.

April 16, 2015 12:30pm Below are final exam practice questions! Questions are randomly color-coded. I recommend trying to answer one set of colored questions first (for example, orange questions), review the answers to those questions, and then move on to another set of colored questions (for example, green).

April 21, 2015 12:35pm You will not need to know logarithms for Exam 2 or for the final. In other words, you can ignore slide 18 on "estimating max" in Lecture 5.

April 16, 2015 12:30pm Below are exam 2 practice questions! Questions are randomly color-coded. I recommend trying to answer one set of colored questions first (for example, orange questions), review the answers to those questions, and then move on to another set of colored questions (for example, green).

April 9, 2015 5:50pm We will have the final exam on May 7 at 9:30am.

April 8, 2015 12:05am We will have Exam 2 on April 23, covering material from Lectures 4 and 5 (homeworks 3 and 4) and concepts in SciLab. Also, I will likely be unavailable for office hours Thursday April 9, but will be happy to schedule separate meetings times with anyone by e-mail as desired.

March 30, 2015 11:45am We will start class on Wednesday in JMH 331 (as we did today).

March 12, 2015 2:50pm There is a laptop policy embedded in our online syllabus. It says laptop usage is generally discouraged, but you may use laptops to read course-related material and to take notes. Do not use your laptops for general surfing during class. Also, if you do plan on using a laptop (preferably you should not use one), sit towards the back of the class so as not to distact students sitting behind you who can see the amazing online brain pictures you are loading and the complex systems equations you are devising.

Also, please note Wednesday, April 1 will be a Monday schedule! We will have class that day.

March 2, 2015 9:12pm The lab section of HW2 is now due next Monday, March 9. Good luck on midterms!

Exam 1 will be held on February 19 23 26
Practice questions     Practice answers
on Feb 25, 5:50pm, three corrections made in red to the answer key, however in each case the final answer has remained the same
35% neuron/anatomy facts, 65% HW-related math

February 10, 2015 1:45pm As announced by e-mail yesterday, I will shift my Thursday office hours this week to Wednesday, 3-4pm.

February 9, 2015 9:20am Due to the weather forecast, class was cancelled this morning! I should have your graded homeworks in my office available for pickup starting at 11am. I also will delay Exam 1 to February 23. I will move Thursday office hours this week to Wednesday -- details to follow. Note, homework 2 is still due this Thursday!

February 3, 2015 10:45pm I will not be available for the regular Thursday office hours this week, but you are welcome to contact me to schedule an alternate time to come by my office to discuss questions on the course material.

February 2, 2015 10:10am It looks like Rose Hill campus is closed all day. For now, I am presuming campus will be open tomorrow and you should drop by my office between noon and 6pm to turn in your homework. If that does not work for you, please e-mail me to let me know.


Readings:
All readings are in Trappenberg. Skip sections on simulations. Readings/equations for later chapters are subject to change closer to the time we reach this material in class.
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, 3.5, 3.6; 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
Neural systems and neuroanatomyChapter 5: 5.1
Representations in the brainChapter 7: 7.1, 7.5.1, 7.5.4 7.25-7.28, 7.40-7.42
Perception(Chapter 10: 10.1 ... optional, we will cover a simpler model in class)
Attention-related cellular mechanisms: 3.5.1, 3.5.3
Online chapter 6		 3.45
Memory/learning7.3.2-3, 8.1, 9.4
Motor control9.5, 9.6 (particularly 9.6.4)


Slides:
Lecture 1, The neuron biology and behavior. Now updated for Thursday January 15!
Animation: movement of action potential down the axon

Lecture 1.5, Introduction to Scilab
Lecture 2, Learning in the neuron; This version has the learned weights on the last several slides, two errors in slide 16 now corrected in green
Lecture 3, Neural systems, neuroanatomy
Lecture 3.5, More on Scilab
Lecture 4, Representations in the brain. Check out the following video demonstration for coding in V1.
Lecture 5, Perception (vision). Try listening to this combined speech recording
Lecture 5.5, Third scilab lecture
Lecture 6, Learning/memory
Lecture 7, Motion - Final motion equation has been corrected: T-(F+S-D) not T-(F+D-S)



Assignments:
Homework 1 — due February 2, 2015
Note: to plot the elements in a vector named vecName, use the instruction plot(vecName)
Answer key
38+ A range
32.5 - 38 B range
27 - 32.5 C range


Homework 2 — due February 12, 2015
Answer key - note lab section has not been assigned (nor graded!) yet
39+ A range
34.5 - 39 B range
30 - 34.5 C range

Homework 2 Lab — due March 5 9, 2015, HW 2 lab instructions updated, regarding column 6 of ExptRecord and regarding question 4
My answers to the HW 2 Lab are now online.
Grade breakdown
10.7+ A range
8.5-10.7 B range
6.2-8.5 C range

Answers to exam 1 are now available
Grade breakdown
55+ A range
49-55 B range
43-49 C range


Homework 3 — due March 26, 2015 - full homework is NOW ONLINE! Last two questions can be handed in on this Thursday as well, or can be handed in the following Monday.
My answers to homework 3 are now online. Answers to Question 2a and b have been corrected, as of April 21!

Homework 4 — due April 9
Example version of problem 2 -- in case there was confusion about the wording of problem 2, here is an example answer. Also, note for the actual problem 2 that Neuron 2 computes a weighted sum and then uses grad to compute the final rout
My answers to homework 4 are now online.

Homework 5 — due April 27 or 30 - hand in on Monday to get it graded for Thursday; or hand it in on Thursday to get the chance to ask me questions next Tuesday at office hours
My answers to homework 5 are now online.

Answers to exam 2 are now available
Grade breakdown
29.9+ A range
26.7-29.9 B range
23.6-26.7 C range