CISC 3250: Systems Neuroscience



Class times: Monday and Thursday, 10:00 – 11:15am, John Mulcahy Hall (JMH) 302
Instructor: Prof. Daniel D. Leeds (my homepage)
Office: JMH 328A
E-mail:
Office hours: Tuesday 12:00 – 1:00pm and 3:00 – 4:00 pm, 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)

Matlab: We will be introduced to the Matlab computing environment in this course and use it selectively in 2-3 homework assignments. 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. Readings
  3. Slides
  4. Resources
  5. Assignments

Announcements:
May 2, 11:25pm: We will have extra office hours this Friday May 6, 11am-12pm at Lincoln Center: computer lab LL812.



April 21, 6:00pm: Our final exam will be May 9, 9:30-11:30am. Also, remember I will be offline 6pm April 22 until around 10 or 11pm April 24.



April 10, 10:35pm: Exam 2 has now been shifted to Monday April 25.



April 7, 10:10pm: We will meet in the JMH 330 computer lab next Monday, April 11. I am considering pushing the exam 2 date to April 25, but currently it is still scheduled for April 21. I will make my final decision over the weekend.



April 6, 4:40pm: We will meet in the JMH 330 computer lab this Thursday, April 7.



March 10, 11:45am: Class on Monday March 14 will begin in the JMH 330 computer lab.
I will be largely out of e-mail contact March 20-March 30. My office hours on Tuesday, March 29 are cancelled.
Also, Exam 2 is tentatively scheduled for April 21.



March 1, 11:40am: I will be out for the second half of my earlier office hour today -- 12:30-1pm. I WILL be in for my full later office hour, 3-4pm.



February 14, 11:20pm: Office hours this coming week will be Thursday, 5:30-6:30pm.



February 8, 11:50am: HW2 will be released Thursday and due February 19. Exam 1 will be Monday February 29.



February 8, 9:30am: As mentioned in class Thursday, class today will meet in the JMH 330 computer lab.



January 29, 1am: Class on Monday February 1, we will meet in the JMH 330 computer lab.

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

Lecture 1, The neuron biology and behavior.
Animation: movement of action potential down the axon

Lecture M1, Intro to Matlab, we will use a MAT file available here and another MAT file available here

Lecture 2, Learning in the neuron.

Lecture 3, Functional neuroanatomy.

Lecture 4, Representations in the brain.

Lecture M2, More on Matlab plotting and loops, we will use a MAT file available here and another MAT file available here

Lecture 5, Perception.

Lecture M3, Matlab vector math and comparisons.

Lecture 6, Motion. - Updated April 21 afternoon; correction about oscillations with delay=2 without forward model. Also, please note I was incorrect in class on one other topic: the right motor cortex controls the LEFT half of the body (contralateral side). Also, see reference video on cerebellar ataxia.

Lecture 7, Memory.

Resources:
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." Exam 1 answers! Below is the grade breakdown:
63-70 "A range"
56-63 "B range"
48-56 "C range"
40-48 "D range"
Exam 2 practice questions! Exam 2 answers! Below is the grade breakdown:
48.5 - 54 "A range"
43 - 48.5 "B range"
37.5 - 43 "C range"
32 - 37.5 "D range"
Final practice questions! -- a few more Matlab practice questions should be up next week

Assignments:
Homework 1 - due February 8. At 1pm on February 3: I modified the description of Question 1 on page 1 to make it more clear. Changes are in bold. The questions are the same, but hopefully slightly better-worded.
Homework 1 answers
44 - 51.5 "A range"
38 - 44 "B range"
32 - 38 "C range"
26 - 32 "D range"

Homework 2 - due February 22; Matlab section uploaded Sunday (Feb 14), also due February 22 - use hw2Data.mat file.
February 16: several corrections (Questions 2, 3b, 5a) and clarifications (Question 4 (second "question 4"), 5c, 5e) made in red
Homework 2 answers
59.5 - 65.5 "A range"
53 - 59.5 "B range"
46.5 - 53 "C range"

Homework 3 - due March 16; I added a few modifications/corrections in red on March 11 to make the questions more clear.
Answers now available (Number to letter grade to be posted tomorrow (same as posted in class).)
63.5 - 71 "A range"
56 - 63.5 "B range"
48 - 56 "C range"
40 - 48 "D range"


Homework 4 - due April 14, with some parts of questions 4-6 due April 18 (see the homework). Use files S11_localizer.mat and convolving.mat
Answers to HW 4
48.5 - 54 "A range"
41 - 48.5 "B range"
31 - 41 "C range"
21 - 31 "D range"


Homework 5 - due May 2, OPTIONAL
Answers to HW 5