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 and Thursday 1:00 – 2:00pm 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" (required); "Lippincott's Pocket Neuroanatomy" (optional)

SciLab: Software website, course resources

Sections below:

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

Announcements:
Now in reverse-chronological order
May 2, 2014 1:35am Below are final exam practice questions! Questions are randomly color-coded. I have not finished the answer key yet, but the answers should hopefully be up by the end of Friday. 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).
Update May 6, 2014 2:20pm A few of the red and blue and green answers have been corrected — the corrected answers are underlined and in larger font size.
      ALSO: For the first blue question I now specify tau=0.1 (NOT tau=2) and vthresh=35mV.
      ALSO: When evaluating a function with a sharp edge, if it is not clear if epsilon(4)=.5 or epsilon(4)=0 either answer acceptable May 1, 11:35am:Office hours today are 11:30am to noon (I am unable to be around for the regular 1-2 office hours). We will have additional hours next week, Monday noon-1pm.

April 27, 4:15pm: Exam 2 answers are now available here.
Grade breakdown (max possible score 68)
56-68: "A range", 3 students
47-56: "B range", 4 students
39-47: "C range", 3 students
31-39: "D range", 2 students


April 24, 11:20pm: Lecture of interest on interpretation of neural firing rates on April 28, 1-2pm: Bioinformatics Seminar from Asohan Amarasingham

April 20, 6:20pm: Our final exam will be on Thursday May 8, 9 – 11am in JMH 302.

 April 14, 11:30am: I will be off campus on Tuesday, April 15 and Tuesday, April 22 — thus, we will not have office hours those two Tuesdays. As always, I am happy to arrange alternate meeting times.

April 7, 2014 10:51pm Below are exam 2 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). April 7, 9:40am: Outline of topics for exam 2 available here.

March 30, 11:50am: Exam 2 will be on April 14, covering material from lecture slides 4, 5, and 6.

March 25, 5:00pm: E-mail me by March 27 to vote whether Exam 2 should be on April 14 or April 24.

March 24, 8:30pm: On May 5 and May 6 we will have class days, making up for the missed snow days, as announced by Fordham University.

March 10, 2:45am: Lecture of interest on hearing and seeing in the brain on March 27, 1-2pm: Clavius Distinguished Lecture from Shinsuke Shimojo

March 6, 11:20pm: Exam 1 answers are now available here.
Grade breakdown (max possible score 52)
46-52: "A range"
39-46: "B range"
32-39: "C range"


February 22, 9:35pm: More clarifications on exam details: February 18, 11:35pm: Practice exam questions (focusing on modeling) are available here. The answers are available here ...see update below. Each answer is placed on a separate page, so you can read the answer to one question without seeing the answer to the next question.
Update! The answers on page 6 of my original answer key are incorrect. The fully correct answer key is availabe here.

February 18, 12:45pm: Outline of topics for exam 1 available here.

February 3, 8:35am: We will have Exam 1 on Monday, February 24.

January 22, 9:15pm: Code and data for tomorrow's class in the computer lab can be found here, not including the SciLab software itself available here.

January 21, 11:40am: FYI, there is a typo in the syllabus. CISC 3250 does not "fulfill the Mathematical Reasoning requirement of the Core Curriculum." This does not affect anyone in the class, but I have corrected the course-description online nonetheless.

January 16, 2:15pm: We will be meeting in the computer lab in JMH 330 on Thursday, January 23. I encourage everyone to bring a laptop if they have one, but it is not required. Also, you are invited (but not required) to download scilab before class.

January 15, 8:30pm: Here is my policy towards laptops in class: I generally encourage students to avoid using laptops during class — the temptation for distraction can be hard to fight. That said, I do presently allow laptops to be used for note-taking or reading online course materials.

Readings:
All readings are in Trappenberg. Skip sections on simulations. TBA means the relevant parts of the chapter/book will be announced later in the semester. Key equations are listed — we wish to understand the intuition behind these equations. Equations that are crossed out (e.g., 3.5) are equations I originally was planning to cover but have now decided to skip due to time constraints.
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
Information representation with features in computer scienceChapter 6: 6.1, 6.2 6.6, 6.10, 6.12, 6.16; 6.18, 6.19, 6.23, 6.25, also look at 6.28, 6.31
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)
Optional reading on HMAX model here
Attention-related cellular mechanisms: 3.5.1, 3.5.3		 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. Most recent version of slides (January 27, noon) here.

Lecture 2, Learning in the Neuron. Most recent version of slides (February 6, noon) here.

Lecture 3, Neuroanatomy. Most recent version of slides (February 10, noon) here.

Lecture 4, Information representation in computer science. Most recent version of slides (February 27, early early morning) here. Final version available here (it is misleadingly labeled "March 3 edition").

Lecture 5, Representations in the brain. Most recent version of slides (March 24, 1:05pm, 3 extra slides added on March 27 to further illustrate population coding) here. The video shown in class showing excitation and suppression in V1 (primary visual cortex) is here ... we only watched the first three minutes dealing with "simple cells".

Lecture 6, Perception. Most recent version of slides (March 30, 1:00pm) here.

Lecture 7, Memory. Most recent version of slides (April 24, 12:40pm) here.

Lecture 8, Motor control. Most recent version of slides (May 1, 12:45pm) here.

Assignments:
HW1 due February 6. Assignment questions available here. Answers now available
Clarification: In Question 2, parts d-f, I am requesting weights that best detect one object and decrease the firing output of neuron 4 if either of the other two objects are shown — for example, in part d, best detect a Bird and decrease firing for plane and superman.
Suggestion: In Question 1, part b, you can assume tau=1 and v(0)=-70mV (though you can answer the question without these assumputions if you want). You also can try simulating the change of voltage with pen and paper and with a time step (delta t) of 1 s.
Grade breakdown (max possible score 13)
11.5-13: "A range," 7 students
9-11.5: "B range," 4 students
7-9: "C range," 1 students


HW2 due February 18. Assignment questions available here. Answers now available ... updated answers here
Update: Summation notation in question 2 corrected on Feb 11 at noon (switched from "wij rij" to "wij rij" — no change to meaning of the question
Grade breakdown (max possible score 16.5)
14-16.5: "A range," 3 students
10.5-14: "B range," 6 students
7-10.5: "C range," 3 students

HW3 due March 27. Assignment questions available here. Answers now available
Grade breakdown (max possible score 43)
37-43: "A range," 6 students
31-37: "B range," 2 students
25-31: "C range," 2 students

HW4 due April 7. Assignment questions available here. Answers now available
20.2-23: "A range," 10 students
17.5-20.2: "B range," 1 students
15-17.5: "C range," 0 students

HW5 due May 1. Assignment questions available here. Answers now available here.
Grade breakdown (max possible score 36)
32-36: "A range", 7 students
27-32: "B range", 4 students
23-27: "C range", 1 students
18-23: "D range", 1 students