Cogs 180: Neural Coding in Sensory Systems (Spring 2017)

Tue & Thr 3:30-4:50
HSS 2321

Course website:


Angela Yu (Professor)

/ phone: 858-822-3317

Office Hours: Tue & Thr 4:50-5:45 - by appointment in SSRB 246

Course Description

This course covers recent advances in the understanding of common neural mechanisms and computational principles underlying the brain’s ability to process multiple sources of sensory information—vision, audition, touch, and multimodal inputs — and translate them into percepts and actions.

This seminar course will consist of lectures, reading, discussion, and writing related to research articles (primary and reviews). Students are especially encouraged to think deeply through some of these major questions in sensory neuroscience and bring their thoughts to class for active discussions.

Pre-reqs for Cogs 180: Cogs 1, Cogs 14B, Cogs 101A, Cogs 108/109 (or Math 18 & 20C; familiarity with PCA is helpful), or consent of instructor.


All required readings will be posted on the course website.

Recommended readings: Principles of Neural Science (Kandel, Schwartz, Jessell), Part V (Perception), Ed. 3, 4, or 5.

Course Details and Policies


Participation (20%): read papers and submit questions on Piazza before class; attend and actively participate in class (ask and answer questions). Course announcements will also be made on Piazza:

Discussion leading (25%): Email a link or pdf of draft slides by Monday/Wednesday 12 PM (, “Cogs 180 slides for <date>”), final slides (revised based on feedback, if necessary) by Tuesday/Thursday 12 PM. Use week 2 slides as an example: use illuminating figures (can be from referenced papers instead of assigned reading itself) and bullet points to highlight important messages and potential discussion points. Plan for 45 minutes of presentation, and 30 minutes of discussion. Include some suggested discussion questions/topics. Collect/organize questions from Piazza as appropriate.

Weekly assignments (30%): posted every Friday, due following Friday (5 PM) by email,, PDF format. Especially insightful answers may be awarded with extra credit. Late submission incurs 10% penalty for each day of delay, submission allowed until Sunday 5 PM (with 20% penalty).

Final in-class assignment (15%): open course material

Final project & presentation (10%): summarize three research talks and present them in class; see relevant talk series at bottom of this page.

Extra credit: SONA participation (up to 3 credits, equivalent to 3% of final grade)

Course Schedule

Week Date Topic Readings Assignments due (Fri) Presenter(s)
1 Tue Apr 04 Course overview (slides)
    Prof. Yu
Thu Apr 06 Introduction to vision (slides) Marr, D.   Prof. Yu
2 Tue Apr 11 Retina
Gollisch & Meister, 2010   Kay, Yvonne
Thu Apr 13 Retina
Gollisch & Meister, 2010   Kay, Yvonne
3 Tue Apr 18 LGN & V1
Nassi & Callaway, 2009   Kay, Yvonne
Thu Apr 20 V1
Ng, Bharath, & Zhaoping, 2007 (sec 3)

Optional reading:
Heeger notes
HW 1
Kay, Yvonne
4 Tue Apr 25 Visual attention Treue, 2001   Aamir, Alex
Thu Apr 27 Visual attention
Cohen & Maunsell, 2009 HW 2
Aamir, Alex
5 Tue May 02 Multistable perception Blake & Logothetis, 2002   Jocelyn, Darlene
Thu May 04 Multistable perception Blake & Logothetis, 2002 HW 3
Jocelyn, Darlene
6 Tue May 09 Perceptual decision-making Gold & Shadlen, 2002

Optional Reading:
slides on SPRT
  Aamir, Jong Hwi
Thu May 11 Perceptual decision-making Gold & Shadlen, 2002 HW 4
Aamir, Jong Hwi
7 Tue May 16 Auditory processing Kraus et al, 2009
  Jocelyn, Alex
Thu May 18 Auditory processing Machens et al, 2005
HW 5
Jocelyn, Alex
8 Tue May 23 Visual attention
Robert Desimone seminar @
CNCB Marilyn G. Farquhar Seminar Room
Thu May 25 Somatosensory processing
Petersen, 2007 HW 6
Mary, Darlene
9 Tue May 30 Visual working memory
Luck & Vogel, 2013 Final project talk selection
Mary, Jong Hwi
Thu Jun 01 Visual working memory Luck & Vogel, 2013   Mary, Jong Hwi
10 Tue Jun 06 In-class essay assignment
Thu Jun 08 Research talk/paper presentation   Final project writeup