SAMPLE SYLLABUS:

Special Topics: Decisions and Actions
NEURL-GA 3042-001
Instructor: Dora Angelaki (da93@nyu.edu)
Time: Mondays 10am-11.55 pm
This course will present the fundamental of the fields of sensory perception, actions and decision making, as well as the links between them.

Course Organization

Most classes other than Guest lectures and Project presentations will have two sections:

  • The first part will consist of a background discussion that is based on classical papers, book chapters, or reviews. All students are expected to have read the background material before the class. It will not be a formal lecture, but I will have slides which will lead a discussion among us. You should be prepared to present and explain figures from the mandatory reading materials when I call upon you.
  • In the second part of each class, one student will present in class and critically evaluate a published manuscript (see list below in blue). The goal of each presentation is not simply to go over what the authors wrote in the manuscript, but rather to think deeply about why and how the experiment was conducted and how it can be improved. It is expected that each student will make 2 such presentations throughout the course. During or after the presentation, the other students, who must also have read the paper, will ask a minimum of 2 questions each. These can be questions of clarity, but also deeper more insightful debates. On those weeks there is no assigned presentation, each student must again be prepared to formulate 2 insightful questions based on the required reading.

Evaluation

Each student’s grade will be determined by a combination of performance on paper and project presentation, class participation and final written paper. These components will be weighted as follows:

  • 30% Class presentations (selected papers)
  • 30% Class participation (questions/discussions)
  • 40% Final paper (see details below)

Final paper - Research grant proposal:

In this research paper, you should come up with a couple of novel hypotheses or questions, and design an experiment to test them. The paper will follow a short grant format, with 3 sections (single-spaced, 11 pt):

  • Specific aims (1 page, describing 2-3 questions or hypotheses you would like to test).
  • Background and Significance (2-3 pages) – why is this question important and significant and what has been done previously to motivate it? What would be the broader benefits from answering this question/testing this hypothesis?
  • Experimental plan (2-3 pages) – details about the experiment and data analyses themselves. What outcome would support or refute your hypothesis? Alternative outcomes and interpretations?

The written research paper will be due by May 12th at 11 pm. A few days before (Monday, May 10th and possibly May 3rd), students will make a 20-minute presentation of their research proposal in class. I am available to discuss ideas and give feedback throughout the course.

Special Arrangements: Students needing special arrangements should contact Dr. Angelaki (da93@nyu.edu) and arrange an office visit.

 

SCHEDULE

Class 1: Monday, February 1 2021: Introduction and Basic Organization – Choice of paper presentation by each student

 

Class 2: Monday, February 8 2021: Basic principles of perceptual decision making – sensory representation (Angelaki)

Background Reading:

(1) Britten KH, Shadlen MN, Newsome WT, Movshon JA. The analysis of visual motion: a comparison of neuronal and psychophysical performance. J Neurosci. 1992 Dec;12(12):4745-65;

(2) Britten KH, Newsome WT, Shadlen MN, Celebrini S, Movshon JA. A relationship between behavioral choice and the visual responses of neurons in macaque MT. Vis Neurosci. 1996 Jan-Feb;13(1):87-100.

Paper Presentation (in class by student):  Purushothaman G, Bradley DC. Nat Neurosci. 2005 Jan;8(1):99-106. Epub 2004 Dec 19.

 

Monday, February 15: No class

 

Class 3: Monday, February 22 2021: Basic principles of perceptual decision making – evidence accumulation (Angelaki)

Background Reading:

(1) Gold JI, Shadlen MN. The neural basis of decision making. Annu Rev Neurosci. 2007;30:535-74. Review.

(2) Shadlen MN, Kiani R. Decision making as a window on cognition. Neuron. 2013 Oct 30;80(3):791-806. doi: 10.1016/j.neuron.2013.10.047. Review.

(3) Brody CD, Hanks TD. Neural underpinnings of the evidence accumulator. Curr Opin Neurobiol. 2016 Apr;37:149-157. doi: 10.1016/j.conb.2016.01.003. Epub 2016 Feb 12. Review.

Paper Presentation (in class by student): Akrami A, Kopec CD, Diamond ME, Brody CD. Posterior parietal cortex represents sensory history and mediates its effects on behaviour. Nature. 2018 Feb 15;554(7692):368-372. doi: 10.1038/nature25510. Epub 2018 Feb 7.  

 

Class 4: Monday, March 1 2021: Multisensory Decisions (Angelaki)

Background Reading:

Fetsch CR, DeAngelis GC, Angelaki DE. Bridging the gap between theories of sensory cue integration and the physiology of multisensory neurons Nat Rev Neurosci. 2013 Jun;14(6):429-42. doi: 10.1038/nrn3503. Review.

Paper Presentation (in class by student): Drugowitsch J, DeAngelis GC, Klier EM, Angelaki DE, Pouget A. Elife. 2014 Jun 14;3. doi: 10.7554/eLife.03005.

Paper Presentation (in class by student): Hou H, Zheng Q, Zhao Y, Pouget A, Gu Y. Neural Correlates of Optimal Multisensory Decision Making under Time-Varying Reliabilities with an Invariant Linear Probabilistic Population Code. Neuron. 2019 Dec 4;104(5):1010-1021.e10. doi: 10.1016/j.neuron.2019.08.038. Epub 2019 Oct 10.

 

Class 5: Monday, March 8 2021: Bayesian decision models (Ma)

Background Reading: Ma WJ. Bayesian Decision Models: A Primer. Neuron. 2019 Oct 9;104(1):164-175. doi: 10.1016/j.neuron.2019.09.037. Review.

 

Class 6: Monday, March 15 2021: Neural network decision models (Wang)

Background Reading:

(1) Wang XJ. Probabilistic decision making by slow reverberation in cortical circuits. Neuron. 2002 Dec 5;36(5):955-68.

(2) Wang XJ. Decision making in recurrent neuronal circuits. Neuron. 2008 Oct 23;60(2):215-34. doi: 10.1016/j.neuron.2008.09.034. Review.

 

Class 7: Monday, March 22 2021: Causal Manipulations: microstimulation and inactivation (Angelaki)

Background Reading:

(1) Salzman CD, Murasugi CM, Britten KH, Newsome WT. Microstimulation in visual area MT: effects on direction discrimination performance J Neurosci. 1992 Jun;12(6):2331-55.

(2) Hanks TD, Ditterich J, Shadlen MN. Microstimulation of macaque area LIP affects decision-making in a motion discrimination task. Nat Neurosci. 2006 May;9(5):682-9. Epub 2006 Apr 9.

(3) Gu Y, DeAngelis GC, Angelaki DE. Causal links between dorsal medial superior temporal area neurons and multisensory heading perception. J Neurosci. 2012 Feb 15;32(7):2299-313. doi: 10.1523/JNEUROSCI.5154-11.2012.

Paper Presentation (in class by student): Pinto L, Rajan K, DePasquale B, Thiberge SY, Tank DW, Brody CD. Task-Dependent Changes in the Large-Scale Dynamics and Necessity of Cortical Regions. Neuron. 2019 Nov 20;104(4):810-824.e9. doi: 10.1016/j.neuron.2019.08.025. Epub 2019 Sep 26.

 

Class 8: Monday, March 29 2021: Caveats in causal manipulations (Savin)

Paper Presentation (in class by student): Katz LN, Yates JL, Pillow JW, Huk AC. Dissociated functional significance of decision-related activity in the primate dorsal stream. Nature. 2016 Jul 14;535(7611):285-8. doi: 10.1038/nature18617

 

Class 9: Monday, April 5 2021: Confidence in decisions (Ma)

Background Reading:

Hsin-Hung Li & Wei Ji Ma Confidence reports in decision-making with multiple alternatives violate the Bayesian confidence hypothesis, https://www.biorxiv.org/content/10.1101/583963v1.full

 

Class 10: Monday, April 12 2021: Reinforcement learning and dopamine (Angelaki)

Background Reading:

(1) Chapter 1 of “Reinforcement Learning: An Introduction”, Richard S. Sutton and Andrew G. Barto (read more if you are interested);

(2) Glimcher PW. Understanding dopamine and reinforcement learning: the dopamine reward prediction error hypothesis. Proc Natl Acad Sci U S A. 2011.

Paper Presentation (in class by student): Kim HR, Malik AN, Mikhael JG, Bech P, Tsutsui-Kimura I, Sun F, Zhang Y, Li Y, Watabe-Uchida M, Gershman SJ, Uchida N. (2020) A Unified Framework for Dopamine Signals across Timescales. Cell. S0092-8674(20)31530-0. doi: 10.1016/j.cell.2020.11.013.

Paper Presentation (in class by student): Matthew P. H. Gardner, Geoffrey Schoenbaum, Samuel J. Gershman. Rethinking dopamine as generalized prediction error. Proc Biol Sci. 2018 Nov 21; 285(1891): 20181645;

 

April 19 – NO CLASS

 

Class 11: Monday, April 26 2021: Cognitive maps and flexible behavior – a shift towards cognition (Angelaki)

Background Reading: Read about place and grid cells; there are many reviews available

Paper Presentation (in class by student): Behrens TEJ, Muller TH, Whittington JCR, et al. What Is a Cognitive Map? Organizing Knowledge for Flexible Behavior. Neuron. 2018;100(2):490–509. doi:10.1016/j.neuron.2018.10.002

Paper Presentation (in class by student): Stachenfeld KL, Botvinick MM, Gershman SJ. Nat Neurosci. 2017 Nov;20(11):1643-1653. doi: 10.1038/nn.4650.

 

Class 12: Monday, May 3 2021: Decisions in naturalistic tasks with active sensing (Angelaki)

Background Reading:

Pitkow X, Angelaki DE. Inference in the Brain: Statistics Flowing in Redundant Population Codes. Neuron. 2017 Jun 7;94(5):943-953. doi: 10.1016/j.neuron.2017.05.028. Review.

Paper Presentation (in class by student): Noel JP, Caziot B, Bruni S, Fitzgerald NE, Avila E, Angelaki DE. Supporting generalization in non-human primate behavior by tapping into structural knowledge: Examples from sensorimotor mappings, inference, and decision-making. Prog Neurobiol. 2021 Jan 14:101996. doi: 10.1016/j.pneurobio.2021.101996.

Paper Presentation (in class by student): Lakshminarasimhan KJ, Avila E, Neyhart E, DeAngelis GC, Pitkow X, Angelaki DE. Tracking the Mind's Eye: Primate Gaze Behavior during Virtual Visuomotor Navigation Reflects Belief Dynamics. Neuron. 2020 May 20;106(4):662-674.e5. doi: 10.1016/j.neuron.2020.02.023. Epub 2020 Mar 13.

 

Class 13: Monday, May 10 2021: Project presentations

 

PAPER DUE: May 12th by 11 pm (by email)