NSCI 401: Introduction to Modelling in Neuroscience

Fall 2020 Syllabus

Classroom
: online
Day, time: live Q&A TBD

Office hours: Jonny Coutinho & Brandon Caie (TAs) - please make an appointment!

Office hours with Jonny (for opinion paper and paper presentations) and Brandon (for TBL projects) are for questions on team-based learning projects and paper presentations. For lecture-related questions, please contact me.



Course organization (Sept 7-11)
Paper assignment, course outline
Slides

Health and wellness...
Some health and wellness pointers

Short opinion paper assignment (chose one):
Jonas & Kording (2017)
Krakauer et al. (2017)
Buzsáki (2020)
Hasson et al. (2020)
Nastase et al. (2020)
Richards et al. (2019)
Cisek (2019)
(due Oct 4, 11:59pm; submit on OnQ)


Lecture (Sept 14-18):
Single neuron models
Introduction to the working principles of neurons
Membrane potentials
Ion channels
An excursion into electricity
Modelling single neuron behaviour
Synapses
Synaptic inputs
Integrate and fire models
Hodgkin-Huxley neuron model
Other models
Slides

Seminar:
Izhikevich (2003)
Abbott et al. (2016)


Lecture (Sept 21-25):
Spike coding
What is a code?
Spike train properties
Spike rates
Tuning curves
Spike count variability
Poisson statistics
Spike coding
Cosine tuning
Population coding
A few words about decoding
Slides

Seminar:
Petersen, et al. (2002)
Stevenson et al. (2012)


Lecture (Sept 28 - Oct 2):
Sensory processing
Sensation
World-brain interface
Sensory organs
Sensory pre-processing
Sensory processing
Sensory receptive fields
Gain modulation
Self-organizing maps
Slides

Seminar:
Bradley & Goyal (2008)
Aumentado-Armstrong et al. (2015)


Lecture (Oct 5-9):
Eye movements

Introduction to eye movements
Types
Neural substrates
Control problems
Modelling eye movements
Linear systems theory
Modelling the eye (Laplace formalism)
Gaze holding (the neural integrator)
Motor command generation
Coordinating different eye (and head) movements
Problems and solutions
Slides

Seminar:
Ghasia, et al. (2008)
Orban de Xivry et al. (2013)

Team-based learning project (Oct 12 - 16):

Reading portfolio
Deneve & Pouget (2004)
Körding & Wolpert (2006)
Probabilities primer (optional)

Project - groups

Deadline for submission: Oct 18, 11:59pm


"Tell me, and I will forget.

                                    Show me, and I may remember.
                                    Involve me, and I will understand."
(Chinese proverb)


Lecture (Oct 19-23):
Decision making
What are decisions?
Involved brain structures
Basal ganglia
Cortex
Models of decision making
Race models
Diffusion models
Optimal decision criteria
Conflict resolution - winner-take-all
Slides

Seminar:
Resulaj, et al. (2009)
Perugini et al. (2016)



Nov 2: drop-out deadline


Team-based learning project (Nov 2-6):

Reading portfolio
Scott (2012)
Diedrichsen, et al. (2010)
Shadmehr & Krakauer (2008)

Project - groups

Deadline for submission: Nov 8, 11:59pm


"Any fool can know.
The point is to understand."

(Albert Einstein)



Lecture (Nov 9-13):
Adaptation and learning
Introduction
What is learning?
Reward
Plasticity
Motor learning
Systems level approach
Reinforcement learning (RL)
Synaptic plasticity
Hebbian learning
Physiology and biophysics
Learning in neural networks
Supervised vs. unsupervised learning
Conditioning and reinforcement learning
Slides

Seminar:
Izhikevich (2007)
Kool et al. (2016)

Lecture (Nov 16-20):
Modelling attention
What is attention?
Overt vs. covert attention
Visual attention
Neural mechanisms
Modelling visual attention (Itti & Koch)
Feature maps
Saliency maps
Top-down modulation: expectation & task demands
Selective tuning model & hierarchies (Tsotsos)
Neglect
Slides

Seminar:
Miconi & VanRullen (2016)
Akbas & Eckstein (2017)


Lecture (Nov 23-27):
Memory
Introduction
Definition & processes
Long-term vs. short-term memory
Short-term memory
Neuronal behaviour
Potential mechanisms
Link to attention
Memory theories (long-term)
Associative and auto-associative memory
Distributed memory
Sparse coding and capacity
Disorders
Amnesia
Slides

Seminar:

Wilson & Linster (2008)
Couey, et al. (2013)
Schneegans & Bays (2017)

Lecture (Nov 30 - Dec 4):




Preliminary marks count for 70% of final mark

Final exam questions 
(Fall 2020) - TBA

Time and location:

Fall 2010 exam questions (FYI)
Fall 2011 exam questions (FYI)
Fall 2012 exam questions (FYI)
Fall 2013 exam questions (FYI)
Fall 2014 exam questions (FYI)
Fall 2016 exam questions (FYI)
Fall 2017 exam questions (FYI)
Fall 2018 exam questions (FYI)
Fall 2019 exam questions (FYI)

Peer Support Centre



Further readings:
Peter Dayan & Larry F. Abbott. Theoretical Neuroscience. MIT-Press, 2001
Thomas P. Trappenberg. Fundamentals of Neuroscience (2nd Ed.). Oxford University Press, 2010



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