NSCI 401: Introduction to Modelling in Neuroscience

Fall 2021 Syllabus

: online
Day, time: Mon, 8:30-11:30am

Office hours: Jonny Coutinho (TA) - please make an appointment!

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

Course organization
Paper assignment, course outline

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)
Niv (2021)
Datta et al. (2019)
Poldrack (2020)
Smaldino (2016)
(due Oct 23, 11:59pm; submit on OnQ)

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

Seminar (week 3):
Izhikevich (2003) - PP1
Abbott et al. (2016) - PP2

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 (see OnQ)

Seminar (week 4):
Petersen, et al. (2002) - PP3
Stevenson et al. (2012) - PP4

Sensory processing
World-brain interface
Sensory organs
Sensory pre-processing
Sensory processing
Sensory receptive fields
Gain modulation
Self-organizing maps
Slides (see OnQ)

Seminar (week 5):
Bradley & Goyal (2008) - PP5
Aumentado-Armstrong et al. (2015) - PP6

Eye movements

Introduction to eye movements
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 (see OnQ)

Seminar (week 7):
Ghasia, et al. (2008) - PP7
Orban de Xivry et al. (2013) - PP8

Team-based learning project

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

Project - groups

Deadline for submission: Oct 16, 11:59pm

"Tell me, and I will forget.

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

Decision making
What are decisions?
Involved brain structures
Basal ganglia
Models of decision making
Race models
Diffusion models
Optimal decision criteria
Conflict resolution - winner-take-all
Slides (see OnQ)

Seminar (week 9):
Resulaj, et al. (2009) - PP9
Perugini et al. (2016) - PP10

Team-based learning project

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

Project - groups

Deadline for submission: Nov 6, 11:59pm

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

(Albert Einstein)

Adaptation and learning
What is learning?
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 (see OnQ)

Seminar (week 10):
Izhikevich (2007) - PP11
Kool et al. (2016) - PP12

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)
Slides (see OnQ)

Seminar (week 11):
Miconi & VanRullen (2016) - PP13
Akbas & Eckstein (2017) - PP14

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
Slides (see OnQ)
(week 12):
Wilson & Linster (2008) - PP15
Couey, et al. (2013) - PP16
Schneegans & Bays (2017) - PP17

Preliminary marks count for 70% of final mark

Final exam questions 
(Fall 2021) - TBA

Time and location:

Fall 2010 exam questions (FYI)
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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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