NSCI 401: Introduction to Modelling in Neuroscience

Syllabus (2014-2015)


Classroom: BioSci Building, Room 1120
Day, time: Wednesdays, 11:30am - 2:30pm

Office hours: Parisa Abedi Khoozani (TA) - Mon, Thu, Fri - 2:30-4:30pm (please make an appointment!)
Botterell Hall, Rm 223
Office hours with Parisa are for questions on team-based learning projects and paper presentations. For lecture-related questions, please contact myself.



Course organization (Sept 10)
Paper selection, course outline
Slides

Lecture (Sept 10):
The computational anatomy of the brain
Hierarchy
Brain structures and their functional role
Information flow
Cortical organization
Slides

Health and wellness...


Lecture (Sept 17):
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

Sept 20: drop-out limit

Seminar (Sept 24):
Izhikevich (2003) - none
Rolls, et al. (2008) - Muir C, Lu M


Lecture (Sept 24):
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 (Oct 8):
Petersen, et al. (2002) - de Kroon S, Green A, Song J
de la Rocha, et al. (2007) - none


Team-based learning project (Sept 24 - Oct 7):

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

Project - groups

Deadline for submission: Oct 7, 11:59pm


"Tell me, and I will forget.

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


Lecture (Oct 8):
Sensory processing
Sensation
World-brain interface
Sensory organs
Sensory pre-processing
Sensory processing
Sensory receptive fields
Gain modulation
Self-organizing maps
Slides

Seminar (Oct 15):
Bradley & Goyal (2008) - Ramanihar P, Trought K, Khan R
Keller & Hahnloser (2009)  - Solarski M, Pow K, Badger C


Lecture (Oct 15):
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 (Oct 22):
Ghasia, et al. (2008) - Sampieri G, Relke N, Jeyachandra J
Ramat, et al. (2007) - Sheculski M, Leisk H, Cho K

Lecture (Oct 22):
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 (Oct 29):
Resulaj, et al. (2009) - Janeteas C, Wang Y, Shannon K
Barraclough, et al. (2004) - Meyers D, Vincent A, Rodrigues J


Lecture (Oct 29):
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 (Nov 5):
Itti & Koch (2001) - Huang J, Wu L, Sasaki K
Cohen & Maunsell (2009) - Tsang P, Chow T, Poole M


Lecture (Nov 5):
Adaptation and learning
Introduction
What is learning?
Reward
Plasticity
Motor learning
Systems level approach
Synaptic plasticity
Hebbian learning
Physiology and biophysics
Learning in neural networks
Supervised vs. unsupervised learning
Conditioning and reinforcement learning
Slides

Seminar (Nov 12):
Izhikevich (2007) - Beauchamp B, Siu D
Law & Gold (2009) - Lee O, Hicks P, Lee J

Lecture (Nov 12):
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
Alzheimer's
Slides

Seminar (Nov 26):

Wilson & Linster (2008) - Hache P, Levac C, Lee S
Couey, et al. (2013) - Zhou J, Micu M, Zheng H


Team-based learning project (Nov 12-25):

Reading portfolio
Scott (2004)
Diedrichsen, et al. (2010)
Shadmehr & Krakauer (2008)

Project - groups

Deadline for submission: Nov 25, 11:59pm


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

(Albert Einstein)


Lecture (Nov 26):

Bayesian TBL Project debriefing slides
Optimal Control Theory TBL Project debriefing slides



Preliminary marks (60% of final mark)

Exam questions
(Fall 2014) - TBD

Time and location: Dec 9, 2pm, Grant Hall
(3h exam)
Fall 2010 exam questions (FYI)
Fall 2011 exam questions (FYI)
Fall 2012 exam questions (FYI)
Fall 2013 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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