COMS30017

Computational Neuroscience

This is a 3rd year Computer Science and MSc unit. We will try to understand how the brain works, from a computational point of view.

Staff

Cian O’Donnell [cian.odonnell@bristol.ac.uk] (unit director)
Laurence Aitchison [laurence.aitchison@bristol.ac.uk]
Rahul Gupta [xv20319@bristol.ac.uk]
Beatriz Mizusaki [fv18192@bristol.ac.uk]

Teaching Assistants

David Rios Santini | Jack Bond-Preston | Katie Marquand | Sandra Montes Olivas | Yash Agarwal

Important info

All live sessions will be hosted on Microsoft Teams. To join the Team for this unit please login to the unit Blackboard page and click on the “Live Sessions” link on the left. You can download the MS Teams app free here, using your UoB email address. Please also use your UoB email address when joining the unit MS Team.

Overall structure

Weeks 1-7: Video lectures for the week released each Monday. Please watch when you can during the week. Each week will cover a different topic.
Weeks 2-8: Monday 10-11am, live Q+A session with lecturer(s). Chance to ask questions to the lecturer about the previous week’s material. Hosted on Microsoft Teams.
Weeks 2-7: Wednesday 1-2pm, live bubble discussion seminars. Each bubble will be moderated by a TA or lecturer with pre-set discussion topics related to the lecture material. Hosted on Microsoft Teams.
Weeks 1-7: Thursday 5-6pm, live peer bubble discussion groups. Students’ chance to ask each other questions and discuss the material! Hosted on Microsoft Teams.
Weeks 8-10: Coursework time, for those taking the 20-credit coursework version of the unit (COMS30015).
Week 11: Consolidation week. Catch up week for any further lecture material.
Week 12: Revision week. Preparation week for those students taking the 10-credit written exam version of unit (COMS30016 or COMSM0039).

Coursework exam for COMS30015

The coursework description is here: https://github.com/cs-uob/COMS30017/raw/master/coursework/COMS30017_coursework_2020.pdf. The data files needed for the coursework are in a zip file here: https://github.com/cs-uob/COMS30017/raw/master/coursework/datafiles_COMS30017_coursework_2020.zip. Submit your work on Blackboard, the deadline is 1pm on Friday 11th December (week 10). There will be drop-in support sessions on MS Teams from 2-3pm each Wednesday in weeks 8, 9 and 10.

Resit (summer 2021) coursework exam for COMS30015

The coursework description is here: https://github.com/cs-uob/COMS30017/raw/master/coursework_resit/COMS30017_coursework_summer21.pdf. The data files needed for the coursework are in a zip file here: https://github.com/cs-uob/COMS30017/raw/master/coursework_resit/datafiles_COMS30017_coursework_summer21.zip. Submit your work on Blackboard, the deadline is 13:00 on Monday 16th August 2021.

Past exams

The 2020/21 January exams with solutions can be found here:

Previous years’ exams can be found here (note they were a different format): https://github.com/coms30127/exam_papers

Intro meeting with Q+A

Recorded 10-10.45am 5/10/20. [Stream link] [pdf slides] (note the slides have been edited to correct the peer discussion timeslot.)

Weekly lecture material

Week 1: 5/10/2020 (Cian)

Background on brains.

Lecture	video	slides
1. Why brains?	19:47 [Stream link]	[pdf]
2. Brain anatomy.	21:37 [Stream link]	[pdf]
3. Neuron anatomy: axons, dendrites, synapses.	12:02 [Stream link]	[pdf]
4. Neuronal communication.	14:37 [Stream link]	[pdf]
5. Measuring, recording and stimulating the brain.	19:54 [Stream link]	[pdf]
Problem sheet	—	[pdf]
Live Q+A 12/10/20	[Stream link]	—

Week 2: 12/10/2020 (Rahul)

Differential equations, numerical methods, leaky integrate-and-fire neurons.

Lecture	video	slides
1. Introduction to Differential Equations: Part1	24:48 [Stream link]	[pdf]
2. Introduction to Differential Equations: Part2	17:44 [Stream link]	[pdf]
3. Numerical Methods for Differential Equations: Part1	17:43 [Stream link]	[pdf]
3.1 Simulation: Nonlinear_becomes_linear	00:36 [Stream link]	—
3.2 Simulation: Taylor_fits_better	00:40 [Stream link]	—
3.3 Simulation: Euler_does_poor	00:36 [Stream link]	—
3.4 Simulation: Euler_does_better	01:03 [Stream link]	—
4. Numerical Methods for Differential Equations: Part2	08:31 [Stream link]	[pdf]
5. Leaky Integrate-and-Fire Model of Neuron: Part1	20:17 [Stream link]	[pdf]
6. Leaky Integrate-and-Fire Model of Neuron: Part2	16:41 [Stream link]	[pdf]
Problem Sheet	—	[pdf]
Live Q+A 19/10/20	[Stream link]	—

Week 3: 19/10/2020 (Cian)

Hodgkin Huxley, modelling neurons, analysing spiking data.

Lecture	video	slides
1. Modelling neurons	26:29 [Stream link]	[pdf]
2. Ion channels & dendritic integration.	23:24 [Stream link]	[pdf]
3. Hodgkin-Huxley model.	33:51 [Stream link]	[pdf]
4. Analysing spike data.	17:05 [Stream link]	[pdf]
5. Neural decoding.	23:02 [Stream link]	[pdf]
Problem Sheet	—	[pdf]
Live Q+A 26/10/20	[Stream link]	—

Week 4: 26/10/2020 (Beatriz)

Synapses and synaptic plasticity

Lecture	video	slides
1. What is a synapse?	27:55 [Stream link]	[pdf]
2. Computational modelling of a synapse	18:10 [Stream link]	[pdf]
3. Synaptic plasticity	15:43 [Stream link]	[pdf]
4. Short-term plasticity	17:43 [Stream link]	[pdf]
5a. Long-term plasticity - part 1	26:03 [Stream link]	[pdf]
5b. Long-term plasticity - part 2 (start at slide #10)	21:31 [Stream link]	[pdf]
Video of simulation of synaptic activity	3:00 [Stream link]
Problem Sheet	—	[pdf]
Live Q+A 2/11/20	[Stream link]	—

Week 5: 2/11/2020 (Laurence)

Hippocampus + Hopfield networks

Lecture	video	slides
1. The Hippocampus and long-term memory	16:32 [Stream link]	[pdf]
2. The Hippocampus and spatial navigation	10:37 [Stream link]	[pdf]
3. Pattern Separation	20:43 [Stream link]	[pdf]
4. Hopfield networks (discrete attractors)	12:35 [Stream link]	[pdf]
5. Continuous attractors and navigation	12:28 [Stream link]	[pdf]
Problem sheet	—	[pdf]
Live Q+A 9/11/20	[Stream link]	—

Week 6: 9/11/2020 (Laurence)

Visual system + rate coding.

Lecture	video	slides
1. Firing rates and receptive fields	16:51 [Stream link]	[pdf]
2. The visual pathway	15:17 [Stream link]	[pdf]
3. Retina	7:08 [Stream link]	[pdf]
4. V1 and the cortical microcircuit	15:46 [Stream link]	[pdf]
5. Topographic maps and sparse coding	20:43 [Stream link]	[pdf]
Problem sheet	—	[pdf]
Live Q+A 16/11/20	[Stream link]	—

Week 7: 16/11/2020 (Laurence)

Cerebellum/basal ganglia, perceptrons, Rescorla-Wagner, blocking.

Lecture	video	slides
1. Supervised learning using the delta rule	12:00 [Stream link]	[pdf]
2. Cerebellar anatomy, function and microstructure	16:27 [Stream link]	[pdf]
3. Classical conditioning	19:32 [Stream link]	[pdf]
4. Temporal difference learning and dopamine	12:17 [Stream link]	[pdf]
Problem sheet	—	[pdf]

Revision Q&A’s

Laurence (week 5-7) [Stream Link])