Andreas Stöckel, Terry Stewart, Chris Eliasmith
Nengo model of the cerebellum presented as a poster at the 42nd Annual Meeting of the Cognitive Science Society, 2020 (CogSci).
-
Link to the presentation video:
https://www.youtube.com/watch?v=vynNYvTUAHo -
Link to the paper:
http://compneuro.uwaterloo.ca/files/publications/stoeckel.2020a.pdf -
Link to the poster:
http://compneuro.uwaterloo.ca/files/publications/stoeckel.2020a.poster.pdf
The code in this repository is the exact codebase used to produce the results presented in the paper. To re-run the experiments, please make sure that a version of NengoBio from the beginning of February 2020 is installed.
The code to execute and visualise the experiments can be found in the notebooks folder, the model itself is located in the model folder.
To reproduce the results from the paper you can use the provided Dockerfile to enter a reproducible environment.
After installing docker on your system, execute the following from the root directory of this repository:
docker build -t cerebellum .
docker run -p 4567:4567 -it cerebellum
This will start a Jupyter lab instance inside the docker container; open the displayed URL (e.g., http://127.0.0.1:4567/lab?token=...) in your browser.
Open notebooks/Run Model.ipynb and select Restart Kernel and Run All Cells from the Kernel menu. Depending on your system, this might take a while (approximately one hour).
Now open the notebooks/Plot - Results - Basic.ipynb notebook; again, select Restart Kernel and Run All Cells from the Kernel menu. The displayed plots should be very similar to those found in the paper.
Note that pytry does not sort the individual trials deterministically; you may have to select a different trial for the final plot (e.g. by replacing data[1] with data[i] where i is between zero and five).
Important:
The experiment results are stored inside the temporary Docker container; once you close the container instance, any changes to the temporary file system are inaccessible.
You can try to convince Docker docker to mount a directory (comment out the ADD line in the Dockerfile; use docker run -v "$PWD:/cogsci2020-cerebellum:rw,z" -p 4567:4567 -it cerebellum) on the host machine, but I was not able to get this to work reliably with Jupyter lab due to file permission issues.
@inproceedings{stoeckel2020biologically,
title={A Biologically Plausible Spiking Neural Model of Eyeblink
Conditioning in the Cerebellum},
author={Andreas St\"ockel and Terrence C. Stewart and Chris Eliasmith},
booktitle={42nd Annual Meeting of the Cognitive Science Society},
year={2020},
pages={1614--1620},
publisher={Cognitive Science Society},
address={Toronto, ON},
}