Towards simulating neurogenesis on real-time neuromorphic hardware

The goal at the outset of my PhD was to simulate hippocampal or striatal adult neurogenesis on SpiNNaker. The network would have been described using the
PyNN simulator-independent language. This process entails several phases of potentially increasing difficulty (this list is not exhaustive):

1. Create a SpiNNaker based framework for defining rewiring synapses

2. sPyNNaker (SpiNNaker's implementation of PyNN) synaptogenesis simulation -- replication of Simeon Bamford's doctoral thesis

3. Extend framework to allow for Neurogenesis

At the time of writing, neurogenesis is not realised. However, extensive experiments have been performed using the synaptic rewiring model implemented on SpiNNaker. For more details, see below.

This repository is a collection of different experiments, mostly revolving around synaptic rewiring (synaptogenesis) with associated analysis scripts(simulation_statistics), sundry experiments (sundry) and ipynb notebooks (notebooks).

Using this research

I have set up a Docker container to easily experiment with structural plasticity on SpiNNaker. It can be found under the tag structural_plasticity for the most up-to-date development version of the tools, while structural_plasticity_5.1.0 contains the most recent (to the time of writing) release of the SpiNNaker tools. These containers include 3 iPython Notebooks which immediately run the most common experiments presented in my thesis which use structural plasticity:

1. Topographic map formation
2. MNIST classification
3. Motion detection

Publications

1. Student Conference Proceedings

   Bogdan PA, Furber SB (2017) "Neurogenesis on SpiNNaker". Proceedings of the 1st HBP Student Conference - Transdisciplinary Research Linking Neuroscience, Brain Medicine and Computer Science, 75-77, ISBN: 978-2-88945-421-1 https://www.frontiersin.org/books/1st_HBP_Student_Conference_-_Transdisciplinary_Research_Linking_Neuroscience_Brain_Medicine_and_Com/1532

2. Conference Proceedings

   Bogdan PA, Pineda-García G, Davidson S, Hopkins M, James R and Furber SB (2019), "Event-based computation: Unsupervised elementary motion decomposition". Proceedings of Emerging Technology Conference

3. Journal Articles

   Bogdan PA, Rowley AGD, Rhodes O and Furber SB (2018) "Structural Plasticity on the SpiNNaker Many-Core Neuromorphic System". Front. Neurosci. 12:434. http://dx.doi.org/10.3389/fnins.2018.00434

   Hopkins M, Pineda-García G, Bogdan PA, Furber SB (2018) "Spiking neural networks for computer vision". Interface Focus 8 20180007.
   http://dx.doi.org/10.1098/rsfs.2018.0007

4. Thesis

   Bogdan, PA (2020). Structural Plasticity on SpiNNaker (The University of Manchester). https://doi.org/10.13140/RG.2.2.33591.06568

5. Data repositories

   Bogdan PA, Rhodes O, Rowley AGD, Furber SB (2018) "Structural plasticity on the SpiNNaker many-core neuromorphic system", Mendeley Data, v1. http://dx.doi.org/10.17632/xfp84r5hb7.1

   Bogdan PA, Furber SB, Pineda-Garcia G, Hopkins M (2018) “Spiking Neural Networks for Computer Vision”, Mendeley Data, v1. http://dx.doi.org/10.17632/84pvnm3rj3.1

   Bogdan PA, Pineda-García G, Davidson S, Hopkins M, James R and Furber SB (2019), "Supporting Data and Software for Event-based computation: Unsupervised elementary motion decomposition", Mendeley Data, v1 http://dx.doi.org/10.17632/wpzxh93vhx.1

6. Posters

   Bogdan PA, Furber SB (2018) "Simulating synaptic rewiring on SpiNNaker". figshare. Poster. https://doi.org/10.6084/m9.figshare.6025460.v1

   Bogdan PA, Furber SB (2018) "Structural plasticity for motion detection on SpiNNaker using PyNN". figshare. Poster. https://doi.org/10.6084/m9.figshare.6949091.v1