Mentors: Bradly Alicea @b.alicea <bradly.alicea@outlook.com>, Mehul Arora <22mehularora22@gmail.com>, Jesse Parent @jparent <jesse@jopro.org>
Skill level: Advanced
Required skills: All of our existing models are built for PyTorch, so experience with Python and PyTorch/Tensorflow workflows is preferred. The ability to work with datasets, such as segmenting video and generating graph visualizations is essential. An ability to build web interfaces, UI design, basic knowledge of biology, open-source practices, and applied mathematical tools will also be useful.
Time commitment: Full time (350 hours)
About: The DevoWorm group has developed an open-source Graph neural network (GNN) framework for embryogenetic data called DevoGraph. Developmental GNNs (D-GNNs) allow us to characterize a growing network that undergoes shape transformations along with increases in size. This is ultimately important for understanding formation of the connectome and the origins of embodied behavior.
Aims: For this year’s project, the successful applicant will work on extending our two outcomes from last year:
- The first direction involves working with Neural Developmental Programs to build growing neural networks. This provides a means to model the function of embryogenetic networks, developing connectomes, and other growth processes
- The second direction involves working with hyper graph representations, enabling multiscale modeling from a network perspective.
We aim to tie our D-GNN work into the group’s ongoing theoretical and computational work. As such, this project will require the ability to work with mathematical models and
associated algorithms. Knowledge of graph and/or network theory is helpful, but not
required.
What can I do before GSoC?
You can ask one of the mentors to direct you to the data source and you can start working on it. Please feel free to join the Openworm Slack or attend our meetings to raise questions/discussions regarding your approach to the problem.
- OpenWorm Foundation: https://openworm.org/
- DevoWorm website: https://devoworm.weebly.com/
- DevoGraph (Github): GitHub - DevoLearn/DevoGraph
- DevoWorm AI: DevoWorm.AI
Project website: https://devoworm.weebly.com