GSoC 2025 Project Idea #4 OpenWorm DevoWorm :: DevoGraph (350h)

GSoC
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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)

Forum for discussion

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.

Project website: https://devoworm.weebly.com

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Dear Mentors,

My name is Nakshatra Piplad, I am an undergraduate student from IIT Kharagpur, and I found this project very interesting and wanted to contribute to it.

I have gone through the provided links and also submitted the form to join the OpenWorm Slack community. While I wait to be added, is there anything else I can do to get started? I am eager to begin contributing and exploring the dataset. I especially found the work around Developmental GNNs and hypergraph representations very interesting. However, I noticed that the following links didn’t open for me:

I’d love to go through these resources as well—please let me know if there are alternative links or any additional reading materials that would help me better understand the project.

Looking forward to your guidance!

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Hi Nakshatra,

To clarify, I’m not a mentor, but I wanted to let you know that the project website https://devoworm.weebly.com/ works fine for me as well. However, I can confirm that the DevoWorm.AI link isn’t working on my end either.

I’d recommend going through the project website for now, as it has plenty of useful information. Hopefully, the DevoWorm.AI link will get sorted out soon!

Feel free to reach out if you have any questions or need help getting started. Looking forward to collaborating!

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Hi @sdivyanshu90,

Thanks for the clarification! I’ll go through the project website for now and keep an eye out for any updates on the DevoWorm.AI link.

Also, is this the right platform for all discussions, or should I reach out via email as well? Let me know what works best.

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Hi @naxatra2,

You’re welcome! Here is the DevoWorm.AI Link. It’s working fine.

Regarding the right platform for discussions, I personally think that email might be a more effective way to reach out, as the mentors are professors and working professionals who may not always have time to check Neurostars frequently. Checking emails could be more feasible for them. However, this is just my personal opinion and not an official stance from any mentor, so I’d recommend being patient, as replies may take some time.

Let me know if you need anything else!

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