D-GNNs: developing DevoGraph for computational developmental biology

Term: Google Summer of Code 2023 Hosts: INCF, OpenWorm Foundation, DevoWorm Project: 3.1 D-GNNs: developing DevoGraph for computational developmental biology — Himanshu Contributor: Himanshu Chougule Mentors: Bradly Alicea, Jiahang Li, Mayukh Deb, Jesse Parent

Summary

This project is about using Graph Neural Networks (GNNs) as a method to discover underlying connectivity to characterize a growing network that undergoes shape as well as size transformations for C. elegans. There are three parts to this project, all of which aim to integrate previous work on embryo networks, developmental connectomes, and embryo differentiation: refining a means to segment raw data and incorporate it into the DevoGraph pipeline; refining the method for deriving graph embeddings; and better integration of DevoGraph as a network structure discovery module of DevoLearn.

Materials

• Google Summer of Code: Archive Page
• INCF Working Group Archive
• Himanshu’s Gist