Research Visit to SciLifeLab by Sorbonne University PhD Student Federico Scarpati
Sorbonne University PhD student, and VOLUMINEX team member, Federico Scarpati recently visited SciLifeLab in Stockholm, Sweden in order to further the ongoing computational work related to VOLUMINEX.
From 11th till 21st May Federico worked together with KTH PhD student David Fernàndez Bonet on a code package intended as a comprehensive toolkit for proximity networks. The package covers several steps from network generation to analysis, denoising, 2D/3D reconstruction and visualization. The final form is intended to be simple, well-documented and ready-to-use. The code package brings together several state-of-the-art methods, including those developed by David during his PhD and others that will be expanded on by Federico within the VOLUMINEX project.
In addition to the code package, Federico and David also worked on a manuscript focusing on denoising methods for proximity networks. Results from the manuscript were recently presented by David at the VOLUMINEX annual meeting in Paris back in April.
Federico enjoyed his visit to SciLifeLab and thanked Professor Ian Hoffecker and his team for the warm welcome. “I especially appreciated collaborating closely with David,” recalled Federico, “as we are both working on the computational side of the VOLUMINEX project. The visit gave us a chance to have an intense exchange of ideas and make good progress through a focused in-person sprint.”
Now back in Paris, Federico is focused on finalizing his work on the generation of synthetic proximity networks, which is the main topic of an upcoming VOLUMINEX deliverable due in August. In parallel, he is continuing his PhD work on denoising proximity networks with graph neural networks, including starting the writing of a manuscript. Federico will also be presenting at the Biological Physics and Statistical Mechanics conference in Turin, Italy on the 9th June.