Molecule Ring & Close Atoms Lifting (Graph to Combinatorial)

[bertranMiquel]

This notebook imports QM9 dataset and applies a lifting from a graph molecular representation to a combinatorial complex. Then, a neural network is run using the loaded data.

Using QM9 dataset, we implement a lifting from a molecule graph to a combinatorial complex based on two points:

• The ring information of the molecule. Rings will be represented as 2-cells in the combinatorial complex.
• The distance between atoms in the molecule. Distances between atoms will be computed. If the atoms are under a predefined threshold, they will be considered as close and groupped together. This clusters will be introduced as hyperedges in the combinatorial complex.

So far, from our knowledge it is the first representation of a cell as a combinatorial complex, combining both hypergraphs and cell complexes.

Here, the elements are the following:

• Nodes: Atoms in the molecule.
• Edges: Bonds between atoms.
• Hyperedges: Clusters of atoms that are close to each other.
• 2-cells: Rings in the molecule.

This pull request is done under the team formed by: Bertran Miquel Oliver, Manel Gil Sorribes, Alexis Molina

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[bertranMiquel]

Hi Guillermo, Answering to fulfill the submission requirements: - Name and last name of the participants: Bertran Miquel-Oliver, Manel Gil-Sorribes, Alexis Molina, Victor Guallar (all of them in cc) - Title: Molecule Ring & Close Atoms Lifting - Input domain: Graph - Output domain: Combinatorial - Pull request: #16 <#16> Best, Bertran Missatge de Guillermo Bernárdez ***@***.***> del dia dl., 8 de jul. 2024 a les 19:12:

…

Hello @bertranMiquel <https://github.com/bertranMiquel>! Thank you for your submission. As we near the end of the challenge, I am collecting participant info for the purpose of selecting and announcing winners. Please email me (or have one member of your team email me) at ***@***.*** so I can share access to the voting form. In your email, please include: - your first and last name (as well as any other team members) - the title of the method you implemented - the input domain of the method you implemented - the output domain of the method you implemented - your pull request number (#16 <#16>) Before July 12, make sure that your submission respects all Submission Requirements laid out on the challenge page <https://pyt-team.github.io/packs/challenge.html>. Any submission that fails to meet this criteria will be automatically disqualified. — Reply to this email directly, view it on GitHub <#16 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHTIUTUULNNZWUSHJVCRXM3ZLLB6XAVCNFSM6AAAAABJUOLSQ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJUG42DEMZTGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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Codecov Report

Attention: Patch coverage is 96.50350% with 5 lines in your changes missing coverage. Please review.

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Files	Patch %	Lines
...gs/graph2combinatorial/ring_close_atoms_lifting.py	95.83%	5 Missing ⚠️

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