Vignac, C;
Osman, N;
Toni, L;
Frossard, P;
(2023)
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation.
In:
Joint European Conference on Machine Learning and Knowledge Discovery in Databases ECML PKDD 2023: Machine Learning and Knowledge Discovery in Databases: Research Track.
(pp. pp. 560-576).
Springer: Cham, Switzerland.
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Abstract
This work introduces MiDi, a novel diffusion model for jointly generating molecular graphs and their corresponding 3D atom arrangements. Unlike existing methods that rely on predefined rules to determine molecular bonds based on the 3D conformation, MiDi offers an end-to-end differentiable approach that streamlines the molecule generation process. Our experimental results demonstrate the effectiveness of this approach. On the challenging GEOM-DRUGS dataset, MiDi generates 92% of stable molecules, against for the previous EDM model that uses interatomic distances for bond prediction, and using EDM followed by an algorithm that directly optimizes bond orders for validity. Our code is available at github.com/cvignac/MiDi.
| Type: | Proceedings paper |
|---|---|
| Title: | MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation |
| Event: | European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases 2023 |
| Location: | Turin, Italy |
| Dates: | 18 Sep 2023 - 22 Sep 2023 |
| ISBN-13: | 9783031434143 |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1007/978-3-031-43415-0_33 |
| Publisher version: | https://doi.org/10.1007/978-3-031-43415-0_33 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
| Keywords: | Diffusion Model, Drug Discovery, Graph Generation |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Electronic and Electrical Eng |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10181491 |
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