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This work introduces MiDi, a novel diffusion model for jointly generatingmolecular graphs and their corresponding 3D arrangement of atoms. Unlikeexisting methods that rely on predefined rules to determine molecular bondsbased on the 3D conformation, MiDi offers an end-to-end differentiable approachthat streamlines the molecule generation process. Our experimental resultsdemonstrate the effectiveness of this approach. On the challenging GEOM-DRUGSdataset, MiDi generates 92% of stable molecules, against 6% for the previousEDM model that uses interatomic distances for bond prediction, and 40% usingEDM followed by an algorithm that directly optimize bond orders for validity.Our code is available at github.com/cvignac/MiDi.

MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation