MiDi: 混合图和3D去噪扩散在分子生成中的应用

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

C Vignac, N Osman, L Toni, P Frossard
[EPFL & University College London]

MiDi: 混合图和3D去噪扩散在分子生成中的应用

要点:

1. MiDi是一种扩散模型，可以联合生成分子图和相应的 3D 构象体；
2. MiDi 在复杂数据集上的表现优于现有的基于 3D 的模型和专用算法；
3. MiDi 有一个新的 rEGNN 层，利用了更多的表达性特征，并仍然保证 SE(3) 的等变性；
4. MiDi 可用于不局限于非条件生成的各种药物发现应用。

一句话总结:
MiDi 是一种扩散模型，可以生成分子图和相应的 3D 构象体，性能优于现有的基于 3D 的模型和专门算法。

This work introduces MiDi, a diffusion model for jointly generating molecular graphs and corresponding 3D conformers. In contrast to existing models, which derive molecular bonds from the conformation using predefined rules, MiDi streamlines the molecule generation process with an end-to-end differentiable model. Experimental results demonstrate the benefits of this approach: on the complex GEOM-DRUGS dataset, our model generates significantly better molecular graphs than 3D-based models and even surpasses specialized algorithms that directly optimize the bond orders for validity. Our code is available at this http URL.

https://arxiv.org/abs/2302.09048

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