This work introduces MiDi, a novel diffusion model for jointly generating molecular graphs and their corresponding 3D arrangement of atoms. 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 6% for the previous EDM model that uses interatomic distances for bond prediction, and 40% using EDM followed by an algorithm that directly optimize bond orders for validity. Our code is available at github.com/cvignac/MiDi.

翻译：本工作介绍MiDi，一种用于联合生成分子图及其对应原子三维排列的新型扩散模型。与依赖预定义规则基于三维构象确定分子键的现有方法不同，MiDi提供了一种端到端可微方法，简化了分子生成过程。我们的实验结果证明了该方法的有效性。在具有挑战性的GEOM-DRUGS数据集上，MiDi生成了92%的稳定分子，而先前使用原子间距离进行键预测的EDM模型仅生成6%，使用EDM后接直接优化键序以确保有效性的算法则生成40%。我们的代码可在github.com/cvignac/MiDi获取。