A Group Symmetric Stochastic Differential Equation Model
for Molecule Multi-modal Pretraining
ICML 2023

Previous Work (GraphMVP) Main Issue: The generative loss is proxy to the actual generative loss.
Solution (MoleculeSDE): We propose doing the actual conditional generation in the mutual way.

• We start by aiming at maximizing the following objective for MI maximization: $$\mathcal{L}_{\text{MI}} = \frac{1}{2} \mathbb{E}_{p(x,y)} \big[ \log p(y|x) + \log p(x|y) \big],$$ where x and y are for the 2D topologies and 3D structures respectively.
• MoleculeSDE: use diffusion model for estimation.
• One diffusion model (SDE) for 3D structures generation conditioned on 2D topologies.
• One diffusion model (SDE) for 2D topologies generation conditioned on 3D structures.