Why not use VAE model?

[FeilongWuHaa]

Hi, Yuning,

Thanks for your excellent paper.

Have you tried to use VAE model instead of AE model? Can VAE model replace GSSL and generate better molecules?

Best,

[yyou1996]

Thanks for the great question. We don't have the conclusive answer for which must be better. Some points for comments are:

• We use AE for the "dimension reduction" purpose, to compress the complicated data structures in the high-dimensional non-Euclidean space into a low-dimensional (latent) Euclidean space.
• We believe in the "simpler" low-dimensional latent space the generative model can learn easier.
• VAE does not serve for the dimension reduction purpose under our motivation.
• VAE might also work in another perspective: Conceptually, composing VAE and diffusion models together can be viewed as a deep hierarchical VAE, which still capture the distribution in the original space with a larger generative model.

[FeilongWuHaa]

Thank you for your opinions and responses.