Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules
Molecular size is coupled to composition, structure, and function, yet most 3D molecular generators require a predefined atom count. We introduce Equivariant-Free Transformer-Autoencoded Latent Flow Matching, a two-stage framework that samples a fixed-dimensional latent vector using flow matching and uses an autoregressive Transformer to determine molecular size, atom types, coordinates, and chemical attributes. Canonical atom ordering and rigid-pose alignment enable Transformers without equivariant layers, while decoded attributes guide bond reconstruction. On PCQM4Mv2, unconditional generation yields 87.9\% unique, novel molecules passing sanitization and PoseBusters checks, exceeding b...
| Authors | Weichi Yao, Cameron Gruich, Bryan R. Goldsmith et al. |
|---|---|
| Primary category | physics.chem-ph |
| Published | 8 September 2026 |
| Last updated at source | 22 September 2026 |
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