ADT: All-Atom Diffusion Tokenizer for 3D Molecular Structures
Discrete structural tokenization provides a promising route to autoregressive 3D molecular generation. Yet, existing tokenizers face a trade-off between compact representation and all-atom reconstruction: atom-level tokens preserve atomic details but produce long sequences, while compact residue-level protein tokens typically omit side-chain geometry. To overcome this limitation, we propose All-atom Diffusion Tokenizer (ADT), which decouples token granularity from reconstruction resolution. ADT uses one structural token per atom for small molecules and one token per protein residue that jointly represents backbone and side-chain geometry. To mitigate geometric distortion introduced by qua...
| Authors | Xuantuo Huang, Encheng Su, Aoran Wang et al. |
|---|---|
| Primary category | cs.LG |
| Published | 16 October 2026 |
| Last updated at source | 16 October 2026 |
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