ADT: All-Atom Diffusion Tokenizer for 3D Molecular Structures
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ADT (All-atom Diffusion Tokenizer) is a tokenizer for 3D molecular structures that decouples token granularity from reconstruction resolution, achieving all-atom reconstruction from compact discrete representations. It tokenizes small molecules atom by atom and uses a single token per protein residue that jointly encodes backbone and side-chain geometry, with a diffusion model recovering geometric distortion introduced by tokenization. Experiments show ADT supports high-quality autoregressive generation of small molecules and all-atom protein structures.
Excerpted from arxiv.org
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- arxiv.orgADT: All-Atom Diffusion Tokenizer for 3D Molecular Structures
ADT (All-atom Diffusion Tokenizer) is a tokenizer for 3D molecular structures that decouples token granularity from reconstruction resolution, achieving all-atom reconstruction from compact discrete representations. It tokenizes small molecules atom by atom and uses a single token per protein residue that jointly encodes backbone and side-chain geometry, with a diffusion model recovering geometric distortion introduced by tokenization. Experiments show ADT supports high-quality autoregressive generation of small molecules and all-atom protein structures.
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