2024
DOI: 10.26434/chemrxiv-2024-77vhr
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A Tree-Transformer based VAE with fragment tokenization for large chemical models

Tensei Inukai,
Aoi Yamato,
Manato Akiyama
et al.

Abstract: Chemical language model (CLM), a molecular generation model, leverages large language models by utilizing SMILES, a string representation of compounds. Chemical variational auto-encoder (VAE), which explicitly constructs a latent space, demonstrates their strength in molecular optimization and generation on a continuous space. We propose the Fragment Tree-Transformer based VAE (FRATTVAE) for the task of molecular optimization and generation, which treats molecules as a tree structure with fragments as nodes. R… Show more

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