Training Text-to-Molecule Models with Context-Aware Tokenization
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arXiv
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| Autori principali: | , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2025
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| _version_ | 1866915498862575616 |
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| author | Kim, Seojin Song, Hyeontae Nam, Jaehyun Shin, Jinwoo |
| author_facet | Kim, Seojin Song, Hyeontae Nam, Jaehyun Shin, Jinwoo |
| contents | Recently, text-to-molecule models have shown great potential across various chemical applications, e.g., drug-discovery. These models adapt language models to molecular data by representing molecules as sequences of atoms. However, they rely on atom-level tokenizations, which primarily focus on modeling local connectivity, thereby limiting the ability of models to capture the global structural context within molecules. To tackle this issue, we propose a novel text-to-molecule model, coined Context-Aware Molecular T5 (CAMT5). Inspired by the significance of the substructure-level contexts in understanding molecule structures, e.g., ring systems, we introduce substructure-level tokenization for text-to-molecule models. Building on our tokenization scheme, we develop an importance-based training strategy that prioritizes key substructures, enabling CAMT5 to better capture the molecular semantics. Extensive experiments verify the superiority of CAMT5 in various text-to-molecule generation tasks. Intriguingly, we find that CAMT5 outperforms the state-of-the-art methods using only 2% of training tokens. In addition, we propose a simple yet effective ensemble strategy that aggregates the outputs of text-to-molecule models to further boost the generation performance. Code is available at https://github.com/Songhyeontae/CAMT5.git. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_04476 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Training Text-to-Molecule Models with Context-Aware Tokenization Kim, Seojin Song, Hyeontae Nam, Jaehyun Shin, Jinwoo Computation and Language Artificial Intelligence Recently, text-to-molecule models have shown great potential across various chemical applications, e.g., drug-discovery. These models adapt language models to molecular data by representing molecules as sequences of atoms. However, they rely on atom-level tokenizations, which primarily focus on modeling local connectivity, thereby limiting the ability of models to capture the global structural context within molecules. To tackle this issue, we propose a novel text-to-molecule model, coined Context-Aware Molecular T5 (CAMT5). Inspired by the significance of the substructure-level contexts in understanding molecule structures, e.g., ring systems, we introduce substructure-level tokenization for text-to-molecule models. Building on our tokenization scheme, we develop an importance-based training strategy that prioritizes key substructures, enabling CAMT5 to better capture the molecular semantics. Extensive experiments verify the superiority of CAMT5 in various text-to-molecule generation tasks. Intriguingly, we find that CAMT5 outperforms the state-of-the-art methods using only 2% of training tokens. In addition, we propose a simple yet effective ensemble strategy that aggregates the outputs of text-to-molecule models to further boost the generation performance. Code is available at https://github.com/Songhyeontae/CAMT5.git. |
| title | Training Text-to-Molecule Models with Context-Aware Tokenization |
| topic | Computation and Language Artificial Intelligence |
| url | https://arxiv.org/abs/2509.04476 |