RTMol: Rethinking Molecule-text Alignment in a Round-trip View
Fuente:
arXiv
Guardado en:
| Autores principales: | , , , |
|---|---|
| Formato: | Preprint |
| Publicado: |
2025
|
| Materias: | |
| Acceso en línea: | |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| _version_ | 1866918216491597824 |
|---|---|
| author | Chen, Letian Shi, Runhan Yu, Gufeng Yang, Yang |
| author_facet | Chen, Letian Shi, Runhan Yu, Gufeng Yang, Yang |
| contents | Aligning molecular sequence representations (e.g., SMILES notations) with textual descriptions is critical for applications spanning drug discovery, materials design, and automated chemical literature analysis. Existing methodologies typically treat molecular captioning (molecule-to-text) and text-based molecular design (text-to-molecule) as separate tasks, relying on supervised fine-tuning or contrastive learning pipelines. These approaches face three key limitations: (i) conventional metrics like BLEU prioritize linguistic fluency over chemical accuracy, (ii) training datasets frequently contain chemically ambiguous narratives with incomplete specifications, and (iii) independent optimization of generation directions leads to bidirectional inconsistency. To address these issues, we propose RTMol, a bidirectional alignment framework that unifies molecular captioning and text-to-SMILES generation through self-supervised round-trip learning. The framework introduces novel round-trip evaluation metrics and enables unsupervised training for molecular captioning without requiring paired molecule-text corpora. Experiments demonstrate that RTMol enhances bidirectional alignment performance by up to 47% across various LLMs, establishing an effective paradigm for joint molecule-text understanding and generation. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2511_12135 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | RTMol: Rethinking Molecule-text Alignment in a Round-trip View Chen, Letian Shi, Runhan Yu, Gufeng Yang, Yang Artificial Intelligence Machine Learning Biomolecules Aligning molecular sequence representations (e.g., SMILES notations) with textual descriptions is critical for applications spanning drug discovery, materials design, and automated chemical literature analysis. Existing methodologies typically treat molecular captioning (molecule-to-text) and text-based molecular design (text-to-molecule) as separate tasks, relying on supervised fine-tuning or contrastive learning pipelines. These approaches face three key limitations: (i) conventional metrics like BLEU prioritize linguistic fluency over chemical accuracy, (ii) training datasets frequently contain chemically ambiguous narratives with incomplete specifications, and (iii) independent optimization of generation directions leads to bidirectional inconsistency. To address these issues, we propose RTMol, a bidirectional alignment framework that unifies molecular captioning and text-to-SMILES generation through self-supervised round-trip learning. The framework introduces novel round-trip evaluation metrics and enables unsupervised training for molecular captioning without requiring paired molecule-text corpora. Experiments demonstrate that RTMol enhances bidirectional alignment performance by up to 47% across various LLMs, establishing an effective paradigm for joint molecule-text understanding and generation. |
| title | RTMol: Rethinking Molecule-text Alignment in a Round-trip View |
| topic | Artificial Intelligence Machine Learning Biomolecules |
| url | https://arxiv.org/abs/2511.12135 |