Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing
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| Main Authors: | , , , , , , , , |
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| Format: | Preprint |
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2022
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| _version_ | 1866929227631165440 |
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| author | Liu, Shengchao Nie, Weili Wang, Chengpeng Lu, Jiarui Qiao, Zhuoran Liu, Ling Tang, Jian Xiao, Chaowei Anandkumar, Anima |
| author_facet | Liu, Shengchao Nie, Weili Wang, Chengpeng Lu, Jiarui Qiao, Zhuoran Liu, Ling Tang, Jian Xiao, Chaowei Anandkumar, Anima |
| contents | There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2212_10789 |
| institution | arXiv |
| publishDate | 2022 |
| record_format | arxiv |
| spellingShingle | Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing Liu, Shengchao Nie, Weili Wang, Chengpeng Lu, Jiarui Qiao, Zhuoran Liu, Ling Tang, Jian Xiao, Chaowei Anandkumar, Anima Machine Learning Computation and Language Quantitative Methods There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks. |
| title | Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing |
| topic | Machine Learning Computation and Language Quantitative Methods |
| url | https://arxiv.org/abs/2212.10789 |