UniMAP: Universal SMILES-Graph Representation Learning
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arXiv
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| Autori principali: | , , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2023
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| _version_ | 1866910682936508416 |
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| author | Feng, Shikun Yang, Lixin Huang, Yanwen Ni, Yuyan Ma, Weiying Lan, Yanyan |
| author_facet | Feng, Shikun Yang, Lixin Huang, Yanwen Ni, Yuyan Ma, Weiying Lan, Yanyan |
| contents | Molecular representation learning is fundamental for many drug related applications. Most existing molecular pre-training models are limited in using single molecular modality, either SMILES or graph representation. To effectively leverage both modalities, we argue that it is critical to capture the fine-grained 'semantics' between SMILES and graph, because subtle sequence/graph differences may lead to contrary molecular properties. In this paper, we propose a universal SMILE-graph representation learning model, namely UniMAP. Firstly, an embedding layer is employed to obtain the token and node/edge representation in SMILES and graph, respectively. A multi-layer Transformer is then utilized to conduct deep cross-modality fusion. Specially, four kinds of pre-training tasks are designed for UniMAP, including Multi-Level Cross-Modality Masking (CMM), SMILES-Graph Matching (SGM), Fragment-Level Alignment (FLA), and Domain Knowledge Learning (DKL). In this way, both global (i.e. SGM and DKL) and local (i.e. CMM and FLA) alignments are integrated to achieve comprehensive cross-modality fusion. We evaluate UniMAP on various downstream tasks, i.e. molecular property prediction, drug-target affinity prediction and drug-drug interaction. Experimental results show that UniMAP outperforms current state-of-the-art pre-training methods.We also visualize the learned representations to demonstrate the effect of multi-modality integration. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2310_14216 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | UniMAP: Universal SMILES-Graph Representation Learning Feng, Shikun Yang, Lixin Huang, Yanwen Ni, Yuyan Ma, Weiying Lan, Yanyan Machine Learning Artificial Intelligence Biomolecules Molecular representation learning is fundamental for many drug related applications. Most existing molecular pre-training models are limited in using single molecular modality, either SMILES or graph representation. To effectively leverage both modalities, we argue that it is critical to capture the fine-grained 'semantics' between SMILES and graph, because subtle sequence/graph differences may lead to contrary molecular properties. In this paper, we propose a universal SMILE-graph representation learning model, namely UniMAP. Firstly, an embedding layer is employed to obtain the token and node/edge representation in SMILES and graph, respectively. A multi-layer Transformer is then utilized to conduct deep cross-modality fusion. Specially, four kinds of pre-training tasks are designed for UniMAP, including Multi-Level Cross-Modality Masking (CMM), SMILES-Graph Matching (SGM), Fragment-Level Alignment (FLA), and Domain Knowledge Learning (DKL). In this way, both global (i.e. SGM and DKL) and local (i.e. CMM and FLA) alignments are integrated to achieve comprehensive cross-modality fusion. We evaluate UniMAP on various downstream tasks, i.e. molecular property prediction, drug-target affinity prediction and drug-drug interaction. Experimental results show that UniMAP outperforms current state-of-the-art pre-training methods.We also visualize the learned representations to demonstrate the effect of multi-modality integration. |
| title | UniMAP: Universal SMILES-Graph Representation Learning |
| topic | Machine Learning Artificial Intelligence Biomolecules |
| url | https://arxiv.org/abs/2310.14216 |