Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel
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arXiv
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| Format: | Preprint |
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2023
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| _version_ | 1866917626627751936 |
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| author | Li, Xuan Zhou, Zhanke Yao, Jiangchao Rong, Yu Zhang, Lu Han, Bo |
| author_facet | Li, Xuan Zhou, Zhanke Yao, Jiangchao Rong, Yu Zhang, Lu Han, Bo |
| contents | Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs mainly excel in leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method to abstract the collective information of atomic groups into a few $\textit{Neural Atoms}$ by implicitly projecting the atoms of a molecular. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection to the traditional LRI calculation method, Ewald Summation. The Neural Atom can enhance GNNs to capture LRI by approximating the potential LRI of the molecular. We conduct extensive experiments on four long-range graph benchmarks, covering graph-level and link-level tasks on molecular graphs. We achieve up to a 27.32% and 38.27% improvement in the 2D and 3D scenarios, respectively. Empirically, our method can be equipped with an arbitrary GNN to help capture LRI. Code and datasets are publicly available in https://github.com/tmlr-group/NeuralAtom. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2311_01276 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel Li, Xuan Zhou, Zhanke Yao, Jiangchao Rong, Yu Zhang, Lu Han, Bo Machine Learning Quantitative Methods Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs mainly excel in leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method to abstract the collective information of atomic groups into a few $\textit{Neural Atoms}$ by implicitly projecting the atoms of a molecular. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection to the traditional LRI calculation method, Ewald Summation. The Neural Atom can enhance GNNs to capture LRI by approximating the potential LRI of the molecular. We conduct extensive experiments on four long-range graph benchmarks, covering graph-level and link-level tasks on molecular graphs. We achieve up to a 27.32% and 38.27% improvement in the 2D and 3D scenarios, respectively. Empirically, our method can be equipped with an arbitrary GNN to help capture LRI. Code and datasets are publicly available in https://github.com/tmlr-group/NeuralAtom. |
| title | Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel |
| topic | Machine Learning Quantitative Methods |
| url | https://arxiv.org/abs/2311.01276 |