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arXiv 2102.10056cs.LGphysics.chem-ph
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基于图神经网络的表征的分子对比学习

Molecular Contrastive Learning of Representations via Graph Neural Networks

Carnegie Mellon University(卡内基梅隆大学)

Yuyang Wang, Jianren Wang, Zhonglin Cao, Amir Barati Farimani

摘要:

分子机器学习(ML)为高效的分子性质预测和药物发现带来了希望。然而,标记的分子数据可能是昂贵的和耗时的获取。由于有限的标记数据,监督学习ML模型推广到巨大的化学空间是一个巨大的挑战。在这项工作中,我们提出了Molten:通过图神经网络(GNNs)进行表征的分子对比学习,这是一个利用大型未标记数据(约10M独特分子)的自监督学习框架。在molecular预训练中,我们构建分子图并开发GNN编码器来学习可微表示。提出了三种分子图增强方法:原子掩蔽、键删除和子图删除。一个对比估计最大限度地提高同一分子的协议,同时最大限度地减少不同分子的协议。实验表明,我们的对比学习框架显着提高了GNN在各种分子特性基准测试(包括分类和回归任务)上的性能。得益于在大型未标记数据库上进行的预训练,Moltron甚至在微调后在几个具有挑战性的基准测试中达到了最先进的水平。此外,进一步的研究表明,Molly学会将分子嵌入到可以区分化学上合理的分子相似性的表示中。

英文摘要:

Molecular Machine Learning (ML) bears promise for efficient molecule property prediction and drug discovery. However, labeled molecule data can be expensive and time-consuming to acquire. Due to the limited labeled data, it is a great challenge for supervised-learning ML models to generalize to the giant chemical space. In this work, we present MolCLR: Molecular Contrastive Learning of Representations via Graph Neural Networks (GNNs), a self-supervised learning framework that leverages large unlabeled data (~10M unique molecules). In MolCLR pre-training, we build molecule graphs and develop GNN encoders to learn differentiable representations. Three molecule graph augmentations are proposed: atom masking, bond deletion, and subgraph removal. A contrastive estimator maximizes the agreement of augmentations from the same molecule while minimizing the agreement of different molecules. Experiments show that our contrastive learning framework significantly improves the performance of GNNs on various molecular property benchmarks including both classification and regression tasks. Benefiting from pre-training on the large unlabeled database, MolCLR even achieves state-of-the-art on several challenging benchmarks after fine-tuning. Additionally, further investigations demonstrate that MolCLR learns to embed molecules into representations that can distinguish chemically reasonable molecular similarities.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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