Yuyan Ni, Shikun Feng, Xin Hong, Yuancheng Sun, Wei-Ying Ma, Zhi-Ming Ma, Qiwei Ye, Yanyan Lan
{"title":"利用分数去噪进行预训练,提高分子特性预测能力","authors":"Yuyan Ni, Shikun Feng, Xin Hong, Yuancheng Sun, Wei-Ying Ma, Zhi-Ming Ma, Qiwei Ye, Yanyan Lan","doi":"10.1038/s42256-024-00900-z","DOIUrl":null,"url":null,"abstract":"Deep learning methods have been considered promising for accelerating molecular screening in drug discovery and material design. Due to the limited availability of labelled data, various self-supervised molecular pre-training methods have been presented. Although many existing methods utilize common pre-training tasks in computer vision and natural language processing, they often overlook the fundamental physical principles governing molecules. In contrast, applying denoising in pre-training can be interpreted as an equivalent force learning, but the limited noise distribution introduces bias into the molecular distribution. To address this issue, we introduce a molecular pre-training framework called fractional denoising, which decouples noise design from the constraints imposed by force learning equivalence. In this way, the noise becomes customizable, allowing for incorporating chemical priors to substantially improve the molecular distribution modelling. Experiments demonstrate that our framework consistently outperforms existing methods, establishing state-of-the-art results across force prediction, quantum chemical properties and binding affinity tasks. The refined noise design enhances force accuracy and sampling coverage, which contribute to the creation of physically consistent molecular representations, ultimately leading to superior predictive performance. Denoising methods introduce useful priors in pre-training methods for molecular property prediction, but chemically unaware noise can lead to inaccurate predictions in downstream tasks. A molecular pre-training framework that uses fractional denoising to improve molecular distribution modelling is proposed, resulting in better predictions in various property prediction tasks.","PeriodicalId":48533,"journal":{"name":"Nature Machine Intelligence","volume":"6 10","pages":"1169-1178"},"PeriodicalIF":18.8000,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Pre-training with fractional denoising to enhance molecular property prediction\",\"authors\":\"Yuyan Ni, Shikun Feng, Xin Hong, Yuancheng Sun, Wei-Ying Ma, Zhi-Ming Ma, Qiwei Ye, Yanyan Lan\",\"doi\":\"10.1038/s42256-024-00900-z\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Deep learning methods have been considered promising for accelerating molecular screening in drug discovery and material design. Due to the limited availability of labelled data, various self-supervised molecular pre-training methods have been presented. Although many existing methods utilize common pre-training tasks in computer vision and natural language processing, they often overlook the fundamental physical principles governing molecules. In contrast, applying denoising in pre-training can be interpreted as an equivalent force learning, but the limited noise distribution introduces bias into the molecular distribution. To address this issue, we introduce a molecular pre-training framework called fractional denoising, which decouples noise design from the constraints imposed by force learning equivalence. In this way, the noise becomes customizable, allowing for incorporating chemical priors to substantially improve the molecular distribution modelling. Experiments demonstrate that our framework consistently outperforms existing methods, establishing state-of-the-art results across force prediction, quantum chemical properties and binding affinity tasks. The refined noise design enhances force accuracy and sampling coverage, which contribute to the creation of physically consistent molecular representations, ultimately leading to superior predictive performance. Denoising methods introduce useful priors in pre-training methods for molecular property prediction, but chemically unaware noise can lead to inaccurate predictions in downstream tasks. 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Pre-training with fractional denoising to enhance molecular property prediction
Deep learning methods have been considered promising for accelerating molecular screening in drug discovery and material design. Due to the limited availability of labelled data, various self-supervised molecular pre-training methods have been presented. Although many existing methods utilize common pre-training tasks in computer vision and natural language processing, they often overlook the fundamental physical principles governing molecules. In contrast, applying denoising in pre-training can be interpreted as an equivalent force learning, but the limited noise distribution introduces bias into the molecular distribution. To address this issue, we introduce a molecular pre-training framework called fractional denoising, which decouples noise design from the constraints imposed by force learning equivalence. In this way, the noise becomes customizable, allowing for incorporating chemical priors to substantially improve the molecular distribution modelling. Experiments demonstrate that our framework consistently outperforms existing methods, establishing state-of-the-art results across force prediction, quantum chemical properties and binding affinity tasks. The refined noise design enhances force accuracy and sampling coverage, which contribute to the creation of physically consistent molecular representations, ultimately leading to superior predictive performance. Denoising methods introduce useful priors in pre-training methods for molecular property prediction, but chemically unaware noise can lead to inaccurate predictions in downstream tasks. A molecular pre-training framework that uses fractional denoising to improve molecular distribution modelling is proposed, resulting in better predictions in various property prediction tasks.
期刊介绍:
Nature Machine Intelligence is a distinguished publication that presents original research and reviews on various topics in machine learning, robotics, and AI. Our focus extends beyond these fields, exploring their profound impact on other scientific disciplines, as well as societal and industrial aspects. We recognize limitless possibilities wherein machine intelligence can augment human capabilities and knowledge in domains like scientific exploration, healthcare, medical diagnostics, and the creation of safe and sustainable cities, transportation, and agriculture. Simultaneously, we acknowledge the emergence of ethical, social, and legal concerns due to the rapid pace of advancements.
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