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基于Copeland 指数的分类器和集成分类器在纳米粒子体外毒性预测中的比较研究

Machine learning prediction of nanoparticle in vitro toxicity: A comparative study of classifiers and ensemble-classifiers using the Copeland Index.

机构信息

Dept. of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93, Ireland.

ELEGI/Colt Laboratory, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom.

出版信息

Toxicol Lett. 2019 Sep 15;312:157-166. doi: 10.1016/j.toxlet.2019.05.016. Epub 2019 May 15.

Abstract

Nano-Particles (NPs) are well established as important components across a broad range of products from cosmetics to electronics. Their utilization is increasing with their significant economic and societal potential yet to be fully realized. Inroads have been made in our understanding of the risks posed to human health and the environment by NPs but this area will require continuous research and monitoring. In recent years Machine Learning (ML) techniques have exploited large datasets and computation power to create breakthroughs in diverse fields from facial recognition to genomics. More recently, ML techniques have been applied to nanotoxicology with very encouraging results. In this study, categories of ML classifiers (rules, trees, lazy, functions and bayes) were compared using datasets from the Safe and Sustainable Nanotechnology (S2NANO) database to investigate their performance in predicting NPs in vitro toxicity. Physicochemical properties, toxicological and quantum-mechanical attributes and in vitro experimental conditions were used as input variables to predict the toxicity of NPs based on cell viability. Voting, an ensemble meta-classifier, was used to combine base models to optimize the classification prediction of toxicity. To facilitate inter-comparison, a Copeland Index was applied that ranks the classifiers according to their performance and suggested the optimal classifier. Neural Network (NN) and Random forest (RF) showed the best performance in the majority of the datasets used in this study. However, the combination of classifiers demonstrated an improved prediction resulting meta-classifier to have higher indices. This proposed Copeland Index can now be used by researchers to identify and clearly prioritize classifiers in order to achieve more accurate classification predictions for NP toxicity for a given dataset.

摘要

纳米颗粒(NPs)已被广泛应用于从化妆品到电子产品等各种产品中,是重要的组成部分。尽管它们具有巨大的经济和社会潜力尚未得到充分实现,但它们的利用率正在增加。我们对纳米颗粒对人类健康和环境造成的风险有了更深入的了解,但这一领域仍需要持续的研究和监测。近年来,机器学习(ML)技术利用大型数据集和计算能力在人脸识别、基因组学等各个领域取得了突破。最近,ML 技术已应用于纳米毒理学,并取得了非常令人鼓舞的结果。在这项研究中,使用来自安全和可持续纳米技术(S2NANO)数据库的数据集比较了几种 ML 分类器(规则、树、懒惰、函数和贝叶斯),以研究它们在预测纳米颗粒体外毒性方面的性能。物理化学特性、毒理学和量子力学属性以及体外实验条件被用作输入变量,根据细胞活力预测纳米颗粒的毒性。投票,一种集成元分类器,被用于组合基础模型,以优化毒性分类预测。为了便于比较,应用了 Copeland 指数,根据性能对分类器进行排名,并建议使用最优分类器。神经网络(NN)和随机森林(RF)在本研究中使用的大多数数据集上表现出最佳性能。然而,分类器的组合显示出改进的预测结果,使得元分类器具有更高的指数。现在,研究人员可以使用这个提出的 Copeland 指数来识别和明确优先考虑的分类器,以便为给定数据集的纳米毒性实现更准确的分类预测。

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