In silico toxicology: comprehensive benchmarking of multi-label classification methods applied to chemical toxicity data

Wiley Interdisciplinary Reviews. Computational Molecular Science
Arwa B Raies, Vladimir B Bajic

Abstract

One goal of toxicity testing, among others, is identifying harmful effects of chemicals. Given the high demand for toxicity tests, it is necessary to conduct these tests for multiple toxicity endpoints for the same compound. Current computational toxicology methods aim at developing models mainly to predict a single toxicity endpoint. When chemicals cause several toxicity effects, one model is generated to predict toxicity for each endpoint, which can be labor and computationally intensive when the number of toxicity endpoints is large. Additionally, this approach does not take into consideration possible correlation between the endpoints. Therefore, there has been a recent shift in computational toxicity studies toward generating predictive models able to predict several toxicity endpoints by utilizing correlations between these endpoints. Applying such correlations jointly with compounds' features may improve model's performance and reduce the number of required models. This can be achieved through multi-label classification methods. These methods have not undergone comprehensive benchmarking in the domain of predictive toxicology. Therefore, we performed extensive benchmarking and analysis of over 19,000 multi-label classifi...Continue Reading

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Citations

Nov 15, 2018·Journal of Environmental Science and Health. Part C, Environmental Carcinogenesis & Ecotoxicology Reviews·Yan LiPing Gong
Mar 19, 2020·Briefings in Bioinformatics·Natesh SinghBruno O Villoutreix
Mar 2, 2019·Journal of Environmental Science and Health. Part C, Environmental Carcinogenesis & Ecotoxicology Reviews·Weihao TangHuixiao Hong
Jun 1, 2018·Oxidative Medicine and Cellular Longevity·Andressa Brito LiraHilzeth de Luna Freire Pessôa
Dec 12, 2019·Frontiers in Chemistry·Maha ThafarVladimir B Bajic
Dec 29, 2020·Chemical Research in Toxicology·Marcus W H WangTimothy E H Allen
Mar 9, 2021·Critical Reviews in Food Science and Nutrition·Georg SandnerJulian Weghuber
Feb 27, 2019·Journal of Chemical Information and Modeling·Lixia SunYun Tang
Sep 14, 2019·Journal of Chemical Information and Modeling·José Pérez-Parras ToledanoGonzalo Cerruela-García
Oct 12, 2019·Journal of Chemical Information and Modeling·Xiaoqi ShanDong-Qing Wei

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Software Mentioned

PADEL
ToxTree
PADEL QSAR
Ambit Discovery
OECD QSAR toolbox
Derek Nexus

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