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Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles
A wide range of environmental factors heavily impact aquatic ecosystems, in turn, affecting human health. Toxic organic compounds resulting from anthropogenic activity are a source of pollution in aquatic ecosystems. To evaluate these contaminants, current approaches mainly rely on acute and chronic...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9503646/ https://www.ncbi.nlm.nih.gov/pubmed/36143479 http://dx.doi.org/10.3390/life12091443 |
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author | Choi, Tae-June An, Hyung-Eun Kim, Chang-Bae |
author_facet | Choi, Tae-June An, Hyung-Eun Kim, Chang-Bae |
author_sort | Choi, Tae-June |
collection | PubMed |
description | A wide range of environmental factors heavily impact aquatic ecosystems, in turn, affecting human health. Toxic organic compounds resulting from anthropogenic activity are a source of pollution in aquatic ecosystems. To evaluate these contaminants, current approaches mainly rely on acute and chronic toxicity tests, but cannot provide explicit insights into the causes of toxicity. As an alternative, genome-wide gene expression systems allow the identification of contaminants causing toxicity by monitoring the organisms’ response to toxic substances. In this study, we selected 22 toxic organic compounds, classified as pesticides, herbicides, or industrial chemicals, that induce environmental problems in aquatic ecosystems and affect human-health. To identify toxic organic compounds using gene expression data from Daphnia magna, we evaluated the performance of three machine learning based feature-ranking algorithms (Learning Vector Quantization, Random Forest, and Support Vector Machines with a Linear kernel), and nine classifiers (Linear Discriminant Analysis, Classification And Regression Trees, K-nearest neighbors, Support Vector Machines with a Linear kernel, Random Forest, Boosted C5.0, Gradient Boosting Machine, eXtreme Gradient Boosting with tree, and eXtreme Gradient Boosting with DART booster). Our analysis revealed that a combination of feature selection based on feature-ranking and a random forest classification algorithm had the best model performance, with an accuracy of 95.7%. This is a preliminary study to establish a model for the monitoring of aquatic toxic substances by machine learning. This model could be an effective tool to manage contaminants and toxic organic compounds in aquatic systems. |
format | Online Article Text |
id | pubmed-9503646 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-95036462022-09-24 Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles Choi, Tae-June An, Hyung-Eun Kim, Chang-Bae Life (Basel) Brief Report A wide range of environmental factors heavily impact aquatic ecosystems, in turn, affecting human health. Toxic organic compounds resulting from anthropogenic activity are a source of pollution in aquatic ecosystems. To evaluate these contaminants, current approaches mainly rely on acute and chronic toxicity tests, but cannot provide explicit insights into the causes of toxicity. As an alternative, genome-wide gene expression systems allow the identification of contaminants causing toxicity by monitoring the organisms’ response to toxic substances. In this study, we selected 22 toxic organic compounds, classified as pesticides, herbicides, or industrial chemicals, that induce environmental problems in aquatic ecosystems and affect human-health. To identify toxic organic compounds using gene expression data from Daphnia magna, we evaluated the performance of three machine learning based feature-ranking algorithms (Learning Vector Quantization, Random Forest, and Support Vector Machines with a Linear kernel), and nine classifiers (Linear Discriminant Analysis, Classification And Regression Trees, K-nearest neighbors, Support Vector Machines with a Linear kernel, Random Forest, Boosted C5.0, Gradient Boosting Machine, eXtreme Gradient Boosting with tree, and eXtreme Gradient Boosting with DART booster). Our analysis revealed that a combination of feature selection based on feature-ranking and a random forest classification algorithm had the best model performance, with an accuracy of 95.7%. This is a preliminary study to establish a model for the monitoring of aquatic toxic substances by machine learning. This model could be an effective tool to manage contaminants and toxic organic compounds in aquatic systems. MDPI 2022-09-16 /pmc/articles/PMC9503646/ /pubmed/36143479 http://dx.doi.org/10.3390/life12091443 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Brief Report Choi, Tae-June An, Hyung-Eun Kim, Chang-Bae Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles |
title | Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles |
title_full | Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles |
title_fullStr | Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles |
title_full_unstemmed | Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles |
title_short | Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles |
title_sort | machine learning models for identification and prediction of toxic organic compounds using daphnia magna transcriptomic profiles |
topic | Brief Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9503646/ https://www.ncbi.nlm.nih.gov/pubmed/36143479 http://dx.doi.org/10.3390/life12091443 |
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