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Bioactive Molecule Prediction Using Extreme Gradient Boosting
Following the explosive growth in chemical and biological data, the shift from traditional methods of drug discovery to computer-aided means has made data mining and machine learning methods integral parts of today’s drug discovery process. In this paper, extreme gradient boosting (Xgboost), which i...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6273295/ https://www.ncbi.nlm.nih.gov/pubmed/27483216 http://dx.doi.org/10.3390/molecules21080983 |
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author | Babajide Mustapha, Ismail Saeed, Faisal |
author_facet | Babajide Mustapha, Ismail Saeed, Faisal |
author_sort | Babajide Mustapha, Ismail |
collection | PubMed |
description | Following the explosive growth in chemical and biological data, the shift from traditional methods of drug discovery to computer-aided means has made data mining and machine learning methods integral parts of today’s drug discovery process. In this paper, extreme gradient boosting (Xgboost), which is an ensemble of Classification and Regression Tree (CART) and a variant of the Gradient Boosting Machine, was investigated for the prediction of biological activity based on quantitative description of the compound’s molecular structure. Seven datasets, well known in the literature were used in this paper and experimental results show that Xgboost can outperform machine learning algorithms like Random Forest (RF), Support Vector Machines (LSVM), Radial Basis Function Neural Network (RBFN) and Naïve Bayes (NB) for the prediction of biological activities. In addition to its ability to detect minority activity classes in highly imbalanced datasets, it showed remarkable performance on both high and low diversity datasets. |
format | Online Article Text |
id | pubmed-6273295 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-62732952018-12-28 Bioactive Molecule Prediction Using Extreme Gradient Boosting Babajide Mustapha, Ismail Saeed, Faisal Molecules Article Following the explosive growth in chemical and biological data, the shift from traditional methods of drug discovery to computer-aided means has made data mining and machine learning methods integral parts of today’s drug discovery process. In this paper, extreme gradient boosting (Xgboost), which is an ensemble of Classification and Regression Tree (CART) and a variant of the Gradient Boosting Machine, was investigated for the prediction of biological activity based on quantitative description of the compound’s molecular structure. Seven datasets, well known in the literature were used in this paper and experimental results show that Xgboost can outperform machine learning algorithms like Random Forest (RF), Support Vector Machines (LSVM), Radial Basis Function Neural Network (RBFN) and Naïve Bayes (NB) for the prediction of biological activities. In addition to its ability to detect minority activity classes in highly imbalanced datasets, it showed remarkable performance on both high and low diversity datasets. MDPI 2016-07-28 /pmc/articles/PMC6273295/ /pubmed/27483216 http://dx.doi.org/10.3390/molecules21080983 Text en © 2016 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Babajide Mustapha, Ismail Saeed, Faisal Bioactive Molecule Prediction Using Extreme Gradient Boosting |
title | Bioactive Molecule Prediction Using Extreme Gradient Boosting |
title_full | Bioactive Molecule Prediction Using Extreme Gradient Boosting |
title_fullStr | Bioactive Molecule Prediction Using Extreme Gradient Boosting |
title_full_unstemmed | Bioactive Molecule Prediction Using Extreme Gradient Boosting |
title_short | Bioactive Molecule Prediction Using Extreme Gradient Boosting |
title_sort | bioactive molecule prediction using extreme gradient boosting |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6273295/ https://www.ncbi.nlm.nih.gov/pubmed/27483216 http://dx.doi.org/10.3390/molecules21080983 |
work_keys_str_mv | AT babajidemustaphaismail bioactivemoleculepredictionusingextremegradientboosting AT saeedfaisal bioactivemoleculepredictionusingextremegradientboosting |