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Int. J. Mol. Sci. 2018, 19(1), 30; doi:10.3390/ijms19010030

Descriptor Selection via Log-Sum Regularization for the Biological Activities of Chemical Structure

1
State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau 999078, China
2
Ministry of Education Key Lab of Intelligent Networks and Network Security, Xi’an Jiaotong University, Xi’an 710049, China
*
Author to whom correspondence should be addressed.
Received: 17 November 2017 / Revised: 10 December 2017 / Accepted: 21 December 2017 / Published: 22 December 2017
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
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Abstract

The quantitative structure-activity relationship (QSAR) model searches for a reliable relationship between the chemical structure and biological activities in the field of drug design and discovery. (1) Background: In the study of QSAR, the chemical structures of compounds are encoded by a substantial number of descriptors. Some redundant, noisy and irrelevant descriptors result in a side-effect for the QSAR model. Meanwhile, too many descriptors can result in overfitting or low correlation between chemical structure and biological bioactivity. (2) Methods: We use novel log-sum regularization to select quite a few descriptors that are relevant to biological activities. In addition, a coordinate descent algorithm, which uses novel univariate log-sum thresholding for updating the estimated coefficients, has been developed for the QSAR model. (3) Results: Experimental results on artificial and four QSAR datasets demonstrate that our proposed log-sum method has good performance among state-of-the-art methods. (4) Conclusions: Our proposed multiple linear regression with log-sum penalty is an effective technique for both descriptor selection and prediction of biological activity. View Full-Text
Keywords: QSAR; biological activity; descriptor selection; regularization; log-sum QSAR; biological activity; descriptor selection; regularization; log-sum
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Xia, L.-Y.; Wang, Y.-W.; Meng, D.-Y.; Yao, X.-J.; Chai, H.; Liang, Y. Descriptor Selection via Log-Sum Regularization for the Biological Activities of Chemical Structure. Int. J. Mol. Sci. 2018, 19, 30.

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