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Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs)
BACKGROUND: Several topological (2D) and geometric (3D) molecular descriptors (MDs) are calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation process. To this end, norm-, mean- and statistic-based (non-fuzzy) operators are used, under the assumption that LOVIs/LOEIs...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755596/ https://www.ncbi.nlm.nih.gov/pubmed/30362050 http://dx.doi.org/10.1186/s13321-018-0306-7 |
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author | García-Jacas, César R. Cabrera-Leyva, Lisset Marrero-Ponce, Yovani Suárez-Lezcano, José Cortés-Guzmán, Fernando Pupo-Meriño, Mario Vivas-Reyes, Ricardo |
author_facet | García-Jacas, César R. Cabrera-Leyva, Lisset Marrero-Ponce, Yovani Suárez-Lezcano, José Cortés-Guzmán, Fernando Pupo-Meriño, Mario Vivas-Reyes, Ricardo |
author_sort | García-Jacas, César R. |
collection | PubMed |
description | BACKGROUND: Several topological (2D) and geometric (3D) molecular descriptors (MDs) are calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation process. To this end, norm-, mean- and statistic-based (non-fuzzy) operators are used, under the assumption that LOVIs/LOEIs are independent (orthogonal) values of one another. These operators are based on additive and/or linear measures and, consequently, they cannot be used to encode information from interrelated criteria. Thus, as LOVIs/LOEIs are not orthogonal values, then non-additive (fuzzy) measures can be used to encode the interrelation among them. RESULTS: General approaches to compute fuzzy 2D/3D-MDs from the contribution of each atom (LOVIs) or covalent bond (LOEIs) within a molecule are proposed, by using the Choquet integral as fuzzy aggregation operator. The Choquet integral-based operator is rather different from the other operators often used for the 2D/3D-MDs calculation. It performs a reordering step to fuse the LOVIs/LOEIs according to their magnitudes and, in addition, it considers the interrelation among them through a fuzzy measure. With this operator, fuzzy definitions can be derived from traditional or recent MDs; for instance, fuzzy Randic-like connectivity indices, fuzzy Balaban-like indices, fuzzy Kier–Hall connectivity indices, among others. To demonstrate the feasibility of using this operator, the QuBiLS-MIDAS 3D-MDs were used as study case and, as a result, a module was built into the corresponding software to compute them (http://tomocomd.com/qubils-midas). Thus, it is the only software reported in the literature that can be employed to determine Choquet integral-based fuzzy MDs. Moreover, regression models were created on eight chemical datasets. In this way, a comparison between the results achieved by the models based on the non-fuzzy QuBiLS-MIDAS 3D-MDs with regard to the ones achieved by the models based on the fuzzy QuBiLS-MIDAS 3D-MDs was made. As a result, the models built with the fuzzy QuBiLS-MIDAS 3D-MDs achieved the best performance, which was statistically corroborated through the Wilcoxon signed-rank test. CONCLUSIONS: All in all, it can be concluded that the Choquet integral constitutes a prominent alternative to compute fuzzy 2D/3D-MDs from LOVIs/LOEIs. In this way, better characterizations of the compounds can be obtained, which will be ultimately useful in enhancing the modelling ability of existing traditional 2D/3D-MDs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13321-018-0306-7) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6755596 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-67555962019-09-26 Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs) García-Jacas, César R. Cabrera-Leyva, Lisset Marrero-Ponce, Yovani Suárez-Lezcano, José Cortés-Guzmán, Fernando Pupo-Meriño, Mario Vivas-Reyes, Ricardo J Cheminform Research Article BACKGROUND: Several topological (2D) and geometric (3D) molecular descriptors (MDs) are calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation process. To this end, norm-, mean- and statistic-based (non-fuzzy) operators are used, under the assumption that LOVIs/LOEIs are independent (orthogonal) values of one another. These operators are based on additive and/or linear measures and, consequently, they cannot be used to encode information from interrelated criteria. Thus, as LOVIs/LOEIs are not orthogonal values, then non-additive (fuzzy) measures can be used to encode the interrelation among them. RESULTS: General approaches to compute fuzzy 2D/3D-MDs from the contribution of each atom (LOVIs) or covalent bond (LOEIs) within a molecule are proposed, by using the Choquet integral as fuzzy aggregation operator. The Choquet integral-based operator is rather different from the other operators often used for the 2D/3D-MDs calculation. It performs a reordering step to fuse the LOVIs/LOEIs according to their magnitudes and, in addition, it considers the interrelation among them through a fuzzy measure. With this operator, fuzzy definitions can be derived from traditional or recent MDs; for instance, fuzzy Randic-like connectivity indices, fuzzy Balaban-like indices, fuzzy Kier–Hall connectivity indices, among others. To demonstrate the feasibility of using this operator, the QuBiLS-MIDAS 3D-MDs were used as study case and, as a result, a module was built into the corresponding software to compute them (http://tomocomd.com/qubils-midas). Thus, it is the only software reported in the literature that can be employed to determine Choquet integral-based fuzzy MDs. Moreover, regression models were created on eight chemical datasets. In this way, a comparison between the results achieved by the models based on the non-fuzzy QuBiLS-MIDAS 3D-MDs with regard to the ones achieved by the models based on the fuzzy QuBiLS-MIDAS 3D-MDs was made. As a result, the models built with the fuzzy QuBiLS-MIDAS 3D-MDs achieved the best performance, which was statistically corroborated through the Wilcoxon signed-rank test. CONCLUSIONS: All in all, it can be concluded that the Choquet integral constitutes a prominent alternative to compute fuzzy 2D/3D-MDs from LOVIs/LOEIs. In this way, better characterizations of the compounds can be obtained, which will be ultimately useful in enhancing the modelling ability of existing traditional 2D/3D-MDs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13321-018-0306-7) contains supplementary material, which is available to authorized users. Springer International Publishing 2018-10-25 /pmc/articles/PMC6755596/ /pubmed/30362050 http://dx.doi.org/10.1186/s13321-018-0306-7 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article García-Jacas, César R. Cabrera-Leyva, Lisset Marrero-Ponce, Yovani Suárez-Lezcano, José Cortés-Guzmán, Fernando Pupo-Meriño, Mario Vivas-Reyes, Ricardo Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs) |
title | Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs) |
title_full | Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs) |
title_fullStr | Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs) |
title_full_unstemmed | Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs) |
title_short | Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs) |
title_sort | choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (lovis/loeis) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755596/ https://www.ncbi.nlm.nih.gov/pubmed/30362050 http://dx.doi.org/10.1186/s13321-018-0306-7 |
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