Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure–Activity Relationship (QSAR) Analysis
Numerous chemical compounds are distributed around the world and may affect the homeostasis of the endocrine system by disrupting the normal functions of hormone receptors. Although the risks associated with these compounds have been evaluated by acute toxicity testing in mammalian models, the chron...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-03-01
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| Series: | Frontiers in Bioengineering and Biotechnology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fbioe.2019.00065/full |
| _version_ | 1818022811519680512 |
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| author | Yasunari Matsuzaka Yoshihiro Uesawa |
| author_facet | Yasunari Matsuzaka Yoshihiro Uesawa |
| author_sort | Yasunari Matsuzaka |
| collection | DOAJ |
| description | Numerous chemical compounds are distributed around the world and may affect the homeostasis of the endocrine system by disrupting the normal functions of hormone receptors. Although the risks associated with these compounds have been evaluated by acute toxicity testing in mammalian models, the chronic toxicity of many chemicals remains due to high cost of the compounds and the testing, etc. However, computational approaches may be promising alternatives and reduce these evaluations. Recently, deep learning (DL) has been shown to be promising prediction models with high accuracy for recognition of images, speech, signals, and videos since it greatly benefits from large datasets. Recently, a novel DL-based technique called DeepSnap was developed to conduct QSAR analysis using three-dimensional images of chemical structures. It can be used to predict the potential toxicity of many different chemicals to various receptors without extraction of descriptors. DeepSnap has been shown to have a very high capacity in tests using Tox21 quantitative qHTP datasets. Numerous parameters must be adjusted to use the DeepSnap method but they have not been optimized. In this study, the effects of these parameters on the performance of the DL prediction model were evaluated in terms of the loss in validation as an indicator for evaluating the performance of the DL using the toxicity information in the Tox21 qHTP database. The relations of the parameters of DeepSnap such as (1) number of molecules per SDF split into (2) zoom factor percentage, (3) atom size for van der waals percentage, (4) bond radius, (5) minimum bond distance, and (6) bond tolerance, with the validation loss following quadratic function curves, which suggests that optimal thresholds exist to attain the best performance with these prediction models. Using the parameter values set with the best performance, the prediction model of chemical compounds for CAR agonist was built using 64 images, at 105° angle, with AUC of 0.791. Thus, based on these parameters, the proposed DeepSnap-DL approach will be highly reliable and beneficial to establish models to assess the risk associated with various chemicals. |
| first_indexed | 2024-12-10T03:34:21Z |
| format | Article |
| id | doaj.art-df77122c4cd1437cb591bfe21ba2f55e |
| institution | Directory Open Access Journal |
| issn | 2296-4185 |
| language | English |
| last_indexed | 2024-12-10T03:34:21Z |
| publishDate | 2019-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioengineering and Biotechnology |
| spelling | doaj.art-df77122c4cd1437cb591bfe21ba2f55e2022-12-22T02:03:44ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852019-03-01710.3389/fbioe.2019.00065427670Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure–Activity Relationship (QSAR) AnalysisYasunari MatsuzakaYoshihiro UesawaNumerous chemical compounds are distributed around the world and may affect the homeostasis of the endocrine system by disrupting the normal functions of hormone receptors. Although the risks associated with these compounds have been evaluated by acute toxicity testing in mammalian models, the chronic toxicity of many chemicals remains due to high cost of the compounds and the testing, etc. However, computational approaches may be promising alternatives and reduce these evaluations. Recently, deep learning (DL) has been shown to be promising prediction models with high accuracy for recognition of images, speech, signals, and videos since it greatly benefits from large datasets. Recently, a novel DL-based technique called DeepSnap was developed to conduct QSAR analysis using three-dimensional images of chemical structures. It can be used to predict the potential toxicity of many different chemicals to various receptors without extraction of descriptors. DeepSnap has been shown to have a very high capacity in tests using Tox21 quantitative qHTP datasets. Numerous parameters must be adjusted to use the DeepSnap method but they have not been optimized. In this study, the effects of these parameters on the performance of the DL prediction model were evaluated in terms of the loss in validation as an indicator for evaluating the performance of the DL using the toxicity information in the Tox21 qHTP database. The relations of the parameters of DeepSnap such as (1) number of molecules per SDF split into (2) zoom factor percentage, (3) atom size for van der waals percentage, (4) bond radius, (5) minimum bond distance, and (6) bond tolerance, with the validation loss following quadratic function curves, which suggests that optimal thresholds exist to attain the best performance with these prediction models. Using the parameter values set with the best performance, the prediction model of chemical compounds for CAR agonist was built using 64 images, at 105° angle, with AUC of 0.791. Thus, based on these parameters, the proposed DeepSnap-DL approach will be highly reliable and beneficial to establish models to assess the risk associated with various chemicals.https://www.frontiersin.org/article/10.3389/fbioe.2019.00065/fullchemical structureconstitutive androgen receptorDeep SnapTox21deep learningQSAR |
| spellingShingle | Yasunari Matsuzaka Yoshihiro Uesawa Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure–Activity Relationship (QSAR) Analysis Frontiers in Bioengineering and Biotechnology chemical structure constitutive androgen receptor Deep Snap Tox21 deep learning QSAR |
| title | Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure–Activity Relationship (QSAR) Analysis |
| title_full | Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure–Activity Relationship (QSAR) Analysis |
| title_fullStr | Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure–Activity Relationship (QSAR) Analysis |
| title_full_unstemmed | Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure–Activity Relationship (QSAR) Analysis |
| title_short | Optimization of a Deep-Learning Method Based on the Classification of Images Generated by Parameterized Deep Snap a Novel Molecular-Image-Input Technique for Quantitative Structure–Activity Relationship (QSAR) Analysis |
| title_sort | optimization of a deep learning method based on the classification of images generated by parameterized deep snap a novel molecular image input technique for quantitative structure activity relationship qsar analysis |
| topic | chemical structure constitutive androgen receptor Deep Snap Tox21 deep learning QSAR |
| url | https://www.frontiersin.org/article/10.3389/fbioe.2019.00065/full |
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