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DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning
Synergistic drug combinations have demonstrated effective therapeutic effects in cancer treatment. Deep learning methods accelerate identification of novel drug combinations by reducing the search space. However, potential adverse drug–drug interactions (DDIs), which may increase the risks for combi...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9861702/ https://www.ncbi.nlm.nih.gov/pubmed/36677903 http://dx.doi.org/10.3390/molecules28020844 |
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author | Wang, Zhongming Dong, Jiahui Wu, Lianlian Dai, Chong Wang, Jing Wen, Yuqi Zhang, Yixin Yang, Xiaoxi He, Song Bo, Xiaochen |
author_facet | Wang, Zhongming Dong, Jiahui Wu, Lianlian Dai, Chong Wang, Jing Wen, Yuqi Zhang, Yixin Yang, Xiaoxi He, Song Bo, Xiaochen |
author_sort | Wang, Zhongming |
collection | PubMed |
description | Synergistic drug combinations have demonstrated effective therapeutic effects in cancer treatment. Deep learning methods accelerate identification of novel drug combinations by reducing the search space. However, potential adverse drug–drug interactions (DDIs), which may increase the risks for combination therapy, cannot be detected by existing computational synergy prediction methods. We propose DEML, an ensemble-based multi-task neural network, for the simultaneous optimization of five synergy regression prediction tasks, synergy classification, and DDI classification tasks. DEML uses chemical and transcriptomics information as inputs. DEML adapts the novel hybrid ensemble layer structure to construct higher order representation using different perspectives. The task-specific fusion layer of DEML joins representations for each task using a gating mechanism. For the Loewe synergy prediction task, DEML overperforms the state-of-the-art synergy prediction method with an improvement of 7.8% and 13.2% for the root mean squared error and the R2 correlation coefficient. Owing to soft parameter sharing and ensemble learning, DEML alleviates the multi-task learning ‘seesaw effect’ problem and shows no performance loss on other tasks. DEML has a superior ability to predict drug pairs with high confidence and less adverse DDIs. DEML provides a promising way to guideline novel combination therapy strategies for cancer treatment. |
format | Online Article Text |
id | pubmed-9861702 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-98617022023-01-22 DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning Wang, Zhongming Dong, Jiahui Wu, Lianlian Dai, Chong Wang, Jing Wen, Yuqi Zhang, Yixin Yang, Xiaoxi He, Song Bo, Xiaochen Molecules Article Synergistic drug combinations have demonstrated effective therapeutic effects in cancer treatment. Deep learning methods accelerate identification of novel drug combinations by reducing the search space. However, potential adverse drug–drug interactions (DDIs), which may increase the risks for combination therapy, cannot be detected by existing computational synergy prediction methods. We propose DEML, an ensemble-based multi-task neural network, for the simultaneous optimization of five synergy regression prediction tasks, synergy classification, and DDI classification tasks. DEML uses chemical and transcriptomics information as inputs. DEML adapts the novel hybrid ensemble layer structure to construct higher order representation using different perspectives. The task-specific fusion layer of DEML joins representations for each task using a gating mechanism. For the Loewe synergy prediction task, DEML overperforms the state-of-the-art synergy prediction method with an improvement of 7.8% and 13.2% for the root mean squared error and the R2 correlation coefficient. Owing to soft parameter sharing and ensemble learning, DEML alleviates the multi-task learning ‘seesaw effect’ problem and shows no performance loss on other tasks. DEML has a superior ability to predict drug pairs with high confidence and less adverse DDIs. DEML provides a promising way to guideline novel combination therapy strategies for cancer treatment. MDPI 2023-01-14 /pmc/articles/PMC9861702/ /pubmed/36677903 http://dx.doi.org/10.3390/molecules28020844 Text en © 2023 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 | Article Wang, Zhongming Dong, Jiahui Wu, Lianlian Dai, Chong Wang, Jing Wen, Yuqi Zhang, Yixin Yang, Xiaoxi He, Song Bo, Xiaochen DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning |
title | DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning |
title_full | DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning |
title_fullStr | DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning |
title_full_unstemmed | DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning |
title_short | DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning |
title_sort | deml: drug synergy and interaction prediction using ensemble-based multi-task learning |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9861702/ https://www.ncbi.nlm.nih.gov/pubmed/36677903 http://dx.doi.org/10.3390/molecules28020844 |
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