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DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis
Zhao, Lianhe1,2; Dong, Qiongye1; Luo, Chunlong1,2; Wu, Yang1; Bu, Dechao1; Qi, Xiaoning1,2; Luo, Yufan1,2; Zhao, Yi1,3
2021
发表期刊COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
ISSN2001-0370
卷号19页码:2719-2725
摘要Integrative analysis of multi-omics data can elucidate valuable insights into complex molecular mechanisms for various diseases. However, due to their different modalities and high dimension, utilizing and integrating different types of omics data suffers from great challenges. There is an urgent need to develop a powerful method to improve survival prediction and detect functional gene modules from multi-omics data. To deal with these problems, we present DeepOmix (a scalable and interpretable multi-Omics Deep learning framework and application in cancer survival analysis), a flexible, scalable, and interpretable method for extracting relationships between the clinical survival time and multi-omics data based on a deep learning framework. DeepOmix enables the non-linear combination of variables from different omics datasets and incorporates prior biological information defined by users (such as signaling pathways and tissue networks). Benchmark experiments demonstrate that DeepOmix outperforms the other five cutting-edge prediction methods. Besides, Lower Grade Glioma (LGG) is taken as the case study to perform the prognosis prediction and illustrate the functional module nodes which are associated with the prognostic result in the prediction model. (C) 2021 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
关键词Multi-omics Deep learning Survival analysis Prognosis prediction Interpretable model
DOI10.1016/j.csbj.2021.04.067
收录类别SCI
语种英语
资助项目National Key R&D Program of China[2019YFC1709801] ; Zhejiang Provincial Research Center for Cancer Intelligent Diagnosis and Molecular Technology[JBZX-202003] ; National Natural Science Foundation of China[32070670] ; Zhejiang Provincial Natural Science Foundation of China[LY21C060003] ; Zhejiang Provincial Natural Science Foundation of China[LY20C060001]
WOS研究方向Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS类目Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS记录号WOS:000684856500007
出版者ELSEVIER
引用统计
被引频次:30[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://119.78.100.204/handle/2XEOYT63/17242
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Zhao, Yi
作者单位1.Chinese Acad Sci, Inst Comp Technol, Adv Comp Res Ctr, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Univ Chinese Acad Sci, Hwa Mei Hosp, Ningbo 315000, Peoples R China
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Zhao, Lianhe,Dong, Qiongye,Luo, Chunlong,et al. DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis[J]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,2021,19:2719-2725.
APA Zhao, Lianhe.,Dong, Qiongye.,Luo, Chunlong.,Wu, Yang.,Bu, Dechao.,...&Zhao, Yi.(2021).DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis.COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,19,2719-2725.
MLA Zhao, Lianhe,et al."DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis".COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 19(2021):2719-2725.
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