OmiEmbed: A Unified Multi-Task Deep Learning Framework for Multi-Omics Data

Xiaoyu Zhang*, Yuting Xing, Kai Sun, Yike Guo*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

39 Citations (Scopus)


High-dimensional omics data contain intrinsic biomedical information that is crucial for personalised medicine. Nevertheless, it is challenging to capture them from the genome-wide data, due to the large number of molecular features and small number of available samples, which is also called “the curse of dimensionality” in machine learning. To tackle this problem and pave the way for machine learning-aided precision medicine, we proposed a unified multi-task deep learning framework named OmiEmbed to capture biomedical information from high-dimensional omics data with the deep embedding and downstream task modules. The deep embedding module learnt an omics embedding that mapped multiple omics data types into a latent space with lower dimensionality. Based on the new representation of multi-omics data, different downstream task modules were trained simultaneously and efficiently with the multi-task strategy to predict the comprehensive phenotype profile of each sample. OmiEmbed supports multiple tasks for omics data including dimensionality reduction, tumour type classification, multi-omics integration, demographic and clinical feature reconstruction, and survival prediction. The framework outperformed other methods on all three types of downstream tasks and achieved better performance with the multi-task strategy compared to training them individually. OmiEmbed is a powerful and unified framework that can be widely adapted to various applications of high-dimensional omics data and has great potential to facilitate more accurate and personalised clinical decision making.
Original languageEnglish
Article number3047
Number of pages22
Issue number12
Publication statusPublished - 18 Jun 2021

Scopus Subject Areas

  • Oncology
  • Cancer Research

User-Defined Keywords

  • Cancer classification
  • Deep learning
  • Multi-omics data
  • Multi-task learning
  • Survival prediction


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