OmiEmbed: a unified multi-task deep learning framework for multi-omics data

TL;DR

OmiEmbed is a versatile deep learning framework that effectively captures biomedical information from high-dimensional multi-omics data, enabling multiple predictive tasks to support personalized medicine.

Contribution

It introduces a unified multi-task deep learning approach with a deep embedding module for multi-omics data, improving performance over existing methods.

Findings

Outperformed other methods on all downstream tasks

Achieved better results with multi-task learning compared to single-task training

Supports various applications like dimensionality reduction and survival prediction

Abstract

High-dimensional omics data contains 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 support 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 comparing to training them individually. OmiEmbed is a powerful and unified framework that can be widely adapted to various application of high-dimensional omics data and has a great potential to facilitate more accurate and personalised clinical decision making.