A deep learning pipeline for cross-sectional and longitudinal multiview data integration

TL;DR

This paper introduces a deep learning pipeline that effectively integrates cross-sectional and longitudinal multi-omics data to identify key biological variables and improve disease classification, demonstrated on IBD data.

Contribution

It presents a novel pipeline combining statistical and deep learning methods for multi-view, multi-timepoint data integration with class outcome consideration.

Findings

Identified microbial pathways, metabolites, and genes associated with IBD.

Compared feature extraction methods via simulations.

Provided a publicly available implementation.

Abstract

Biomedical research now commonly integrates diverse data types or views from the same individuals to better understand the pathobiology of complex diseases, but the challenge lies in meaningfully integrating these diverse views. Existing methods often require the same type of data from all views (cross-sectional data only or longitudinal data only) or do not consider any class outcome in the integration method, presenting limitations. To overcome these limitations, we have developed a pipeline that harnesses the power of statistical and deep learning methods to integrate cross-sectional and longitudinal data from multiple sources. Additionally, it identifies key variables contributing to the association between views and the separation among classes, providing deeper biological insights. This pipeline includes variable selection/ranking using linear and nonlinear methods, feature extraction using functional principal component analysis and Euler characteristics, and joint integration and classification using dense feed-forward networks and recurrent neural networks. We applied this pipeline to cross-sectional and longitudinal multi-omics data (metagenomics, transcriptomics, and metabolomics) from an inflammatory bowel disease (IBD) study and we identified microbial pathways, metabolites, and genes that discriminate by IBD status, providing information on the etiology of IBD. We conducted simulations to compare the two feature extraction methods. The proposed pipeline is available from the following GitHub repository: https://github.com/lasandrall/DeepIDA-GRU.