SGUQ: Staged Graph Convolution Neural Network for Alzheimer's Disease Diagnosis using Multi-Omics Data

TL;DR

This paper introduces SGUQ, a staged graph convolutional network that efficiently diagnoses Alzheimer's disease by selectively integrating multi-omics data, reducing costs and improving accuracy over existing methods.

Contribution

The paper presents a novel staged GCN with uncertainty quantification that adaptively incorporates multi-omics data for AD diagnosis, enhancing efficiency and accuracy.

Findings

46.23% samples predicted with single-omics data

16.04% samples improved with two-omics data

Achieved 0.858 accuracy on ROSMAP dataset

Abstract

Alzheimer's disease (AD) is a chronic neurodegenerative disorder and the leading cause of dementia, significantly impacting cost, mortality, and burden worldwide. The advent of high-throughput omics technologies, such as genomics, transcriptomics, proteomics, and epigenomics, has revolutionized the molecular understanding of AD. Conventional AI approaches typically require the completion of all omics data at the outset to achieve optimal AD diagnosis, which are inefficient and may be unnecessary. To reduce the clinical cost and improve the accuracy of AD diagnosis using multi-omics data, we propose a novel staged graph convolutional network with uncertainty quantification (SGUQ). SGUQ begins with mRNA and progressively incorporates DNA methylation and miRNA data only when necessary, reducing overall costs and exposure to harmful tests. Experimental results indicate that 46.23% of the samples can be reliably predicted using only single-modal omics data (mRNA), while an additional 16.04% of the samples can achieve reliable predictions when combining two omics data types (mRNA + DNA methylation). In addition, the proposed staged SGUQ achieved an accuracy of 0.858 on ROSMAP dataset, which outperformed existing methods significantly. The proposed SGUQ can not only be applied to AD diagnosis using multi-omics data but also has the potential for clinical decision-making using multi-viewed data. Our implementation is publicly available at https://github.com/chenzhao2023/multiomicsuncertainty.