UMMAN: Unsupervised Multi-graph Merge Adversarial Network for Disease Prediction Based on Intestinal Flora

TL;DR

UMMAN is a novel unsupervised multi-graph neural network that effectively captures complex microbial associations for improved disease prediction from gut microbiome data.

Contribution

It introduces the first combination of Graph Neural Networks with intestinal flora disease prediction, utilizing multi-graph embeddings and adversarial training.

Findings

Outperforms existing methods on five gut microbiome datasets.

Effectively learns complex microbial associations.

Demonstrates stable and robust prediction performance.

Abstract

The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit connection among gut microbes poses a significant challenge for disease prediction using abundance information from OTU data. Recently, several methods have shown potential in predicting corresponding diseases. However, these methods fail to learn the inner association among gut microbes from different hosts, leading to unsatisfactory performance. In this paper, we present a novel architecture, Unsupervised Multi-graph Merge Adversarial Network (UMMAN). UMMAN can obtain the embeddings of nodes in the Multi-Graph in an unsupervised scenario, so that it helps learn the multiplex association. Our method is the first to combine Graph Neural Network with the task of intestinal flora disease prediction. We employ complex relation-types to construct the Original-Graph and disrupt the relationships among nodes to generate corresponding Shuffled-Graph. We introduce the Node Feature Global Integration (NFGI) module to represent the global features of the graph. Furthermore, we design a joint loss comprising adversarial loss and hybrid attention loss to ensure that the real graph embedding aligns closely with the Original-Graph and diverges from the Shuffled-Graph. Comprehensive experiments on five classical OTU gut microbiome datasets demonstrate the effectiveness and stability of our method. (We will release our code soon.)