Predicting Microbial Interactions Using Graph Neural Networks

TL;DR

This paper introduces a Graph Neural Network approach to predict and classify microbial interactions, outperforming previous methods on a large dataset of co-culture experiments.

Contribution

The study presents a novel GNN-based model for predicting and classifying microbial interactions, leveraging shared information across experiments, with superior performance over existing models.

Findings

Achieved an F1-score of 80.44% in interaction prediction.

Outperformed XGBoost with an F1-score of 72.76%.

Successfully classified complex interaction types like mutualism and parasitism.

Abstract

Predicting interspecies interactions is a key challenge in microbial ecology, as these interactions are critical to determining the structure and activity of microbial communities. In this work, we used data on monoculture growth capabilities, interactions with other species, and phylogeny to predict a negative or positive effect of interactions. More precisely, we used one of the largest available pairwise interaction datasets to train our models, comprising over 7,500 interactions be- tween 20 species from two taxonomic groups co-cultured under 40 distinct carbon conditions, with a primary focus on the work of Nestor et al.[28 ]. In this work, we propose Graph Neural Networks (GNNs) as a powerful classifier to predict the direction of the effect. We construct edge-graphs of pairwise microbial interactions in order to leverage shared information across individual co-culture experiments, and use GNNs to predict modes of interaction. Our model can not only predict binary interactions (positive/negative) but also classify more complex interaction types such as mutualism, competition, and parasitism. Our initial results were encouraging, achieving an F1-score of 80.44%. This significantly outperforms comparable methods in the literature, including conventional Extreme Gradient Boosting (XGBoost) models, which reported an F1-score of 72.76%.