Predicting Microbial Interactions Using Graph Neural Networks

Elham Gholamzadeh, Kajal Singla, Nico Scherf

Keywords: Graph Neural Networks, Edge graphs, Microbial communities, Microbial interactions, Computational biology

TL;DR: We develop a graph neural network framework leveraging edge-graph representations of pairwise microbial co-cultures to classify interaction with higher accuracy than XGBoost and other baseline models.

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 between 20 species from two taxonomic groups co-cultured under 40 distinct carbon conditions, with a primary focus on the work of Nestor et al.\cite{nestor2023interactions}. 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\%.

Submission Number: 28