MegaD: Deep Learning for Rapid and Accurate Disease Status Prediction of Metagenomic Samples

The diversity within different microbiome communities that drive biogeochemical processes influences many different phenotypes. Analyses of these communities and their diversity by countless microbiome projects have revealed an important role of metagenomics in understanding the complex relation between microbes and their environments. This relationship can be understood in the context of microbiome composition of specific known environments. These compositions can then be used as a template for predicting the status of similar environments. Machine learning has been applied as a key component to this predictive task. Several analysis tools have already been published utilizing machine learning methods for metagenomic analysis. Despite the previously proposed machine learning models, the performance of deep neural networks is still under-researched. Given the nature of metagenomic data, deep neural networks could provide a strong boost to growth in the prediction accuracy in metagenomic analysis applications. To meet this urgent demand, we present a deep learning based tool that utilizes a deep neural network implementation for phenotypic prediction of unknown metagenomic samples. (1) First, our tool takes as input taxonomic profiles from 16S or WGS sequencing data. (2) Second, given the samples, our tool builds a model based on a deep neural network by computing multi-level classification. (3) Lastly, given the model, our tool classifies an unknown sample with its unlabeled taxonomic profile. In the benchmark experiments, we deduced that an analysis method facilitating a deep neural network such as our tool can show promising results in increasing the prediction accuracy on several samples compared to other machine learning models.