Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach.

Derek Reiman, Ali M Farhat, Yang Dai

Methods in molecular biology (Clifton, N.J.) 2021

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Accurate prediction of the host phenotypes from a microbial sample and identification of the associated microbial markers are important in understanding the impact of the microbiome on the pathogenesis and progression of various diseases within the host. A deep learning tool, PopPhy-CNN, has been developed for the task of predicting host phenotypes using a convolutional neural network (CNN). By representing samples as annotated taxonomic trees and further representing these trees as matrices, PopPhy-CNN utilizes the CNN's innate ability to explore locally similar microbes on the taxonomic tree. Furthermore, PopPhy-CNN can be used to evaluate the importance of each taxon in the prediction of host status. Here, we describe the underlying methodology, architecture, and core utility of PopPhy-CNN. We also demonstrate the use of PopPhy-CNN on a microbial dataset.

Citation

Derek Reiman, Ali M Farhat, Yang Dai. Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach. Methods in molecular biology (Clifton, N.J.). 2021;2190:249-266