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 STYLE
Reiman, D., Farhat, A. M., & Dai, Y. (2021). Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach. In Methods in Molecular Biology (Vol. 2190, pp. 249–266). Humana Press Inc. https://doi.org/10.1007/978-1-0716-0826-5_12
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