This repository contains a Julia package for using a compositional Neural Ordinary Differential Equation (cNODE) associated with the paper: "Predicting microbiome compositions from species assemblages through deep learning" (doi: https://doi.org/10.1101/2021.06.17.448886).
Check out the documentation for the usage of the Package.
This package is build for Julia at the long term support release. Download: Julia 1.6.5 from the webpage.
To install cNODE.jl, on Julia REPL press ] to acces Pkg utilities and add package:
(@v1.6) pkg> add https://github.com/michel-mata/cNODE.jl.git
Synthetic Data. For generating synthetic data and validating cNODE, check the tutorial:
tutorial_synthetic_data.jl
Real Data. For using cNODE with real data, check the tutorial:
tutorial_real_data.jl
The results from our paper were obtained in Julia 0.6.4, check the repository for this version.