Commit 9b05bc4c authored by Valerio Maggio's avatar Valerio Maggio
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# Install MLPY 3.5.0 Dependency
`mlpy` package is required for some opetions included in the DAP procedure.
`mlpy` package is required for some operations included in the DAP procedure.
To install `mlpy` dependency, the following steps must be accomplished:
# Phylogenetic Convolutional Neural Network
A novel architecture for metagenomic classification defined as phylogenetic convolutional neural network, as presented in the paper [Phylogenetic Convolutiona -Neural Networks in Metagenomics](
## Getting Started
These instructions will get you a copy of the project up and running on your local machine.
### Cloning
We recommend to clone the repository with the --recursive option in order to clone the submodule too.
### Prerequisites
A complete conda environment is provided as a yml file in the folder `envs`. Additionally it is required to install the mlpy library as described in the readme included in the `envs/deps` folder.
## Running the program
In order to run the program one needs to modify the following files:
* `` - where it can be chose which type of data we want to load, where are the data, where to output, etc...
* `dap/` - where it can be set how the DAP is supposed to operate. More informations are available in the readme in the `dap` folder and in the paper.
* `dap/` - where all the settings specific for deep learning can be set.
Once done that one can select the algormthm (SVM, random forrest, MLP, ph-cnn) to be used by simply decide which runner to execute. For example:
will execute the phylogenetic convolutional neural network on the selected data with the selected settings.
## Replication
| disease | | | | |
| cdf | [IBD data]( | [IBD results]( | [Synthetic data]( | [Synthetic results]( |
| cdr | [IBD data]( | [IBD results]( | [Synthetic data]( | [Synthetic results]( |
| icdf | [IBD data]( | [IBD results]( | [Synthetic data]( | [Synthetic results]( |
| icdr | [IBD data]( | [IBD results]( | [Synthetic data]( | [Synthetic results]( |
| ucf | [IBD data]( | [IBD results]( | [Synthetic data]( | [Synthetic results]( |
| ucr | [IBD data]( | [IBD results]( | [Synthetic data]( | [Synthetic results]( |
## Authors
* Valerio Maggio - [website]()
* Diego Fioravanti- [website](
## License
This project is licensed under SOMETHING - see the []( file for details
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