Merge branch 'master' of gitlab.fbk.eu:MPBA/phylogenetic-cnn

envs/deps/README.md

 # 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:
 

readme.md

+# 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](https://arxiv.org/abs/1709.02268).
+
+## 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:
+
+* `settings.py` - where it can be chose which type of data we want to load, where are the data, where to output, etc...
+* `dap/settings.py` - 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/deep_learning_settings.py` - 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:
+
+```
+python3 phylocnn_runner.py
+```
+will execute the phylogenetic convolutional neural network on the selected data with the selected settings.
+
+## Replication
+| disease |                                                                           |                                                                              |                                                                                 |                                                                                    |
+|:-------:|---------------------------------------------------------------------------|------------------------------------------------------------------------------|---------------------------------------------------------------------------------|------------------------------------------------------------------------------------|
+|   cdf   | [IBD data](https://drive.google.com/open?id=0B5ihbogwrsACZ292WW9Qd0oteFE) | [IBD results](https://drive.google.com/open?id=0BwWtRh6l0dHGUXhwbmpJQ0VMNVU) | [Synthetic data](https://drive.google.com/open?id=0B5ihbogwrsACM3F1M0dIM3NkX0k) | [Synthetic results](https://drive.google.com/open?id=0BwWtRh6l0dHGckJjWlBYQ2gyYjQ) |
+|   cdr   | [IBD data](https://drive.google.com/open?id=0B5ihbogwrsACLTJfaEYwNlNZaDg) | [IBD results](https://drive.google.com/open?id=0BwWtRh6l0dHGbVdVNHprSFpvdTg) | [Synthetic data](https://drive.google.com/open?id=0B5ihbogwrsACZHNvd3pocG94RXM) | [Synthetic results](https://drive.google.com/open?id=0BwWtRh6l0dHGU2RHN2VXbWhsdk0) |
+|   icdf  | [IBD data](https://drive.google.com/open?id=0B5ihbogwrsACa0I1XzNCSnIzNDA) | [IBD results](https://drive.google.com/open?id=0BwWtRh6l0dHGSjhhOVJFQUZUMHc) | [Synthetic data](https://drive.google.com/open?id=0B5ihbogwrsACTjhBck5fVDV3QnM) | [Synthetic results](https://drive.google.com/open?id=0BwWtRh6l0dHGT2VndEp2QzdSZHM) |
+|   icdr  | [IBD data](https://drive.google.com/open?id=0B5ihbogwrsACa0dsRjVzTzkydlk) | [IBD results](https://drive.google.com/open?id=0BwWtRh6l0dHGWjlqdmhucnRFRUU) | [Synthetic data](https://drive.google.com/open?id=0B5ihbogwrsACc2JScTRqUXJfWjQ) | [Synthetic results](https://drive.google.com/open?id=0BwWtRh6l0dHGZ1ZhWVpDQ2oza1E) |
+|   ucf   | [IBD data](https://drive.google.com/open?id=0B5ihbogwrsACYWVEOHZzVWZzM1k) | [IBD results](https://drive.google.com/open?id=0BwWtRh6l0dHGYUc2cng5OUpKTk0) | [Synthetic data](https://drive.google.com/open?id=0B5ihbogwrsACOW5rNjAxX1pQbUE) | [Synthetic results](https://drive.google.com/open?id=0BwWtRh6l0dHGX1RNNWhWM1RsREU) |
+|   ucr   | [IBD data](https://drive.google.com/open?id=0B5ihbogwrsACRFpwQTVYa1h1ekE) | [IBD results](https://drive.google.com/open?id=0BwWtRh6l0dHGZEJ0eTVEem1QR28) | [Synthetic data](https://drive.google.com/open?id=0B5ihbogwrsACc25OclVvald0N28) | [Synthetic results](https://drive.google.com/open?id=0BwWtRh6l0dHGaWFVbUg0Wm9WNFU) |
+
+## Authors
+
+* Valerio Maggio - [website]()
+* Diego Fioravanti- [website](https://is.tuebingen.mpg.de/people/dfioravanti)
+
+## License
+
+This project is licensed under SOMETHING - see the [LICENSE.md](LICENSE.md) file for details