Constructing Phylogenetic Networks via Cherry Picking and Machine Learning
Giulia Bernardini, Leo van Iersel, Esther Julien and Leen Stougie
To run the code, the following packages have to be installed: numpy, pandas, scikit-learn, networkx, and
joblib.
The CPH is implemented in CPH.py. To experiment with this file,
In the file test_data_gen_rets.py, tree sets used for testing can be generated.
The code for initializing and updating the features can be found in Features.py.
For training the random forest, we first have to generate training data.
The code for this is given in train_data_gen.py.
In the folder LearningCherries you can find the code for training a random forest.
In the folder data/RFModels, there are some trained random forests in joblib format.