vbpi-gnn

Code for learnable topological features for phylogenetic inference via graph neural networks

Please cite our paper if you find the code useful

@inproceedings{
zhang2023learnable,
title={Learnable Topological Features For Phylogenetic Inference via Graph Neural Networks},
author={Cheng Zhang},
booktitle={The Eleventh International Conference on Learning Representations },
year={2023},
url={https://openreview.net/forum?id=hVVUY7p64WL}
}

Mini demo

Use command line

python run_tde.py --gnn_type edge --batch_size 20 --hL 2 --hdim 100 --maxIter 200000
python main.py --dataset DS1  --brlen_model gnn --gnn_type edge --hL 2 --hdim 100 --maxIter 400000 --empFreq --psp

You can also load the data, set up and train the model on your own. See more details in main.py and run_tde.py.