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vbpi-torch's Introduction

vbpi-torch

Pytorch Implementation of Variational Bayesian Phylogenetic Inference

Dependencies

You can build and enter a conda environment with all of the dependencies built in using the supplied environment.yml file via:

conda env create -f environment.yml
conda activate vbpi-torch

Preparation

Unzip DENV4_constant_golden_run.trees.zip in the rooted/data/DENV4 directory.

Running

Examples:

In the unrooted/ folder

python main.py --dataset DS1 --psp --empFreq
python main.py --dataset DS1 --psp --nParticle 20 --gradMethod rws --empFreq
python main.py --dataset flu100 --psp
python main.py --dataset flu100 --psp --supportType mcmc -cf 100000

In the rooted/ folder

python main.py --dataset DENV4 --burnin 2501 --coalescent_type constant --clock_type strict --init_clock_rate 1e-3 --sample_info --psp --empFreq
python main.py --dataset HCV --burnin 251 --coalescent_type skyride --clock_type fixed_rate --init_clock_rate 7.9e-4 --psp

vbpi-torch's People

Contributors

zcrabbit avatar matsen avatar

Stargazers

Amine M. Remita avatar

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