MtBNN

The python script for MtBNN. The objective function of MtBNN is the ELBO

The task-dependent part is and the task-commom part is . The help information can be obtain by

python main.py -h

Some toy data are given in testdata folder. The format of input files should be the same as these toy examples.

Updated in 2022.09

• Reconstruct the code
• Discard edward and make the sampling process transparent
• Add the code for generating data
• Use Python 3.8 & torch
• Optimize the model architecture, hyperparameters and training process. The model has better performance than the previous version.
• Update scripts for making data/running experiments
• Optimize the memory usage

Prepare data

Set genome.fa path in globalconfig.py

bash script/preparejsonfile.sh # it might take a while

Run experiments

Pretrain the Bayesian model:

bash script/run_pretrain.sh;

Eval with the pretrain model:

bash script/run_eval.sh

Five-fold cross-validation:

bash script/run_cv.sh;

requirement

Python==3.8

torch==1.11.0