BFReg

Supplements of toy data and code for Biological Regulatory Network.

We provide a preprossed toy dataset for missing value prediction task. Other data and preprocessing codes will be released after the paper is accepted.

File introductions

c_main.py cell classification task.

mask_main.py missing value prediction task.

c_model.py model construction.

module.py BFReg-NN blocks.

d_main.py dynamic prediction task.

dataset.py dataset file for gene trajectory prediction task.

cnf_model.py model file for gene trajectory prediction task.

gt_main.py gene trajectory prediction task.

Usage

enviroment

python == 3.7

pytorch == 1.31

pygeometric

geomloss

torchdiff

run toy data

missing value task.

$ python mask_main.py

cell classification task.

$ python c_main.py

future prediction task.

$ python d_main.py

cell trajectory task. Data are available without preprocessing at https://www.synapse.org/#!Synapse:syn20366914/wiki/593925

$ python gt_main.py