Error when working with Norman pretrained model

[igrabski]

Thanks for making this tool available!

I am trying to run the tutorial located here, but have been encountering some issues. When I run the following code:

from gears import PertData, GEARS
from gears.utils import dataverse_download
from zipfile import ZipFile

dataverse_download('https://dataverse.harvard.edu/api/access/datafile/6979957', 'norman_umi_go.tar.gz')

## Extract and set up dataloader directory
import tarfile
with tarfile.open('norman_umi_go.tar.gz', 'r:gz') as tar:
    tar.extractall()

dataverse_download('https://dataverse.harvard.edu/api/access/datafile/6979956', 'model.zip')

## Extract and set up model directory
with ZipFile(('model.zip'), 'r') as zip:
    zip.extractall(path = './')

data_path = './'
data_name = 'norman_umi_go'
model_name = 'gears_misc_umi_no_test'

pert_data = PertData(data_path)
pert_data.load(data_path = data_path + data_name)
pert_data.prepare_split(split = 'no_test', seed = 1)
pert_data.get_dataloader(batch_size = 32, test_batch_size = 128)

gears_model = GEARS(pert_data, device = 'cpu',
                        weight_bias_track = False,
                        proj_name = 'gears',
                        exp_name = model_name)

I get the error below:

AttributeError: 'Series' object has no attribute 'nonzero'

I was able to resolve the error by running:

pert_data.adata.X = pert_data.adata.X.toarray()

and the gears_model command works. However, when I then run:

gears_model.load_pretrained('./model_ckpt')

I get this error:

TypeError: GEARS.model_initialize() got an unexpected keyword argument 'cell_fitness_pred'

Please let me know how I can resolve this -- thanks so much!