Questions about creating pertdata with own data files

[HelloWorldLTY]

Hi, thanks for your work. I wonder if it is possible for us to access the sample_adata.h5ad file in the dataset tutorial. I intend to test if creating dataset functions have other errors or not. Thanks.

[HelloWorldLTY]

Moreover, I found that I met nan when training GEARs with own datasets

What could be the possible reasons? Thanks.

Start Training...
Epoch 1 Step 1 Train Loss: 0.2541
Epoch 1 Step 51 Train Loss: 0.0840
Epoch 1 Step 101 Train Loss: 0.1225
Epoch 1 Step 151 Train Loss: 0.1427
Epoch 1 Step 201 Train Loss: 0.0407
Epoch 1 Step 251 Train Loss: nan

[yhr91]

Can you provide more details on what dataset you are using for training. Did you use the data tutorial as is or did you make modifications

Very likely this is a problem of data normalization or maybe there are zeroes or nans in your data

[HelloWorldLTY]

Hi, I used datasets from this paper (https://www.biorxiv.org/content/10.1101/2024.07.03.601903v1.abstract) which contains two large-scale perturbation datasets. I follow the recommended pre-processing step and verify that there are no nan values.

Thanks.