mahmoodlab / PathomicFusion

Fusing Histology and Genomics via Deep Learning - IEEE TMI

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options.py

rongyua opened this issue · comments

parser.add_argument('--use_bilinear', type=int, default=1)
parser.add_argument('--path_gate', type=int, default=1)
parser.add_argument('--grph_gate', type=int, default=1)
parser.add_argument('--omic_gate', type=int, default=1)
parser.add_argument('--path_scale', type=int, default=1)
parser.add_argument('--grph_scale', type=int, default=1)
parser.add_argument('--omic_scale', type=int, default=1)
Can you tell me the use of these parameters in the options.py file?
When I run the GCN+SNN code, I get an error using the command you gave me.
FileNotFoundError: [Errno 2] No such file or directory: './data/TCGA_GBMLGG/all_st_patches_512_cpc/TCGA-12-0616-01Z-00-DX3.b426f381-b175-4a6d-957e-2dbfed42caeb_2_256_0.pt'.
But it can run after deleting some of the above parameters in the code you gave.
Can you please answer this?

Hi, I met the same issue you mentioned. When I was running the CNN+GCN+SNN model with the exact same command in README, the error is [Errno 2] No such file or directory: './data/TCGA_GBMLGG/all_st_patches_512_cpc/TCGA-S9-A6UA-01Z-00-DX1.99AB8786-858B-46A0-94BA-C5AA1CD5351B_1_512_256.pt'. I am wondering how you delete some of the parameters to let the code run? Much appreciated.