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Published 20 hours ago • verified publisher icon mahmoodlab

Survival Code

Open pazadimo opened this issue 3 years ago • 1 comments
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Hi, Thanks for sharing the code. It seems that hipt_lgp is implemented in the MCAT repo yet, but it says in this repo that we should use the below command which I assume is related to MCAT repo(Please correct me if I'm wrong):

python main.py --data_root_dir $DATAROOT --which_splits 5foldcv --split_dir tcga_brca --mode pyramid --model_type hipt_lgp --pretrain_4k vit4k_xs_dino --freeze_4k

I wonder if you can provide more info on how to use MCAT code with hipt_lgp backbone for survival prediction especially when there is no omics data available in the dataset? or the main file with other required files for this task.

Thanks.

pazadimo avatar Jul 18 '22 06:07 pazadimo

Hi @pazadimo - will send an update soon. I am still thinking whether it would be better to re-hash the MCAT survival code in this repository, or update MCAT with the hipt_lgp method (leaning towards the former than the latter).

Richarizardd avatar Jul 21 '22 21:07 Richarizardd