Survival Code

[pazadimo]

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.

[Richarizardd]

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).

[zzbuzzard]

Hi @Richarizardd been a while but would appreciate an update here; it's really unclear how to actually run HIPT for survival prediction as things are at the moment.