MCAT

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Hello, I want to ask whether you can provide these extracted WSI featues stored in pt files? Because when I use CLAM to extract featues, there are some differences. So,...

JIaqiYang78

Hi there, Thank you for sharing your nice work! I met a problem when I try to train your model, it returned the nan loss and risk like below: batch...

folkaholic

Hi, I am trying to reproduce your results but am having trouble with MI-FC as i do not have the required fast_cluster_ids.pkl file. I saw quite a bit of discussion...

ValentinKoch

https://github.com/mahmoodlab/MCAT/blob/b9cca63be83c67de7f95308d54a58f80b78b0da1/main.py#L106C1-L107C1 #16 The default setting of fusion now is concat, which will cause "float division by zero" error for WSI only baselines.

sofan110

Hello author, I would like to ask if you have ever encountered the problem that loss decreases in the training set and verification set, and C-Index increases in the training...

Hanminghao

Hello!Thanks for you contributions.Why don't you add the test mode to the model?I notice that you only use the validation set to examine the performance of the model,but you have...

ljhOfGithub

Co-attention visualizations?

4

Hi, Thanks for the publishing the nice code. I can't find code in this repo that makes the slide attention visualizations similar to that seen in Figures 2 and 3...

benlansdell

Questions about the computation of the survival layer in `MCAT_Surv`

1

It seems that the computation of the survival layer in `MCAT_Surv`([link](https://github.com/mahmoodlab/MCAT/blob/b9cca63be83c67de7f95308d54a58f80b78b0da1/models/model_coattn.py#L100)) is wrong, and `logits = self.classifier(h).unsqueeze(0)` should be `logits = self.classifier(h)`. With the old version, supposing that the `batch_size=6`...

huangmozhilv

Dear authors, Please help check the following line: https://github.com/mahmoodlab/MCAT/blob/b9cca63be83c67de7f95308d54a58f80b78b0da1/datasets/dataset_survival.py#L63 I have tested the code as follows: import pandas as pd import numpy as np csv_path = 'MCAT_master/datasets_sig_csv/tcga_brca_all_clean.csv.zip' slide_data = pd.read_csv(csv_path,...

hachikong