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Dear Greg - thanks for your continued work on this and for this follow up paper with updated pipeline. I'm the lead author of [Hermida et al. Nat Commun 2022](https://www.nature.com/articles/s41467-02…
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**Error occurred:**
Prov-gigapath main \ finetune \ training -->evaluate function
```
def evaluate(loader, model, fp16_scaler, loss_fn, epoch, args):
model.eval()
# set the evaluatio…
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In the WebApp, configure this filter:
COLLECTION IN (TCGA-LUAD) AND TCGA>AGE AT DIAGNOSIS in (85-90)
I.E., select TCGA-LUAD, then set the age_at_diagnosis slider to 85-90 (probably anything that is …
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Hi Sam, its me again here.
Tried running the program again with TCGA samples, but unfortunately immediately ran into this new error.
When running the preprocessing, I realise that the tag direc…
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Could you please provide the `TCGA_RCC` and `TCGA_Lung` datasets through an alternative method, such as Google Drive? I have encountered difficulties downloading them from the provided [link](https://…
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Hi, thanks for creating this tool!
I have a few questions about how to create the input files and what the output represents:
1. I understand I should convert TCGA .svs files to .tif using this sc…
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Hi,
I've practiced the model training following the tutorial you provided.
The gdcCancer.bb file was downloaded from the link in the tutorial, and later was converted to bed file using bigBedToB…
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Hi,
I was wondering what threshold was used for the TCGA data shown in the article to determine which samples are MSI.
Thank you in advance!
Kind regards,
Miranda
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Hi @GeorgeBatch @binli123 ! Thanks for the incredible work! I was wondering if you have the patch level labels as well beside the patch level features for the TCGA dataset. Thanks.
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When I come to the website, it says: “All slide and diagnostic images from the TCGA program are currently unavailable for download”. Could you share the lung datasets by using a Google Cloud link? : )…