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mahmoodlab / CLAM

Open source tools for computational pathology - Nature BME
http://clam.mahmoodlab.org
GNU General Public License v3.0
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The time that CONCH takes #266

Closed TXPsim closed 2 months ago

TXPsim commented 3 months ago

Thanks for your excellent work!

May I ask the approximate time it takes to extract the features of a WSI using CONCH in a single GPU? Because I noticed that CONCH takes longer to extract features than ResNet50.

I'm looking forward to your reponse. Thank you so much!

fedshyvana commented 3 months ago

Hi, I don't have concrete comparison numbers but yes it is expected since CONCH is quite a bit larger than the truncated ResNet50 (for the same reason, UNI is expected take even longer). If the forward pass becomes too much of a bottleneck I think you can try to perform inference in torch autocast fp16 for a pretty significant speed up.

TXPsim commented 3 months ago

Thanks for your quick reply！It is very helpful to me and I would like to try your advice!