Model checkpoints missing data file

[andanison]

Hi

I am trying to use the model checkpoints to try to predict on a new patch/image. Generally for each checkpoint we have three files: meta file, index file, data file. However for the checkpoints in path DeepPATH/DeepPATH_code/example_TCGA_lung/checkpoints/, all of them only contain meta file and index file but the data file containing model weights is missing. Is it still possible to load the weights used in the paper after training for evaluation-- If yes, can you point me how to? or is it that the checkpoints are dummy and serve only as a purpose to be able to run the pipeline?

When I try to load the model, it says run1a_3D_classifier/model.ckpt-69000.data-00000-of-00001; No such file or directory

[ncoudray]

Hi,

Indeed, the missing file is to big to be shared via github. Please email me an invit to a shared box/folder and I'll upload them there

Best, Nicolas

[andanison]

Hi Nicolas

Thank you for your quick reply. I have sent you an invite on your nyumc.org email address

In case it doesn't work, let me know.

Kind regards Sonali

On Tue, Feb 25, 2020 at 9:21 PM Nicolas Coudray notifications@github.com wrote:

Hi,

Indeed, the missing file is to big to be shared via github. Please email me an invit to a shared box/folder and I'll upload them there

Best, Nicolas

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[ncoudray]

done

Best N.

[afrankel]

I am trying to do something similar by using transfer learning with the run1a_3D_classifier. I am getting ...run1a_3D_classifier/model.ckpt-69000.data-00000-of-00001; No such file or directory

I suppose I need the same large file. Also, I noticed that the transfer learning using the inception-v3 checkpoint includes the following files:

• checkpoint
• model.ckpt-157585

I assume I create my own checkpoint file for run1a_3D_classifier and then the large file I am missing is the equivalent of the model.ckpt-157585 file. Is that correct?

[ncoudray]

Hi - Yes, one of the files is too big to be shared on github, but if you send me an invit on box, I can drop them there for you

[afrankel]

https://www.dropbox.com/request/YLVtInDEH54kaAhe1436

Hopefully, that works and has enough space. Thank you!

[ncoudray]

did it - let me know if you got them

[afrankel]

Thank you

[fredafredaf]

Hi Nicholas,

I am trying to do perform mutation transfer learning with the run1b_10way_MutationClassifier, could you please share with me the .data file? thank you.

https://drive.google.com/drive/folders/1_Urcuw9i3U8EPMAhG3EQ2Gl33N1mJwvn?usp=sharing

[ncoudray]

Hi Fred - Done. HTH