Understanding the prediction_dir format for leaderboard submission

[jmamath]

I wonder if the log folder used during training is the prediction_dir described in Get Started: Evaluating trained models.

I tried to reproduce the ERM result on a subset of camelyon with the following command:

python examples/run_expt.py --dataset camelyon17 --algorithm ERM--root_dir data --frac 0.1 --log_dir log_erm_01.

Training goes well.

But my file camelyon17_split:id_val_seed:0_epoch is empty.

Then I ran the following command:
python examples/evaluate.py log_erm_01 erm_01_output --root-dir data --dataset camelyon17

And I got this:

Traceback (most recent call last):
  File "examples/evaluate.py", line 282, in <module>
    main()
  File "examples/evaluate.py", line 244, in main
    evaluate_benchmark(
  File "examples/evaluate.py", line 136, in evaluate_benchmark
    predictions_file = get_prediction_file(
  File "examples/evaluate.py", line 89, in get_prediction_file
    raise FileNotFoundError(
FileNotFoundError: Could not find CSV or pth prediction file that starts with camelyon17_split:id_val_seed:0.

So my question is whether the log file is the prediction_dir described in Get Started ?

[kohpangwei]

Hi Jean-Michel,

Those log files should be in the log_dir that you specified (i.e,. log_erm_01). Is that folder empty?

[jmamath]

Hi, thank for your response.

No the folder isn't empty. After training it has the following files:

• camelyon17_seed:0_epoch:best_model.pth
• camelyon17_seed:0_epoch:last_model.pth
• camelyon17_split:id_val_seed:0_epoch
• camelyon17_split:test_seed:0_epoch
• camelyon17_split:val_seed:0_epoch
• id_val_algo.csv
• id_val_eval.csv
• log
• test_algo.csv
• test_eval.csv
• train_algo.csv
• train_eval.csv
• val_algo.csv
• val_eval.csv

But the files camelyon17_split:id_val_seed:0_epoch, camelyon17_split:test_seed:0_epoch, camelyon17_split:val_seed:0_epoch are the only empty files.

(EDIT)

I think I get it, once we have finished training, we should run the same command with --eval_only True to get the prediction results. So in this specific case it would be:
python examples/run_expt.py --dataset camelyon17 --algorithm ERM--root_dir data --log_dir log_erm_01 --eval_only True. This would result in the files asked in the leaderboard submission: https://wilds.stanford.edu/submit/.

Note that in the previous command, I did not used --frac, as it would get predictions on a fraction of the dataset, however, it is not possible to specify such parameter when evaluating later:
python examples/evaluate.py log_erm_01 erm_01_output --root-dir data --dataset camelyon17

I think that precising how to get the predictions in the readme could help.

The problem I faced is that using Windows as operating system does not allow to have colons ":" in filenames, so I used a hack: https://stackoverflow.com/questions/10386344/how-to-get-a-file-in-windows-with-a-colon-in-the-filename to change the colons in many files and functions to save the model and result. Then it becames difficult to see where I use the hacky colon or the normal colon. Maybe it would be more democratic to use underscore "_" in place of colon ":".

[kohpangwei]

Hi Jean-Michel,

Hmm, you shouldn't need to run it with --eval_only to get the prediction results. The prediction files are for some reason incorrectly named in your case. Instead of

camelyon17_split:id_val_seed:0_epoch
camelyon17_split:test_seed:0_epoch
camelyon17_split:val_seed:0_epoch

it should look like

camelyon17_split:id_val_seed:0_epoch:best_pred.csv
camelyon17_split:id_val_seed:0_epoch:last_pred.csv
camelyon17_split:test_seed:0_epoch:best_pred.csv
camelyon17_split:test_seed:0_epoch:last_pred.csv
camelyon17_split:val_seed:0_epoch:best_pred.csv
camelyon17_split:val_seed:0_epoch:last_pred.csv

Perhaps this is related to the Windows colon issue? I hadn't known about that. Sorry for the trouble. (If it helps, using Windows Subsystem for Linux would allow you to bypass these issues.)