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Building segmentation ensemble models is slow because of full image inference in the child runs #328

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ant0nsc opened this issue Nov 25, 2020 · 2 comments · Fixed by #502
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workflow Improvements to workflows (recovery, speed)

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@ant0nsc
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ant0nsc commented Nov 25, 2020

When building ensemble models, we are usually just interested in the metrics of the final ensemble. But we still do full image inference on validation and test set, before actually starting the ensemble building. We could speed that up by disabling full image inference in the child runs, and only run it with the ensemble model.

AB#3942

@ant0nsc ant0nsc added the workflow Improvements to workflows (recovery, speed) label Feb 2, 2021
@ant0nsc ant0nsc added no changelog needed CHANGELOG.md does not need to be updated in this PR and removed no changelog needed CHANGELOG.md does not need to be updated in this PR labels Apr 9, 2021
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ant0nsc commented Jun 21, 2021

  • Ensure that we trigger full image inference on training, validation and test set separately. (current: Training set on/off, Val+Test set on/off)
  • Trigger full image inference for ensemble model separate from child runs (single checkpoint)
  • one solution could be to have a total of 6 flag, we probably want that internally in any case. Externally facing flags could be "smart"

@JonathanTripp JonathanTripp self-assigned this Jun 22, 2021
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The flags currently are:

  • perform_training_set_inference: bool =
    param.Boolean(False,
    doc="If True, run full image inference on the training set at the end of training. If False and "
    "perform_validation_and_test_set_inference is True (default), only run inference on "
    "validation and test set. If both flags are False do not run inference.")
  • perform_validation_and_test_set_inference: bool =
    param.Boolean(True,
    doc="If True (default), run full image inference on validation and test set after training.")

In class WorkflowParams

@JonathanTripp JonathanTripp linked a pull request Jun 22, 2021 that will close this issue
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