Update Multiple Instance Learning Pipeline #728
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Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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@Nic-Ma Here is the accuracy metric of the updated pipeline with respect to the original one that Andriy has run the experiment and produced the figures. The dark blue is the original one and the orange is the updated one (ignore the other colors). Both dark blue and orange ones are performing very similarly considering the different randomness that they have. |
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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pathology/multiple_instance_learning/panda_mil_train_evaluate_pytorch_gpu.py
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Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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* Update mil pipeline Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix a typo Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Tiffile to cucim Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update to RandGridPatchd Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix import Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add sort_key Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * sort key max to min Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix patch_size Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Stack patch locations Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove location Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change to fix_num_patches Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update grid patch Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add threshold_filter Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update threshold and add pad_mode=None Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update mil pipeline with new grid patch Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update GridPatch args Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update LabelEncodeIntegerGraded and sort imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com>
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Fixes #637
Description
This PR updates Multiple Instance Learning Pipeline with the new components in MONAI.
Status
Ready
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./runner [-p <regex_pattern>]