Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ENH: Enable custom SSL encoder checkpoint #562

Merged
merged 8 commits into from
Aug 8, 2022
Merged

ENH: Enable custom SSL encoder checkpoint #562

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
edf76c6
Add command line arg for custom SSL encoder checkpoint
mebristo Aug 8, 2022
76e1f30
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 8, 2022
2ea1327
Add smoke test to workflow
mebristo Aug 8, 2022
6f168b3
Merge branch 'mebristo/custom_ckpt_ssl' of https://github.com/microso…
mebristo Aug 8, 2022
f12af83
Remove uneccessary change
mebristo Aug 8, 2022
c5816eb
Address PR comments
mebristo Aug 8, 2022
c5d9b6a
remove warning
mebristo Aug 8, 2022
bffcc88
Add variable to makefile
mebristo Aug 8, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 16 additions & 0 deletions .github/workflows/cpath-pr.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -151,6 +151,22 @@ jobs:
cd ${{ env.folder }}
make smoke_test_tilespandaimagenetmil_aml

smoke_test_tcgacrcksslmil_aml:
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v3
with:
lfs: true

- name: Set up smoke test environment
id: setup-sslmil-smoke-test-environment
uses: ./.github/actions/prepare_smoke_test_environment

- name: smoke test
run: |
cd ${{ env.folder }}
make smoke_test_tcgacrcksslmil_aml

smoke_test_crck_simclr_aml:
runs-on: ubuntu-20.04
steps:
Expand Down
7 changes: 3 additions & 4 deletions hi-ml-cpath/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,8 @@ pytest:
pytest_coverage:
pytest --cov=health_cpath --cov SSL --cov-branch --cov-report=html --cov-report=xml --cov-report=term-missing --cov-config=.coveragerc

SSL_CKPT_RUN_ID_CRCK := CRCK_SimCLR_1655731022_85790606

# Run regression tests and compare performance
define BASE_CPATH_RUNNER_COMMAND
cd ../ ; \
Expand All @@ -92,7 +94,7 @@ define DEEPSMILEPANDATILES_ARGS
endef

define TCGACRCKSSLMIL_ARGS
--model=health_cpath.TcgaCrckSSLMIL
--model=health_cpath.TcgaCrckSSLMIL --ssl_checkpoint_run_id=${SSL_CKPT_RUN_ID_CRCK}
endef

define CRCKSIMCLR_ARGS
Expand Down Expand Up @@ -193,9 +195,6 @@ smoke_test_tilespandaimagenetmil_aml:
{ ${BASE_CPATH_RUNNER_COMMAND} ${DEEPSMILEPANDATILES_ARGS} ${DEFAULT_SMOKE_TEST_ARGS} \
${DEEPSMILEPANDATILES_SMOKE_TEST_ARGS} ${AML_MULTIPLE_DEVICE_ARGS};}

# Note: this test doesn't currently run in hi-ml Workspace since the checkpoint run specified in run_ids
# innereye_ssl_checkpoint_crck_4ws does not exist there. Once we can specify alternative checkpoints
# this can be run with any Workspace
# The following test takes about 30 seconds
smoke_test_tcgacrcksslmil_local:
{ ${BASE_CPATH_RUNNER_COMMAND} ${TCGACRCKSSLMIL_ARGS} ${DEFAULT_SMOKE_TEST_ARGS} \
Expand Down
11 changes: 5 additions & 6 deletions hi-ml-cpath/src/health_cpath/configs/classification/BaseMIL.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,8 @@ class BaseMIL(LightningContainer, EncoderParams, PoolingParams):
"generating outputs.")
maximise_primary_metric: bool = param.Boolean(True, doc="Whether the primary validation metric should be "
"maximised (otherwise minimised).")
ssl_checkpoint_run_id: str = param.String(default="", doc="Optional run id from which to load checkpoint if "
"using SSLEncoder")

def __init__(self, **kwargs: Any) -> None:
super().__init__(**kwargs)
Expand All @@ -82,9 +84,6 @@ def __init__(self, **kwargs: Any) -> None:
def cache_dir(self) -> Path:
return Path(f"/tmp/himl_cache/{self.__class__.__name__}-{self.encoder_type}/")

def setup(self) -> None:
self.ssl_ckpt_run_id = ""

def get_test_plot_options(self) -> Set[PlotOption]:
options = {PlotOption.HISTOGRAM, PlotOption.CONFUSION_MATRIX}
if self.num_top_slides > 0:
Expand Down Expand Up @@ -206,7 +205,7 @@ def get_dataloader_kwargs(self) -> dict:

def get_transforms_dict(self, image_key: str) -> Dict[ModelKey, Union[Callable, None]]:
if self.is_caching:
encoder = create_from_matching_params(self, EncoderParams).get_encoder(self.ssl_ckpt_run_id,
encoder = create_from_matching_params(self, EncoderParams).get_encoder(self.ssl_checkpoint_run_id,
self.outputs_folder)
transform = Compose([
LoadTilesBatchd(image_key, progress=True),
Expand All @@ -226,7 +225,7 @@ def create_model(self) -> TilesDeepMILModule:
class_weights=self.data_module.class_weights,
dropout_rate=self.dropout_rate,
outputs_folder=self.outputs_folder,
ssl_ckpt_run_id=self.ssl_ckpt_run_id,
ssl_ckpt_run_id=self.ssl_checkpoint_run_id,
encoder_params=create_from_matching_params(self, EncoderParams),
pooling_params=create_from_matching_params(self, PoolingParams),
optimizer_params=create_from_matching_params(self, OptimizerParams),
Expand Down Expand Up @@ -266,7 +265,7 @@ def create_model(self) -> SlidesDeepMILModule:
class_weights=self.data_module.class_weights,
dropout_rate=self.dropout_rate,
outputs_folder=self.outputs_folder,
ssl_ckpt_run_id=self.ssl_ckpt_run_id,
ssl_ckpt_run_id=self.ssl_checkpoint_run_id,
encoder_params=create_from_matching_params(self, EncoderParams),
pooling_params=create_from_matching_params(self, PoolingParams),
optimizer_params=create_from_matching_params(self, OptimizerParams),
Expand Down
3 changes: 2 additions & 1 deletion hi-ml-cpath/src/health_cpath/configs/classification/DeepSMILECrck.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,8 @@ def __init__(self, **kwargs: Any) -> None:

def setup(self) -> None:
super().setup()
self.ssl_ckpt_run_id = innereye_ssl_checkpoint_crck_4ws
# If no SSL checkpoint is provided, use the default one
self.ssl_checkpoint_run_id = self.ssl_checkpoint_run_id or innereye_ssl_checkpoint_crck_4ws

def get_data_module(self) -> TilesDataModule:
return TcgaCrckTilesDataModule(
Expand Down
6 changes: 4 additions & 2 deletions hi-ml-cpath/src/health_cpath/configs/classification/DeepSMILEPanda.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,8 @@ def __init__(self, **kwargs: Any) -> None:

def setup(self) -> None:
BaseMILTiles.setup(self)
self.ssl_ckpt_run_id = innereye_ssl_checkpoint_binary
# If no SSL checkpoint is provided, use the default one
self.ssl_checkpoint_run_id = self.ssl_checkpoint_run_id or innereye_ssl_checkpoint_binary

def get_data_module(self) -> PandaTilesDataModule:
return PandaTilesDataModule(
Expand Down Expand Up @@ -135,7 +136,8 @@ def __init__(self, **kwargs: Any) -> None:

def setup(self) -> None:
BaseMILSlides.setup(self)
self.ssl_ckpt_run_id = innereye_ssl_checkpoint_binary
# If no SSL checkpoint is provided, use the default one
self.ssl_checkpoint_run_id = self.ssl_checkpoint_run_id or innereye_ssl_checkpoint_binary

def get_dataloader_kwargs(self) -> dict:
return dict(
Expand Down
2 changes: 1 addition & 1 deletion hi-ml-cpath/src/health_cpath/configs/classification/DeepSMILESlidesPandaBenchmark.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ def create_model(self) -> SlidesDeepMILModule:
class_weights=self.data_module.class_weights,
dropout_rate=self.dropout_rate,
outputs_folder=self.outputs_folder,
ssl_ckpt_run_id=self.ssl_ckpt_run_id,
ssl_ckpt_run_id=self.ssl_checkpoint_run_id,
encoder_params=create_from_matching_params(self, EncoderParams),
pooling_params=create_from_matching_params(self, PoolingParams),
optimizer_params=create_from_matching_params(self, OptimizerParams),
Expand Down