Merge branch 'master' into dynunet_set_automaticaly_strides_kernels

.github/workflows/python-test.yml

@@ -115,7 +115,7 @@ jobs:
           flags: unittests
 
       - name: Upload coverage to Codacy
-        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        if: github.ref == 'refs/heads/master' # only run when on master
         uses: codacy/[email protected]
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

GANDLF/compute/inference_loop.py

@@ -89,7 +89,16 @@ def inference_loop(
             assert file_to_load != None, "The 'best_file' was not found"
 
         main_dict = torch.load(file_to_load, map_location=parameters["device"])
-        model.load_state_dict(main_dict["model_state_dict"])
+        state_dict = main_dict["model_state_dict"]
+        if parameters.get("differential_privacy"):
+            # this is required for torch==1.11 and for DP inference
+            new_state_dict = {}
+            for key, val in state_dict.items():
+                new_key = key.replace("_module.", "")
+                new_state_dict[new_key] = val  # remove `module.`
+            state_dict = new_state_dict
+
+        model.load_state_dict(state_dict)
         parameters["previous_parameters"] = main_dict.get("parameters", None)
         model.eval()
     elif parameters["model"]["type"].lower() == "openvino":

GANDLF/compute/training_loop.py

@@ -31,6 +31,10 @@
 from .forward_pass import validate_network
 from .generic import create_pytorch_objects
 
+from GANDLF.privacy.opacus.model_handling import empty_collate
+from GANDLF.privacy.opacus import handle_dynamic_batch_size, prep_for_opacus_training
+from opacus.utils.batch_memory_manager import wrap_data_loader
+
 # hides torchio citation request, see https://github.com/fepegar/torchio/issues/235
 os.environ["TORCHIO_HIDE_CITATION_PROMPT"] = "1"
 
@@ -91,6 +95,14 @@ def train_network(
     for batch_idx, (subject) in enumerate(
         tqdm(train_dataloader, desc="Looping over training data")
     ):
+        if params.get("differential_privacy"):
+            subject, params["batch_size"] = handle_dynamic_batch_size(
+                subject=subject, params=params
+            )
+            assert not isinstance(
+                model, torch.nn.DataParallel
+            ), "Differential privacy is not supported with DataParallel or DistributedDataParallel. Please use a single GPU or DDP with Opacus."
+
         optimizer.zero_grad()
         image = (  # 5D tensor: (B, C, H, W, D)
             torch.cat(
@@ -212,6 +224,23 @@ def train_network(
     return average_epoch_train_loss, average_epoch_train_metric
 
 
+def train_network_wrapper(model, train_dataloader, optimizer, params):
+    """
+    Wrapper Function to handle train_dataloader for benign and DP cases and pass on to train a network for a single epoch
+    """
+
+    if params.get("differential_privacy"):
+        with train_dataloader as memory_safe_data_loader:
+            epoch_train_loss, epoch_train_metric = train_network(
+                model, memory_safe_data_loader, optimizer, params
+            )
+    else:
+        epoch_train_loss, epoch_train_metric = train_network(
+            model, train_dataloader, optimizer, params
+        )
+    return epoch_train_loss, epoch_train_metric
+
+
 def training_loop(
     training_data: pd.DataFrame,
     validation_data: pd.DataFrame,
@@ -368,6 +397,7 @@ def training_loop(
         logger_csv_filename=os.path.join(output_dir, "logs_validation.csv"),
         metrics=metrics_log,
         mode="valid",
+        add_epsilon=bool(params.get("differential_privacy")),
     )
     if testingDataDefined:
         test_logger = Logger(
@@ -392,6 +422,36 @@ def training_loop(
 
     print("Using device:", device, flush=True)
 
+    if params.get("differential_privacy"):
+        print(
+            "Using Opacus to make training differentially private with respect to the training data."
+        )
+
+        model, optimizer, train_dataloader, privacy_engine = prep_for_opacus_training(
+            model=model,
+            optimizer=optimizer,
+            train_dataloader=train_dataloader,
+            params=params,
+        )
+
+        train_dataloader.collate_fn = empty_collate(train_dataloader.dataset[0])
+
+        # train_dataloader = BatchMemoryManager(
+        #     data_loader=train_dataloader,
+        #     max_physical_batch_size=MAX_PHYSICAL_BATCH_SIZE,
+        #     optimizer=optimizer,
+        # )
+        batch_size = params["batch_size"]
+        max_physical_batch_size = params["differential_privacy"].get(
+            "physical_batch_size"
+        )
+        if max_physical_batch_size and max_physical_batch_size != batch_size:
+            train_dataloader = wrap_data_loader(
+                data_loader=train_dataloader,
+                max_batch_size=max_physical_batch_size,
+                optimizer=optimizer,
+            )
+
     # Iterate for number of epochs
     for epoch in range(start_epoch, epochs):
         if params["track_memory_usage"]:
@@ -453,6 +513,14 @@ def training_loop(
 
         patience += 1
 
+        # if training with differential privacy, print privacy epsilon
+        if params.get("differential_privacy"):
+            delta = params["differential_privacy"]["delta"]
+            this_epsilon = privacy_engine.get_epsilon(delta)
+            print(f"     Epoch Final   Privacy: (ε = {this_epsilon:.2f}, δ = {delta})")
+            # save for logging
+            epoch_valid_metric["epsilon"] = this_epsilon
+
         # Write the losses to a logger
         train_logger.write(epoch, epoch_train_loss, epoch_train_metric)
         valid_logger.write(epoch, epoch_valid_loss, epoch_valid_metric)

GANDLF/config_manager.py

@@ -7,6 +7,7 @@
 
 from .utils import version_check
 from GANDLF.data.post_process import postprocessing_after_reverse_one_hot_encoding
+from GANDLF.privacy.opacus import parse_opacus_params
 
 from GANDLF.metrics import surface_distance_ids
 from importlib.metadata import version
@@ -710,6 +711,10 @@ def _parseConfig(
         temp_dict["type"] = params["optimizer"]
         params["optimizer"] = temp_dict
 
+    # initialize defaults for DP
+    if params.get("differential_privacy"):
+        params = parse_opacus_params(params, initialize_key)
+
     # initialize defaults for inference mechanism
     inference_mechanism = {"grid_aggregator_overlap": "crop", "patch_overlap": 0}
     initialize_inference_mechanism = False

GANDLF/logger.py

@@ -12,14 +12,21 @@
 
 
 class Logger:
-    def __init__(self, logger_csv_filename: str, metrics: List[str], mode: str) -> None:
+    def __init__(
+        self,
+        logger_csv_filename: str,
+        metrics: List[str],
+        mode: str,
+        add_epsilon: bool = False,
+    ) -> None:
         """
-        Logger class to log the training and validation metrics to a csv file.
-            May append to existing file if headers match; elsewise raises an error.
+        Logger class to log the training and validation metrics to a csv file. May append to existing file if headers match; elsewise raises an error.
 
         Args:
             logger_csv_filename (str): Path to a filename where the csv has to be stored.
             metrics (Dict[str, float]): The metrics to be logged.
+            mode (str): The mode of the logger, used as suffix to metric names. Normally may be `train` / `val` / `test`
+            add_epsilon (bool): Whether to log epsilon values or not (differential privacy measurement)
         """
         self.filename = logger_csv_filename
         mode = mode.lower()
@@ -28,6 +35,8 @@ def __init__(self, logger_csv_filename: str, metrics: List[str], mode: str) -> N
         new_header = ["epoch_no", f"{mode}_loss"] + [
             f"{mode}_{metric}" for metric in metrics
         ]
+        if add_epsilon:
+            new_header.append(f"{self.mode}_epsilon")
 
         # TODO: do we really need to support appending to existing files?
         if os.path.exists(self.filename):

GANDLF/models/imagenet_unet.py

@@ -252,6 +252,10 @@ def __init__(self, parameters) -> None:
             aux_params=classifier_head_parameters,
         )
 
+        # all BatchNorm should be replaced with InstanceNorm for DP experiments
+        if "differential_privacy" in parameters:
+            self.replace_batchnorm(self.model)
+
         if self.n_dimensions == 3:
             self.model = self.converter(self.model).model
 

GANDLF/privacy/opacus/__init__.py

@@ -0,0 +1,3 @@
+from .config_parsing import parse_opacus_params
+from .model_handling import opacus_model_fix, prep_for_opacus_training
+from .training_utils import handle_dynamic_batch_size

GANDLF/privacy/opacus/config_parsing.py

@@ -0,0 +1,59 @@
+from typing import Callable
+
+
+def parse_opacus_params(params: dict, initialize_key: Callable) -> dict:
+    """
+    Function to set defaults and augment the parameters related to making a trained model differentially
+    private with respect to the training data.
+
+    Args:
+        params (dict): Training parameters.
+        initialize_key (Callable): Function to fill in value for a missing key.
+
+    Returns:
+        dict: Updated training parameters.
+    """
+
+    if not isinstance(params["differential_privacy"], dict):
+        print(
+            "WARNING: Non dictionary value for the key: 'differential_privacy' was used, replacing with default valued dictionary."
+        )
+        params["differential_privacy"] = {}
+    # these are some defaults
+    params["differential_privacy"] = initialize_key(
+        params["differential_privacy"], "noise_multiplier", 10.0
+    )
+    params["differential_privacy"] = initialize_key(
+        params["differential_privacy"], "max_grad_norm", 1.0
+    )
+    params["differential_privacy"] = initialize_key(
+        params["differential_privacy"], "accountant", "rdp"
+    )
+    params["differential_privacy"] = initialize_key(
+        params["differential_privacy"], "secure_mode", False
+    )
+    params["differential_privacy"] = initialize_key(
+        params["differential_privacy"], "allow_opacus_model_fix", True
+    )
+    params["differential_privacy"] = initialize_key(
+        params["differential_privacy"], "delta", 1e-5
+    )
+    params["differential_privacy"] = initialize_key(
+        params["differential_privacy"], "physical_batch_size", params["batch_size"]
+    )
+
+    if params["differential_privacy"]["physical_batch_size"] > params["batch_size"]:
+        print(
+            f"WARNING: The physical batch size {params['differential_privacy']['physical_batch_size']} is greater"
+            f"than the batch size {params['batch_size']}, setting the physical batch size to the batch size."
+        )
+    params["differential_privacy"]["physical_batch_size"] = params["batch_size"]
+
+    # these keys need to be parsed as floats, not strings
+    for key in ["noise_multiplier", "max_grad_norm", "delta", "epsilon"]:
+        if key in params["differential_privacy"]:
+            params["differential_privacy"][key] = float(
+                params["differential_privacy"][key]
+            )
+
+    return params