Fix for weighted BCE loss

.gitignore

@@ -176,3 +176,7 @@ lightning_logs
 logs
 .isort.cfg
 /.vscode
+
+*.out
+*.err
+*.sh

README.md

@@ -81,7 +81,7 @@ The `classes_path` is the path to the dataset's `raw/classes.txt` file that cont
 You can evaluate a model trained on the ontology extension task in one of two ways:
 
 ### 1. Using the Jupyter Notebook
-An example notebook is provided at `tutorials/eval_model_basic.ipynb`.  
+An example notebook is provided at `tutorials/eval_model_basic.ipynb`.
 - Load your finetuned model and run the evaluation cells to compute metrics on the test set.
 
 ### 2. Using the Lightning CLI

chebai/cli.py

@@ -70,6 +70,10 @@ def call_data_methods(data: Type[XYBaseDataModule]):
             "data.num_of_labels", "trainer.callbacks.init_args.num_labels"
         )
 
+        parser.link_arguments(
+            "data", "model.init_args.criterion.init_args.data_extractor"
+        )
+
     @staticmethod
     def subcommands() -> Dict[str, Set[str]]:
         """

chebai/loss/bce_weighted.py

@@ -10,7 +10,6 @@
 class BCEWeighted(torch.nn.BCEWithLogitsLoss):
     """
     BCEWithLogitsLoss with weights automatically computed according to the beta parameter.
-    If beta is None or data_extractor is None, the loss is unweighted.
 
     This class computes weights based on the formula from the paper by Cui et al. (2019):
     https://openaccess.thecvf.com/content_CVPR_2019/papers/Cui_Class-Balanced_Loss_Based_on_Effective_Number_of_Samples_CVPR_2019_paper.pdf
@@ -22,7 +21,7 @@ class BCEWeighted(torch.nn.BCEWithLogitsLoss):
 
     def __init__(
         self,
-        beta: Optional[float] = None,
+        beta: float = 0.99,
         data_extractor: Optional[XYBaseDataModule] = None,
         **kwargs,
     ):
@@ -32,11 +31,26 @@ def __init__(
         if isinstance(data_extractor, LabeledUnlabeledMixed):
             data_extractor = data_extractor.labeled
         self.data_extractor = data_extractor
+
+        assert (
+            isinstance(beta, float) and beta > 0.0
+        ), f"Beta parameter must be a float with value greater than 0.0, for loss class {self.__class__.__name__}."
+
+        assert (
+            self.data_extractor is not None
+        ), f"Data extractor must be provided if this loss class ({self.__class__.__name__}) is used."
+
+        assert all(
+            os.path.exists(os.path.join(self.data_extractor.processed_dir, file_name))
+            for file_name in self.data_extractor.processed_file_names
+        ), "Dataset files not found. Make sure the dataset is processed before using this loss."
+
         assert (
             isinstance(self.data_extractor, _ChEBIDataExtractor)
             or self.data_extractor is None
         )
         super().__init__(**kwargs)
+        self.pos_weight: Optional[torch.Tensor] = None
 
     def set_pos_weight(self, input: torch.Tensor) -> None:
         """
@@ -45,17 +59,7 @@ def set_pos_weight(self, input: torch.Tensor) -> None:
         Args:
             input (torch.Tensor): The input tensor for which to set the positive weights.
         """
-        if (
-            self.beta is not None
-            and self.data_extractor is not None
-            and all(
-                os.path.exists(
-                    os.path.join(self.data_extractor.processed_dir, file_name)
-                )
-                for file_name in self.data_extractor.processed_file_names
-            )
-            and self.pos_weight is None
-        ):
+        if self.pos_weight is None:
             print(
                 f"Computing loss-weights based on v{self.data_extractor.chebi_version} dataset (beta={self.beta})"
             )
@@ -96,3 +100,9 @@ def forward(
         """
         self.set_pos_weight(input)
         return super().forward(input, target)
+
+
+class UnWeightedBCEWithLogitsLoss(torch.nn.BCEWithLogitsLoss):
+    def forward(self, input, target, **kwargs):
+        # As the custom passed kwargs are not used in BCEWithLogitsLoss, we can ignore them
+        return super().forward(input, target)

tests/unit/cli/bce_loss.yml

@@ -0,0 +1 @@
+class_path: chebai.loss.bce_weighted.UnWeightedBCEWithLogitsLoss

tests/unit/cli/testCLI.py

@@ -15,8 +15,7 @@ def setUp(self):
             "--model.pass_loss_kwargs=false",
             "--trainer.min_epochs=1",
             "--trainer.max_epochs=1",
-            "--model.criterion=configs/loss/bce.yml",
-            "--model.criterion.init_args.beta=0.99",
+            "--model.criterion=tests/unit/cli/bce_loss.yml",
         ]
 
     def test_mlp_on_chebai_cli(self):