Fix PubChem pretraining (#159)

* allow input_dim and out_dim of 0

* dont pass config to base model

* catch missing labels if no labels exist

* only create classes.txt path for dynamic datasets

* change message for loading properties

Author: sfluegel05

chebai/models/base.py

@@ -48,8 +48,8 @@ def __init__(
         if exclude_hyperparameter_logging is None:
             exclude_hyperparameter_logging = tuple()
         self.criterion = criterion
-        assert out_dim is not None and out_dim > 0, "out_dim must be specified"
-        assert input_dim is not None and input_dim > 0, "input_dim must be specified"
+        assert out_dim is not None, "out_dim must be specified"
+        assert input_dim is not None, "input_dim must be specified"
         self.out_dim = out_dim
         self.input_dim = input_dim
         print(

chebai/models/electra.py

@@ -39,8 +39,8 @@ class ElectraPre(ChebaiBaseNet):
         replace_p (float): Probability of replacing tokens during training.
     """
 
-    def __init__(self, config: Dict[str, Any] = None, **kwargs: Any):
-        super().__init__(config=config, **kwargs)
+    def __init__(self, config: Dict[str, Any], **kwargs: Any):
+        super().__init__(**kwargs)
 
         self.generator_config = ElectraConfig(**config["generator"])
         self.generator = ElectraForMaskedLM(self.generator_config)

chebai/preprocessing/collate.py

@@ -87,7 +87,11 @@ def __call__(self, data: List[Union[Dict, Tuple]]) -> XYData:
                 *((d["features"], d["labels"], d.get("ident")) for d in data)
             )
             missing_labels = [
-                d.get("missing_labels", [False for _ in y[0]]) for d in data
+                d.get(
+                    "missing_labels",
+                    [False for _ in y[0]] if y[0] is not None else [False],
+                )
+                for d in data
             ]
 
         if any(x is not None for x in y):

chebai/preprocessing/datasets/base.py

@@ -514,11 +514,13 @@ def setup(self, *args, **kwargs) -> None:
 
         rank_zero_info(f"Check for processed data in {self.processed_dir}")
         rank_zero_info(f"Cross-validation enabled: {self.use_inner_cross_validation}")
-        rank_zero_info(f"Looking for files: {self.processed_file_names}")
         if any(
             not os.path.isfile(os.path.join(self.processed_dir, f))
             for f in self.processed_file_names
         ):
+            rank_zero_info(
+                f"Did not find one of: {', '.join(self.processed_file_names)} in {self.processed_dir}"
+            )
             self.setup_processed()
 
         self._after_setup(**kwargs)
@@ -627,17 +629,17 @@ def raw_file_names_dict(self) -> dict:
         raise NotImplementedError
 
     @property
-    def classes_txt_file_path(self) -> str:
+    def classes_txt_file_path(self) -> Optional[str]:
         """
-        Returns the filename for the classes text file.
+        Returns the filename for the classes text file (for labeled datasets that produce a list of labels).
 
         Returns:
-            str: The filename for the classes text file.
+            Optional[str]: The filename for the classes text file.
         """
         # This property also used in following places:
         #   - chebai/result/prediction.py: to load class names for csv columns names
         #   - chebai/cli.py: to link this property to `model.init_args.classes_txt_file_path`
-        return os.path.join(self.processed_dir_main, "classes.txt")
+        return None
 
 
 class MergedDataset(XYBaseDataModule):
@@ -1264,3 +1266,16 @@ def processed_file_names_dict(self) -> dict:
         if self.n_token_limit is not None:
             return {"data": f"data_maxlen{self.n_token_limit}.pt"}
         return {"data": "data.pt"}
+
+    @property
+    def classes_txt_file_path(self) -> str:
+        """
+        Returns the filename for the classes text file.
+
+        Returns:
+            str: The filename for the classes text file.
+        """
+        # This property also used in following places:
+        #   - chebai/result/prediction.py: to load class names for csv columns names
+        #   - chebai/cli.py: to link this property to `model.init_args.classes_txt_file_path`
+        return os.path.join(self.processed_dir_main, "classes.txt")

chebai/preprocessing/datasets/pubchem.py

@@ -195,8 +195,9 @@ def _set_processed_data_props(self):
         self._num_of_labels = 0
         self._feature_vector_size = 0
 
-        print(f"Number of labels for loaded data: {self._num_of_labels}")
-        print(f"Feature vector size: {self._feature_vector_size}")
+        print(
+            f"Number of labels and feature vector size set to: {self._num_of_labels} / {self._feature_vector_size} (default values, not used for self-supervised learning)"
+        )
 
     def _perform_data_preparation(self, *args, **kwargs):
         """